Patent Grant
11697668
The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. The ASCII copy, created on Apr. 20, 2020, is named 44854-708_301_SL.txt and is 5,878 bytes in size.
Highly efficient chemical gene synthesis with high fidelity and low cost has a central role in biotechnology and medicine, and in basic biomedical research. De novo gene synthesis is a powerful tool for basic biological research and biotechnology applications. While various methods are known for the synthesis of relatively short fragments in a small scale, these techniques suffer from scalability, automation, speed, accuracy, and cost. There is a need for devices for simple, reproducible, scalable, less error-prone and cost-effective methods that guarantee successful synthesis of desired genes and are amenable to automation.
Provided herein are methods for preparing a surface for oligonucleic acid synthesis, comprising: providing a structure comprising a surface, wherein the structure comprises silicon dioxide; depositing a first molecule on the surface at a first region, wherein the first molecule binds to the surface and lacks a reactive group that binds to a nucleoside phosphoramidite; depositing a second molecule on the surface at a second region, wherein the second region comprises a plurality of loci surrounded by the first region, wherein the second molecule binds to the surface and lacks a reactive group that binds to the nucleoside phosphoramidite; and depositing a mixture on the surface at the second region, wherein the mixture comprises the second molecule and a third molecule, wherein the third molecule binds to the surface and nucleoside phosphoramidite, and wherein the mixture comprises a greater amount of the second molecule than the third molecule. Methods are further provided wherein the second molecule and the third molecule both have a higher surface energy than a surface energy of the first molecule, and wherein surface energy is a measurement of water contact angle on a smooth planar surface. Methods are further provided wherein the difference in water contact angle between the first region and the second region is at least 10, 20, 50, or 75 degrees. Methods are further provided wherein the third molecule is a silane. Methods are further provided wherein the third molecule is N-(3-triethoxysilylpropyl)-4-hydroxybutyramide (HAPS), 11-acetoxyundecyltriethoxysilane, n-decyltriethoxysilane, (3-aminopropyl)trimethoxysilane, (3-aminopropyl)triethoxysilane, 3-glycidoxypropyltrimethoxysilane, 3-iodo-propyltrimethoxysilane, or octylchlorosilane. Methods are further provided wherein the third molecule is 3-glycidoxypropyltrimethoxysilane. Methods are further provided wherein the silane is an aminosilane. Methods are further provided wherein the second molecule is propyltrimethoxysilane. Methods are further provided wherein the first molecule is a fluorosilane. Methods are further provided wherein the fluorosilane is (tridecafluoro-1,1,2,2-tetrahydrooctyl)trichlorosilane. Methods are further provided wherein the mixture comprises the second molecule and the third molecule present in a molar ratio of about 100:1 to about 2500:1. Methods are further provided wherein the mixture comprises the second molecule and the third molecule present in a molar ratio of about 2000:1. Methods are further provided wherein the mixture comprises the second molecule and the third molecule present in a molar ratio of 2000:1. Methods are further provided wherein the first molecule lacks a free hydroxyl, amino, or carboxyl group. Methods are further provided wherein the second molecule lacks a free hydroxyl, amino, or carboxyl group. Methods are further provided wherein the mixture is in a gaseous state when deposited on the surface. Methods are further provided wherein the first molecule is in a gaseous state when deposited on the surface. Methods are further provided wherein the surface comprises a layer of silicon oxide. Provided herein is a device for oligonucleic acid synthesis prepared by any one of the methods described herein.
Provide herein are methods for preparing a surface for oligonucleic acid synthesis, comprising: providing a structure comprising a surface, wherein the structure comprises silicon dioxide, and wherein the surface comprises a layer of silicon oxide; coating the surface with a light-sensitive material that binds silicon oxide; exposing predetermined regions of the surface to a light source to remove a portion of the light-sensitive material coated on the surface; depositing a first molecule on the surface, wherein the first molecule binds the surface at the predetermined regions and lacks a reactive group that binds to a nucleoside phosphoramidite; removing a remaining portion of the light-sensitive material coated on the surface to expose loci, wherein each of the loci are surrounded by the predetermined regions comprising the first molecule; depositing a second molecule on the surface at the loci, wherein the second molecule binds to the loci and lacks a reactive group that binds to the nucleoside phosphoramidite; and depositing a mixture on the surface at the loci, the mixture comprises the second molecule and a third molecule, and wherein the third molecule binds to the surface and nucleoside phosphoramidite. Methods are further provided wherein the second molecule and the third molecule both have a higher surface energy than a surface energy of the first molecule, wherein the second molecule and the third molecule both have a higher surface energy than a surface energy of the first molecule, and wherein surface energy is a measurement of water contact angle on a smooth planar surface. Methods are further provided wherein the difference in water contact angle between the first region and the second region is at least 10, 20, 50, or 75 degrees. Methods are further provided wherein the difference in water contact angle between the first region and the second region is at least 50 degrees. Methods are further provided wherein the third molecule is a silane. Methods are further provided wherein the third molecule is N-(3-triethoxysilylpropyl)-4-hydroxybutyramide (HAPS), 11-acetoxyundecyltriethoxysilane, n-decyltriethoxysilane, (3-aminopropyl)trimethoxysilane, (3-aminopropyl)triethoxysilane, 3-glycidoxypropyltrimethoxysilane, 3-iodo-propyltrimethoxysilane, or octylchlorosilane. Methods are further provided wherein the third molecule is 3-glycidoxypropyltrimethoxysilane. Methods are further provided wherein the silane is an aminosilane. Methods are further provided wherein the second molecule is propyltrimethoxysilane. Methods are further provided wherein the first molecule is a fluorosilane. Methods are further provided wherein the fluorosilane is (tridecafluoro-1,1,2,2-tetrahydrooctyl)trichlorosilane. Methods are further provided wherein the mixture comprises the second molecule and the third molecule present in a molar ratio of about 100:1 to about 2500:1. Methods are further provided wherein the mixture comprises the second molecule and the third molecule present in a molar ratio of about 2000:1. Methods are further provided wherein the mixture comprises the second molecule and the third molecule present in a molar ratio of 2000:1. Methods are further provided wherein the first molecule lacks a free hydroxyl, amino, or carboxyl group. Methods are further provided wherein the second molecule lacks a free hydroxyl, amino, or carboxyl group. Methods are further provided wherein the mixture is in a gaseous state when deposited on the surface. Methods are further provided wherein the first molecule is in a gaseous state when deposited on the surface. Methods are further provided wherein the method further comprises applying oxygen plasma to the surface prior to coating the surface with the light-sensitive material that binds silicon oxide. Methods are further provided wherein the method further comprises applying oxygen plasma to the surface after exposing predetermined regions of the surface to light. Provided herein is a device for oligonucleic acid synthesis prepared by any one of the methods described herein.
Provided herein are methods for oligonucleic acid synthesis, comprising: providing predetermined sequences for at least 30,000 non-identical oligonucleic acids; providing a structure comprising a patterned surface, wherein the structure comprises silicon dioxide; wherein the patterned surface is generated by: depositing a first molecule on the surface at a first region, wherein the first molecule binds to the surface and lacks a reactive group that binds to a nucleoside phosphoramidite; and depositing a second molecule on the surface at a second region, wherein the second region comprises a plurality of loci surrounded by the first region, wherein the second molecule binds to the surface and lacks a reactive group that binds to the nucleoside phosphoramidite; and depositing a mixture on the surface at the second region, wherein the mixture comprises the second molecule and a third molecule, wherein the third molecule binds to the surface and nucleoside phosphoramidite, wherein the mixture comprises a greater amount of the second molecule than the third molecule; and synthesizing the at least 30,000 non-identical oligonucleic acids each at least 10 bases in length, wherein the at least 30,000 non-identical oligonucleic acids encode sequences with an aggregate deletion error rate of less than 1 in 1500 bases compared to the predetermined sequences, and wherein each of the at least 30,000 non-identical oligonucleic acids extends from a different locus. Methods are further provided wherein the second molecule and the third molecule both have a higher surface energy than a surface energy of the first molecule, and surface energy is a measurement of water contact angle on a smooth planar surface. Methods are further provided wherein a difference in water contact angle between the first region and the second region is at least 10, 20, 50, or 75 degrees. Methods are further provided wherein the difference in water contact angle between the first region and the second region is at least 50 degrees. Methods are further provided wherein the third molecule is a silane. Methods are further provided wherein the third molecule is N-(3-triethoxysilylpropyl)-4-hydroxybutyramide (HAPS), 11-acetoxyundecyltriethoxysilane, n-decyltriethoxysilane, (3-aminopropyl)trimethoxysilane, (3-aminopropyl)triethoxysilane, 3-glycidoxypropyltrimethoxysilane, 3-iodo-propyltrimethoxysilane, or octylchlorosilane. Methods are further provided wherein the silane is an aminosilane. Methods are further provided wherein the third molecule is 3-glycidoxypropyltrimethoxysilane. Methods are further provided wherein the second molecule is propyltrimethoxysilane. Methods are further provided wherein the first molecule is a fluorosilane. Methods are further provided wherein the fluorosilane is (tridecafluoro-1,1,2,2-tetrahydrooctyl)trichlorosilane. Methods are further provided wherein the mixture comprises the second molecule and the third molecule present in a molar ratio of about 100:1 to about 2500:1. Methods are further provided wherein the mixture comprises the second molecule and the third molecule present in a molar ratio of about 2000:1. Methods are further provided wherein the mixture comprises the second molecule and the third molecule present in a molar ratio of 2000:1. Methods are further provided wherein the first molecule lacks a free hydroxyl, amino, or carboxyl group. Methods are further provided wherein the second molecule lacks a free hydroxyl, amino, or carboxyl group. Methods are further provided wherein the mixture is in a gaseous state when deposited on the surface. Methods are further provided wherein the first molecule is in a gaseous state when deposited on the surface. Methods are further provided wherein each of the at least 30,000 non-identical oligonucleic acids is at least 30 bases in length. Methods are further provided wherein each of the at least 30,000 non-identical oligonucleic acids is 10 bases to 1 kb in length. Methods are further provided wherein each of the at least 30,000 non-identical oligonucleic acids is about 50 to about 120 bases in length. Methods are further provided wherein the aggregate deletion error rate is less than about 1 in 1700 bases compared to the predetermined sequences. Methods are further provided wherein the aggregate deletion error rate is achieved without correcting errors. Methods are further provided wherein the at least 30,000 non-identical oligonucleic acids synthesized encode sequences with an aggregate error rate of less than 1 in 1500 bases compared to the predetermined sequences without correcting errors. Methods are further provided wherein the aggregate error rate is less than 1 in 2000 bases compared to the predetermined sequences. Methods are further provided wherein the aggregate error rate is less than 1 in 3000 bases compared to the predetermined sequences. Methods are further provided wherein the surface comprises a layer of silicon oxide.
Provided herein are methods for nucleic acid synthesis, comprising: providing predetermined sequences for at least 200 preselected nucleic acids; providing a structure comprising a patterned surface, wherein the structure comprises silicon dioxide; wherein the patterned surface is generated by: depositing a first molecule on the surface at a first region, wherein the first molecule binds to the surface and lacks a reactive group that binds to a nucleoside phosphoramidite; and depositing a second molecule on the surface at a second region, wherein the second region comprises a plurality of loci surrounded by the first region, wherein the second molecule binds to the surface and lacks a reactive group that binds to the nucleoside phosphoramidite; and depositing a mixture on the surface at the second region, wherein the mixture comprises the second molecule and a third molecule, wherein the third molecule binds to the surface and nucleoside phosphoramidite, wherein the mixture comprises a greater amount of the second molecule than the third molecule; and synthesizing at least 20,000 non-identical oligonucleic acids each at least 50 bases in length, wherein each of the at least 20,000 non-identical oligonucleic acids extends from a different locus of the patterned surface; releasing the at least 20,000 non-identical oligonucleic acids from the patterned surface; suspending the at least 20,000 non-identical oligonucleic acids in a solution; and subjecting the solution comprising at least 20,000 non-identical oligonucleic acids to a polymerase chain assembly reaction to assemble at least 200 genes, wherein the assembled at least 200 preselected nucleic acids encode sequences with an aggregate deletion error rate of less than 1 in 1500 bases compared to the predetermined sequences. Methods are further provided wherein the second molecule and the third molecule both have a higher surface energy than a surface energy of the first molecule, and wherein surface energy is a measurement of water contact angle on a smooth planar surface. Methods are further provided wherein the difference in water contact angle between the first region and the second region is at least 10, 20, 50, or 75 degrees. Methods are further provided wherein the difference in water contact angle between the first region and the second region is at least 50 degrees. Methods are further provided wherein the third molecule is N-(3-triethoxysilylpropyl)-4-hydroxybutyramide (HAPS), 11-acetoxyundecyltriethoxysilane, n-decyltriethoxysilane, (3-aminopropyl)trimethoxysilane, (3-aminopropyl)triethoxysilane, 3-glycidoxypropyltrimethoxysilane, 3-iodo-propyltrimethoxysilane, or octylchlorosilane. Methods are further provided wherein the third molecule is a silane. Methods are further provided wherein the third molecule is 3-glycidoxypropyltrimethoxysilane. Methods are further provided wherein the silane is an aminosilane. Methods are further provided wherein the second molecule is propyltrimethoxysilane. Methods are further provided wherein the first molecule is a fluorosilane. Methods are further provided wherein the fluorosilane is (tridecafluoro-1,1,2,2-tetrahydrooctyl)trichlorosilane. Methods are further provided wherein the mixture comprises the second molecule and the third molecule present in a molar ratio of about 100:1 to about 2500:1. Methods are further provided wherein the mixture comprises the second molecule and the third molecule present in a molar ratio of about 2000:1. Methods are further provided wherein the mixture comprises the second molecule and the third molecule present in a molar ratio of 2000:1. Methods are further provided wherein the first molecule lacks a free hydroxyl, amino, or carboxyl group. Methods are further provided wherein the second molecule lacks a free hydroxyl, amino, or carboxyl group. Methods are further provided wherein each of the at least 20,000 non-identical oligonucleic acids is about 50 to about 120 bases in length. Methods are further provided wherein the aggregate deletion error rate is less than about 1 in 1700 bases compared to the predetermined sequences. Methods are further provided wherein the aggregate deletion error rate is achieved without correcting errors. Methods are further provided wherein the assembled at least 200 preselected nucleic acids encode sequences with an aggregate error rate of less than 1 in 1500 bases compared to the predetermined sequences without correcting errors. Methods are further provided wherein the aggregate error rate is less than 1 in 2000 bases compared to the predetermined sequences. Methods are further provided wherein the surface comprises a layer of silicon oxide.
Provided here are devices for oligonucleic acid synthesis, comprising: a structure having a surface, wherein the structure comprises silicon dioxide; a plurality of recesses or posts on the surface, wherein each recess or post comprises: a width length that is 6.8 nm to 500 nm, a pitch length that is about twice the width length, and a depth length that is about 60% to about 125% of the pitch length; a plurality of loci on the surface, wherein each locus has a diameter of 0.5 to 100 μm, wherein each locus comprises at least two of the plurality of recesses or posts; and a plurality of clusters on the surface, wherein each of the clusters comprise 50 to 500 loci and has a cross-section of 0.5 to 2 mm. Devices are further provided wherein each of the clusters comprise 100 to 150 loci. Devices are further provided wherein the structure comprises at least 30,000 loci. Devices are further provided wherein the pitch length is 1 μm or less. Devices are further provided wherein the depth length is 1 μm or less. Devices are further provided wherein each of the loci has a diameter of 0.5 μm. Devices are further provided wherein each of the loci has a diameter of 10 μm. Devices are further provided wherein each of the loci has a diameter of 50 μm. Devices are further provided wherein the cross-section of each of the clusters is about 1.125 mm. Devices are further provided wherein each of the clusters has a pitch of about 1.125 mm. Devices are further provided wherein each locus comprises a molecule that binds to the surface and a nucleoside phosphoramidite. Devices are further provided wherein the molecule that binds to the surface and the nucleoside phosphoramidite is a silane. Devices are further provided wherein the molecule that binds to the surface and the nucleoside phosphoramidite is N-(3-triethoxysilylpropyl)-4-hydroxybutyramide (HAPS), 11-acetoxyundecyltriethoxysilane, n-decyltriethoxysilane, (3-aminopropyl)trimethoxysilane, (3-aminopropyl)triethoxysilane, 3-glycidoxypropyltrimethoxysilane, 3-iodo-propyltrimethoxysilane, or octylchlorosilane. Devices are further provided wherein the silane is 3-glycidoxypropyltrimethoxysilane. Devices are further provided wherein the silane is an aminosilane. Devices are further provided wherein a region surrounding the plurality of loci comprises a molecule that binds to the surface and lacks a nucleoside phosphoramidite. Devices are further provided wherein the molecule that binds to the surface and lacks the nucleoside phosphoramidite is a fluorosilane. Devices are further provided wherein the fluorosilane is (tridecafluoro-1,1,2,2-tetrahydrooctyl)trichlorosilane or perfluorooctyltrichlorosilane. Devices are further provided wherein the surface comprises a layer of silicon oxide.
Provided herein are methods for oligonucleic acid synthesis, comprising: providing predetermined sequences; providing a device for oligonucleic acid synthesis prepared by any one of methods described herein; synthesizing a plurality of non-identical oligonucleic acids at least 10 bases in length, wherein each of the non-identical oligonucleic acids extends from a different locus. Methods are further provided wherein the aggregate deletion error rate is less than about 1 in 1700 bases compared to the predetermined sequences. Methods are further provided wherein the aggregate deletion error rate is achieved without correcting errors. Methods are further provided wherein the plurality of non-identical oligonucleic acids synthesized encode sequences with an aggregate error rate of less than 1 in 1500 bases compared to the predetermined sequences without correcting errors. Methods are further provided wherein the aggregate error rate is less than 1 in 2000 bases compared to the predetermined sequences. Methods are further provided wherein the aggregate error rate is less than 1 in 3000 bases compared to the predetermined sequences.
Provided herein are methods for nucleic acid synthesis, comprising: providing predetermined sequences for at least 200 preselected nucleic acids; providing the device described herein; synthesizing at least 20,000 non-identical oligonucleic acids each at least 50 bases in length, wherein each of the at least 20,000 non-identical oligonucleic acids extends from a different locus; releasing the at least 20,000 non-identical oligonucleic acids from the surface; suspending the at least 20,000 non-identical oligonucleic acids in a solution; and subjecting the solution comprising at least 20,000 non-identical oligonucleic acids to a polymerase chain assembly reaction to assemble at least 200 genes, wherein the assembled at least 200 preselected nucleic acids encode sequences with an aggregate deletion error rate of less than 1 in 1500 bases compared to the predetermined sequences. Methods are further provided wherein the aggregate deletion error rate is less than about 1 in 1700 bases compared to the predetermined sequences. Methods are further provided wherein the aggregate deletion error rate is achieved without correcting errors. Methods are further provided wherein the assembled at least 200 preselected nucleic acids encode sequences with an aggregate error rate of less than 1 in 1500 bases compared to the predetermined sequences without correcting errors. Methods are further provided wherein the aggregate error rate is less than 1 in 2000 bases compared to the predetermined sequences.
Provide herein are devices for oligonucleic acid synthesis, comprising: a structure having a surface, wherein the structure comprises silicon dioxide; a plurality of recesses or posts on the surface, wherein each recess or post comprises (i) a width length that is 6.8 nm to 500 nm, (ii) a pitch length that is about twice the width length, and (iii) a depth length that is about 60% to about 125% of the pitch length; a plurality of loci on the surface, wherein each locus has a diameter of 0.5 to 100 um, wherein each locus comprises at least two of the plurality of recesses or posts; a plurality of clusters on the surface, wherein each of the clusters comprise 50 to 500 loci and has a cross-section of 0.5 to 2 mm, wherein the plurality of loci comprise a less than saturating amount of a molecule that binds the surface and couples to nucleoside phosphoramidite; and a plurality of regions surrounding each loci comprise a molecule that binds the surface and does not couple to nucleoside phosphoramidite, wherein the plurality of loci have a higher surface energy than the plurality of regions surrounding each loci. Devices are further provided wherein the molecule that binds the surface and couples to nucleoside phosphoramidite is a silane disclosed herein. Devices are further provided wherein the molecule that binds the surface and does not couple to nucleoside phosphoramidite is a fluorosilane disclosed herein. Devices are further provided wherein the plurality of loci are coated with a molecule that binds the surface, does not couple to nucleoside phosphoramidite, and has a higher surface energy than the molecule on plurality of regions surrounding each loci. Devices are further provided wherein the surface comprises a layer of silicon oxide.
All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.
The present disclosure provides devices and methods for the rapid parallel synthesis of oligonucleic acids with low error rates. The oligonucleotide synthesis steps described here are “de novo,” meaning that oligonucleotides are built one monomer at a time to form a polymer. During de novo synthesis of oligonucleic acids, the crowding of single stranded oligonucleic acids extending from a surface results in an increase in error rates. To reduce the frequency of crowding-related errors, methods are provided herein to reduce the density of nucleoside-coupling agent bound to specific regions of the surface.
An exemplary method for generating a surface having a reduction in nucleoside-coupling agent density is illustrated in
As a consequence of reducing the amount of nucleoside coupling molecules on the surface of a structure, the oligonucleic acid yields are also reduced. If the oligonucleic acid yields are too low, insufficient amounts of material will be produced for subsequent downstream molecular biology processes utilizing oligonucleic acids synthesized, e.g., as gene assembly. In order to increase the oligonucleic acid yields, methods are also provided for increasing the surface area at the site of oligonucleic acid extension by creating textured surface. To increase the surface area, the surface of a device may have a field of protrusions (see, for example, FIG. 3A) or a field of recesses (
A number of steps are performed to make a textured surface. A exemplary structure 101 (e.g., silicon-based) disclosed herein is polished (
Throughout this disclosure, numerical features are presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of any embodiments. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range to the tenth of the unit of the lower limit unless the context clearly dictates otherwise. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual values within that range, for example, 1.1, 2, 2.3, 5, and 5.9. This applies regardless of the breadth of the range. The upper and lower limits of these intervening ranges may independently be included in the smaller ranges, and are also encompassed within the invention, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in the invention, unless the context clearly dictates otherwise.
The terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting of any embodiment. As used herein, the singular forms “a,” “an” and “the” are intended to include the plural forms as well, unless the context clearly indicates otherwise. It will be further understood that the terms “comprises” and/or “comprising,” when used in this specification, specify the presence of stated features, integers, steps, operations, elements, and/or components, but do not preclude the presence or addition of one or more other features, integers, steps, operations, elements, components, and/or groups thereof. As used herein, the term “and/or” includes any and all combinations of one or more of the associated listed items.
Unless specifically stated or obvious from context, as used herein, the term “about” in reference to a number or range of numbers is understood to mean the stated number and numbers +/−10% thereof, or 10% below the lower listed limit and 10% above the higher listed limit for the values listed for a range.
As used herein, the terms “preselected sequence”, “predefined sequence” or “predetermined sequence” are used interchangeably. The terms mean that the sequence of the polymer is known and chosen before synthesis or assembly of the polymer. In particular, various aspects of the invention are described herein primarily with regard to the preparation of nucleic acids molecules, the sequence of the oligonucleotide or polynucleotide being known and chosen before the synthesis or assembly of the nucleic acid molecules.
Surface Materials
Structures for oligonucleic acid synthesis provided herein are fabricated from a variety of materials capable of modification to support a de novo oligonucleic acid synthesis reaction. In some cases, the structures are sufficiently conductive, e.g., are able to form uniform electric fields across all or a portion of the structure. A structure described herein can comprise a flexible material. Exemplary flexible materials include, without limitation, modified nylon, unmodified nylon, nitrocellulose, and polypropylene. A structure described herein can comprise a rigid material. Exemplary rigid materials include, without limitation, glass, fuse silica, silicon, silicon dioxide, silicon nitride, plastics (for example, polytetrafluoroethylene, polypropylene, polystyrene, polycarbonate, and blends thereof, and metals (for example, gold, platinum). Structure disclosed herein can be fabricated from a material comprising silicon, polystyrene, agarose, dextran, cellulosic polymers, polyacrylamides, polydimethylsiloxane (PDMS), glass, or any combination thereof. In some cases, a structure disclosed herein is manufactured with a combination of materials listed herein or any other suitable material known in the art. In some cases, a structure disclosed herein comprises a silicon dioxide base and a surface layer of silicon oxide. Alternatively, the structure can have a base of silicon oxide. Surface of the structure provided here can be textured, resulting in an increase overall surface area for oligonucleic acid synthesis. Structure disclosed herein may comprise at least 5%, 10%, 25%, 50%, 80%, 90%, 95%, or 99% silicon. A device disclosed herein may be fabricated from a silicon on insulator (SOI) wafer.
Patterned Surfaces
Disclosed herein are surfaces for the synthesis of oligonucleic acids at a low error rate. Surfaces disclosed herein comprise predetermined regions having varying wettability characteristics and varying ability to couple nucleoside. For example, a surface disclosed herein comprises high energy regions comprising a molecule that binds to the surface and also couples to nucleoside, and the high energy regions are surrounded by low energy regions comprising a molecule that binds to the surface and does not couple to nucleoside. In some instances, the high energy regions comprise a mixture of molecules having varying ability to couple nucleoside, e.g., a nucleoside phosphoramidite.
To set stage for coupling monomers extending from a structure, surfaces of a structure disclosed herein can be coated with a layer of material comprising an active functionalization agent, such as a nucleoside-coupling agent. An nucleoside-coupling agent is one that binds to the surface and also binds to nucleic acid monomer, thereby supporting a coupling reaction to the surface. Nucleoside-coupling agents are molecules having a reactive group, for example, a hydroxyl, amino or carboxyl group, available for binding to a nucleoside in a coupling reaction. A surface can be additionally coated with a layer of material comprising a passive functionalization agent. A passive functionalization agent or material binds to the surface but does not efficiently bind to nucleic acid, thereby preventing nucleic acid attachment at sites where passive functionalization agent is bound. Passive functionalization agents are molecules lacking an available reactive group (e.g., a hydroxyl, amino or carboxyl group) for binding a nucleoside in a coupling reaction. Surfaces can be configured for both active and passive functionalization agents bound to the surface at within predetermined regions of the surface, generating distinct regions for oligonucleic acid synthesis, wherein the region comprises a less than saturating amount of active functionalization agent, compare
A first exemplary method of functionalizing a surface is discussed above with reference to
The surface energy of a chemical layer coated on a surface can facilitate localization of droplets on the surface. Depending on the patterning arrangement selected, the proximity of loci and/or area of fluid contact at the loci can be altered. In the context of silicon surfaces, certain aminosilane molecules can bind their silicon atom to the oxygen atom of the surface and also have additional chemical interactions for both binding photoresist or biomolecules. For example, for both (3-aminopropyl)trimethoxysilane (APTMS), or (3-aminopropyl)triethoxysilane (APTES), the silicon atom binds to the oxygen atom of the surface and the amine groups bind to the organic molecules. Exemplary activate functionalizing chemical coating agents include (3-aminopropyl)trimethoxysilane, (3-aminopropyl)triethoxysilane or N-(3-triethoxysilylpropyl)-4-hydroxybutyramide.
Surfaces, or more specifically resolved loci, onto which nucleic acids or other molecules are deposited, e.g., for oligonucleic acid synthesis, can be smooth or substantially planar or are textured, having raised or lowered features (e.g., three-dimensional features). Surfaces disclosed herein can be layered with one or more different layers of compounds. Such modification layers of interest include, without limitation, inorganic and organic layers such as metals, metal oxides, polymers, small organic molecules and the like. Non-limiting polymeric layers include peptides, proteins, nucleic acids or mimetics thereof (e.g., peptide nucleic acids and the like), polysaccharides, phospholipids, polyurethanes, polyesters, polycarbonates, polyureas, polyamides, polyetheyleneamines, polyarylene sulfides, polysiloxanes, polyimides, polyacetates, and any other suitable compounds described herein or otherwise known in the art. In some cases, polymers are heteropolymeric. In some cases, polymers are homopolymeric. In some cases, polymers comprise functional moieties or are conjugated.
Loci disclosed herein can be functionalized with one or more molecules that increase and/or decrease surface energy. The molecule can be chemically inert. The surface energy, or hydrophobicity, of a surface is a factor for determining the affinity of a nucleotide to attach onto the surface. Provided herein is a method for functionalization of a surface disclosed herein comprises: (a) providing a structure having a surface that comprises silicon dioxide; and (b) silanizing the surface using, a suitable silanizing agent described herein or otherwise known in the art, for example, an organofunctional alkoxysilane molecule. In some cases, the organofunctional alkoxysilane molecule comprises dimethylchloro-octodecyl-silane, methyldichloro-octodecyl-silane, trichloro-octodecyl-silane, trimethyl-octodecyl-silane, triethyl-octodecyl-silane, or any combination thereof. In some cases, a surface comprises functionalization with polyethylene/polypropylene (functionalized by gamma irradiation or chromic acid oxidation, and reduction to hydroxyalkyl surface), highly crosslinked polystyrene-divinylbenzene (derivatized by chloromethylation, and aminated to benzylamine functional surface), nylon (the terminal aminohexyl groups are directly reactive), or etched with reduced polytetrafluoroethylene.
A surface disclosed herein can be functionalized by contact with a derivatizing composition that contains a mixture of silanes, under reaction conditions effective to couple the silanes to the surface. Silanization generally can be used to cover a surface through self-assembly with organofunctional alkoxysilane molecules. A variety of siloxane functionalizing reagents can further be used as currently known in the art, e.g., for lowering or increasing surface energy. The organofunctional alkoxysilanes are classified according to their organic functions. Non-limiting examples of siloxane functionalizing reagents include hydroxyalkyl siloxanes (silylate surface, functionalizing with diborane and oxidizing the alcohol by hydrogen peroxide), diol (dihydroxyalkyl) siloxanes (silylate surface, and hydrolyzing to diol), aminoalkyl siloxanes (amines require no intermediate functionalizing step), glycidoxysilanes (3-glycidoxypropyl-dimethyl-ethoxysilane, glycidoxy-trimethoxysilane), mercaptosilanes (3-mercaptopropyl-trimethoxysilane, 3-4 epoxycyclohexyl-ethyltrimethoxysilane or 3-mercaptopropyl-methyl-dimethoxysilane), bicyclohepthenyl-trichlorosilane, butyl-aldehyde-trimethoxysilane, or dimeric secondary aminoalkyl siloxanes. The hydroxyalkyl siloxanes can include 3-(chloro)allyltrichlorosilane turning into 3-hydroxypropyl, or 7-octenyltrichlorosilane turning into 8-hydroxyoctyl. The diol (dihydroxyalkyl) siloxanes include glycidyl trimethoxysilane-derived (3-glycidyloxypropyl)trimethoxysilane (GOPS). The aminoalkyl siloxanes include 3-aminopropyl trimethoxysilane turning into 3-aminopropyl (3-aminopropyl-triethoxysilane, 3-aminopropyl-diethoxy-methylsilane, 3-aminopropyl-dimethyl-ethoxysilane, or 3-aminopropyl-trimethoxysilane). The dimeric secondary aminoalkyl siloxanes can be bis (3-trimethoxysilylpropyl) amine turning into bis(silyloxylpropyl)amine. In some cases, the functionalizing agent comprises 11-acetoxyundecyltriethoxysilane, n-decyltriethoxysilane, (3-aminopropyl)trimethoxysilane, (3-aminopropyl)triethoxysilane, glycidyloxypropyl/trimethoxysilane and N-(3-triethoxysilylpropyl)-4-hydroxybutyramide.
Desired surface tensions, wettabilities, water contact angles, and/or contact angles for other suitable solvents are achieved by providing a surface with a suitable ratio of functionalization agents. A surface disclosed herein can be functionalized to enable covalent binding of molecular moieties that can lower the surface energy so that wettability can be reduced. A portion of a surface disclosed herein may be prepared to have a high surface energy and increased wettability. Surfaces disclosed herein can also be modified to comprise reactive hydrophilic moieties such as hydroxyl groups, carboxyl groups, thiol groups, and/or substituted or unsubstituted amino groups. Suitable materials that can be used for solid phase chemical synthesis, e.g., cross-linked polymeric materials (e.g., divinylbenzene styrene-based polymers), agarose (e.g., Sepharose®), dextran (e.g., Sephadex®), cellulosic polymers, polyacrylamides, silica, glass (particularly controlled pore glass, or “CPG”), ceramics, and the like. The supports may be obtained commercially and used as is, or they may be treated or coated prior to functionalization.
Dilution of Active Functionalization Agent to Form Regions of High Surface Energy
To achieve surfaces with low density of nucleoside-coupling agents, a mixture of both active and passive functionalization agents is mixed and deposited at a predetermined region of a surface disclosed herein. Such a mixture provides for a region having a less than saturating amount of active functionalization agent bound to the surface and therefore lowers the density of functionalization agent in a particular region. A mixture of agents that bind to a surface disclosed herein can be deposited on predetermined region of the surface, wherein coated surface provides for a density of synthesized oligonucleic acids that is about 10%, 20%, 30%, 40%, 50%, 60%, 70%, or 80% less than the density of synthesized oligonucleic acids extended from a region of the surface comprising only the active functionalization agent. The mixture can comprise (i) a silane that binds the surface and couples nucleoside and (ii) a silane that binds the surface and does not couple nucleoside is deposited on predetermined region of a surface disclosed herein, wherein coated surface provides for a density of synthesized oligonucleic acids that is about 10%, 20%, 30%, 40%, 50%, 60%, 70%, or 80% less than the density of synthesized oligonucleic acids extended from a region of the surface comprising (i) the silane that binds the surface and couples nucleoside and not (ii) the silane that binds the surface and does not couple nucleoside. A predetermined region of a surface can be treated with a diluted amount of an active functionalization agent disclosed herein provides for a reduction in density of synthesized oligonucleic acids that is about 50% compared to an identical surface coated with a non-diluted amount of the active functionalization agents. One exemplary active functionalization agent is 3-glycidoxypropyltrimethoxysilane, which can optionally be included in a mixture disclosed herein. For example, the mixture can include 3-glycidoxypropyltrimethoxysilane or propyltrimethoxysilane; or 3-glycidoxypropyltrimethoxysilane and propyltrimethoxysilane. Regions surrounding those regions deposited with the mixture can be coated with a passive functionalization agent having a lower surface energy. In some cases, the passive functionalization agent having a lower surface energy is a fluorosilane. Exemplary fluorosilanes include (tridecafluoro-1,1,2,2-tetrahydrooctyl)trichlorosilane and perfluorooctyltrichlorosilane.
More broadly, active functionalization agent can comprise a silane, such as an aminosilane. In some cases, the active functionalization agent comprises a silane that, once activated, couples nucleoside, e.g., a nucleoside phosphoramidite. The active functionalization agent can be a silane that has a higher surface energy than the passive functionalization agent deposited on areas of the surface located outside of predetermined regions where the silane is deposited. In some cases, both molecules types in the mixture comprise silanes, and the mixture is deposited on the surface. For example, one of the molecules in the mixture is a silane that binds the surface and couples to nucleoside, and another one of the molecules in the surface is a silane that binds the surface and does not couple to nucleoside. In such cases, both molecules in the mixture, when deposited on the surface, provide for a region having a higher surface energy than regions surrounding where the mixture is deposited.
Agents in a mixture disclosed here are chosen from suitable reactive and inert moieties, thus diluting the surface density of reactive groups to a desired level for downstream reactions, where both molecules have similar surface energy. In some cases, the density of the fraction of a surface functional group that reacts to form a growing oligonucleotide in an oligonucleotide synthesis reaction is about 0.005, 0.01, 0.05, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 3.0, 3.5, 4.0, 4.5, 5.0, 7.0, 10.0, 15.0, 20.0, 50.0, 75.0, 100.0 μmol/m2.
Mixtures disclosed herein can comprise at least 2, 3, 4, 5 or more different types of functionalization agents. A mixture can comprises 1, 2, 3 or more silanes. The ratio of the at least two types of surface functionalization agents in a mixture deposited on a surface disclosed herein may range from about 1:1 to 1:100 with the active functionalization agent being diluted to a greater amount compared to a functionalization agent that does not couple nucleoside. In some cases, the ratio of the at least two types of surface functionalization agents in a mixture deposited on a surface disclosed herein is about 1:100 to about 1:2500, with the active functionalization agent being diluted to a greater amount compared to a functionalization agent that does not couple nucleoside. Exemplary ratios of the at least two types of surface functionalization agents in a mixture deposited on a surface disclosed herein include at least 1:10, 1:50, 1:100, 1:200, 1:500, 1:1000, 1:2000, 1:2500, 1:3000, or 1:5000, with the active functionalization agent being diluted to a greater amount compared to a functionalization agent that does not couple nucleoside. An exemplary specific ratio of the at least two types of surface functionalization agents in a mixture is about 1:2000, with the active functionalization agent being diluted to a greater amount compared to a functionalization agent that does not couple nucleoside. Another exemplary specific ratio of the at least two types of surface functionalization agents in a mixture is 1:2000, with the active functionalization agent being diluted to a greater amount compared to a functionalization agent that does not couple nucleoside. The passive functionalization agent deposited on the surface can be a fluorosilane molecule. Exemplary fluorosilane molecules are (tridecafluoro-1,1,2,2-tetrahydrooctyl)trichlorosilane and perfluorooctyltrichlorosilane. The mixture deposited on a surfaced disclosed herein may comprise a silane that binds the surface and nucleoside phosphoramidite and is diluted about 1:100 to about 1:2500 with a silane that bind the surface and does not bind nucleoside phosphoramidite. In some cases, the silane molecule deposited on a surfaced disclosed herein is diluted about 1:2000.
To attain a reduction in active agent density at particular locations on a surface disclosed herein, deposition at regions for nucleic acid extension with the non-nucleoside molecule of the mixture occurs prior to deposition with the mixture itself. In some case, the mixture deposited on a surfaced disclosed herein comprises 3-glycidoxypropyltrimethoxysilane diluted at a ratio of about 1:2000. The mixture deposited on a surfaced disclosed herein may comprise 3-glycidoxypropyltrimethoxysilane diluted at a ratio of about 1:2000 in propyltrimethoxysilane. In one example, a surface disclosed herein is first deposited at regions for nucleic acid extension with propyltrimethoxysilane prior to deposition of a mixture of propyltrimethoxysilane and 3-glycidoxypropyltrimethoxysilane. In some cases, a silane deposited at sites of oligonucleic acid synthesis are selected from the group consisting of 11-acetoxyundecyltriethoxysilane, n-decyltriethoxysilane, (3-aminopropyl)trimethoxysilane, (3-aminopropyl)triethoxysilane, 3-glycidyloxypropyl/trimethoxysilane and N-(3-triethoxysilylpropyl)-4-hydroxybutyramide.
Hydrophilic and Hydrophobic Surfaces
The surface energy, or hydrophobicity of a surface, can be evaluated or measured by measuring a water contact angle. Water contact angle is the angle between the drop surface and a solid surface where a water droplet meets the solid surface. A surface with a water contact angle of smaller than 90°, the solid surface can be considered hydrophilic or polar. A surface with a water contact angle of greater than 90°, the solid surface can be considered hydrophobic or apolar. Highly hydrophobic surfaces with low surface energy can have water contact angle that is greater than 120°.
Surface characteristics of coated surfaces can be adjusted in various ways suitable for oligonucleotide synthesis. A surface described herein is selected to be inert to the conditions of ordinary oligonucleotide synthesis; e.g. the solid surface may be devoid of free hydroxyl, amino, or carboxyl groups to the bulk solvent interface during monomer addition, depending on the selected chemistry. In some cases, the surface may comprise reactive moieties prior to the start of a first cycle, or first few cycles of an oligonucleotide synthesis process, wherein the reactive moieties can be quickly depleted to unmeasurable densities after one, two, three, four, five, or more cycles of the oligonucleotide synthesis reaction. The surface can further be optimized for well or pore wetting, e.g., by common organic solvents such as acetonitrile and the glycol ethers or aqueous solvents, relative to surrounding surfaces.
Without being bound by theory, the wetting phenomenon is understood to be a measure of the surface tension or attractive forces between molecules at a solid-liquid interface, and is expressed in dynes/cm2. For example, fluorocarbons have very low surface tension, which is typically attributed to the unique polarity (electronegativity) of the carbon-fluorine bond. In tightly structured Langmuir-Blodgett type films, surface tension of a layer can be primarily determined by the percent of fluorine in the terminus of the alkyl chains. For tightly ordered films, a single terminal trifluoromethyl group can render a surface nearly as lipophobic as a perfluoroalkyl layer. When fluorocarbons are covalently attached to an underlying derivatized solid (e.g. a highly crosslinked polymeric) support, the density of reactive sites can be lower than Langmuir-Blodgett and group density. For example, surface tension of a methyltrimethoxysilane surface can be about 22.5 mN/m and aminopropyltriethoxysilane surface can be about 35 mN/m. Briefly, hydrophilic behavior of surfaces is generally considered to occur when critical surface tensions are greater than 45 mN/m. As the critical surface tension increases, the expected decrease in contact angle is accompanied with stronger adsorptive behavior. Hydrophobic behavior of surfaces is generally considered to occur when critical surface tensions are less than 35 mN/m. At first, the decrease in critical surface tension is associated with oleophilic behavior, i.e. the wetting of the surfaces by hydrocarbon oils. As the critical surface tensions decrease below 20 mN/m, the surfaces resist wetting by hydrocarbon oils and are considered both oleophobic as well as hydrophobic. For example, silane surface modification can be used to generate a broad range of critical surface tensions. Devices and methods disclosed herein include surface coatings, e.g. those involving silanes, to achieve surface tensions of less than 5, 6, 7, 8, 9, 10, 12, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 110, 115, 120 mN/m, or higher. Further, in some cases, the methods and devices disclosed herein use surface coatings, e.g. those involving silanes, to achieve surface tensions of more than 115, 110, 100, 90, 80, 70, 60, 50, 45, 40, 35, 30, 25, 20, 15, 12, 10, 9, 8, 7, 6 mN/m or less. The water contact angle and the surface tension of non-limiting examples of surface coatings, e.g., those involving silanes, are described in Table 1 and Table 2 of Arkles et al. (Silanes and Other Coupling Agents, Vol. 5v: The Role of Polarity in the Structure of Silanes Employed in Surface Modification. 2009), which is incorporated herein by reference in its entirety. The tables are replicated below.
Provided herein are surfaces, or a portion of the surface, functionalized or modified to be more hydrophilic or hydrophobic as compared to the surface or the portion of the surface prior to the functionalization or modification. One or more surfaces may be modified to have a difference in water contact angle of greater than 90°, 85°, 80°, 75°, 70°, 65°, 60°, 55°, 50°, 45°, 40°, 35°, 30°, 25°, 20°, 15° or 10° as measured on one or more uncurved, smooth or planar equivalent surfaces. In some cases, the surface of microstructures, channels, wells, resolved loci, resolved reactor caps or other parts of structure is modified to have a differential hydrophobicity corresponding to a difference in water contact angle that is greater than 90°, 85°, 80°, 75°, 70°, 65°, 60°, 55°, 50°, 45°, 40°, 35°, 30°, 25°, 20°, 15° or 10° as measured on uncurved, smooth or planar equivalent surfaces of such structures.
Provided herein are surfaces have a predetermined first region comprising two or more molecules having different ability to couple nucleoside and have a similarity in water contact angle. In some cases, the similarity is less than 40°, 35°, 30°, 25°, 20°, 15° or 10° as measured on one or more smooth or planar equivalent surfaces. In some cases, the first region is surrounded by a second region, where the first and second region have a difference in water contact angle of greater than 90°, 85°, 80°, 75°, 70°, 65°, 60°, 55°, 50°, 45°, 40°, 35°, 30°, 25°, 20°, 15° or 10° as measured on one or more smooth or planar equivalent surfaces. In some cases, the first region is surrounded by a second region, where the first and second region have a difference in water contact angle of at least 90°, 85°, 80°, 75°, 70°, 65°, 60°, 55°, 50°, 45°, 40°, 35°, 30°, 25°, 20°, 15° or 10° as measured on one or more smooth or planar equivalent surfaces. Unless otherwise stated, water contact angles mentioned herein correspond to measurements that would be taken on uncurved, smooth or planar equivalents of the surfaces in question.
Surface Preparation
Surfaces provided herein comprise or are modified to support oligonucleic acid synthesis at predetermined locations and with a resulting low error rate. A common method for functionalization comprises selective deposition of an organosilane molecule onto a surface of a structure disclosed herein. Selective deposition refers to a process that produces two or more distinct areas on a structure, wherein at least one area has a different surface or chemical property that another area of the same structure. Such properties include, without limitation, surface energy, chemical termination, surface concentration of a chemical molecule, and the like. Any suitable process that changes the chemical properties of the surface described herein or known in the art may be used to functionalize the surface, for example chemical vapor deposition of an organosilane. Typically, this results in the deposition of a self-assembled monolayer (SAM) of the functionalization species.
Provided herein are methods for functionalizing a surface of a structure disclosed herein for oligonucleic acid synthesis which include photolithography. An exemplary photolithographic method comprises 1) applying a photoresist to a surface, 2) exposing the resist to light, e.g., using a binary mask opaque in some areas and clear in others, and 3) developing the resist; wherein the areas that were exposed are patterned. The patterned resist can then serve as a mask for subsequent processing steps, for example, etching, ion implantation, and deposition. After processing, the resist is typically removed, for example, by plasma stripping or wet chemical removal. Oxygen plasma cleaning may optionally be used to facilitate the removal of residual organic contaminants in resist cleared areas, for example, by using a typically short plasma cleaning step (e.g., oxygen plasma). Resist can be stripped by dissolving it in a suitable organic solvent, plasma etching, exposure and development, etc., thereby exposing the areas of the surface that had been covered by the resist. Resist can be removed in a process that does not remove functionalization groups or otherwise damage the functionalized surface.
Provided herein is a method for functionalizing a surface of a structure disclosed herein for oligonucleic acid synthesis comprises a resist or photoresist coat. Photoresist, in many cases, refers to a light-sensitive material useful in photolithography to form patterned coatings. It is applied as a liquid to solidify on a surface as volatile solvents in the mixture evaporate. In some cases, the resist is applied in a spin coating process as a thin film, e.g., 1 μm to 100 μm. The coated resist can be patterned by exposing it to light through a mask or reticle, changing its dissolution rate in a developer. In some cases, the resist coat is used as a sacrificial layer that serves as a blocking layer for subsequent steps that modify the underlying surface, e.g., etching, and then is removed by resist stripping. Surface of a structure can be functionalized while areas covered in resist are protected from active or passive functionalization.
Provide herein are methods where a chemical cleaning is a preliminary step in surface preparation. In some exemplary methods, active functionalization is performed prior to lithography. A structure may be first cleaned, for example, using a piranha solution. An example of a cleaning process includes soaking a structure in a piranha solution (e.g., 90% H2SO4, 10% H2O2) at an elevated temperature (e.g., 120° C.) and washing (e.g., water) and drying the structure (e.g., nitrogen gas). The process optionally includes a post piranha treatment comprising soaking the piranha treated structure in a basic solution (e.g., NH4OH) followed by an aqueous wash (e.g., water). Alternatively, a structure can be plasma cleaned, optionally following the piranha soak and optional post piranha treatment. An example of a plasma cleaning process comprises an oxygen plasma etch.
Provided herein are methods for surface preparation where, an active chemical vapor (CVD) deposition step is done after photolithography. An exemplary first step includes optionally cleaning the surface cleaning the surface of a structure using cleaning methods disclosed herein. Cleaning can include oxygen plasma treatment. In some cases, the CVD step is for deposition of a mixture, the mixture having at least two molecules resulting in a high surface energy region and the region coated with the first chemical layer is a lower surface energy region. The mixture may comprise a molecule that binds the surface and couple nucleoside phosphoramidite mixed with a greater amount of a molecule that binds the surface and does not couple nucleoside phosphoramidite. For the two step dilution protocol, prior to depositing the mixture on the surface, a step includes deposition of 100% of the mixture ingredient molecule that binds the surface and does not couple nucleoside phosphoramidite. The first chemical layer can comprise a fluorosilane disclosed herein, for example, tridecafluoro-1,1,2,2-tetrahydrooctyl)-trichlorosilane. The second chemical layer can comprise at least two silanes disclosed herein. In some cases, the two silanes are GOPS and propyltrimethoxysilane. In an exemplary method, the surface is treated with propyltrimethoxysilane prior to treatment with the mixture. The above workflow is an example process and any step or component may be omitted or changed in accordance with properties desired of the final functionalized surface.
A surface of a structure disclosed herein can be coated with a resist, subject to functionalization and/or after lithography, and then treated to remove the resist. In some cases, the resist is removed with a solvent, for example, with a stripping solution comprising N-methyl-2-pyrrolidone. In some cases, resist stripping comprises sonication or ultrasonication. After stripping resist, the surface can be further subjected to deposition of an active functionalization agent binding to exposed areas to create a desired differential functionalization pattern. In some cases, the active functionalization areas comprise one or more different species of silanes, for example, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more silanes. One of the one or more silanes may b present in the functionalization composition in an amount greater than another silane. The composition and density of functionalization agent can contribute to a low error rate of oligonucleic acid synthesis, e.g., an error rate of less than 1 in 1000, less than 1 in 1500, less than 1 in 2000, less than 1 in 3000, less than 1 in 4000, less than 1 in 5000 bases).
Provided herein are methods which include applying an adhesion promoter to the surface. The adhesion promoter is applied in addition to applying the light sensitive lack. In some cases, applying both the adhesion promoter and light sensitive lack is done to surfaces including, without limitation, glass, silicon, silicon dioxide and silicon nitride. Exemplary adhesion promoters include silanes, e.g., aminosilanes. Exemplary aminosilanes include, without limitation, (3-aminopropyl)trimethoxysilane, (3-aminopropyl)triethoxysilane and N-(3-triethoxysilylpropyl)-4-hydroxybutyramide. In addition, a passive layer can be deposited on the surface, which may or may not have reactive oxide groups. The passive layer can comprise silicon nitride (Si3N4) or polyamide. The photolithographic step can be used to define regions where loci form on the passivation layer.
Provided here are methods for producing a substrate having a plurality of loci starts with a structure. The structure (e.g., silicon) can have any number of layers disposed upon it, including but not limited to a conducting layer such as a metal (e.g., silicon dioxide, silicon oxide, or aluminum). The structure can have a protective layer (e.g., titanium nitride). The layers can be deposited with the aid of various deposition techniques, such as, for example, chemical vapor deposition (CVD), atomic layer deposition (ALD), plasma enhanced CVD (PECVD), plasma enhanced ALD (PEALD), metal organic CVD (MOCVD), hot wire CVD (HWCVD), initiated CVD (iCVD), modified CVD (MCVD), vapor axial deposition (VAD), outside vapor deposition (OVD) and physical vapor deposition (e.g., sputter deposition, evaporative deposition).
An oxide layer can be deposited on the structure. The oxide layer can comprise silicon dioxide. The silicon dioxide can be deposited using tetraethyl orthosilicate (TEOS), high density plasma (HDP), or any combination thereof. The silicon dioxide can be deposited to a thickness suitable for the manufacturing of suitable microstructures described in further detail elsewhere herein. In some cases, silicon dioxide is grown in a conformal way on a silicon substrate. Growth on a silicon substrate can performed in a wet or dry atmosphere. An exemplary wet growth method is provided where wet growth is conducted at high temperatures, e.g., about 1000 degrees Celsius and in water vapor. The dry growth method can be conducted in the presence of oxygen.
Loci can be created using photolithographic techniques such as those used in the semiconductor industry. For example, a photo-resist (e.g., a material that changes properties when exposed to electromagnetic radiation) can be coated onto the silicon dioxide (e.g., by spin coating of a wafer) to any suitable thickness. Exemplary coating thicknesses include about 1, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, or 500 μm. An exemplary photoresist material is MEGAPOSIT SPR 3612 photoresist (Dow Electronic Material) or a similar product. The substrate including the photo-resist can be exposed to an electromagnetic radiation source. A mask can be used to shield radiation from portions of the photo-resist in order to define the area of the loci. The photo-resist can be a negative resist or a positive resist (e.g., the area of the loci can be exposed to electromagnetic radiation or the areas other than the loci can be exposed to electromagnetic radiation as defined by the mask). The area overlying the location in which the resolved loci are to be created is exposed to electromagnetic radiation to define a pattern that corresponds to the location and distribution of the resolved loci in the silicon dioxide layer. The photoresist can be exposed to electromagnetic radiation through a mask defining a pattern that corresponds to the resolved loci. Next, the exposed portion of the photoresist can be removed, such as, e.g., with the aid of wet chemical etching and a washing operation. The removed portion of the mask can then be exposed to a chemical etchant to etch the substrate and transfer the pattern of resolved loci into the silicon dioxide layer. The etchant can include an acid, such as, for example, buffered HF in the case of silicon dioxide.
Various etching procedures can be used to etch the silicon in the area where the resolved loci are to be formed. The etch can be an isotropic etch (i.e., the etch rate alone one direction substantially equal or equal to the etch rate along an orthogonal direction), or an anisotropic etch (i.e., the etch rate along one direction is less than the etch rate alone an orthogonal direction), or variants thereof. The etching techniques can be both wet silicon etches such as KOH, TMAH, EDP and the like, and dry plasma etches (for example DRIE). Both may be used to etch micro structures wafer through interconnections.
The dry etch can be an anisotropic etch that etches substantially vertically (e.g., toward the substrate) but not laterally or substantially laterally (e.g., parallel to the substrate). In some cases, the dry etch comprises etching with a fluorine based etchant such as CF4, CHF3, C2F6, C3F6, or any combination thereof. In some cases, the etching is performed for 400 seconds with an Applied Materials eMax-CT machine having settings of 100 mT, 1000 W, 20 G, and 50 CF4. The substrates described herein can be etched by deep reactive-ion etching (DRIE). DRIE is a highly anisotropic etch process used to create deep penetration, steep-sided holes and trenches in wafers/substrates, typically with high aspect ratios. The substrates can be etched using two main technologies for high-rate DRIE: cryogenic and Bosch. Methods of applying DRIE are described in the U.S. Pat. No. 5,501,893, which is herein incorporated by reference in its entirety.
The wet etch can be an isotropic etch that removes material in all directions. In some cases, the wet oxide etches are performed at room temperature with a hydrofluoric acid base that can be buffered (e.g., with ammonium fluoride) to slow down the etch rate. In some cases, a chemical treatment can be used to etch a thin surface material, e.g., silicon dioxide or silicon nitride. Exemplary chemical treatments include buffered oxide etch (BOE), buffered HF and/or NH4F. The etch time needed to completely remove an oxide layer is typically determined empirically. In one example, the etch is performed at 22° C. with 15:1 BOE (buffered oxide etch).
The silicon dioxide layer can be etched up to an underlying material layer. For example, the silicon dioxide layer can be etched until a titanium nitride layer. In some cases, the silicon dioxide is grown at a temperature of 1000 degrees Celsius and the underlying layer is typically silicon.
An additional surface layer can be added on top of an etched silicon layer subsequent to etching. In an exemplary arrangement, the additional surface layer is one that effectively binds to an adhesion promoter. Exemplary additional surface layers include, without limitation, silicon dioxide and silicon nitride. In the case of silicon dioxide, the additional layer can be added by conformal growth of a thin layer of this material on the silicon.
Clusters and Loci
Provided herein are devices having surfaces which comprises 50 to 10000 clusters 400, each cluster located in a predetermined position. The surface of a device disclosed herein can comprise more than 10000 clusters, each cluster located in a predetermined position. The term “locus” as used herein refers to a discrete region on the surface of a structure which provides support for synthesis of oligonucleotides encoding for a single sequence to extend from the surface. In an exemplary arrangement, each cluster comprises 121 loci 425, each loci being located in a predetermined position. The loci can comprise a molecule that binds the surface and also couples to nucleoside. Moreover, loci can comprise a mixture of (i) a molecule that binds the surface and couples to a nucleoside; and (ii) a molecule that binds the surface and does not couple to nucleoside. In some cases, the regions surrounding the loci comprise a molecule that binds the surface and does not couple to nucleoside, wherein the surface of regions surrounding the loci results a lower surface energy than the surface energy at the loci.
The loci can be located on a substantially planar surface. In some arrangements, a locus is located on a well, microwell, channel, post, or other raised or lowered feature of a surface disclosed herein. A region of a locus can span a plurality of wells, microwells, channels, posts, or other raised or lowered features of a surface disclosed herein.
Provided herein are structures comprising a surface that supports the synthesis of a plurality of oligonucleic acids having different predetermined sequences at addressable locations on a common support. The surface of a structure disclosed herein can support for the synthesis of more than 2,000; 5,000; 10,000; 20,000; 50,000; 100,000; 200,000; 300,000; 400,000; 500,000; 600,000; 700,000; 800,000; 900,000; 1,000,000; 1,200,000; 1,400,000; 1,600,000; 1,800,000; 2,000,000; 2,500,000; 3,000,000; 3,500,000; 4,000,000; 4,500,000; 5,000,000; 10,000,000 or more non-identical oligonucleic acids. In some case, at least a portion of the oligonucleic acids have an identical sequence or are configured to be synthesized with an identical sequence. Structures disclosed herein provides for a surface environment for the growth of oligonucleic acids having at least about 10, 20, 30, 50, 60, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 1000, 2000 bases or more in length.
Provided herein are surfaces in which oligonucleic acids are synthesized on distinct loci of a surface disclosed herein, wherein each locus supports the synthesis of a population of oligonucleic acids. In some cases, each locus supports the synthesis of a population of oligonucleic acids having a different sequence than a population of oligonucleic acids grown on another locus. Loci of a surface disclosed herein are each located within a cluster of a plurality of clusters. Provided herein are surfaces which comprise at least 10, 100, 500, 1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000, 10000, 11000, 12000, 13000, 14000, 15000, 20000, 30000, 40000, 50000 or more clusters. Provided herein are surfaces which comprise more than 2,000; 5,000; 10,000; 100,000; 200,000; 300,000; 400,000; 500,000; 600,000; 700,000; 800,000; 900,000; 1,000,000; 1,100,000; 1,200,000; 1,300,000; 1,400,000; 1,500,000; 1,600,000; 1,700,000; 1,800,000; 1,900,000; 2,000,000; 300,000; 400,000; 500,000; 600,000; 700,000; 800,000; 900,000; 1,000,000; 1,200,000; 1,400,000; 1,600,000; 1,800,000; 2,000,000; 2,500,000; 3,000,000; 3,500,000; 4,000,000; 4,500,000; 5,000,000; or 10,000,000 or more distinct loci. In some cases, each cluster includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 120, 130, 150, 200, 500 or more loci. In some cases, each cluster includes 50 to 500, 50 to 200, 50 to 150, or 100 to 150 loci. In some cases, each cluster includes 100 to 150 loci. In exemplary arrangements, each cluster includes 109, 121, 130 or 137 loci.
The number of distinct oligonucleic acids synthesized on a surface disclosed herein can be dependent on the number of distinct loci available on the surface. Provided herein are structures wherein the density of loci within a cluster of a structure disclosed herein is at least or about 1 locus per mm2, 10 loci per mm2, 25 loci per mm2, 50 loci per mm2, 65 loci per mm2, 75 loci per mm2, 100 loci per mm2, 130 loci per mm2, 150 loci per mm2, 175 loci per mm2, 200 loci per mm2, 300 loci per mm2, 400 loci per mm2, 500 loci per mm2, 1,000 loci per mm2 or more. In some cases, a the surface of a structure disclosed herein comprises from about 10 loci per mm2 to about 500 mm2, from about 25 loci per mm2 to about 400 mm2, or from about 50 loci per mm2 to about 200 mm2.
Provided herein are structures wherein the distance between the centers of two adjacent loci within a cluster is from about 10 μm to about 500 μm, from about 10 μm to about 200 μm, or from about 10 μm to about 100 μm. Provided herein are structures wherein the distance between two centers of adjacent loci is greater than about 10 μm, 20 μm, 30 μm, 40 μm, 50 μm, 60 μm, 70 μm, 80 μm, 90 μm or 100 μm. In some cases, the distance between the centers of two adjacent loci is less than about 200 μm, 150 μm, 100 μm, 80 μm, 70 μm, 60 μm, 50 μm, 40 μm, 30 μm, 20 μm or 10 μm.
Provided herein are structures wherein the number of distinct nucleic acids or genes assembled from a plurality of oligonucleic acids synthesized on the structure is dependent on the number of clusters available in the surface of the structure. In some case, the density of clusters within a region of the surface is at least or about 1 cluster per 100 mm2, 1 cluster per 10 mm2, 1 cluster per 5 mm2, 1 cluster per 4 mm2, 1 cluster per 3 mm2, 1 cluster per 2 mm2, 1 cluster per 1 mm2, 2 clusters per 1 mm2, 3 clusters per 1 mm2, 4 clusters per 1 mm2, 5 clusters per 1 mm2, 10 clusters per 1 mm2, 50 clusters per 1 mm2 or more. In some cases, a region of a surface disclosed herein comprises from about 1 cluster per 10 mm2 to about 10 clusters per 1 mm2. Provided herein are structures wherein the distance between the centers of two adjacent clusters is less than about 50 μm, 100 μm, 200 μm, 500 μm, 1000 μm, or 2000 μm or 5000 μm. Provided herein are structures wherein the distance between the centers of two adjacent clusters is 1.125 mm. In some cases, the distance between the centers of two adjacent clusters is between about 50 μm and about 100 μm, between about 50 μm and about 200 μm, between about 50 μm and about 300 μm, between about 50 μm and about 500 μm, or between about 100 μm to about 2000 μm. In some cases, the distance between the centers of two adjacent clusters is between about 0.05 mm to about 50 mm, between about 0.05 mm to about 10 mm, between about 0.05 mm and about 5 mm, between about 0.05 mm and about 4 mm, between about 0.05 mm and about 3 mm, between about 0.05 mm and about 2 mm, between about 0.1 mm and 10 mm, between about 0.2 mm and 10 mm, between about 0.3 mm and about 10 mm, between about 0.4 mm and about 10 mm, between about 0.5 mm and 10 mm, between about 0.5 mm and about 5 mm, or between about 0.5 mm and about 2 mm. In some cases, the distance between two clusters is about or at least about 0.3 mm, 0.4 mm, 0.5 mm, 0.6 mm, 0.7 mm, 0.8 mm. 0.9 mm, 1 mm, 1.2 mm, 1.4 mm, 1.6 mm, 1.8 mm, 2 mm, 2.2 mm, 2.4 mm, 2.6 mm, 2.8 mm, 3 mm, 3.2 mm, 3.4 mm, 3.6 mm, 3.8 mm, 4 mm, 4.2 mm, 4.4 mm, 4.6 mm, 4.8 mm, 5 mm, 5.2 mm, 5.4 mm, 5.6 mm, 5.8 mm, 6 mm, 6.2 mm, 6.4 mm, 6.6 mm, 6.8 mm, 7 mm, 7.2 mm, 7.4 mm, 7.6 mm, 7.8 mm, 8 mm, 8.2 mm, 8.4 mm, 8.6 mm, 8.8 mm, or 9 mm. The distance between two clusters may range between 0.3-9 mm, 0.4-8 mm, 0.5-7 mm, 0.6-6 mm, 0.7-5 mm, 0.7-4 mm, 0.8-3 mm, or 0.9-2 mm. Those of skill in the art appreciate that the distance may fall within any range bound by any of these values, for example 0.8 mm-2 mm.
Provided herein are structures having a surface wherein one or more loci on the surface comprise a channel or a well. In some cases, the channels or wells are accessible to reagent deposition via a deposition device such as an oligonucleic acid synthesizer. In some cases, reagents and/or fluids may collect in a larger well in fluid communication one or more channels or wells. In some case, a structure disclosed herein comprises a plurality of channels corresponding to a plurality of loci with a cluster, and the plurality of channels or wells are in fluid communication with one well of the cluster. In some cases, a library of oligonucleic acids is synthesized in a plurality of loci of a cluster, followed by the assembly of the oligonucleic acids into a large nucleic acid such as gene, wherein the assembly of the large nucleic acid optionally occurs within a well of the cluster, e.g., by using PCA.
Provided herein are structures wherein a cluster located on a surface disclosed herein has the same or different width, height, and/or volume as another cluster of the surface. A well located on a surface disclosed herein may have the same or different width, height, and/or volume as another well of the surface. Provided herein are structures wherein a channel located on a surface disclosed herein has the same or different width, height, and/or volume as another channel of the surface. Provided herein are structures wherein the diameter of a cluster is between about 0.05 mm to about 50 mm, between about 0.05 mm to about 10 mm, between about 0.05 mm and about 5 mm, between about 0.05 mm and about 4 mm, between about 0.05 mm and about 3 mm, between about 0.05 mm and about 2 mm, between about 0.05 mm and about 1 mm, between about 0.05 mm and about 0.5 mm, between about 0.05 mm and about 0.1 mm, between about 0.1 mm and 10 mm, between about 0.2 mm and 10 mm, between about 0.3 mm and about 10 mm, between about 0.4 mm and about 10 mm, between about 0.5 mm and 10 mm, between about 0.5 mm and about 5 mm, or between about 0.5 mm and about 2 mm. Provided herein are structures wherein the diameter of a cluster is less than or about 5 mm, 4 mm, 3 mm, 2 mm, 1 mm, 0.5 mm, 0.1 mm, 0.09 mm, 0.08 mm, 0.07 mm, 0.06 mm or 0.05 mm. In some cases, the diameter of a cluster is between about 1.0 and about 1.3 mm. In some cases, the diameter of a cluster is between about 0.5 to 2.0 mm. In some cases, the diameter of a cluster is about 1.150 mm. In some cases, the diameter of a cluster or well, or both is about 0.08 mm.
Provided herein are structures wherein the height of a well is from about 20 μm to about 1000 μm, from about 50 μm to about 1000 μm, from about 100 μm to about 1000 μm, from about 200 μm to about 1000 μm, from about 300 μm to about 1000 μm, from about 400 μm to about 1000 μm, or from about 500 μm to about 1000 μm. In some cases, the height of a well is less than about 1000 μm, less than about 900 μm, less than about 800 μm, less than about 700 μm, or less than about 600 μm.
Provided herein are structures wherein the structure disclosed herein comprises a plurality of channels corresponding to a plurality of loci within a cluster, wherein the height or depth of a channel is from about 5 μm to about 500 μm, from about 5 μm to about 400 μm, from about 5 μm to about 300 μm, from about 5 μm to about 200 μm, from about 5 μm to about 100 μm, from about 5 μm to about 50 μm, or from about 10 μm to about 50 μm. In some cases, the height of a channel is less than 100 μm, less than 80 μm, less than 60 μm, less than 40 μm or less than 20 μm.
Provided herein are structures wherein the diameter of a channel, well, or substantially planar locus is from about 0.5 μm to about 1000 μm, from about 0.5 μm to about 500 μm, from about 0.5 μm to about 200 μm, from about 0.5 μm to about 100 μm, from about 1 μm to about 100 μm, from about 5 μm to about 100 μm, or from about 10 μm to about 100 μm. In some cases, the diameter of a locus is about 90 μm, 80 μm, 70 μm, 60 μm, 50 μm, 40 μm, 30 μm, 20 μm, 10 μm, 1 μm, or 0.5 μm. In some cases, the diameter of a channel, well, or substantially planar locus is less than about 100 μm, 90 μm, 80 μm, 70 μm, 60 μm, 50 μm, 40 μm, 30 μm, 20 μm, 10 μm, 1 μm, or 0.5 μm. In some cases, the distance between the center of two adjacent loci is from about 1 μm to about 500 μm, from about 1 μm to about 200 μm, from about 1 μm to about 100 μm, from about 5 μm to about 200 μm, from about 5 μm to about 100 μm, from about 5 μm to about 50 μm, or from about 5 μm to about 30 μm, for example, about 20 μm.
Each of the resolved loci on the substrate can have any shape that is known in the art, or the shapes that can be made by methods known in the art. For example, each of the resolved loci can have an area that is in a circular shape, a rectangular shape, elliptical shape, or irregular shape. In some instances, the resolved loci can be in a shape that allows liquid to easily flow through without creating air bubbles. Resolved loci can have a circular shape, with a diameter that can be about, at least about, or less than about 0.5, 1 micrometers (μm), 2 μm, 3 μm, 4 μm, 5 μm, 6 μm, 7 μm, 8 μm, 9 μm, 10 μm, 11 μm, 12 μm, 13 μm, 14 μm, 15 μm, 16 μm, 17 μm, 18 μm, 19 μm, 20 μm, 25 μm, 30 μm, 35 μm, 40 μm, 45 μm, 50 μm, 55 μm, 60 μm, 65 μm, 70 μm, 75 μm, 80 μm, 85 μm, 90 μm, 95 μm, 100 μm, 110 μm, 120 μm, 130 μm, 140 μm, 150 μm, 160 μm, 170 μm, 180 μm, 190 μm, 200 μm, 250 μm, 300 μm, 350 μm, 400 μm, 450 μm, 500 μm, 550 μm, 600 μm, 650 μm, 700 μm or 750 μm. In some cases, the resolved loci have a diameter of 80 μm. The resolved loci may have a monodisperse size distribution, i.e. all of the microstructures may have approximately the same width, height, and/or length. A resolved loci of may have a limited number of shapes and/or sizes, for example the resolved loci may be represented in 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 15, 20, or more distinct shapes, each having a monodisperse size. The same shape can be repeated in multiple monodisperse size distributions, for example, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 15, 20, or more monodisperse size distributions. A monodisperse distribution may be reflected in a unimodular distribution with a standard deviation of less than 25%, 20%, 15%, 10%, 5%, 3%, 2%, 1%, 0.1%, 0.05%, 0.01%, 0.001% of the mode or smaller.
Textured Surfaces
Structures disclosed herein can be manufactured to increase the surface area such that, at particular regions for oligonucleic acid growth, the yield is increased. For example a textured surface is provided which comprises raised or recessed textured features, such as posts, wells, or other shapes. Texture features of the surfaces (e.g., posts or wells) are measured by the following parameters: S=surface area per unit cell; S0=surface area without texture; d=depth length; w=width length; and p=pitch length. In exemplary arrangements, the ratio of pitch length to width length is about 2. If the ratio of pitch length to width length is 2, then the following equation may be used to calculate the surface area of a chip with texture:
If the ratio of pitch length to width length is 2, then the following equation may be used to calculate the surface area of a chip with texture:
Provided herein are structures wherein the width length is at least twice the desired oligonucleic acid length to be synthesized on a surface disclosed herein. In some instances, the width length of a textured feature disclosed herein is greater than about 0.68 nm, 1 nm, 2 nm, 3 nm, 4 nm, 5 nm, 6 nm, 7 nm, 8 nm, 9 nm, 10 nm, 15 nm, 20 nm, 50 nm, 100 nm, 200 nm, 300 nm, 400 nm, 500 nm, 600 nm, 700 nm, 800 nm, 900 nm, 1 μm, 2 μm, 3 μm, 4 μm, 5 μm, 6 μm, 7 μm, 8 μm, 9 μm, or 10 μm. In some instances, the width length of a textured feature disclosed herein is about 0.1 nm, 0.5 nm, 1 nm, 2 nm, 3 nm, 4 nm, 5 nm, 6 nm, 7 nm, 8 nm, 9 nm, 10 nm, 15 nm, 20 nm, 50 nm, 100 nm, 200 nm, 300 nm, 400 nm, 500 nm, 600 nm, 700 nm, 800 nm, 900 nm, 1 μm, 2 μm, 3 μm, 4 μm, 5 μm, 6 μm, 7 μm, 8 μm, 9 μm, or 10 μm. Those of skill in the art appreciate that the width length may fall within any range bound by any of these values, for example 10 nm to 400 nm, 100 nm to 800 nm, or 200 nm to 1 μm. In some instances, the width length is 7 nm to 500 nm. In some case, the width length is 6.8 nm to 500 nm.
Provided herein are structures wherein the pitch length of a textured feature disclosed herein is greater than about 0.1 nm, 0.5 nm, 1 nm, 2 nm, 3 nm, 4 nm, 5 nm, 6 nm, 7 nm, 8 nm, 9 nm, 10 nm, 15 nm, 20 nm, 50 nm, 100 nm, 200 nm, 300 nm, 400 nm, 500 nm, 600 nm, 700 nm, 800 nm, 900 nm, 1 μm, 2 μm, 3 μm, 4 μm, 5 μm, 6 μm, 7 μm, 8 μm, 9 μm, or 10 μm. In some instances, the pitch length of a textured feature disclosed herein is about 0.1 nm, 0.5 nm, 1 nm, 2 nm, 3 nm, 4 nm, 5 nm, 6 nm, 7 nm, 8 nm, 9 nm, 10 nm, 15 nm, 20 nm, 50 nm, 100 nm, 200 nm, 300 nm, 400 nm, 500 nm, 600 nm, 700 nm, 800 nm, 900 nm, 1 μm, 2 μm, 3 μm, 4 μm, 5 μm, 6 μm, 7 μm, 8 μm, 9 μm, or 10 μm. Those of skill in the art appreciate that the pitch length may fall within any range bound by any of these values, for example 10 nm to 400 nm, 100 nm to 800 nm, or 200 nm to 1 μm. In some cases, the pitch length is 14 nm to 1 μm. In some cases, the pitch length is 13.6 nm to 1 μm. In some instances, the pitch length is about twice the width length.
Provided herein are structures wherein the depth length of a textured feature disclosed herein is greater than about 0.1 nm, 0.5 nm, 1 nm, 2 nm, 3 nm, 4 nm, 5 nm, 6 nm, 7 nm, 8 nm, 9 nm, 10 nm, 15 nm, 20 nm, 50 nm, 100 nm, 200 nm, 300 nm, 400 nm, 500 nm, 600 nm, 700 nm, 800 nm, 900 nm, 1 μm, 2 μm, 3 μm, 4 μm, 5 μm, 6 μm, 7 μm, 8 μm, 9 μm, or 10 μm. In some cases, the depth length of a textured feature disclosed herein is about 0.1 nm, 0.5 nm, 1 nm, 2 nm, 3 nm, 4 nm, 5 nm, 6 nm, 7 nm, 8 nm, 9 nm, 10 nm, 15 nm, 20 nm, 50 nm, 100 nm, 200 nm, 300 nm, 400 nm, 500 nm, 600 nm, 700 nm, 800 nm, 900 nm, 1 μm, 2 μm, 3 μm, 4 μm, 5 μm, 6 μm, 7 μm, 8 μm, 9 μm, or 10 μm. Those of skill in the art appreciate that the depth length may fall within any range bound by any of these values, for example 10 nm to 400 nm, 100 nm to 800 nm, or 200 nm to 1 μm. In some instances, the depth length is 8 nm to 1 μm. In some cases, the depth length is 13.6 nm to 2 μm. In some instances, the depth length is about 60% to about 125% of the pitch length.
Provided herein are structures wherein the width length and the pitch length are of a predetermined ratio. The ratio of pitch length to width length can be greater than about 0.1, 0.5, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, or 10. The ratio of pitch length to width length can be about 0.1, 0.5, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, or 10. In some instances, the ratio of pitch length to width length is about 1. In some instances, the ratio of pitch length to width length is about 2.
Provided herein are structures wherein the depth length and the pitch length are of a predetermined ratio. In some instances, the ratio of pitch length to width length is greater than about 0.1, 0.5, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, or 10. In some instances, the ratio of pitch length to width length is about 0.1, 0.5, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, or 10. In some instances, the ratio of depth length to pitch length is about 0.5. In some instances, the ratio of depth length to pitch length is about 0.6 to about 1.2. In some instances, the ratio of pitch length to width length is about 1. In some instances, the ratio of depth length to pitch length is about 0.6 to 1.25, or about 0.6 to about 2.5.
Provided herein are structures wherein a surface disclosed herein comprises a plurality of clusters, each cluster comprising a plurality of loci 400, wherein in each loci has a distance apart from each other 415 of about 25.0 μm, a diameter 410 of about 50 μm, a distance from the center of one loci to the center of another loci 405, 420 of 75 μm in X and Y axis directions,
Provided herein are structures wherein the surface of a structure described herein is substantially planar or comprises recesses/lowered or protruding/raised features. In some cases, the protrusions comprise wells and/or channels. The raised or lowered features may have sharp or rounded edges and may have cross-sections (widths) of any desired geometric shape, such as rectangular, circular, etc. The lowered features may form channels along the entire substrate surface or a portion of it.
The raised or lowered features may have an aspect ratio of at least or about at least 1:20, 2:20, 3:20, 4:20, 5:20, 6:20, 10:20, 15:20, 20:20, 20:10, 20:5, 20:1, or more. The raised or lowered features may have an aspect ratio of at most or about at most 20:1, 20:5, 20:10, 20:20, 20:15, 20:10, 20:10, 6:20, 5:20, 4:20, 3:20, 2:20, 1:20, or less. The raised or lowered features may have an aspect ratio that falls between 1:20-20:1, 2:20-20:5, 3:20-20:10, 4-20:20:15, 5:20-20:20, 6:20-20:20. Those of skill in the art appreciate that the raised or lowered features may have an aspect ratio that may fall within any range bound by any of these values, for example 3:20-4:20. In some cases, the raised or lowered features have an aspect ratio that falls within any range defined by any of the values serving as endpoints of the range.
Provided herein are structures wherein raised or lowered features have cross-sections of at least or about at least 10 nanometers (nm), 11 nm, 12 nm, 20 nm, 30 nm, 100 nm, 500 nm, 1000 nm, 10000 nm, 100000 nm, 1000000 nm, or more. The raised or lowered features may have cross-sections of at least or most or about at most 1000000 nm, 100000 nm, 10000 nm, 1000 nm, 500 nm, 100 nm, 30 nm, 20 nm, 12 nm, 11 nm, 10 nm, or less. The raised or lowered features may have cross-sections that fall between 10 nm-1000000 nm, 11 nm-100000 nm, 12 nm-10000 nm, 20 nm-1000 nm, 30 nm-500 nm. Those of skill in the art appreciate that the raised or lowered features may have cross-sections that may fall within any range bound by any of these values, for example 10 nm-100 nm. The raised or lowered features may have cross-sections that fall within any range defined by any of the values serving as endpoints of the range.
Provided herein are structures wherein, raised or lowered features have heights of at least or about at least 10 nanometers (nm), 11 nm, 12 nm, 20 nm, 30 nm, 100 nm, 500 nm, 1000 nm, 10000 nm, 100000 nm, 1000000 nm, or more. The raised or lowered features may have heights of at most or about at most 1000000 nanometers (nm), 100000 nm, 10000 nm, 1000 nm, 500 nm, 100 nm, 30 nm, 20 nm, 12 nm, 11 nm, 10 nm, or less. The raised or lowered features may have heights that fall between 10 nm-1000000 nm, 11 nm-100000 nm, 12 nm-10000 nm, 20 nm-1000 nm, 30 nm-500 nm. Those of skill in the art appreciate that the raised or lowered features may have heights that may fall within any range bound by any of these values, for example 100 nm-1000 nm. The raised or lowered features may have heights that fall within any range defined by any of the values serving as endpoints of the range. The individual raised or lowered features may be separated from a neighboring raised or lowered feature by a distance of at least or at least about 5 nanometers (nm), 10 nm, 11 nm, 12 nm, 20 nm, 30 nm, 100 nm, 500 nm, 1000 nm, 10000 nm, 100000 nm, 1000000 nm, or more. The individual raised or lowered features may be separated from a neighboring raised or lowered feature by a distance of at most or about at most 1000000 nanometers (nm), 100000 nm, 10000 nm, 1000 nm, 500 nm, 100 nm, 30 nm, 20 nm, 12 nm, 11 nm, 10 nm, 5 nm, or less. The raised or lowered features may have heights that fall between 5-1000000 nm, 10-100000 nm, 11-10000 nm, 12-1000 nm, 20-500 nm, 30-100 nm. Those of skill in the art appreciate that the individual raised or lowered features may be separated from a neighboring raised or lowered feature by a distance that may fall within any range bound by any of these values, for example 100-1000 nm. The individual raised or lowered features may be separated from a neighboring raised or lowered feature by a distance that falls within any range defined by any of the values serving as endpoints of the range. In some cases, the distance between two raised or lowered features is at least or about at least 0.1, 0.2, 0.5, 1.0, 2.0, 3.0, 5.0, 10.0 times, or more, the cross-section (width) or average cross-section of the raised or lowered features. The distance between the two raised or lowered features is at most or about at most 10.0, 5.0, 3.0, 2.0, 1.0, 0.5, 0.2, 0.1 times, or less, the cross-section (width) or average cross-section of the raised or lowered features. The distance between the two raised or lowered features may be between 0.1-10, 0.2-5.0, 1.0-3.0 times, the cross-section (width) or average cross-section of the raised or lowered features. Those of skill in the art appreciate that the distance between the two raised or lowered features may be between any times the cross-section (width) or average cross-section of the raised or lower features within any range bound by any of these values, for example 5-10 times. The distance between the two raised or lowered features may be within any range defined by any of the values serving as endpoints of the range.
Provided herein are structures wherein groups of raised or lowered features are separated from each other. Perimeters of groups of raised or lowered features may be marked by a different type of structural feature or by differential functionalization. A group of raised or lowered features may be dedicated to the synthesis of a single oligonucleotide. A group of raised or lowered features may span an area that is at least or about at least 10 μm, 11 μm, 12 μm, 13, 14 μm, 15 μm, 20 μm, 50 μm, 70 μm, 90 μm, 100 μm, 150 μm, 200 μm, or wider in cross section. A group of raised or lowered features may span an area that is at most or about at most 200 μm, 150 μm, 100 μm, 90 μm, 70 μm, 50 μm, 20 μm, 15 μm, 14 μm, 13 μm, 12 μm, 11 μm, 10 μm, or narrower in cross section. A group of raised or lowered features may span an area that is between 10-200 μm, 11-150 μm, 12-100 μm, 13-90 μm, 14-70 μm, 15-50 μm, 13-20 μm, wide in cross-section. Those of skill in art appreciate that a group of raised or lowered features may span an area that falls within any range bound by any of these values, for example 12-200 μm. A group of raised or lowered features may span an area that fall within any range defined by any of the values serving as endpoints of the range.
Provided herein are structures wherein a structure comprising a surface is about the size of a standard 96 well plate, for example between about 100 and 200 mm by between about 50 and 150 mm. In some cases, a structure comprising a surface disclosed herein has a diameter less than or equal to about 1000 mm, 500 mm, 450 mm, 400 mm, 300 mm, 250 nm, 200 mm, 150 mm, 100 mm or 50 mm. In some cases, the diameter of a structure comprising a surface disclosed herein is between about 25 mm and 1000 mm, between about 25 mm and about 800 mm, between about 25 mm and about 600 mm, between about 25 mm and about 500 mm, between about 25 mm and about 400 mm, between about 25 mm and about 300 mm, or between about 25 mm and about 200. Non-limiting examples of structure size include about 300 mm, 200 mm, 150 mm, 130 mm, 100 mm, 76 mm, 51 mm and 25 mm. In some cases, a structure comprising a surface disclosed herein has a planar surface area of at least about 100 mm2; 200 mm2; 500 mm2; 1,000 mm2; 2,000 mm2; 5,000 mm2; 10,000 mm2; 12,000 mm2; 15,000 mm2; 20,000 mm2; 30,000 mm2; 40,000 mm2; 50,000 mm2 or more. In some cases, the thickness of a structure comprising a surface disclosed herein is between about 50 μm and about 2000 μm, between about 50 um and about 1000 um, between about 100 um and about 1000 um, between about 200 um and about 1000 um, or between about 250 um and about 1000 um. Non-limiting examples of structure thickness include 275 um, 375 um, 525 um, 625 um, 675 um, 725 um, 775 um and 925 um. In some cases, the thickness of a structure varies with diameter and depends on the composition of the structure. For example, a structure comprising materials other than silicon has a different thickness than a silicon structure of the same diameter. Structure thickness may be determined by the mechanical strength of the material used and the structure must be thick enough to support its own weight without cracking during handling. Provided herein is a wafer comprises multiple structures (e.g., 1 to 30 or more) disclosed herein.
Provided herein are structures wherein a surface is configured to allow for controlled flow and mass transfer paths for oligonucleic acid synthesis on a surface. The configuration allows for the controlled and even distribution of mass transfer paths, chemical exposure times, and/or wash efficacy during oligonucleic acid synthesis. In some case, the configuration allows for increased sweep efficiency, for example by providing sufficient volume for a growing an oligonucleic acid such that the excluded volume by the growing oligonucleic acid does not take up more than 50, 45, 40, 35, 30, 25, 20, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1%, or less of the initially available volume that is available or suitable for growing the oligonucleic acid.
Provided herein are structures wherein a surface of the structure comprises features with a density of about or greater than about 1, 5, 10, 20, 30, 40, 50, 60, 70, 80, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 300, 400 or 500 features per mm2. Standard silicon wafer processes can be employed to create a structure surface that will have a high surface area as described above and a managed flow, allowing rapid exchange of chemical exposure. In some cases, the oligonucleotide synthesis surface comprises series of structural features with sufficient separation to allow oligomer chains greater than at least or about at least 20 mer, 25 mer, 30 mer, 50 mer, 100 mer, 200 mer, 250 mer, 300 mer, 400 mer, 500 mer, or more to be synthesized without substantial influence on the overall channel or pore dimension, for example due to excluded volume effects, as the oligonucleotide grows. In some cases, the oligonucleotide synthesis surface comprises a series of structures with sufficient separation to allow oligomer chains greater than at most or about at most 500 mer, 200 mer, 100 mer, 50 mer, 30 mer, 25 mer, 20 mer, or less to be synthesized without substantial influence on the overall channel or pore dimension, for example due to excluded volume effects, as the oligonucleotide grows.
Provided herein are structures wherein the distance between the features is greater than at least or about at least 5 nm, 10 nm, 20 nm, 100 nm, 1000 nm, 10000 nm, 100000 nm, 1000000 nm, or more. In some case, the distance between the features is greater than at most or about at most 1000000 nm, 100000 nm, 10000 nm, 1000 nm, 100 nm, 20 nm, 10 nm, 5 nm, or less. In some case, the distance between the features falls between 5-1000000 nm, 10-100000 nm, 20-10000 nm, or 100-1000 nm. In some case, the distance between the features is greater than 200 nm. The features may be created by any suitable MEMS processes described elsewhere herein or otherwise known in the art, such as a process employing a timed reactive ion etch process. Such semiconductor manufacturing processes can typically create feature sizes smaller than 200 nm, 100 nm, 50 nm, 40 nm, 30 nm, 25 nm, 20 nm, 10 nm, 5 nm, or less. Those of skill in the art appreciate that the feature size smaller than 200 nm can be between any of these values, for example, 20-100 nm. The feature size can fall within any range defined by any of these values serving as endpoints of the range. In some cases, an array of 40 μm wide posts are etched with 30 μm depth, which about doubles the surface area available for synthesis.
Provided herein are devices for oligonucleic acid synthesis, the device comprising a structure having a surface disclosed herein; a plurality of recesses or posts on the surface, wherein each recess or post comprises (i) a width length that is 6.8 nm to 500 nm, (ii) a pitch length that is about twice the width length, and (iii) a depth length that is about 60% to about 125% of the pitch length; a plurality of loci on the surface, wherein each locus has a diameter of 0.5 to 100 um, wherein each locus comprises at least two of the plurality of recesses or posts; a plurality of clusters on the surface, wherein each of the clusters comprise 50 to 500 loci and has a cross-section of 0.5 to 2 mm, wherein the plurality of loci comprise a less than saturating amount of a molecule that binds the surface and couples to nucleoside phosphoramidite; and a plurality of regions surrounding each loci comprise a molecule that binds the surface and does not couple to nucleoside phosphoramidite, wherein the plurality of loci have a higher surface energy than the plurality of regions surrounding each loci. In some cases, the molecule that binds the surface and couples to nucleoside phosphoramidite is a silane disclosed herein. In some cases, the molecule that binds the surface and does not couple to nucleoside phosphoramidite is a fluorosilane disclosed herein. In some cases, the plurality of loci are coated with a molecule that binds the surface, does not couple to nucleoside phosphoramidite, and has a higher surface energy than the molecule on plurality of regions surrounding each loci.
Preparation of Textured Surfaces
As discussed above,
To resist coat only a small region of the surface (e.g., lowered features such as a well and/or channel), a droplet of resist may be deposited into the lowered feature where it optionally spreads. In some cases, a portion of the resist is removed, for example, by etching (e.g., oxygen plasma etch) to leave a smooth surface covering only a select area.
The surface can be wet cleaned, for example, using a piranha solution. Alternatively, the surface can be plasma cleaned, for example, by dry oxygen plasma exposure. The photoresist may be coated by a process governed by wicking into the device layer channels. The photoresist may be patterned using photolithography to expose areas that are desired to be passive (i.e., areas where oligonucleic acid synthesis is not designed to take place). Patterning by photolithography may occur by exposing the resist to light through a binary mask that has a pattern of interest. After exposure, the resist in the exposed regions may be removed in developer solution.
Alignment Marks
During the deposition process, references points on a surface are used by a machine for calibration purposes. Surfaces described herein may comprise fiducial marks, global alignment marks, lithography alignment marks or a combination thereof. Fiducial marks are generally placed on the surface of a structure, such as an array of clusters 800 to facilitate alignment of such devices with other components of a system,
Fiducial marks may have various shapes and sizes. In some cases, a fiducial mark has the shape of a square, circle, triangle, cross, “X”, addition or plus sign, subtraction or minus sign, or any combination thereof. In some one example, a fiducial mark is in the shape of an addition or a plus sign 805. In some cases, a fiducial mark comprises a plurality of symbols. Exemplary fiducial mark may comprises one or more plus signs 810, e.g., 2, 3, 4, or more plus signs. In one example, a fiducial mark comprises 4 plus signs.
Fiducial marks may be located on the surface of structures disclosed herein. A fiducial mark may be about 0.5 μm, 1 μm, 2 μm, 3 μm, 4 μm, 5 μm, 6 μm, 7 μm, 8 μm, 9 μm, 10 μm, 100 μm, 1000 μm, 2000 μm, 5000 μm, 7000 μm, 8000 μm, 9000 μm, or 10,000 μm, from the center of the surface. In some cases, the fiducial mark is located from about 0.1 mm to about 10 mm from the edge of the surface portion, e.g., about 0.5 mm from the edge. In some case, the fiducial is located from about 1 mm to about 10 mm form a cluster, e.g., 1.69 mm. In some instances, a distance from the center of a fiducial mark and a nearest corner of a surface in one dimension is from about 0.5 mm to about 10 mm, e.g., about 1 mm. In some instances, a length of a fiducial mark in one dimension is from about 0.5 mm to about 5 mm, e.g., about 1 mm. In some instances, the width of a fiducial mark is from about 0.01 mm to about 2 mm, e.g., 0.05 mm.
Global alignment marks may have various shapes and sizes. Global alignment marks are placed on the surface of a structure described herein to facilitate alignment of such devices with other components of a system,
A global alignment mark may be located on the surface of a structure disclosed herein. In some cases, the global alignment mark is about 0.5 μm, 1 μm, 2 μm, 3 μm, 4 μm, 5 μm, 6 μm, 7 μm, 8 μm, 9 μm, 10 μm, 100 μm, 1000 μm, 2000 μm, 5000 μm, 7000 μm, 8000 μm, 9000 μm, or 10,000 μm, from the center of the surface. In some case, the global alignment mark is about 0.5 μm, 1 μm, 2 μm, 3 μm, 4 μm, 5 μm, 6 μm, 7 μm, 8 μm, 9 μm, 10 μm, 100 μm, 1000 μm, 2000 μm, 5000 μm, 7000 μm, 8000 μm, 9000 μm, or 10,000 μm, from the edge of the surface. In some cases, the global alignment mark is about 0.5 μm, 1 μm, 2 μm, 3 μm, 4 μm, 5 μm, 6 μm, 7 μm, 8 μm, 9 μm, 10 μm, 100 μm, 200 μm, 300 μm, 400 μm, 500 μm, 750 μm, or 1000 μm in size. In an example arrangement, the global alignment mark is about 125 μm in diameter and is located about 1000 μm from the edge of the surface of the structure. Surface disclosed herein may comprise one or more global alignment marks, e.g. 2, 3, 4, 5, 6, 7, 8, 9, 10, or more marks. The distance between the global alignment marks may be about 1 μm, 2 μm, 3 μm, 4 μm, 5 μm, 6 μm, 7 μm, 8 μm, 9 μm, 10 μm, 100 μm, 500 μm, 1000 μm, 2000 μm, 5000 μm, 7000 μm, 8000 μm, 9000 μm, or 10,000 μm.
Oligonucleic Acid Synthesis
De Novo Synthesis Workflow
Structures having modified surfaces described herein may be used for de novo synthesis processes. An exemplary workflow for one such process is divided generally into phases: (1) de novo synthesis of a single stranded oligonucleic acid library, (2) joining oligonucleic acids to form larger fragments, (3) error correction, (4) quality control, and (5) shipment,
Once preselected nucleic acids for generation are selected, a predetermined library of oligonucleic acids is designed for de novo synthesis. Various suitable methods are known for generating high density oligonucleic acid arrays. In the workflow example, a surface layer 1001 is provided. In the example, chemistry of the surface is altered in order to improve the oligonucleic acid synthesis process. Areas of low surface energy are generated to repel liquid while areas of high surface energy are generated to attract liquids. The surface itself may be in the form of a planar surface or contain variations in shape, such as protrusions or microwells which increase surface area. In the workflow example, high surface energy molecules selected serve a dual function of supporting DNA chemistry, as disclosed in International Patent Application Publication WO/2015/021080, which is herein incorporated by reference in its entirety.
In situ preparation of oligonucleic acid arrays is generated on a solid support and utilizes single nucleotide extension process to extend multiple oligomers in parallel. A device, such as an oligonucleic acid synthesizer, is designed to release reagents in a step wise fashion such that multiple oligonucleic acids extend, in parallel, one residue at a time to generate oligomers with a predetermined nucleic acid sequence 1002. In some cases, oligonucleic acids are cleaved from the surface at this stage. Cleavage may include gas cleavage, e.g., with ammonia or methylamine.
The generated oligonucleic acid libraries are placed in a reaction chamber. In this exemplary workflow, the reaction chamber (also referred to as “nanoreactor”) is a silicon coated well, containing PCR reagents and lowered onto the oligonucleic acid library 1003. Prior to or after the sealing 1004 of the oligonucleic acids, a reagent is added to release the oligonucleic acids from the surface. In the exemplary workflow, the oligonucleic acids are released subsequent to sealing of the nanoreactor 1005. Once released, fragments of single stranded oligonucleic acids hybridize in order to span an entire long range sequence of DNA. Partial hybridization 1005 is possible because each synthesized oligonucleic acid is designed to have a small portion overlapping with at least one other oligonucleic acid in the pool.
After hybridization, a PCA reaction is commenced. During the polymerase cycles, the oligonucleic acids anneal to complementary fragments and gaps are filled in by a polymerase. Each cycle increases the length of various fragments randomly depending on which oligonucleic acids find each other. Complementarity amongst the fragments allows for forming a complete large span of double stranded DNA 1006.
After PCA is complete, the nanoreactor is separated from the surface 1007 and positioned for interaction with a polymerase 1008. After sealing, the nanoreactor is subject to PCR 1009 and the larger nucleic acids are formed. After PCR 1010, the nanochamber is opened 1011, error correction reagents are added 1012, the chamber is sealed 1013 and an error correction reaction occurs to remove mismatched base pairs and/or strands with poor complementarity from the double stranded PCR amplification products 1014. The nanoreactor is opened and separated 1015. Error corrected product is next subject to additional processing steps, such as PCR and molecular bar coding, and then packaged 1022 for shipment 1023.
In some cases, quality control measures are taken. After error correction, quality control steps include for example interaction with a wafer having sequencing primers for amplification of the error corrected product 1016, sealing the wafer to a chamber containing error corrected amplification product 1017, and performing an additional round of amplification 1018. The nanoreactor is opened 1019 and the products are pooled 1020 and sequenced 1021. After an acceptable quality control determination is made, the packaged product 1022 is approved for shipment 1023.
The structures described herein comprise actively functionalized surfaces configured to support the attachment and synthesis of oligonucleic acids. Synthesized oligonucleic acids include oligonucleic acids comprising modified and/or non-canonical bases and/or modified backbones. In various methods, a library of oligonucleic acids having pre-selected sequences is synthesized on a structure disclosed herein. In some cases, one or more of the oligonucleic acids has a different sequence and/or length than another oligonucleic acid in the library. The stoichiometry of each oligonucleic acid synthesized on a surface is controlled and tunable by varying one or more features of the surface (e.g., functionalized surface) and/or oligonucleic acid sequence to be synthesized; one or more methods for surface functionalization and/or oligonucleic acid synthesis; or a combination thereof. In many instances, controlling the density of a growing oligonucleic acid on a resolved locus of a structure disclosed herein allows for oligonucleic acids to be synthesized with a low error rate.
Oligonucleic acids synthesized using the methods and/or devices described herein include at least about 50, 60, 70, 75, 80, 90, 100, 120, 150, 200, 300, 400, 500, 600, 700, 800 or more bases. A library of oligonucleic acids may be synthesized, wherein a population of distinct oligonucleic acids are assembled to generate a larger nucleic acid comprising at least about 500; 1,000; 2,000; 3,000; 4,000; 5,000; 6,000; 7,000; 8,000; 9,000; 10,000; 11,000; 12,000; 13,000; 14,000; 15,000; 16,000; 17,000; 18,000; 19,000; 20,000; 25,000; 30,000; 40,000; or 50,000 bases. Oligonucleic acid synthesis methods described herein are useful for the generation of an oligonucleic acid library comprising at least 500; 1,000; 5,000; 10,000; 20,000; 50,000; 100,000; 200,000; 300,000; 400,000; 500,000; 600,000; 700,000; 800,000; 900,000; 1,000,000; 1,100,000; 1,200,000; 1,300,000; 1,400,000; 1,500,000; 1,600,000; 1,700,000; 1,800,000; 1,900,000; 2,000,000; 2,200,000; 2,400,000; 2,600,000; 2,800,000; 3,000,000; 3,500,000; 4,000,000; or 5,000,000 distinct oligonucleic acids. In some case, at least about 1 pmol, 10 pmol, 20 pmol, 30 pmol, 40 pmol, 50 pmol, 60 pmol, 70 pmol, 80 pmol, 90 pmol, 100 pmol, 150 pmol, 200 pmol, 300 pmol, 400 pmol, 500 pmol, 600 pmol, 700 pmol, 800 pmol, 900 pmol, 1 nmol, 5 nmol, 10 nmol, 100 nmol or more of an oligonucleic acid is synthesized within a locus.
Oligonucleic acids are synthesized on a surface described herein using a system comprising an oligonucleic acid synthesizer that deposits reagents necessary for synthesis,
Methods are provided herein where at least or about at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 1000, 10000, 50000, 100000 or more nucleic acids can be synthesized in parallel. Total molar mass of nucleic acids synthesized within the device or the molar mass of each of the nucleic acids may be at least or at least about 10, 20, 30, 40, 50, 100, 250, 500, 750, 1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000, 10000, 25000, 50000, 75000, 100000 picomoles, or more.
Oligonucleic acid synthesis methods disclosed herein include those which are enzyme independent. An example of a synthesis method that is useful with the devices provided herein is one that incorporates phosphoramidite chemistry,
Provided herein are methods wherein an oligonucleic acid error rate is dependent on the efficiency of one or more chemical steps of oligonucleic acid synthesis. In some cases, oligonucleic acid synthesis comprises a phosphoramidite method, wherein a base of a growing oligonucleic acid chain is coupled to phosphoramidite. Coupling efficiency of the base is related to the error rate. For example, higher coupling efficiency correlates to lower error rates. In some cases, the devices and/or synthesis methods described herein allow for a coupling efficiency greater than 98%, 98.5%, 99%, 99.5%, 99.6%, 99.7%, 99.8%, 99.9%, 99.95%, 99.96%, 99.97%, 99.98%, or 99.99%. In some cases, an oligonucleic acid synthesis method comprises a double coupling process, wherein a base of a growing oligonucleic acid chain is coupled with a phosphoramidite, the oligonucleic acid is washed and dried, and then treated a second time with a phosphoramidite. Efficiency of deblocking in a phosphoramidite oligonucleic acid synthesis method also contributes to error rate. In some cases, the devices and/or synthesis methods described herein allow for removal of 5′-hydroxyl protecting groups at efficiencies greater than 98%, 98.5%, 99%, 99.5%, 99.6%, 99.7%, 99.8%, 99.9%, 99.95%, 99.96%, 99.97%, 99.98%, or 99.99%. Error rate may be reduced by minimization of depurination side reactions.
Methods for the synthesis of oligonucleic acids typically involve an iterating sequence of the following steps: application of a protected monomer to an actively functionalized surface (e.g., locus) to link with either the activated surface, a linker or with a previously deprotected monomer; deprotection of the applied monomer so that it can react with a subsequently applied protected monomer; and application of another protected monomer for linking. One or more intermediate steps include oxidation or sulfurization. In some cases, one or more wash steps precede or follow one or all of the steps.
In an exemplary method, at least 20,000 or more non-identical oligonucleic acids each at least 10, 50, 100 or more bases in length are synthesized, wherein each of the at least 20,000 non-identical oligonucleic acids extends from a different locus of the patterned surface. Methods disclosed herein provides for at least 20,000 non-identical oligonucleic acids collectively encoding for at least 200 preselected nucleic acids, and have an aggregate error rate of less than 1 in 1500 bases compared to predetermined sequences without correcting errors. In some cases, the aggregate error rate is less than 1 in 2000, less than 1 in 3000 bases or less compared to the predetermined sequences. Surfaces provided herein provide for the low error rates.
Oligonucleotide Libraries with Low Error Rates
The term “error rate” may also be referred to herein as a comparison of the collective sequence encoded by oligonucleic acids generated compared to the sequence of one or more predetermined longer nucleic acid, e.g., a gene. An aggregate “error rate” refers to the collective error rate of synthesized nucleic acids compared to the predetermined sequences for which the nucleic acids are intended to encode. Error rates include mismatch error rate, deletion error rate, insertion error rate, insertion/deletion error rate, any combination thereof. Methods and devices herein provide for low error rates are for synthesized oligonucleic acid libraries having at least 20,000; 40,000; 60,000; 80,000; 100,000; 200,000; 300,000; 400,000; 500,000; 600,000; 700,000; 800,000; 1,000,000; or 2,000,000 or more oligonucleic acids. Loci may be configured to comprise a population of oligonucleic acids, wherein the population may be configured to comprise oligonucleic acids having the same or different sequences.
Devices and methods described herein provide for a low overall error rate for the individual types of errors are achieved. Individual types of error rates include deletions, insertions, or substitutions for an oligonucleic acid library synthesized. In some cases, oligonucleic acids synthesized have an average error rate of about 1:500, 1:1000, 1:2000, 1:3000, 1:4000, 1:5000, 1:6000, 1:7000, 1:8000, 1:9000, 1:10000 or less. These error rates may be for at least 50%, 60%, 70%, 80%, 90%, 95%, 98%, 99%, 99.5%, or more of the oligonucleic acids synthesized.
Methods described herein provide synthesis of oligonucleic acids having an average deletion error rate of about 1:500, 1:1000, 1:1700, 1:2000, 1:3000, 1:4000, 1:5000, 1:6000, 1:7000, 1:8000, 1:9000, 1:10000 or less. Methods described herein provide synthesis of oligonucleic acids having an deletion error rate of about 1:500, 1:1000, 1:1700, 1:2000, 1:3000, 1:4000, 1:5000, 1:6000, 1:7000, 1:8000, 1:9000, 1:10000 or less. Methods described herein provide synthesis of oligonucleic acids having an average insertion error rate of about 1:500, 1:1000, 1:2000, 1:3000, 1:4000, 1:5000, 1:6000, 1:7000, 1:8000, 1:9000, 1:10000 or less. Methods described herein provide synthesis of oligonucleic acids having an insertion error rate of about 1:500, 1:1000, 1:2000, 1:3000, 1:4000, 1:5000, 1:6000, 1:7000, 1:8000, 1:9000, 1:10000 or less. Methods described herein provide synthesis of oligonucleic acids having an average substitution error rate of about 1:500, 1:1000, 1:2000, 1:3000, 1:4000, 1:5000, 1:6000, 1:7000, 1:8000, 1:9000, 1:10000 or less. Methods described herein provide synthesis of oligonucleic acids having a substitution error rate of about 1:500, 1:1000, 1:2000, 1:3000, 1:4000, 1:5000, 1:6000, 1:7000, 1:8000, 1:9000, 1:10000 or less. The overall error rate or error rates for individual types of errors such as deletions, insertions, or substitutions for each oligonucleotide synthesized, may be for at least 50%, 60%, 70%, 80%, 90%, 95%, 98%, 99%, 99.5%, or more of the oligonucleotides synthesized.
Oligonucleic Acid Release and Assembly
Oligonucleic acids synthesized using the methods and devices described herein, are optionally released from the surface from which they were synthesized. In some cases, oligonucleic acids are cleaved from the surface at this stage. Cleavage may include gaseous cleavage, e.g., with gaseous ammonia or gaseous methylamine. Loci in a single cluster collectively correspond to sequence encoding for a single gene, and, when cleaved, may remain on the surface of the loci within a cluster. The application of ammonia gas is used to simultaneously deprotect phosphates groups protected during the synthesis steps, i.e. removal of electron-withdrawing cyano group. Once released from the surface, oligonucleic acids may be assembled into larger nucleic acids. Synthesized oligonucleic acids are useful, for example, as components for gene assembly/synthesis, site-directed mutagenesis, nucleic acid amplification, microarrays, and sequencing libraries.
Provided herein are methods where oligonucleic acids of predetermined sequence are designed to collectively span a large region of a target sequence, such as a gene. In some cases, larger oligonucleic acids are generated through ligation reactions to join the synthesized oligonucleic acids. One example of a ligation reaction is polymerase chain assembly (PCA). In some cases, at least of a portion of the oligonucleic acids are designed to include an appended region that is a substrate for universal primer binding. For PCA reactions, the presynthesized oligonucleic acids include overlaps with each other (e.g., 4, 20, 40 or more bases with overlapping sequence). During the polymerase cycles, the oligonucleic acids anneal to complementary fragments and then are filled in by polymerase. Each cycle thus increases the length of various fragments randomly depending on which oligonucleic acids find each other. Complementarity amongst the fragments allows for forming a complete large span of double stranded DNA. In some cases, after the PCA reaction is complete, an error correction step is conducted using mismatch repair detecting enzymes to remove mismatches in the sequence. Once larger fragments of a target sequence are generated, they can be amplified. For example, in some cases, a target sequence comprising 5′ and 3′ terminal adaptor sequences is amplified in a polymerase chain reaction (PCR) which includes modified primers, e.g., uracil containing primers the hybridize to the adaptor sequences.
Provided herein are methods wherein following oligonucleic acid synthesis, oligonucleic acids within one cluster are released from their respective surfaces and pooled into the common area, such as a ell. In some cases, the pooled oligonucleic acids are assembled into a larger nucleic acid, such as a gene, within the well. In some cases, at least about 1, 10, 50, 100, 200, 240, 500, 1000, 10000, 20000, 50000, 100000, 1000000 or more nucleic acids are assembled from oligonucleic acids synthesized on a surface disclosed herein. A pass-printing scheme may be used to deliver reagents to loci in a cluster, as wells as to transfer synthesis reaction products to another location. At least 2, 3, 4, 5, 6, 7, 8, 9, or 10 passes may be used to deliver reagents. For example, four passes of the may be used to deliver reagents to a second structure for assembly or analysis,
Computer Systems
Methods are provided herein for attachment of pre-synthesized oligonucleotide and/or polynucleotide sequences to a support and in situ synthesis of the same using light-directed methods, flow channel and spotting methods, inkjet methods, pin-based methods and/or bead-based methods are used. In some cases, pre-synthesized oligonucleotides are attached to a support or are synthesized using a spotting methodology wherein monomers solutions are deposited drop wise by a dispenser that moves from region to region. In one example, oligonucleotides are spotted on a support using a mechanical wave actuated dispenser.
The systems described herein can further include a member for providing a droplet to a first spot (or feature) having a plurality of support-bound oligonucleotides. The droplet can include one or more compositions comprising nucleotides or oligonucleotides (also referred herein as nucleotide addition constructs) having a specific or predetermined nucleotide to be added and/or reagents that allow one or more of hybridizing, denaturing, chain extension reaction, ligation, and digestion. In some cases, different compositions or different nucleotide addition constructs may be deposited at different addresses on the support during any one iteration so as to generate an array of predetermined oligonucleotide sequences (the different features of the support having different predetermined oligonucleotide sequences). One particularly useful way of depositing the compositions is by depositing one or more droplet, each droplet containing the desired reagent (e.g. nucleotide addition construct) from a pulse jet device spaced apart from the support surface, onto the support surface or features built into the support surface.
A substrate with resolved features is “addressable” when it has multiple regions of different moieties (e.g., different polynucleotide sequences) such that a region (i.e., a “feature” or “spot” of the substrate) at a particular predetermined location (i.e., an “address”) on the substrate will detect a particular target or class of targets (although a feature may incidentally detect non-targets of that location). Substrate features are typically, but need not be, separated by intervening spaces. In some cases, features may be built into a substrate and may create one-, two-, or three-dimensional microfluidic geometries. A “substrate layout” refers to one or more characteristics of the features, such as feature positioning on the substrate, one or more feature dimensions, and an indication of a molecule at a given location.
Any of the systems described herein, may be operably linked to a computer and may be automated through a computer either locally or remotely. Methods and disclosed herein may further comprise software programs on computer systems and use thereof. Accordingly, computerized control for the synchronization of the dispense/vacuum/refill functions such as orchestrating and synchronizing the material deposition device movement, dispense action and vacuum actuation are within the bounds of the invention. The computer systems may be programmed to interface between the user specified base sequence and the position of a material deposition device to deliver the correct reagents to specified regions of the substrate.
The computer system 1400 illustrated in
A high speed cache 1504 can be connected to, or incorporated in, the processor 1502 to provide a high speed memory for instructions or data that have been recently, or are frequently, used by processor 1502. The processor 1502 is connected to a north bridge 1506 by a processor bus 1508. The north bridge 1506 is connected to random access memory (RAM) 1510 by a memory bus 1512 and manages access to the RAM 1510 by the processor 1502. The north bridge 1506 is also connected to a south bridge 1514 by a chipset bus 1516. The south bridge 1514 is, in turn, connected to a peripheral bus 1518. The peripheral bus can be, for example, PCI, PCI-X, PCI Express, or other peripheral bus. The north bridge and south bridge are often referred to as a processor chipset and manage data transfer between the processor, RAM, and peripheral components on the peripheral bus 1518. In some alternative architectures, the functionality of the north bridge can be incorporated into the processor instead of using a separate north bridge chip. In some embodiments, system 1500 can include an accelerator card 1522 attached to the peripheral bus 1518. The accelerator can include field programmable gate arrays (FPGAs) or other hardware for accelerating certain processing. For example, an accelerator can be used for adaptive data restructuring or to evaluate algebraic expressions used in extended set processing.
Software and data are stored in external storage 1524 and can be loaded into RAM 1510 and/or cache 1504 for use by the processor. The system 1500 includes an operating system for managing system resources; non-limiting examples of operating systems include: Linux, Windows™, MACOS™, BlackBerry OS™, iOS™, and other functionally-equivalent operating systems, as well as application software running on top of the operating system for managing data storage and optimization in accordance with example embodiments of the present invention. In this example, system 1500 also includes network interface cards (NICs) 1520 and 1521 connected to the peripheral bus for providing network interfaces to external storage, such as Network Attached Storage (NAS) and other computer systems that can be used for distributed parallel processing.
The above computer architectures and systems are examples only, and a wide variety of other computer, cell phone, and personal data assistant architectures and systems can be used in connection with example embodiments, including systems using any combination of general processors, co-processors, FPGAs and other programmable logic devices, system on chips (SOCs), application specific integrated circuits (ASICs), and other processing and logic elements. In some cases, all or part of the computer system can be implemented in software or hardware. Any variety of data storage media can be used in connection with example embodiments, including random access memory, hard drives, flash memory, tape drives, disk arrays, Network Attached Storage (NAS) and other local or distributed data storage devices and systems.
The computer system can be implemented using software modules executing on any of the above or other computer architectures and systems. In other examples, the functions of the system can be implemented partially or completely in firmware, programmable logic devices such as field programmable gate arrays (FPGAs), system on chips (SOCs), application specific integrated circuits (ASICs), or other processing and logic elements. For example, the Set Processor and Optimizer can be implemented with hardware acceleration through the use of a hardware accelerator card, such as accelerator card 1522.
The following examples are set forth to illustrate more clearly the principle and practice of embodiments disclosed herein to those skilled in the art and are not to be construed as limiting the scope of any claimed embodiments. Unless otherwise stated, all parts and percentages are on a weight basis.
In this example, a silicon dioxide wafer was treated with a single organic layer deposited at different locations on the wafer to create loci with a high surface energy and coupling ability to nucleoside. A surface of 1000 Angstroms of silicon dioxide on top of polished silicon was selected. A controlled surface density of hydroxyl groups was achieved on the surface by a wet process using a 1% solution of N-(3-TRIETHOXYSILYLPROPYL-4HYDROXYBUTYRAMIDE in ethanol and acetic acid deposited on the surface and treated for 4 hours, followed by placing the wafers on a hot plate at 150 degrees C. for 14 hours.
A layer of MEGAPOSIT SPR 3612 photoresist was deposited on top of the aminosilane. In this case, the organic layer was an adhesion promoter for the photoresist. The photoresist layer was patterned by exposure to ultraviolet light through a shadow mask. The photoresist pattern was transferred into the organic layer by oxygen plasma. The photoresist was then stripped, revealing a pattern of regions for biomolecular coupling. Clusters of 80 discs with a diameter of about 80 μm were well resolved.
Oligonucleic acids were extended from the surface. The photolithographic process performed without adhesion promoter layer did not result in organized loci having oligonucleic acids extended (data not shown). Oligonucleic acids extension performed a surface treated with the photolithographic process performed using the aminosilane layer resulted in clarified small discs of oligonucleic acids 80 μm in diameter (
A CVD process was performed by delivering silane to the surface in gaseous state and applying a controlled deposition pressure of about 200 mTor and a controlled temperature of about 150 degrees C. (Data not shown.)
A oligonucleic acid synthesis device was assembled into a flowcell, which was connected to an Applied Biosystems (ABI394 DNA Synthesizer). The oligonucleic acid synthesis device was uniformly functionalized with N-(3-TRIETHOXYSILYLPROPYL)-4-HYDROXYBUTYRAMIDE (Gelest, CAS No. 156214-80-1) and was used to synthesize an exemplary oligonucleotide of 50 bp (“50-mer oligonucleotide”) using oligonucleotide synthesis methods described herein. The sequence of the 50-mer was as described in SEQ ID NO.: 1.
5′AGACAATCAACCATTTGGGGTGGACAGCCTTGACCTCTAGACTTCGGCAT ## TTTTTTTTTT3′ (SEQ ID NO.: 1), where # denotes Thymidine-succinyl hexamide CED phosphoramidite (CLP-2244 from ChemGenes), which is a cleavable linker enabling the release of oligos from the surface during deprotection. The synthesis was done using standard DNA synthesis chemistry (coupling, capping, oxidation, and deblocking) according to the protocol in Table 3 and an ABI synthesizer.
The phosphoramidite/activator combination was delivered similar to the delivery of bulk reagents through the flowcell. No drying steps were performed as the environment stays “wet” with reagent the entire time. The flow restrictor was removed from the ABI 394 synthesizer to enable faster flow. Without flow restrictor, flow rates for amidites (0.1M in ACN), Activator, (0.25M Benzoylthiotetrazole (“BTT”; 30-3070-xx from GlenResearch) in ACN), and Ox (0.02M 12 in 20% pyridine, 10% water, and 70% THF) were roughly ˜100 uL/sec, for acetonitrile (“ACN”) and capping reagents (1:1 mix of CapA and CapB, wherein CapA is acetic anhydride in THF/Pyridine and CapB is 16% 1-methylimidizole in THF), roughly ˜200 uL/sec, and for Deblock (3% dichloroacetic acid in toluene), roughly ˜300 uL/sec (compared to ˜50 uL/sec for all reagents with flow restrictor). The time to completely push out Oxidizer was observed, the timing for chemical flow times was adjusted accordingly and an extra ACN wash was introduced between different chemicals. After oligonucleotide synthesis, the chip was deprotected in gaseous ammonia overnight at 75 psi. Five drops of water were applied to the surface to recover oligonucleic acids (
The same process as described in Example 3 for the synthesis of the 50-mer sequence was used for the synthesis of a 100-mer oligonucleotide (“100-mer oligonucleotide”; 5′ CGGGATCCTTATCGTCATCGTCGTACAGATCCCGACCCATTTGCTGTCCACCAGTCATGCTAGCCATACCATGATGATGATGATGATGAGAACCCCGCAT ## TTTTTTTTTT3′, where # denotes Thymidine-succinyl hexamide CED phosphoramidite (CLP-2244 from ChemGenes); SEQ ID NO.: 2) on two different silicon chips, the first one uniformly functionalized with N-(3-TRIETHOXYSILYLPROPYL)-4-HYDROXYBUTYRAMIDE and the second one functionalized with 5/95 mix of 11-acetoxyundecyltriethoxysilane and n-decyltriethoxysilane, and the oligos extracted from the surface were analyzed on a BioAnalyzer instrument (
All ten samples from the two chips were further PCR amplified using a forward (5′ATGCGGGGTTCTCATCATC3′; SEQ ID NO.: 3) and a reverse (5′CGGGATCCTTATCGTCATCG3′; SEQ ID NO.: 4) primer in a 50 uL PCR mix (25 uL NEB Q5 mastermix, 2.5 uL 10 uM Forward primer, 2.5 uL 10 uM Reverse primer, 1 uL oligo extracted from the surface, and water up to 50 uL) using the following thermalcycling program:
98 C, 30 sec
98 C, 10 sec; 63 C, 10 sec; 72 C, 10 sec; repeat 12 cycles
72 C, 2 min
The PCR products were also run on a BioAnalyzer (data not shown), demonstrating sharp peaks at the 100-mer position. Next, the PCR amplified samples were cloned, and Sanger sequenced. Table 4 summarizes the results from the Sanger sequencing for samples taken from spots 1-5 from chip 1 and for samples taken from spots 6-10 from chip 2.
Thus, the high quality and uniformity of the synthesized oligonucleotides were repeated on two chips with different surface chemistries. Overall, 89%, corresponding to 233 out of 262 of the 100-mers that were sequenced were perfect sequences with no errors.
Finally, Table 5 summarizes key error characteristics for the sequences obtained from the oligonucleotides samples from spots 1-10.
A nanoreactor was sealed to a silicon wafer. The wafer contained nucleic acids generated from the DNA synthesis reaction. Gene assembly reagents were added to the reaction chamber. Gene amplification occurred in the resolved enclosure. The reaction chamber included nucleic acids encoding for different predetermined sequences. A series of enzymatic reactions resulted in the linking of amplified nucleic acids into a 2 kilobase gene.
A gene of about 1 kb (SEQ ID NO.: 5; Table 6) was assembled using 6 purchased oligonucleotides (5 nM each during PCA) (Ultramer; SEQ ID NO.: 6-11; Table 6) and assembled in a PCA reaction using a 1×NEB Q5 buffer with 0.02 U/uL Q5 hot-start high-fidelity polymerase and 100 uM dNTP as follows:
1 cycle: 98 C, 30 sec
15 cycles: 98 C, 7 sec; 62 C 30 sec; 72 C, 30 sec
1 cycle: 72 C, 5 min
Ultramer oligonucleotides are expected to have error rates of at least 1 in 500 nucleotides, more likely at least 1 in 200 nucleotides or more.
The assembled gene was amplified in a PCR reaction using a forward primer (5′ ATGACCATGATTACGGATTCACTGGCC3′ SEQ ID NO.: 12) and a reverse primer (5′GATAGAGATTCGGGATTTCGGCGCTCC3′ SEQ ID NO.: 13), using 1×NEB Q5 buffer with 0.02 U/uL Q5 hot-start high-fidelity polymerase, 200 uM dNTP, and 0.5 uM primers as follows:
1 cycle: 98 C, 30 sec
30 cycles: 98 C, 7 sec; 65 C 30 sec; 72 C, 45 sec
1 cycle: 72 C, 5 min
The amplified assembled gene was analyzed in a BioAnalyzer and cloned. Mini-preps from ˜24 colonies were Sanger sequenced. The BioAnalyzer analysis provided a broad peak and a tail for the uncorrected gene, indicated a high error rate. The sequencing indicated an error rate of 1/789 (data not shown). Two rounds of error correction were followed using CorrectASE (Life Technologies, www.lifetechnologies.com/order/catalog/product/A14972) according to the manufacturer's instructions. The resulting gene samples were similarly analyzed in the BioAnalyzer after round one and round two and cloned. (Data not shown.) 24 colonies were picked for sequencing. The sequencing results indicated an error rate of 1/5190 bp and 1/6315 bp after the first and second rounds of error correction, respectively.
240 genes were selected for de novo synthesis wherein the genes ranged from 701 to 1796 base pairs in length. The gene sequence for each of the genes was divided into smaller fragments encoding for oligonucleic acids ranging between 50 to 90 nucleotides in length, with each nucleotide having 20 to 25 nucleotides overlapping sequences A distribution chart is depicted in
Gene sequence for a single gene that was larger than 1.8 kb in length was divided into smaller fragments encoding for oligonucleic acids ranging between 50 to 120 nucleotides in length, with each nucleotide having 20 to 25 nucleotides overlapping sequences. A total of 90 different design arrangement were synthesized. A distribution chart is depicted in
Various methods for surface preparation were preformed, which include: (i) performing an active chemical vapor (CVD) deposition step before photolithography; (ii) performing an active chemical vapor (CVD) deposition step after photolithography; and (i) performing a dilution active chemical vapor (CVD) deposition step after photolithograph.
A first silicon dioxide structure having a silicon oxide layer was individually cleaned in an oxygen plasma (referred to as the “HAPS” chip. An aminosilane, N-(3-TRIETHOXYSILYLPROPYL)-4-HYDROXYBUTYRAMIDE, HAPS), was deposited on the silicon oxide at predetermined locations, referred to as loci. The surface was coated with AZ resist and then baked. The surface was cleaned again in an oxygen plasma, fluorinated (depositing (tridecafluoro-1,1,2,2-tetrahydrooctyl)-trichlorosilane), and then stripped.
A second silicon dioxide structure having a silicon oxide layer was individually cleaned in an oxygen plasma (referred to as the “100% GOPS-1” chip). A silane, 3-glycidoxypropyltrimethoxysilane (GOPS), was deposited on the silicon oxide at predetermined locations, referred to as loci. The surface was coated with AZ resist and then baked. The surface was cleaned again in an oxygen plasma, fluorinated (depositing (tridecafluoro-1,1,2,2-tetrahydrooctyl)-trichlorosilane), and then stripped.
A third silicon dioxide structure having a silicon oxide layer was individually cleaned in an oxygen plasma (referred to as the “100% GOPS-2” chip). Directly after cleaning, the surface was coated with AZ resist and then baked at 90 degrees Celsius for 7 min. The surface was cleaned again in an oxygen plasma, fluorinated in the YES CVD system (depositing (tridecafluoro-1,1,2,2-tetrahydrooctyl)-trichlorosilane), and then stripped. The surface was treated with 100% GOPS at 1 Torr for 1 hour at chamber temperature of 100 degrees Celsius. Lastly, the surface was activated in water for 30 minutes at room temperature.
For the diluted active agent deposition protocol, a fourth silicon dioxide structure having a silicon oxide layer was individually cleaned in an oxygen plasma (referred to as the “GOPS-diluted” chip). Directly after cleaning, the surface was coated with AZ resist and then baked at 90 degrees Celsius for 7 min. The surface was cleaned again in an oxygen plasma, fluorinated in the YES CVD system (depositing (tridecafluoro-1,1,2,2-tetrahydrooctyl)-trichlorosilane), and then stripped. The surface was treated with 100% propyltrimethoxysilane at 3.5 Torr for 15 hours at chamber temperature of 100 C degrees Celsius. The surface was treated with water for 30 minutes, followed by a second deposition step. In the second deposition step, a mixture of 0.05% GOPS and 99.95% propyltrimethoxysilane was deposited on the surface and treated at 3.5 Torr for 1.5 hours at chamber temperature of 100 C. Lastly, the surface was activated in water for 30 minute at room temperature. For each structure prepared, the molecules able to couple nucleoside (HAPS and GOPS) were deposited in described locations on the surfaces, loci, and the loci were arranged in clusters.
Oligonucleic acids of 30, 50 and 80 nucleotides in length were synthesized on the surfaces prepared in Example 9. A FRT tool (MicroProf 100, Fries Research and Technology, GmbH, Germany) was used to measure the thickness of DNA post-synthesis. The FRT tool scans across a cluster and measure reflectivity of light, which corresponds to the amount of material on the surface. A summary of the results is shown in
Qubit analysis from fluorometric measurement of the clusters was also performed. A summary of the analysis from growth of 30, 50 and 80-mers is in the chart in
Oligonucleic acids of 30, 50 and 80 nucleotides in length were synthesized on the surfaces prepared in Example 9, gas cleaved from the surface, and subject to sequence analysis using an Illumina MiSeq. Deletion error rates were determined for oligonucleic acids synthesized on the GOPS-diluted surfaces. The total deletion error rate was 0.060%, or 1 in 1674 bases. Sequencing of control oligonucleic acids from the GOPS-diluted chips resulted in a deletion rate of 0.070%. Analysis of the deletion error rate frequency at particular bases in terms of distance from the surface was performed, and results are shown in the plot in
A microfluidic device is manufactured to have increased surface area. An array of recesses or posts is etched into a silicon dioxide wafer to increase surface area by a factor of 2 to 3. A number of steps are performed to make a textured surface. To the starting silicon dioxide wafer, with one side polished, is added a textured layer via a pass printing scheme lithography. A silicon reactive ion etching and resist strip is added to the chip, followed by oxidation of the surface. The fiducial layer is printed on via lithography, after which a final oxide etching results in a textured silicon ship. The surface has a recess or post width that is about 2 times the length of the desired oligonucleic acids to be extended. A chart of exemplary widths is provided in Table 8 based on an approximate length of 0.34 nm/base.
A silicon dioxide structure is prepared having a 16×16 array of clusters. Each cluster includes multiple groups of 4 loci, wherein each loci resides on top of a different design feature, as outlined in Table 9.
Each loci is coated with an silane that binds the surface and couples to nucleoside phosphoramidite. Oligonucleic acid synthesis is perform on the structure and DNA thickness, DNA mass and error rates of the synthesized oligonucleic acids are measured.
A microfluidic device is manufactured. Each device is 200 mm, double-side polished. A SOI wafer has 21 chips arranged in a 200 mm wafer. Each chip is 32 mm×32 mm in size, and comprised a 16×16 array of clusters. A total of 256 clusters are present in the array. 121 reaction sites are located in a single cluster, providing 30,976 individually addressable oligo sites per chip. Each cluster pitch is 1.125 mm. Each of the reaction sites are about 50 μm.
A silicon dioxide structure is prepared having a 16×16 array of clusters. Each cluster includes groups of 4 loci, wherein each loci is in close proximity to a one of three fiducial marks having a plurality of lines, wherein the line weight is listed in Table 10. Each fiducial design is in the shape of a plus 805. One of the test regions includes a plurality of fiducial marks in close proximity 810.
Each loci is coated with an silane that binds the surface and couples to nucleoside phosphoramidite. Oligonucleic acid synthesis is perform on the structure and measurements are taken using the fiducial marks to calibrate align the surface with other components of a system.
A silicon dioxide structure is prepared having a 16×16 array of clusters. Global alignment marks are used to aligning the surface 900 with other components of a system. Global alignment marks 905, 910, 915, 920, 935, and 940 are located at positions on a substantially planar substrate portion of the surface 900 and near an edge of the structure. Detailed circular mark 925 and plus sign mark 945 are shown in an expanded view in
A structure for oligonucleic acid synthesis is manufactured. Each device is 200 mm, double-side polished. A SOI wafer has 21 chips are arranged in a 200 mm wafer. Each chip is 32 mm×32 mm in size, and comprised a 16×16 array of clusters. A total of 256 clusters are present in the array. 121 reaction sites are located in a single cluster, providing 30,976 individually addressable oligo sites per chip. Each cluster pitch is 1.125 mm. Each of the reaction sites are about 50 μm in diameter. The surface of each chip is textured by methods as describe in Example 12 to include recesses with one of the texture designs listed in Table 9.
The structures for oligonucleic acid synthesis are individually cleaned by treatment with oxygen plasma. Directly after cleaning, the surface is coated with AZ resist and then baked at 90 degrees Celsius for 7 minutes. The surface is cleaned again by treatment with oxygen plasma, fluorinated in a YES CVD system (depositing (tridecafluoro-1,1,2,2-tetrahydrooctyl)-trichlorosilane), and is stripped. The surface is treated with 100% propyltrimethoxysilane at 3.5 Torr for 15 hours at chamber temperature of 100 C degrees Celsius. The surface is treated with water for 30 minutes, followed by a second deposition step. In the second deposition step, a mixture of 0.05% GOPS and 99.95% propyltrimethoxysilane is deposited on the surface and treated at 3.5 Torr for 1.5 hours at chamber temperature of 100 degrees Celsius. Lastly, the surface is activated in water for 30 minute at room temperature. The reaction sites on the surface of each structure comprise diluted GOPS. Each of the reaction sites are surrounded by surface coated with tridecafluoro-1,1,2,2-tetrahydrooctyl)-trichlorosilane.
While preferred embodiments of the present invention have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the invention. It should be understood that various alternatives to the embodiments of the invention described herein may be employed in practicing the invention.
This application is a Continuation of U.S. patent application Ser. No. 15/015,059, filed Feb. 3, 2016, now U.S. Pat. No. 10,669,304, issued Jun. 2, 2020, which claims the benefit of U.S. Provisional Application No. 62/112,083, filed Feb. 4, 2015, each of which is herein incorporated herein by reference in its entirety.
| Number | Name | Date | Kind |
|---|---|---|---|
| 3549368 | Robert et al. | Dec 1970 | A |
| 3920714 | Streck | Nov 1975 | A |
| 4123661 | Wolf et al. | Oct 1978 | A |
| 4415732 | Caruthers et al. | Nov 1983 | A |
| 4613398 | Chiong et al. | Sep 1986 | A |
| 4726877 | Fryd et al. | Feb 1988 | A |
| 4808511 | Holmes | Feb 1989 | A |
| 4837401 | Hirose et al. | Jun 1989 | A |
| 4863557 | Kokaku et al. | Sep 1989 | A |
| 4981797 | Jessee et al. | Jan 1991 | A |
| 4988617 | Landegren et al. | Jan 1991 | A |
| 5102797 | Tucker et al. | Apr 1992 | A |
| 5118605 | Urdea | Jun 1992 | A |
| 5137814 | Rashtchian et al. | Aug 1992 | A |
| 5143854 | Pirrung et al. | Sep 1992 | A |
| 5242794 | Whiteley et al. | Sep 1993 | A |
| 5242974 | Holmes | Sep 1993 | A |
| 5288514 | Ellman | Feb 1994 | A |
| 5299491 | Kawada | Apr 1994 | A |
| 5368823 | McGraw et al. | Nov 1994 | A |
| 5384261 | Winkler et al. | Jan 1995 | A |
| 5387541 | Hodge et al. | Feb 1995 | A |
| 5395753 | Prakash | Mar 1995 | A |
| 5431720 | Nagai et al. | Jul 1995 | A |
| 5445934 | Fodor et al. | Aug 1995 | A |
| 5449754 | Nishioka | Sep 1995 | A |
| 5459039 | Modrich et al. | Oct 1995 | A |
| 5474796 | Brennan | Dec 1995 | A |
| 5476930 | Letsinger et al. | Dec 1995 | A |
| 5487993 | Herrnstadt et al. | Jan 1996 | A |
| 5494810 | Barany et al. | Feb 1996 | A |
| 5501893 | Laermer et al. | Mar 1996 | A |
| 5508169 | Deugau et al. | Apr 1996 | A |
| 5510270 | Fodor et al. | Apr 1996 | A |
| 5514789 | Kempe | May 1996 | A |
| 5527681 | Holmes | Jun 1996 | A |
| 5530516 | Sheets | Jun 1996 | A |
| 5534507 | Cama et al. | Jul 1996 | A |
| 5556750 | Modrich et al. | Sep 1996 | A |
| 5586211 | Dumitrou et al. | Dec 1996 | A |
| 5641658 | Adams et al. | Jun 1997 | A |
| 5677195 | Winkler et al. | Oct 1997 | A |
| 5679522 | Modrich et al. | Oct 1997 | A |
| 5688642 | Chrisey et al. | Nov 1997 | A |
| 5700637 | Southern | Dec 1997 | A |
| 5700642 | Monforte et al. | Dec 1997 | A |
| 5702894 | Modrich et al. | Dec 1997 | A |
| 5707806 | Shuber | Jan 1998 | A |
| 5712124 | Walker | Jan 1998 | A |
| 5712126 | Weissman et al. | Jan 1998 | A |
| 5739386 | Holmes | Apr 1998 | A |
| 5750672 | Kempe | May 1998 | A |
| 5780613 | Letsinger et al. | Jul 1998 | A |
| 5830643 | Yamamoto et al. | Nov 1998 | A |
| 5830655 | Monforte et al. | Nov 1998 | A |
| 5830662 | Soares et al. | Nov 1998 | A |
| 5834252 | Stemmer et al. | Nov 1998 | A |
| 5843669 | Kaiser et al. | Dec 1998 | A |
| 5843767 | Beattie | Dec 1998 | A |
| 5846717 | Brow et al. | Dec 1998 | A |
| 5854033 | Lizardi | Dec 1998 | A |
| 5858754 | Modrich et al. | Jan 1999 | A |
| 5861482 | Modrich et al. | Jan 1999 | A |
| 5863801 | Southgate et al. | Jan 1999 | A |
| 5869245 | Yeung | Feb 1999 | A |
| 5877280 | Wetmur | Mar 1999 | A |
| 5882496 | Northrup et al. | Mar 1999 | A |
| 5922539 | Modrich et al. | Jul 1999 | A |
| 5922593 | Livingston | Jul 1999 | A |
| 5928907 | Woudenberg et al. | Jul 1999 | A |
| 5962272 | Chenchik et al. | Oct 1999 | A |
| 5976842 | Wurst | Nov 1999 | A |
| 5976846 | Passmore et al. | Nov 1999 | A |
| 5989872 | Luo et al. | Nov 1999 | A |
| 5994069 | Hall et al. | Nov 1999 | A |
| 6001567 | Brow et al. | Dec 1999 | A |
| 6008031 | Modrich et al. | Dec 1999 | A |
| 6013440 | Lipshutz et al. | Jan 2000 | A |
| 6015674 | Woudenberg et al. | Jan 2000 | A |
| 6020481 | Benson et al. | Feb 2000 | A |
| 6027898 | Gjerde et al. | Feb 2000 | A |
| 6028189 | Blanchard | Feb 2000 | A |
| 6028198 | Liu et al. | Feb 2000 | A |
| 6040138 | Lockhart et al. | Mar 2000 | A |
| 6077674 | Schleifer et al. | Jun 2000 | A |
| 6087482 | Teng et al. | Jul 2000 | A |
| 6090543 | Prudent et al. | Jul 2000 | A |
| 6090606 | Kaiser et al. | Jul 2000 | A |
| 6103474 | Dellinger et al. | Aug 2000 | A |
| 6107038 | Choudhary et al. | Aug 2000 | A |
| 6110682 | Dellinger et al. | Aug 2000 | A |
| 6114115 | Wagner, Jr. | Sep 2000 | A |
| 6130045 | Wurst et al. | Oct 2000 | A |
| 6132997 | Shannon | Oct 2000 | A |
| 6136568 | Hiatt et al. | Oct 2000 | A |
| 6171797 | Perbost | Jan 2001 | B1 |
| 6180351 | Cattell | Jan 2001 | B1 |
| 6201112 | Ach | Mar 2001 | B1 |
| 6218118 | Sampson et al. | Apr 2001 | B1 |
| 6221653 | Caren et al. | Apr 2001 | B1 |
| 6222030 | Dellinger et al. | Apr 2001 | B1 |
| 6232072 | Fisher | May 2001 | B1 |
| 6235483 | Wolber et al. | May 2001 | B1 |
| 6242266 | Schleifer et al. | Jun 2001 | B1 |
| 6251588 | Shannon et al. | Jun 2001 | B1 |
| 6251595 | Gordon et al. | Jun 2001 | B1 |
| 6251685 | Dorsel et al. | Jun 2001 | B1 |
| 6258454 | Lefkowitz et al. | Jul 2001 | B1 |
| 6262490 | Hsu et al. | Jul 2001 | B1 |
| 6274725 | Sanghvi et al. | Aug 2001 | B1 |
| 6284465 | Wolber | Sep 2001 | B1 |
| 6287776 | Hefti | Sep 2001 | B1 |
| 6287824 | Lizardi | Sep 2001 | B1 |
| 6297017 | Schmidt et al. | Oct 2001 | B1 |
| 6300137 | Earhart et al. | Oct 2001 | B1 |
| 6306599 | Perbost | Oct 2001 | B1 |
| 6309822 | Fodor et al. | Oct 2001 | B1 |
| 6309828 | Schleifer et al. | Oct 2001 | B1 |
| 6312911 | Bancroft et al. | Nov 2001 | B1 |
| 6319674 | Fulcrand et al. | Nov 2001 | B1 |
| 6323043 | Caren et al. | Nov 2001 | B1 |
| 6329210 | Schleifer | Dec 2001 | B1 |
| 6346423 | Schembri | Feb 2002 | B1 |
| 6365355 | McCutchen-Maloney | Apr 2002 | B1 |
| 6372483 | Schleifer et al. | Apr 2002 | B2 |
| 6375903 | Cerrina et al. | Apr 2002 | B1 |
| 6376285 | Joyner et al. | Apr 2002 | B1 |
| 6384210 | Blanchard | May 2002 | B1 |
| 6387636 | Perbost et al. | May 2002 | B1 |
| 6399394 | Dahm et al. | Jun 2002 | B1 |
| 6399516 | Ayon | Jun 2002 | B1 |
| 6403314 | Lange et al. | Jun 2002 | B1 |
| 6406849 | Dorsel et al. | Jun 2002 | B1 |
| 6406851 | Bass | Jun 2002 | B1 |
| 6408308 | Maslyn et al. | Jun 2002 | B1 |
| 6419883 | Blanchard | Jul 2002 | B1 |
| 6428957 | Delenstarr | Aug 2002 | B1 |
| 6440669 | Bass et al. | Aug 2002 | B1 |
| 6444268 | Lefkowitz et al. | Sep 2002 | B2 |
| 6446642 | Caren et al. | Sep 2002 | B1 |
| 6446682 | Viken | Sep 2002 | B1 |
| 6451998 | Perbost | Sep 2002 | B1 |
| 6458526 | Schembri et al. | Oct 2002 | B1 |
| 6458535 | Hall et al. | Oct 2002 | B1 |
| 6458583 | Bruhn et al. | Oct 2002 | B1 |
| 6461812 | Barth et al. | Oct 2002 | B2 |
| 6461816 | Wolber et al. | Oct 2002 | B1 |
| 6469156 | Schafer et al. | Oct 2002 | B1 |
| 6472147 | Janda et al. | Oct 2002 | B1 |
| 6492107 | Kauffman et al. | Dec 2002 | B1 |
| 6518056 | Schembri et al. | Feb 2003 | B2 |
| 6521427 | Evans | Feb 2003 | B1 |
| 6521453 | Crameri et al. | Feb 2003 | B1 |
| 6555357 | Kaiser et al. | Apr 2003 | B1 |
| 6558908 | Wolber et al. | May 2003 | B2 |
| 6562611 | Kaiser et al. | May 2003 | B1 |
| 6566495 | Fodor et al. | May 2003 | B1 |
| 6582908 | Fodor et al. | Jun 2003 | B2 |
| 6582938 | Su et al. | Jun 2003 | B1 |
| 6586211 | Staehler et al. | Jul 2003 | B1 |
| 6587579 | Bass | Jul 2003 | B1 |
| 6589739 | Fisher | Jul 2003 | B2 |
| 6599693 | Webb | Jul 2003 | B1 |
| 6602472 | Zimmermann et al. | Aug 2003 | B1 |
| 6610978 | Yin et al. | Aug 2003 | B2 |
| 6613513 | Parce et al. | Sep 2003 | B1 |
| 6613523 | Fischer | Sep 2003 | B2 |
| 6613560 | Tso et al. | Sep 2003 | B1 |
| 6613893 | Webb | Sep 2003 | B1 |
| 6621076 | Van De Goor et al. | Sep 2003 | B1 |
| 6630581 | Dellinger et al. | Oct 2003 | B2 |
| 6632641 | Brennan et al. | Oct 2003 | B1 |
| 6635226 | Tso et al. | Oct 2003 | B1 |
| 6642373 | Manoharan et al. | Nov 2003 | B2 |
| 6649348 | Bass et al. | Nov 2003 | B2 |
| 6660338 | Hargreaves | Dec 2003 | B1 |
| 6664112 | Mulligan et al. | Dec 2003 | B2 |
| 6670127 | Evans | Dec 2003 | B2 |
| 6670461 | Wengel et al. | Dec 2003 | B1 |
| 6673552 | Frey | Jan 2004 | B2 |
| 6682702 | Barth et al. | Jan 2004 | B2 |
| 6689319 | Fisher et al. | Feb 2004 | B1 |
| 6692917 | Neri et al. | Feb 2004 | B2 |
| 6702256 | Killeen et al. | Mar 2004 | B2 |
| 6706471 | Brow et al. | Mar 2004 | B1 |
| 6706875 | Goldberg et al. | Mar 2004 | B1 |
| 6709841 | Short | Mar 2004 | B2 |
| 6709852 | Bloom et al. | Mar 2004 | B1 |
| 6709854 | Donahue et al. | Mar 2004 | B2 |
| 6713262 | Gillibolian et al. | Mar 2004 | B2 |
| 6716629 | Hess et al. | Apr 2004 | B2 |
| 6716634 | Myerson | Apr 2004 | B1 |
| 6723509 | Ach | Apr 2004 | B2 |
| 6728129 | Lindsey et al. | Apr 2004 | B2 |
| 6743585 | Dellinger et al. | Jun 2004 | B2 |
| 6753145 | Holcomb et al. | Jun 2004 | B2 |
| 6768005 | Mellor et al. | Jul 2004 | B2 |
| 6770748 | Imanishi et al. | Aug 2004 | B2 |
| 6770892 | Corson et al. | Aug 2004 | B2 |
| 6773676 | Schembri | Aug 2004 | B2 |
| 6773888 | Li et al. | Aug 2004 | B2 |
| 6780982 | Lyamichev et al. | Aug 2004 | B2 |
| 6787308 | Balasubramanian et al. | Sep 2004 | B2 |
| 6789965 | Barth et al. | Sep 2004 | B2 |
| 6790620 | Bass et al. | Sep 2004 | B2 |
| 6794499 | Wengel et al. | Sep 2004 | B2 |
| 6796634 | Caren et al. | Sep 2004 | B2 |
| 6800439 | McGall et al. | Oct 2004 | B1 |
| 6814846 | Berndt | Nov 2004 | B1 |
| 6815218 | Jacobson et al. | Nov 2004 | B1 |
| 6824866 | Glazer et al. | Nov 2004 | B1 |
| 6830890 | Lockhart et al. | Dec 2004 | B2 |
| 6833246 | Balasubramanian | Dec 2004 | B2 |
| 6833450 | McGall et al. | Dec 2004 | B1 |
| 6835938 | Ghosh et al. | Dec 2004 | B2 |
| 6838888 | Peck | Jan 2005 | B2 |
| 6841131 | Zimmermann et al. | Jan 2005 | B2 |
| 6845968 | Killeen et al. | Jan 2005 | B2 |
| 6846454 | Peck | Jan 2005 | B2 |
| 6846922 | Manoharan et al. | Jan 2005 | B1 |
| 6852850 | Myerson et al. | Feb 2005 | B2 |
| 6858720 | Myerson et al. | Feb 2005 | B2 |
| 6879915 | Cattell | Apr 2005 | B2 |
| 6880576 | Karp et al. | Apr 2005 | B2 |
| 6884580 | Caren et al. | Apr 2005 | B2 |
| 6887715 | Schembri | May 2005 | B2 |
| 6890723 | Perbost et al. | May 2005 | B2 |
| 6890760 | Webb | May 2005 | B1 |
| 6893816 | Beattie | May 2005 | B1 |
| 6897023 | Fu et al. | May 2005 | B2 |
| 6900047 | Bass | May 2005 | B2 |
| 6900048 | Perbost | May 2005 | B2 |
| 6911611 | Wong et al. | Jun 2005 | B2 |
| 6914229 | Corson et al. | Jul 2005 | B2 |
| 6916113 | Van de Goor et al. | Jul 2005 | B2 |
| 6916633 | Shannon | Jul 2005 | B1 |
| 6919181 | Hargreaves | Jul 2005 | B2 |
| 6927029 | Lefkowitz et al. | Aug 2005 | B2 |
| 6929951 | Corson et al. | Aug 2005 | B2 |
| 6936472 | Earhart et al. | Aug 2005 | B2 |
| 6938476 | Chesk | Sep 2005 | B2 |
| 6939673 | Bass et al. | Sep 2005 | B2 |
| 6943036 | Bass | Sep 2005 | B2 |
| 6946285 | Bass | Sep 2005 | B2 |
| 6950756 | Kincaid | Sep 2005 | B2 |
| 6951719 | Dupret et al. | Oct 2005 | B1 |
| 6958119 | Yin et al. | Oct 2005 | B2 |
| 6960464 | Jessee et al. | Nov 2005 | B2 |
| 6969449 | Maher et al. | Nov 2005 | B2 |
| 6969488 | Bridgham et al. | Nov 2005 | B2 |
| 6976384 | Hobbs et al. | Dec 2005 | B2 |
| 6977223 | George et al. | Dec 2005 | B2 |
| 6987263 | Hobbs et al. | Jan 2006 | B2 |
| 6989267 | Kim et al. | Jan 2006 | B2 |
| 6991922 | Dupret et al. | Jan 2006 | B2 |
| 7008037 | Caren et al. | Mar 2006 | B2 |
| 7025324 | Slocum et al. | Apr 2006 | B1 |
| 7026124 | Barth et al. | Apr 2006 | B2 |
| 7027930 | Cattell | Apr 2006 | B2 |
| 7028536 | Karp et al. | Apr 2006 | B2 |
| 7029854 | Collins et al. | Apr 2006 | B2 |
| 7034290 | Lu et al. | Apr 2006 | B2 |
| 7041445 | Chenchik et al. | May 2006 | B2 |
| 7045289 | Allawi et al. | May 2006 | B2 |
| 7051574 | Peck | May 2006 | B2 |
| 7052841 | Delenstarr | May 2006 | B2 |
| 7062385 | White et al. | Jun 2006 | B2 |
| 7064197 | Rabbani et al. | Jun 2006 | B1 |
| 7070932 | Leproust et al. | Jul 2006 | B2 |
| 7075161 | Barth | Jul 2006 | B2 |
| 7078167 | Delenstarr et al. | Jul 2006 | B2 |
| 7078505 | Bass et al. | Jul 2006 | B2 |
| 7094537 | Leproust et al. | Aug 2006 | B2 |
| 7097974 | Stahler et al. | Aug 2006 | B1 |
| 7101508 | Thompson et al. | Sep 2006 | B2 |
| 7101986 | Dellinger et al. | Sep 2006 | B2 |
| 7105295 | Bass et al. | Sep 2006 | B2 |
| 7115423 | Mitchell | Oct 2006 | B1 |
| 7122303 | Delenstarr et al. | Oct 2006 | B2 |
| 7122364 | Lyamichev et al. | Oct 2006 | B1 |
| 7125488 | Li | Oct 2006 | B2 |
| 7125523 | Sillman | Oct 2006 | B2 |
| 7128876 | Yin et al. | Oct 2006 | B2 |
| 7129075 | Gerard et al. | Oct 2006 | B2 |
| 7135565 | Dellinger et al. | Nov 2006 | B2 |
| 7138062 | Yin et al. | Nov 2006 | B2 |
| 7141368 | Fisher et al. | Nov 2006 | B2 |
| 7141807 | Joyce et al. | Nov 2006 | B2 |
| 7147362 | Caren et al. | Dec 2006 | B2 |
| 7150982 | Allawi et al. | Dec 2006 | B2 |
| 7153689 | Tolosko et al. | Dec 2006 | B2 |
| 7163660 | Lehmann | Jan 2007 | B2 |
| 7166258 | Bass et al. | Jan 2007 | B2 |
| 7179659 | Stolowitz et al. | Feb 2007 | B2 |
| 7183406 | Belshaw et al. | Feb 2007 | B2 |
| 7192710 | Gellibolian et al. | Mar 2007 | B2 |
| 7193077 | Dellinger et al. | Mar 2007 | B2 |
| 7195872 | Agrawal | Mar 2007 | B2 |
| 7198939 | Dorsel et al. | Apr 2007 | B2 |
| 7202264 | Ravikumar et al. | Apr 2007 | B2 |
| 7202358 | Hargreaves | Apr 2007 | B2 |
| 7205128 | Ilsley et al. | Apr 2007 | B2 |
| 7205399 | Vargeese et al. | Apr 2007 | B1 |
| 7205400 | Webb | Apr 2007 | B2 |
| 7206439 | Zhou et al. | Apr 2007 | B2 |
| 7208322 | Stolowitz et al. | Apr 2007 | B2 |
| 7217522 | Brenner | May 2007 | B2 |
| 7220573 | Shea et al. | May 2007 | B2 |
| 7221785 | Curry et al. | May 2007 | B2 |
| 7226862 | Staehler et al. | Jun 2007 | B2 |
| 7227017 | Mellor et al. | Jun 2007 | B2 |
| 7229497 | Stott et al. | Jun 2007 | B2 |
| 7247337 | Leproust et al. | Jul 2007 | B1 |
| 7247497 | Dahm et al. | Jul 2007 | B2 |
| 7252938 | Leproust et al. | Aug 2007 | B2 |
| 7269518 | Corson | Sep 2007 | B2 |
| 7271258 | Dellinger et al. | Sep 2007 | B2 |
| 7276336 | Webb et al. | Oct 2007 | B1 |
| 7276378 | Myerson | Oct 2007 | B2 |
| 7276599 | Moore et al. | Oct 2007 | B2 |
| 7282183 | Peck | Oct 2007 | B2 |
| 7282332 | Caren et al. | Oct 2007 | B2 |
| 7282705 | Brennen | Oct 2007 | B2 |
| 7291471 | Sampson et al. | Nov 2007 | B2 |
| 7302348 | Ghosh et al. | Nov 2007 | B2 |
| 7306917 | Prudent et al. | Dec 2007 | B2 |
| 7314599 | Roitman et al. | Jan 2008 | B2 |
| 7323320 | Oleinikov | Jan 2008 | B2 |
| 7344831 | Wolber et al. | Mar 2008 | B2 |
| 7348144 | Minor | Mar 2008 | B2 |
| 7351379 | Schleifer | Apr 2008 | B2 |
| 7353116 | Webb et al. | Apr 2008 | B2 |
| 7361906 | Ghosh et al. | Apr 2008 | B2 |
| 7364896 | Schembri | Apr 2008 | B2 |
| 7368550 | Dellinger et al. | May 2008 | B2 |
| 7371348 | Schleifer et al. | May 2008 | B2 |
| 7371519 | Wolber et al. | May 2008 | B2 |
| 7371580 | Yakhini et al. | May 2008 | B2 |
| 7372982 | Le Cocq | May 2008 | B2 |
| 7384746 | Lyamichev et al. | Jun 2008 | B2 |
| 7385050 | Dellinger et al. | Jun 2008 | B2 |
| 7390457 | Schembri | Jun 2008 | B2 |
| 7393665 | Brenner | Jul 2008 | B2 |
| 7396676 | Robotti et al. | Jul 2008 | B2 |
| 7399844 | Sampson et al. | Jul 2008 | B2 |
| 7402279 | Schembri | Jul 2008 | B2 |
| 7411061 | Myerson et al. | Aug 2008 | B2 |
| 7413709 | Roitman et al. | Aug 2008 | B2 |
| 7417139 | Dellinger et al. | Aug 2008 | B2 |
| 7422911 | Schembri | Sep 2008 | B2 |
| 7427679 | Dellinger et al. | Sep 2008 | B2 |
| 7432048 | Neri et al. | Oct 2008 | B2 |
| 7435810 | Myerson et al. | Oct 2008 | B2 |
| 7439272 | Xu | Oct 2008 | B2 |
| 7476709 | Moody et al. | Jan 2009 | B2 |
| 7482118 | Allawi et al. | Jan 2009 | B2 |
| 7488607 | Tom-Moy et al. | Feb 2009 | B2 |
| 7504213 | Sana et al. | Mar 2009 | B2 |
| 7514369 | Li et al. | Apr 2009 | B2 |
| 7517979 | Wolber | Apr 2009 | B2 |
| 7524942 | Wang et al. | Apr 2009 | B2 |
| 7524950 | Dellinger et al. | Apr 2009 | B2 |
| 7527928 | Neri et al. | May 2009 | B2 |
| 7531303 | Dorsel et al. | May 2009 | B2 |
| 7534561 | Sana et al. | May 2009 | B2 |
| 7534563 | Hargreaves | May 2009 | B2 |
| 7537936 | Dahm et al. | May 2009 | B2 |
| 7541145 | Prudent et al. | Jun 2009 | B2 |
| 7544473 | Brenner | Jun 2009 | B2 |
| 7556919 | Chenchik et al. | Jul 2009 | B2 |
| 7563600 | Oleinikov | Jul 2009 | B2 |
| 7572585 | Wang | Aug 2009 | B2 |
| 7572907 | Dellinger et al. | Aug 2009 | B2 |
| 7572908 | Dellinger et al. | Aug 2009 | B2 |
| 7585970 | Dellinger et al. | Sep 2009 | B2 |
| 7588889 | Wolber et al. | Sep 2009 | B2 |
| 7595350 | Xu | Sep 2009 | B2 |
| 7604941 | Jacobson | Oct 2009 | B2 |
| 7604996 | Stuelpnagel et al. | Oct 2009 | B1 |
| 7608396 | Delenstarr | Oct 2009 | B2 |
| 7618777 | Myerson et al. | Nov 2009 | B2 |
| 7629120 | Bennett et al. | Dec 2009 | B2 |
| 7635772 | McCormac | Dec 2009 | B2 |
| 7648832 | Jessee et al. | Jan 2010 | B2 |
| 7651762 | Xu et al. | Jan 2010 | B2 |
| 7659069 | Belyaev et al. | Feb 2010 | B2 |
| 7678542 | Lyamichev et al. | Mar 2010 | B2 |
| 7682809 | Sampson | Mar 2010 | B2 |
| 7709197 | Drmanac | May 2010 | B2 |
| 7718365 | Wang | May 2010 | B2 |
| 7718786 | Dupret et al. | May 2010 | B2 |
| 7723077 | Young et al. | May 2010 | B2 |
| 7737088 | Stahler et al. | Jun 2010 | B1 |
| 7737089 | Guimil et al. | Jun 2010 | B2 |
| 7741463 | Gormley et al. | Jun 2010 | B2 |
| 7749701 | Leproust et al. | Jul 2010 | B2 |
| 7759471 | Dellinger et al. | Jul 2010 | B2 |
| 7776021 | Borenstein et al. | Aug 2010 | B2 |
| 7776532 | Gibson et al. | Aug 2010 | B2 |
| 7790369 | Stahler et al. | Sep 2010 | B2 |
| 7790387 | Dellinger et al. | Sep 2010 | B2 |
| 7807356 | Sampson et al. | Oct 2010 | B2 |
| 7807806 | Allawi et al. | Oct 2010 | B2 |
| 7811753 | Eshoo | Oct 2010 | B2 |
| 7816079 | Fischer | Oct 2010 | B2 |
| 7820387 | Neri et al. | Oct 2010 | B2 |
| 7829314 | Prudent et al. | Nov 2010 | B2 |
| 7855281 | Dellinger et al. | Dec 2010 | B2 |
| 7862999 | Zheng et al. | Jan 2011 | B2 |
| 7867782 | Barth | Jan 2011 | B2 |
| 7875463 | Adaskin et al. | Jan 2011 | B2 |
| 7879541 | Kincaid | Feb 2011 | B2 |
| 7879580 | Carr et al. | Feb 2011 | B2 |
| 7894998 | Kincaid | Feb 2011 | B2 |
| 7919239 | Wang | Apr 2011 | B2 |
| 7919308 | Schleifer | Apr 2011 | B2 |
| 7927797 | Nobile et al. | Apr 2011 | B2 |
| 7927838 | Shannon | Apr 2011 | B2 |
| 7932025 | Carr et al. | Apr 2011 | B2 |
| 7932070 | Hogrefe et al. | Apr 2011 | B2 |
| 7935800 | Allawi et al. | May 2011 | B2 |
| 7939645 | Borns | May 2011 | B2 |
| 7943046 | Martosella et al. | May 2011 | B2 |
| 7943358 | Hogrefe et al. | May 2011 | B2 |
| 7960157 | Borns | Jun 2011 | B2 |
| 7977119 | Kronick et al. | Jul 2011 | B2 |
| 7979215 | Sampas | Jul 2011 | B2 |
| 7998437 | Berndt et al. | Aug 2011 | B2 |
| 7999087 | Dellinger et al. | Aug 2011 | B2 |
| 8021842 | Brenner | Sep 2011 | B2 |
| 8021844 | Wang | Sep 2011 | B2 |
| 8034917 | Yamada | Oct 2011 | B2 |
| 8036835 | Sampas et al. | Oct 2011 | B2 |
| 8048664 | Guan et al. | Nov 2011 | B2 |
| 8053191 | Blake | Nov 2011 | B2 |
| 8058001 | Crameri et al. | Nov 2011 | B2 |
| 8058004 | Oleinikov | Nov 2011 | B2 |
| 8058055 | Barrett et al. | Nov 2011 | B2 |
| 8063184 | Allawi et al. | Nov 2011 | B2 |
| 8067556 | Hogrefe et al. | Nov 2011 | B2 |
| 8073626 | Troup et al. | Dec 2011 | B2 |
| 8076064 | Wang | Dec 2011 | B2 |
| 8076152 | Robotti | Dec 2011 | B2 |
| 8097711 | Timar et al. | Jan 2012 | B2 |
| 8137936 | Macevicz | Mar 2012 | B2 |
| 8148068 | Brenner | Apr 2012 | B2 |
| 8154729 | Baldo et al. | Apr 2012 | B2 |
| 8168385 | Brenner | May 2012 | B2 |
| 8168388 | Gormley et al. | May 2012 | B2 |
| 8173368 | Staehler et al. | May 2012 | B2 |
| 8182991 | Kaiser et al. | May 2012 | B1 |
| 8194244 | Wang et al. | Jun 2012 | B2 |
| 8198071 | Goshoo et al. | Jun 2012 | B2 |
| 8202983 | Dellinger et al. | Jun 2012 | B2 |
| 8202985 | Dellinger et al. | Jun 2012 | B2 |
| 8206952 | Carr et al. | Jun 2012 | B2 |
| 8213015 | Kraiczek et al. | Jul 2012 | B2 |
| 8242258 | Dellinger et al. | Aug 2012 | B2 |
| 8247221 | Fawcett et al. | Aug 2012 | B2 |
| 8263335 | Carr et al. | Sep 2012 | B2 |
| 8268605 | Sorge et al. | Sep 2012 | B2 |
| 8283148 | Sorge et al. | Oct 2012 | B2 |
| 8288093 | Hall et al. | Oct 2012 | B2 |
| 8298767 | Brenner et al. | Oct 2012 | B2 |
| 8304273 | Stellacci et al. | Nov 2012 | B2 |
| 8309307 | Barrett et al. | Nov 2012 | B2 |
| 8309706 | Dellinger et al. | Nov 2012 | B2 |
| 8309710 | Sierzchala et al. | Nov 2012 | B2 |
| 8314220 | Mullinax et al. | Nov 2012 | B2 |
| 8318433 | Brenner | Nov 2012 | B2 |
| 8318479 | Domansky et al. | Nov 2012 | B2 |
| 8357489 | Chua et al. | Jan 2013 | B2 |
| 8357490 | Froehlich et al. | Jan 2013 | B2 |
| 8367016 | Quan et al. | Feb 2013 | B2 |
| 8367335 | Staehler et al. | Feb 2013 | B2 |
| 8380441 | Webb et al. | Feb 2013 | B2 |
| 8383338 | Kitzman et al. | Feb 2013 | B2 |
| 8415138 | Leproust | Apr 2013 | B2 |
| 8435736 | Gibson et al. | May 2013 | B2 |
| 8445205 | Brenner | May 2013 | B2 |
| 8445206 | Bergmann et al. | May 2013 | B2 |
| 8470996 | Brenner | Jun 2013 | B2 |
| 8476018 | Brenner | Jul 2013 | B2 |
| 8476598 | Pralle et al. | Jul 2013 | B1 |
| 8481292 | Casbon et al. | Jul 2013 | B2 |
| 8481309 | Zhang et al. | Jul 2013 | B2 |
| 8491561 | Borenstein et al. | Jul 2013 | B2 |
| 8497069 | Hutchison et al. | Jul 2013 | B2 |
| 8500979 | Elibol et al. | Aug 2013 | B2 |
| 8501454 | Liu et al. | Aug 2013 | B2 |
| 8507226 | Carr et al. | Aug 2013 | B2 |
| 8507239 | Lubys et al. | Aug 2013 | B2 |
| 8507272 | Zhang et al. | Aug 2013 | B2 |
| 8530197 | Li et al. | Sep 2013 | B2 |
| 8552174 | Dellinger et al. | Oct 2013 | B2 |
| 8563478 | Gormley et al. | Oct 2013 | B2 |
| 8569046 | Love et al. | Oct 2013 | B2 |
| 8577621 | Troup et al. | Nov 2013 | B2 |
| 8586310 | Mitra et al. | Nov 2013 | B2 |
| 8614092 | Zhang et al. | Dec 2013 | B2 |
| 8642755 | Sierzchala et al. | Feb 2014 | B2 |
| 8664164 | Ericsson et al. | Mar 2014 | B2 |
| 8669053 | Stuelpnagel et al. | Mar 2014 | B2 |
| 8679756 | Brenner et al. | Mar 2014 | B1 |
| 8685642 | Sampas | Apr 2014 | B2 |
| 8685676 | Hogrefe et al. | Apr 2014 | B2 |
| 8685678 | Casbon et al. | Apr 2014 | B2 |
| 8715933 | Oliver | May 2014 | B2 |
| 8715967 | Casbon et al. | May 2014 | B2 |
| 8716467 | Jacobson | May 2014 | B2 |
| 8722368 | Casbon et al. | May 2014 | B2 |
| 8722585 | Wang | May 2014 | B2 |
| 8728766 | Casbon et al. | May 2014 | B2 |
| 8741606 | Casbon et al. | Jun 2014 | B2 |
| 8808896 | Choo et al. | Aug 2014 | B2 |
| 8808986 | Jacobson et al. | Aug 2014 | B2 |
| 8815600 | Liu et al. | Aug 2014 | B2 |
| 8889851 | Leproust et al. | Nov 2014 | B2 |
| 8932994 | Gormley et al. | Jan 2015 | B2 |
| 8962532 | Shapiro et al. | Feb 2015 | B2 |
| 8968999 | Gibson et al. | Mar 2015 | B2 |
| 8980563 | Zheng et al. | Mar 2015 | B2 |
| 9018365 | Brenner | Apr 2015 | B2 |
| 9023601 | Oleinikov | May 2015 | B2 |
| 9051666 | Oleinikov | Jun 2015 | B2 |
| 9073962 | Fracchia et al. | Jul 2015 | B2 |
| 9074204 | Anderson et al. | Jul 2015 | B2 |
| 9085797 | Gebeyehu et al. | Jul 2015 | B2 |
| 9102731 | Boone et al. | Aug 2015 | B2 |
| 9133510 | Andersen et al. | Sep 2015 | B2 |
| 9139874 | Myers et al. | Sep 2015 | B2 |
| 9150853 | Hudson et al. | Oct 2015 | B2 |
| 9187777 | Jacobson et al. | Nov 2015 | B2 |
| 9194001 | Brenner | Nov 2015 | B2 |
| 9216414 | Chu | Dec 2015 | B2 |
| 9217144 | Jacobson et al. | Dec 2015 | B2 |
| 9279149 | Efcavitch et al. | Mar 2016 | B2 |
| 9286439 | Shapiro et al. | Mar 2016 | B2 |
| 9295965 | Jacobson et al. | Mar 2016 | B2 |
| 9315861 | Hendricks et al. | Apr 2016 | B2 |
| 9328378 | Earnshaw et al. | May 2016 | B2 |
| 9347091 | Bergmann et al. | May 2016 | B2 |
| 9375748 | Harumoto et al. | Jun 2016 | B2 |
| 9376677 | Mir | Jun 2016 | B2 |
| 9376678 | Gormley et al. | Jun 2016 | B2 |
| 9384320 | Church | Jul 2016 | B2 |
| 9384920 | Bakulich | Jul 2016 | B1 |
| 9388407 | Jacobson | Jul 2016 | B2 |
| 9394333 | Wada et al. | Jul 2016 | B2 |
| 9403141 | Banyai et al. | Aug 2016 | B2 |
| 9409139 | Banyai et al. | Aug 2016 | B2 |
| 9410149 | Brenner et al. | Aug 2016 | B2 |
| 9410173 | Betts et al. | Aug 2016 | B2 |
| 9416411 | Stuelpnagel et al. | Aug 2016 | B2 |
| 9422600 | Ramu et al. | Aug 2016 | B2 |
| 9487824 | Kutyavin | Nov 2016 | B2 |
| 9499848 | Carr et al. | Nov 2016 | B2 |
| 9523122 | Zheng et al. | Dec 2016 | B2 |
| 9528148 | Zheng et al. | Dec 2016 | B2 |
| 9534251 | Young et al. | Jan 2017 | B2 |
| 9555388 | Banyai et al. | Jan 2017 | B2 |
| 9568839 | Stahler et al. | Feb 2017 | B2 |
| 9580746 | Leproust et al. | Feb 2017 | B2 |
| 9670529 | Osborne et al. | Jun 2017 | B2 |
| 9670536 | Casbon et al. | Jun 2017 | B2 |
| 9677067 | Toro et al. | Jun 2017 | B2 |
| 9695211 | Wada et al. | Jul 2017 | B2 |
| 9718060 | Venter et al. | Aug 2017 | B2 |
| 9745573 | Stuelpnagel et al. | Aug 2017 | B2 |
| 9745619 | Rabbani et al. | Aug 2017 | B2 |
| 9765387 | Rabbani et al. | Sep 2017 | B2 |
| 9771576 | Gibson et al. | Sep 2017 | B2 |
| 9833761 | Banyai et al. | Dec 2017 | B2 |
| 9834774 | Carstens | Dec 2017 | B2 |
| 9839894 | Banyai et al. | Dec 2017 | B2 |
| 9879283 | Ravinder et al. | Jan 2018 | B2 |
| 9889423 | Banyai et al. | Feb 2018 | B2 |
| 9895673 | Peck et al. | Feb 2018 | B2 |
| 9925510 | Jacobson et al. | Mar 2018 | B2 |
| 9932576 | Raymond et al. | Apr 2018 | B2 |
| 9981239 | Banyai et al. | May 2018 | B2 |
| 10053688 | Cox | Aug 2018 | B2 |
| 10272410 | Banyai et al. | Apr 2019 | B2 |
| 10384188 | Banyai et al. | Aug 2019 | B2 |
| 10384189 | Peck | Aug 2019 | B2 |
| 10417457 | Peck | Sep 2019 | B2 |
| 10583415 | Banyai et al. | Mar 2020 | B2 |
| 10632445 | Banyai | Apr 2020 | B2 |
| 10639609 | Banyai | May 2020 | B2 |
| 10669304 | Indermuhle | Jun 2020 | B2 |
| 10754994 | Peck | Aug 2020 | B2 |
| 10773232 | Banyai et al. | Sep 2020 | B2 |
| 10963953 | Sweeder et al. | Mar 2021 | B2 |
| 11214798 | Brown | Jan 2022 | B2 |
| 11236393 | Dubinsky et al. | Feb 2022 | B2 |
| 11268149 | Targan et al. | Mar 2022 | B2 |
| 20010018512 | Blanchard | Aug 2001 | A1 |
| 20010039014 | Bass et al. | Nov 2001 | A1 |
| 20010055761 | Kanemoto et al. | Dec 2001 | A1 |
| 20020012930 | Rothberg et al. | Jan 2002 | A1 |
| 20020025561 | Hodgson | Feb 2002 | A1 |
| 20020058802 | Dellinger et al. | May 2002 | A1 |
| 20020076716 | Sabanayagam et al. | Jun 2002 | A1 |
| 20020081582 | Gao et al. | Jun 2002 | A1 |
| 20020094533 | Hess et al. | Jul 2002 | A1 |
| 20020095073 | Jacobs et al. | Jul 2002 | A1 |
| 20020119459 | Griffiths | Aug 2002 | A1 |
| 20020132308 | Liu et al. | Sep 2002 | A1 |
| 20020155439 | Rodriguez et al. | Oct 2002 | A1 |
| 20020160536 | Regnier et al. | Oct 2002 | A1 |
| 20020164824 | Xiao et al. | Nov 2002 | A1 |
| 20030008411 | Van Dam et al. | Jan 2003 | A1 |
| 20030022207 | Balasubramanian et al. | Jan 2003 | A1 |
| 20030022317 | Jack et al. | Jan 2003 | A1 |
| 20030044781 | Korlach et al. | Mar 2003 | A1 |
| 20030058629 | Hirai et al. | Mar 2003 | A1 |
| 20030064398 | Barnes | Apr 2003 | A1 |
| 20030068633 | Belshaw et al. | Apr 2003 | A1 |
| 20030082618 | Li et al. | May 2003 | A1 |
| 20030082719 | Schumacher et al. | May 2003 | A1 |
| 20030100102 | Rothberg et al. | May 2003 | A1 |
| 20030108903 | Wang et al. | Jun 2003 | A1 |
| 20030120035 | Gao et al. | Jun 2003 | A1 |
| 20030130827 | Bentzien et al. | Jul 2003 | A1 |
| 20030138782 | Evans | Jul 2003 | A1 |
| 20030143605 | Lok et al. | Jul 2003 | A1 |
| 20030148291 | Robotti | Aug 2003 | A1 |
| 20030148344 | Rothberg et al. | Aug 2003 | A1 |
| 20030148401 | Agrawal et al. | Aug 2003 | A1 |
| 20030171325 | Gascoyne et al. | Sep 2003 | A1 |
| 20030186226 | Brennan et al. | Oct 2003 | A1 |
| 20030228602 | Parker et al. | Dec 2003 | A1 |
| 20030228620 | Du Breuil Lastrucci | Dec 2003 | A1 |
| 20040009498 | Short | Jan 2004 | A1 |
| 20040043509 | Stahler et al. | Mar 2004 | A1 |
| 20040053362 | De Luca et al. | Mar 2004 | A1 |
| 20040086892 | Crothers et al. | May 2004 | A1 |
| 20040087008 | Schembri | May 2004 | A1 |
| 20040106130 | Besemer et al. | Jun 2004 | A1 |
| 20040106728 | McGall et al. | Jun 2004 | A1 |
| 20040110133 | Xu et al. | Jun 2004 | A1 |
| 20040175710 | Haushalter | Sep 2004 | A1 |
| 20040175734 | Stahler et al. | Sep 2004 | A1 |
| 20040191810 | Yamamoto | Sep 2004 | A1 |
| 20040219663 | Page et al. | Nov 2004 | A1 |
| 20040236027 | Maeji et al. | Nov 2004 | A1 |
| 20040248161 | Rothberg et al. | Dec 2004 | A1 |
| 20040253242 | Bowdish et al. | Dec 2004 | A1 |
| 20040259146 | Friend et al. | Dec 2004 | A1 |
| 20050022895 | Barth et al. | Feb 2005 | A1 |
| 20050049402 | Babcook et al. | Mar 2005 | A1 |
| 20050049796 | Webb et al. | Mar 2005 | A1 |
| 20050053968 | Bharadwaj et al. | Mar 2005 | A1 |
| 20050079510 | Berka et al. | Apr 2005 | A1 |
| 20050100932 | Lapidus et al. | May 2005 | A1 |
| 20050112608 | Grossman et al. | May 2005 | A1 |
| 20050112636 | Hurt et al. | May 2005 | A1 |
| 20050112679 | Myerson et al. | May 2005 | A1 |
| 20050118706 | Pirrung et al. | Jun 2005 | A1 |
| 20050124022 | Srinivasan et al. | Jun 2005 | A1 |
| 20050137805 | Lewin et al. | Jun 2005 | A1 |
| 20050208513 | Agbo et al. | Sep 2005 | A1 |
| 20050214778 | Peck et al. | Sep 2005 | A1 |
| 20050214779 | Peck et al. | Sep 2005 | A1 |
| 20050227235 | Carr et al. | Oct 2005 | A1 |
| 20050255477 | Carr et al. | Nov 2005 | A1 |
| 20050266045 | Canham et al. | Dec 2005 | A1 |
| 20050277125 | Benn et al. | Dec 2005 | A1 |
| 20050282158 | Landegren | Dec 2005 | A1 |
| 20050287585 | Oleinikov | Dec 2005 | A1 |
| 20060003381 | Gilmore et al. | Jan 2006 | A1 |
| 20060012784 | Ulmer | Jan 2006 | A1 |
| 20060012793 | Harris | Jan 2006 | A1 |
| 20060019084 | Pearson | Jan 2006 | A1 |
| 20060024678 | Buzby | Feb 2006 | A1 |
| 20060024711 | Lapidus et al. | Feb 2006 | A1 |
| 20060024721 | Pedersen | Feb 2006 | A1 |
| 20060076482 | Hobbs et al. | Apr 2006 | A1 |
| 20060078909 | Srinivasan et al. | Apr 2006 | A1 |
| 20060078927 | Peck et al. | Apr 2006 | A1 |
| 20060078937 | Korlach et al. | Apr 2006 | A1 |
| 20060127920 | Church et al. | Jun 2006 | A1 |
| 20060134638 | Mulligan et al. | Jun 2006 | A1 |
| 20060160138 | Church | Jul 2006 | A1 |
| 20060171855 | Yin et al. | Aug 2006 | A1 |
| 20060202330 | Reinhardt et al. | Sep 2006 | A1 |
| 20060203236 | Ji et al. | Sep 2006 | A1 |
| 20060203237 | Ji et al. | Sep 2006 | A1 |
| 20060207923 | Li | Sep 2006 | A1 |
| 20060219637 | Killeen et al. | Oct 2006 | A1 |
| 20060286569 | Bar-Or et al. | Dec 2006 | A1 |
| 20070031857 | Makarov et al. | Feb 2007 | A1 |
| 20070031877 | Stahler et al. | Feb 2007 | A1 |
| 20070043516 | Gustafsson et al. | Feb 2007 | A1 |
| 20070054127 | Hergenrother et al. | Mar 2007 | A1 |
| 20070059692 | Gao et al. | Mar 2007 | A1 |
| 20070087349 | Staehler et al. | Apr 2007 | A1 |
| 20070099196 | Kauppinen et al. | May 2007 | A1 |
| 20070099208 | Drmanac et al. | May 2007 | A1 |
| 20070122817 | Church et al. | May 2007 | A1 |
| 20070128635 | Macevicz | Jun 2007 | A1 |
| 20070141557 | Raab et al. | Jun 2007 | A1 |
| 20070196834 | Cerrina et al. | Aug 2007 | A1 |
| 20070196854 | Stahler et al. | Aug 2007 | A1 |
| 20070207482 | Church et al. | Sep 2007 | A1 |
| 20070207487 | Emig et al. | Sep 2007 | A1 |
| 20070231800 | Roberts et al. | Oct 2007 | A1 |
| 20070238104 | Barrett et al. | Oct 2007 | A1 |
| 20070238106 | Barrett et al. | Oct 2007 | A1 |
| 20070238108 | Barrett et al. | Oct 2007 | A1 |
| 20070259344 | Leproust et al. | Nov 2007 | A1 |
| 20070259345 | Sampas | Nov 2007 | A1 |
| 20070259346 | Gordon et al. | Nov 2007 | A1 |
| 20070259347 | Gordon et al. | Nov 2007 | A1 |
| 20070269870 | Church et al. | Nov 2007 | A1 |
| 20080085511 | Peck et al. | Apr 2008 | A1 |
| 20080085514 | Peck et al. | Apr 2008 | A1 |
| 20080087545 | Jensen et al. | Apr 2008 | A1 |
| 20080161200 | Yu et al. | Jul 2008 | A1 |
| 20080182296 | Chanda et al. | Jul 2008 | A1 |
| 20080214412 | Stahler et al. | Sep 2008 | A1 |
| 20080227160 | Kool | Sep 2008 | A1 |
| 20080233616 | Liss | Sep 2008 | A1 |
| 20080287320 | Baynes et al. | Nov 2008 | A1 |
| 20080300842 | Govindarajan et al. | Dec 2008 | A1 |
| 20080308884 | Kalvesten | Dec 2008 | A1 |
| 20080311628 | Shoemaker | Dec 2008 | A1 |
| 20090036664 | Peter | Feb 2009 | A1 |
| 20090053704 | Novoradovskaya et al. | Feb 2009 | A1 |
| 20090062129 | McKernan et al. | Mar 2009 | A1 |
| 20090074771 | Koenig et al. | Mar 2009 | A1 |
| 20090087840 | Baynes et al. | Apr 2009 | A1 |
| 20090088679 | Wood et al. | Apr 2009 | A1 |
| 20090105094 | Heiner et al. | Apr 2009 | A1 |
| 20090170802 | Stahler et al. | Jul 2009 | A1 |
| 20090176280 | Hutchison, III et al. | Jul 2009 | A1 |
| 20090181861 | Li et al. | Jul 2009 | A1 |
| 20090194483 | Robotti et al. | Aug 2009 | A1 |
| 20090230044 | Bek | Sep 2009 | A1 |
| 20090238722 | Mora-Fillat et al. | Sep 2009 | A1 |
| 20090239759 | Balch | Sep 2009 | A1 |
| 20090263802 | Drmanac | Oct 2009 | A1 |
| 20090285825 | Kini et al. | Nov 2009 | A1 |
| 20090324546 | Notka et al. | Dec 2009 | A1 |
| 20100004143 | Shibahara | Jan 2010 | A1 |
| 20100008851 | Nicolaides et al. | Jan 2010 | A1 |
| 20100009872 | Eid et al. | Jan 2010 | A1 |
| 20100047805 | Wang | Feb 2010 | A1 |
| 20100051967 | Bradley et al. | Mar 2010 | A1 |
| 20100069250 | White, III et al. | Mar 2010 | A1 |
| 20100090341 | Wan et al. | Apr 2010 | A1 |
| 20100099103 | Hsieh et al. | Apr 2010 | A1 |
| 20100111768 | Banerjee et al. | May 2010 | A1 |
| 20100160463 | Wang et al. | Jun 2010 | A1 |
| 20100167950 | Juang et al. | Jul 2010 | A1 |
| 20100173364 | Evans, Jr. et al. | Jul 2010 | A1 |
| 20100216648 | Staehler et al. | Aug 2010 | A1 |
| 20100256017 | Larman et al. | Oct 2010 | A1 |
| 20100258487 | Zelechonok et al. | Oct 2010 | A1 |
| 20100272711 | Feldman et al. | Oct 2010 | A1 |
| 20100286290 | Lohmann et al. | Nov 2010 | A1 |
| 20100292102 | Nouri | Nov 2010 | A1 |
| 20100300882 | Zhang et al. | Dec 2010 | A1 |
| 20100311960 | Dellinger | Dec 2010 | A1 |
| 20100323404 | Lathrop | Dec 2010 | A1 |
| 20110009607 | Komiyama et al. | Jan 2011 | A1 |
| 20110082055 | Fox et al. | Apr 2011 | A1 |
| 20110114244 | Yoo et al. | May 2011 | A1 |
| 20110114549 | Yin et al. | May 2011 | A1 |
| 20110124049 | Li et al. | May 2011 | A1 |
| 20110124055 | Carr et al. | May 2011 | A1 |
| 20110126929 | Velasquez-Garcia et al. | Jun 2011 | A1 |
| 20110171651 | Richmond | Jul 2011 | A1 |
| 20110172127 | Jacobson et al. | Jul 2011 | A1 |
| 20110201057 | Carr et al. | Aug 2011 | A1 |
| 20110201528 | Baek et al. | Aug 2011 | A1 |
| 20110217738 | Jacobson | Sep 2011 | A1 |
| 20110229975 | Matthiesen et al. | Sep 2011 | A1 |
| 20110230653 | Novoradovskaya et al. | Sep 2011 | A1 |
| 20110254107 | Bulovic et al. | Oct 2011 | A1 |
| 20110287435 | Grunenwald et al. | Nov 2011 | A1 |
| 20120003713 | Hansen et al. | Jan 2012 | A1 |
| 20120021932 | Mershin et al. | Jan 2012 | A1 |
| 20120027786 | Gupta et al. | Feb 2012 | A1 |
| 20120028843 | Ramu et al. | Feb 2012 | A1 |
| 20120032366 | Ivniski et al. | Feb 2012 | A1 |
| 20120046175 | Rodesch et al. | Feb 2012 | A1 |
| 20120050411 | Mabritto et al. | Mar 2012 | A1 |
| 20120094847 | Warthmann et al. | Apr 2012 | A1 |
| 20120128548 | West et al. | May 2012 | A1 |
| 20120129704 | Gunderson et al. | May 2012 | A1 |
| 20120149602 | Friend et al. | Jun 2012 | A1 |
| 20120164127 | Short et al. | Jun 2012 | A1 |
| 20120164633 | Laffler | Jun 2012 | A1 |
| 20120164691 | Eshoo et al. | Jun 2012 | A1 |
| 20120184724 | Sierzchala et al. | Jul 2012 | A1 |
| 20120220497 | Jacobson et al. | Aug 2012 | A1 |
| 20120231968 | Bruhn et al. | Sep 2012 | A1 |
| 20120238737 | Dellinger et al. | Sep 2012 | A1 |
| 20120258487 | Chang et al. | Oct 2012 | A1 |
| 20120264653 | Carr et al. | Oct 2012 | A1 |
| 20120270750 | Oleinikov | Oct 2012 | A1 |
| 20120270754 | Blake | Oct 2012 | A1 |
| 20120283140 | Chu | Nov 2012 | A1 |
| 20120288476 | Hartmann et al. | Nov 2012 | A1 |
| 20120289691 | Dellinger et al. | Nov 2012 | A1 |
| 20120315670 | Jacobson et al. | Dec 2012 | A1 |
| 20120322681 | Kung et al. | Dec 2012 | A1 |
| 20130005585 | Anderson et al. | Jan 2013 | A1 |
| 20130005612 | Carr et al. | Jan 2013 | A1 |
| 20130017642 | Milgrew et al. | Jan 2013 | A1 |
| 20130017977 | Oleinikov | Jan 2013 | A1 |
| 20130017978 | Kavanagh et al. | Jan 2013 | A1 |
| 20130035261 | Sierzchala et al. | Feb 2013 | A1 |
| 20130040836 | Himmler et al. | Feb 2013 | A1 |
| 20130045483 | Treusch et al. | Feb 2013 | A1 |
| 20130053252 | Xie et al. | Feb 2013 | A1 |
| 20130059296 | Jacobson et al. | Mar 2013 | A1 |
| 20130059761 | Jacobson et al. | Mar 2013 | A1 |
| 20130065017 | Sieber | Mar 2013 | A1 |
| 20130109595 | Routenberg | May 2013 | A1 |
| 20130109596 | Peterson | May 2013 | A1 |
| 20130123129 | Zeiner et al. | May 2013 | A1 |
| 20130130321 | Staehler et al. | May 2013 | A1 |
| 20130137161 | Zhang et al. | May 2013 | A1 |
| 20130137173 | Zhang et al. | May 2013 | A1 |
| 20130137174 | Zhang et al. | May 2013 | A1 |
| 20130137861 | Leproust et al. | May 2013 | A1 |
| 20130164308 | Foletti et al. | Jun 2013 | A1 |
| 20130165328 | Previte et al. | Jun 2013 | A1 |
| 20130217071 | Montesclaros et al. | Aug 2013 | A1 |
| 20130225421 | Li et al. | Aug 2013 | A1 |
| 20130244884 | Jacobson et al. | Sep 2013 | A1 |
| 20130252849 | Hudson et al. | Sep 2013 | A1 |
| 20130261027 | Li et al. | Oct 2013 | A1 |
| 20130281308 | Kung et al. | Oct 2013 | A1 |
| 20130289246 | Crowe et al. | Oct 2013 | A1 |
| 20130296192 | Jacobson et al. | Nov 2013 | A1 |
| 20130296194 | Jacobson et al. | Nov 2013 | A1 |
| 20130298265 | Cunnac et al. | Nov 2013 | A1 |
| 20130309725 | Jacobson et al. | Nov 2013 | A1 |
| 20130323725 | Peter et al. | Dec 2013 | A1 |
| 20130330778 | Zeiner et al. | Dec 2013 | A1 |
| 20140011226 | Bernick et al. | Jan 2014 | A1 |
| 20140018441 | Fracchia et al. | Jan 2014 | A1 |
| 20140031240 | Behlke et al. | Jan 2014 | A1 |
| 20140038240 | Temme et al. | Feb 2014 | A1 |
| 20140106394 | Ko et al. | Apr 2014 | A1 |
| 20140141982 | Jacobson et al. | May 2014 | A1 |
| 20140170665 | Hiddessen et al. | Jun 2014 | A1 |
| 20140178992 | Nakashima et al. | Jun 2014 | A1 |
| 20140274729 | Kurn et al. | Sep 2014 | A1 |
| 20140274741 | Hunter et al. | Sep 2014 | A1 |
| 20140303000 | Armour et al. | Oct 2014 | A1 |
| 20140309119 | Jacobson et al. | Oct 2014 | A1 |
| 20140309142 | Tian | Oct 2014 | A1 |
| 20150010953 | Lindstrom et al. | Jan 2015 | A1 |
| 20150012723 | Park et al. | Jan 2015 | A1 |
| 20150031089 | Lindstrom | Jan 2015 | A1 |
| 20150038373 | Banyai et al. | Feb 2015 | A1 |
| 20150056609 | Daum et al. | Feb 2015 | A1 |
| 20150057625 | Coulthard | Feb 2015 | A1 |
| 20150065357 | Fox | Mar 2015 | A1 |
| 20150065393 | Jacobson | Mar 2015 | A1 |
| 20150099870 | Bennett et al. | Apr 2015 | A1 |
| 20150119293 | Short | Apr 2015 | A1 |
| 20150120265 | Amirav-Drory | Apr 2015 | A1 |
| 20150159152 | Allen et al. | Jun 2015 | A1 |
| 20150183853 | Sharma et al. | Jul 2015 | A1 |
| 20150191624 | Scheibel et al. | Jul 2015 | A1 |
| 20150191719 | Hudson et al. | Jul 2015 | A1 |
| 20150196917 | Kay et al. | Jul 2015 | A1 |
| 20150203839 | Jacobson et al. | Jul 2015 | A1 |
| 20150211047 | Borns | Jul 2015 | A1 |
| 20150225782 | Walder et al. | Aug 2015 | A1 |
| 20150240232 | Zamore et al. | Aug 2015 | A1 |
| 20150240280 | Gibson et al. | Aug 2015 | A1 |
| 20150261664 | Goldman et al. | Sep 2015 | A1 |
| 20150269313 | Church | Sep 2015 | A1 |
| 20150293102 | Shim | Oct 2015 | A1 |
| 20150307875 | Happe et al. | Oct 2015 | A1 |
| 20150321191 | Kendall et al. | Nov 2015 | A1 |
| 20150322504 | Lao et al. | Nov 2015 | A1 |
| 20150344927 | Sampson et al. | Dec 2015 | A1 |
| 20150353921 | Tian | Dec 2015 | A9 |
| 20150353994 | Myers et al. | Dec 2015 | A1 |
| 20150361420 | Hudson et al. | Dec 2015 | A1 |
| 20150361422 | Sampson et al. | Dec 2015 | A1 |
| 20150361423 | Sampson et al. | Dec 2015 | A1 |
| 20150368687 | Saaem et al. | Dec 2015 | A1 |
| 20150376602 | Jacobson et al. | Dec 2015 | A1 |
| 20160001247 | Oleinikov | Jan 2016 | A1 |
| 20160002621 | Nelson et al. | Jan 2016 | A1 |
| 20160002622 | Nelson et al. | Jan 2016 | A1 |
| 20160010045 | Cohen et al. | Jan 2016 | A1 |
| 20160017394 | Liang et al. | Jan 2016 | A1 |
| 20160017425 | Ruvolo et al. | Jan 2016 | A1 |
| 20160019341 | Harris et al. | Jan 2016 | A1 |
| 20160024138 | Gebeyehu et al. | Jan 2016 | A1 |
| 20160024576 | Chee | Jan 2016 | A1 |
| 20160026753 | Krishnaswami et al. | Jan 2016 | A1 |
| 20160026758 | Jabara et al. | Jan 2016 | A1 |
| 20160032396 | Diehn et al. | Feb 2016 | A1 |
| 20160046973 | Efcavitch et al. | Feb 2016 | A1 |
| 20160046974 | Efcavitch et al. | Feb 2016 | A1 |
| 20160082472 | Perego et al. | Mar 2016 | A1 |
| 20160089651 | Banyai | Mar 2016 | A1 |
| 20160090422 | Reif et al. | Mar 2016 | A1 |
| 20160090592 | Banyai et al. | Mar 2016 | A1 |
| 20160096160 | Banyai et al. | Apr 2016 | A1 |
| 20160097051 | Jacobson et al. | Apr 2016 | A1 |
| 20160102322 | Ravinder et al. | Apr 2016 | A1 |
| 20160108466 | Nazarenko et al. | Apr 2016 | A1 |
| 20160122755 | Hall et al. | May 2016 | A1 |
| 20160122800 | Bernick et al. | May 2016 | A1 |
| 20160152972 | Stapleton et al. | Jun 2016 | A1 |
| 20160168611 | Efcavitch et al. | Jun 2016 | A1 |
| 20160184788 | Hall et al. | Jun 2016 | A1 |
| 20160200759 | Srivastava et al. | Jul 2016 | A1 |
| 20160215283 | Braman et al. | Jul 2016 | A1 |
| 20160229884 | Indermuhle et al. | Aug 2016 | A1 |
| 20160230175 | Carstens | Aug 2016 | A1 |
| 20160230221 | Bergmann et al. | Aug 2016 | A1 |
| 20160251651 | Banyai | Sep 2016 | A1 |
| 20160256846 | Smith et al. | Sep 2016 | A1 |
| 20160264958 | Toro et al. | Sep 2016 | A1 |
| 20160289758 | Akeson et al. | Oct 2016 | A1 |
| 20160289839 | Harumoto et al. | Oct 2016 | A1 |
| 20160297883 | Gallo et al. | Oct 2016 | A1 |
| 20160303535 | Banyai et al. | Oct 2016 | A1 |
| 20160304862 | Igawa et al. | Oct 2016 | A1 |
| 20160304946 | Betts et al. | Oct 2016 | A1 |
| 20160310426 | Wu | Oct 2016 | A1 |
| 20160310927 | Banyai et al. | Oct 2016 | A1 |
| 20160318016 | Hou et al. | Nov 2016 | A1 |
| 20160333340 | Wu | Nov 2016 | A1 |
| 20160339409 | Banyai et al. | Nov 2016 | A1 |
| 20160340672 | Banyai et al. | Nov 2016 | A1 |
| 20160348098 | Stuelpnagel et al. | Dec 2016 | A1 |
| 20160354752 | Banyai et al. | Dec 2016 | A1 |
| 20160355880 | Gormley et al. | Dec 2016 | A1 |
| 20170017436 | Church | Jan 2017 | A1 |
| 20170066844 | Glanville | Mar 2017 | A1 |
| 20170067047 | Link et al. | Mar 2017 | A1 |
| 20170067099 | Zheng et al. | Mar 2017 | A1 |
| 20170073731 | Zheng et al. | Mar 2017 | A1 |
| 20170081660 | Cox et al. | Mar 2017 | A1 |
| 20170081716 | Peck | Mar 2017 | A1 |
| 20170088887 | Makarov et al. | Mar 2017 | A1 |
| 20170095785 | Banyai et al. | Apr 2017 | A1 |
| 20170096706 | Behlke et al. | Apr 2017 | A1 |
| 20170114404 | Behlke et al. | Apr 2017 | A1 |
| 20170141793 | Strauss et al. | May 2017 | A1 |
| 20170147748 | Staehler et al. | May 2017 | A1 |
| 20170151546 | Peck et al. | Jun 2017 | A1 |
| 20170159044 | Toro et al. | Jun 2017 | A1 |
| 20170175110 | Jacobson et al. | Jun 2017 | A1 |
| 20170218537 | Olivares | Aug 2017 | A1 |
| 20170233764 | Young et al. | Aug 2017 | A1 |
| 20170249345 | Malik et al. | Aug 2017 | A1 |
| 20170253644 | Steyaert et al. | Sep 2017 | A1 |
| 20170298432 | Holt | Oct 2017 | A1 |
| 20170320061 | Venter et al. | Nov 2017 | A1 |
| 20170327819 | Banyai et al. | Nov 2017 | A1 |
| 20170355984 | Evans et al. | Dec 2017 | A1 |
| 20170357752 | Diggans | Dec 2017 | A1 |
| 20170362589 | Banyai | Dec 2017 | A1 |
| 20180029001 | Banyai et al. | Feb 2018 | A1 |
| 20180051278 | Cox et al. | Feb 2018 | A1 |
| 20180051280 | Gibson et al. | Feb 2018 | A1 |
| 20180068060 | Ceze et al. | Mar 2018 | A1 |
| 20180104664 | Fernandez | Apr 2018 | A1 |
| 20180126355 | Peck et al. | May 2018 | A1 |
| 20180142289 | Zeitoun | May 2018 | A1 |
| 20180171509 | Cox | Jun 2018 | A1 |
| 20180236425 | Banyai et al. | Aug 2018 | A1 |
| 20180253563 | Peck et al. | Sep 2018 | A1 |
| 20180264428 | Banyai et al. | Sep 2018 | A1 |
| 20180273936 | Cox et al. | Sep 2018 | A1 |
| 20180282721 | Cox et al. | Oct 2018 | A1 |
| 20180291445 | Betts et al. | Oct 2018 | A1 |
| 20180312834 | Cox et al. | Nov 2018 | A1 |
| 20180326388 | Banyai et al. | Nov 2018 | A1 |
| 20180334712 | Singer et al. | Nov 2018 | A1 |
| 20180355351 | Nugent et al. | Dec 2018 | A1 |
| 20190060345 | Harrison et al. | Feb 2019 | A1 |
| 20190083596 | Orentas et al. | Mar 2019 | A1 |
| 20190118154 | Marsh et al. | Apr 2019 | A1 |
| 20190135926 | Glanville | May 2019 | A1 |
| 20190224711 | Demeris, Jr. | Jul 2019 | A1 |
| 20190240636 | Peck et al. | Aug 2019 | A1 |
| 20190244109 | Bramlett et al. | Aug 2019 | A1 |
| 20190314783 | Banyai et al. | Oct 2019 | A1 |
| 20190352635 | Toro et al. | Nov 2019 | A1 |
| 20190366293 | Banyai et al. | Dec 2019 | A1 |
| 20190366294 | Banyai et al. | Dec 2019 | A1 |
| 20200017907 | Zeitoun et al. | Jan 2020 | A1 |
| 20200056229 | Mir | Feb 2020 | A1 |
| 20200102611 | Zeitoun et al. | Apr 2020 | A1 |
| 20200156037 | Banyai et al. | May 2020 | A1 |
| 20200181667 | Wu et al. | Jun 2020 | A1 |
| 20200222875 | Peck et al. | Jul 2020 | A1 |
| 20200283760 | Nugent et al. | Sep 2020 | A1 |
| 20200299684 | Toro et al. | Sep 2020 | A1 |
| 20200308575 | Sato | Oct 2020 | A1 |
| 20200325235 | Tabibiazar et al. | Oct 2020 | A1 |
| 20200342143 | Peck | Oct 2020 | A1 |
| 20210002710 | Gantt et al. | Jan 2021 | A1 |
| 20210040476 | Cox et al. | Feb 2021 | A1 |
| 20210071168 | Nugent et al. | Mar 2021 | A1 |
| 20210102192 | Tabibiazar et al. | Apr 2021 | A1 |
| 20210102195 | Sato et al. | Apr 2021 | A1 |
| 20210102198 | Cox et al. | Apr 2021 | A1 |
| 20210115594 | Cox et al. | Apr 2021 | A1 |
| 20210129108 | Marsh et al. | May 2021 | A1 |
| 20210142182 | Bramlett et al. | May 2021 | A1 |
| 20210147830 | Liss | May 2021 | A1 |
| 20210170356 | Peck et al. | Jun 2021 | A1 |
| 20210179724 | Sato et al. | Jun 2021 | A1 |
| 20210207197 | Gantt et al. | Jul 2021 | A1 |
| 20210332078 | Wu | Oct 2021 | A1 |
| 20210348220 | Zeitoun et al. | Nov 2021 | A1 |
| 20210355194 | Sato et al. | Nov 2021 | A1 |
| 20210395344 | Sato et al. | Dec 2021 | A1 |
| 20220032256 | Lackey et al. | Feb 2022 | A1 |
| 20220064206 | Fernandez et al. | Mar 2022 | A1 |
| 20220064313 | Sato et al. | Mar 2022 | A1 |
| 20220064628 | Toro et al. | Mar 2022 | A1 |
| 20220106586 | Nugent et al. | Apr 2022 | A1 |
| 20220106590 | Arbiza et al. | Apr 2022 | A1 |
| 20220135690 | Sato et al. | May 2022 | A1 |
| 20220135965 | Gantt et al. | May 2022 | A1 |
| 20220138354 | Peck | May 2022 | A1 |
| 20220145289 | Lackey et al. | May 2022 | A1 |
| 20220206001 | Sato | Jun 2022 | A1 |
| 20220243195 | Nugent et al. | Aug 2022 | A1 |
| 20220246236 | Amirav-Drory | Aug 2022 | A1 |
| 20220259319 | Sato et al. | Aug 2022 | A1 |
| 20220259638 | Brown | Aug 2022 | A1 |
| 20220277808 | Arbiza et al. | Sep 2022 | A1 |
| 20220281989 | Glanville | Sep 2022 | A1 |
| 20220307010 | Sato et al. | Sep 2022 | A1 |
| 20220315971 | Wu et al. | Oct 2022 | A1 |
| 20220323924 | Lackey et al. | Oct 2022 | A1 |
| 20220325276 | Banyai et al. | Oct 2022 | A2 |
| 20220325278 | Nugent et al. | Oct 2022 | A1 |
| 20220348659 | Sato et al. | Nov 2022 | A1 |
| 20220356463 | Shen et al. | Nov 2022 | A1 |
| 20220356468 | Sato et al. | Nov 2022 | A1 |
| 20220411784 | Sato et al. | Dec 2022 | A1 |
| 20230002478 | Sato et al. | Jan 2023 | A1 |
| Number | Date | Country |
|---|---|---|
| 3157000 | Sep 2000 | AU |
| 2362939 | Aug 2000 | CA |
| 2720587 | Oct 2009 | CA |
| 1771336 | May 2006 | CN |
| 101277758 | Oct 2008 | CN |
| 102159726 | Aug 2011 | CN |
| 103003431 | Mar 2013 | CN |
| 103907117 | Jul 2014 | CN |
| 104520864 | Apr 2015 | CN |
| 104562213 | Apr 2015 | CN |
| 104734848 | Jun 2015 | CN |
| 104974929 | Oct 2015 | CN |
| 204714802 | Oct 2015 | CN |
| 105637097 | Jun 2016 | CN |
| 10260805 | Jul 2004 | DE |
| 201890763 | Aug 2018 | EA |
| 0090789 | Oct 1983 | EP |
| 0126621 | Aug 1990 | EP |
| 0753057 | Jan 1997 | EP |
| 1314783 | May 2003 | EP |
| 1363125 | Nov 2003 | EP |
| 1546387 | Jun 2005 | EP |
| 1153127 | Jul 2006 | EP |
| 1728860 | Dec 2006 | EP |
| 1072010 | Apr 2010 | EP |
| 2175021 | Apr 2010 | EP |
| 2330216 | Jun 2011 | EP |
| 1343802 | May 2012 | EP |
| 2504449 | Oct 2012 | EP |
| 2751729 | Jul 2014 | EP |
| 2872629 | May 2015 | EP |
| 2928500 | Oct 2015 | EP |
| 2971034 | Jan 2016 | EP |
| 3030682 | Jun 2016 | EP |
| 3044228 | Apr 2017 | EP |
| 2994509 | Jun 2017 | EP |
| 3204518 | Aug 2017 | EP |
| H07505530 | Jun 1995 | JP |
| 2001518086 | Oct 2001 | JP |
| 2002511276 | Apr 2002 | JP |
| 2002536977 | Nov 2002 | JP |
| 2002538790 | Nov 2002 | JP |
| 2003522119 | Jul 2003 | JP |
| 2004521628 | Jul 2004 | JP |
| 2004268394 | Sep 2004 | JP |
| 2006503586 | Feb 2006 | JP |
| 2006238724 | Sep 2006 | JP |
| 2007314746 | Dec 2007 | JP |
| 2008505642 | Feb 2008 | JP |
| 2008097189 | Apr 2008 | JP |
| 2008523786 | Jul 2008 | JP |
| 2008214343 | Sep 2008 | JP |
| 2009294195 | Dec 2009 | JP |
| 2010248084 | Nov 2010 | JP |
| 2012507513 | Mar 2012 | JP |
| 2015521472 | Jul 2015 | JP |
| 2016527313 | Sep 2016 | JP |
| 101339064 | Jan 2014 | KR |
| WO-9015070 | Dec 1990 | WO |
| WO-9210092 | Jun 1992 | WO |
| WO-9210588 | Jun 1992 | WO |
| WO-9309668 | May 1993 | WO |
| WO-9320242 | Oct 1993 | WO |
| WO-9525116 | Sep 1995 | WO |
| WO-9526397 | Oct 1995 | WO |
| WO-9615861 | May 1996 | WO |
| WO-9710365 | Mar 1997 | WO |
| WO-9822541 | May 1998 | WO |
| WO-9841531 | Sep 1998 | WO |
| WO-9942813 | Aug 1999 | WO |
| WO-9953101 | Oct 1999 | WO |
| WO-0013017 | Mar 2000 | WO |
| WO-0018957 | Apr 2000 | WO |
| WO-0042559 | Jul 2000 | WO |
| WO-0042560 | Jul 2000 | WO |
| WO-0042561 | Jul 2000 | WO |
| WO-0049142 | Aug 2000 | WO |
| WO-0053617 | Sep 2000 | WO |
| WO-0156216 | Aug 2001 | WO |
| WO-0210443 | Feb 2002 | WO |
| WO-0156216 | Mar 2002 | WO |
| WO-0220537 | Mar 2002 | WO |
| WO-0224597 | Mar 2002 | WO |
| WO-0227638 | Apr 2002 | WO |
| WO-0233669 | Apr 2002 | WO |
| WO-02072791 | Sep 2002 | WO |
| WO-02072864 | Sep 2002 | WO |
| WO-03040410 | May 2003 | WO |
| WO-03046223 | Jun 2003 | WO |
| WO-03054232 | Jul 2003 | WO |
| WO-03060084 | Jul 2003 | WO |
| WO-03064026 | Aug 2003 | WO |
| WO-03064027 | Aug 2003 | WO |
| WO-03064699 | Aug 2003 | WO |
| WO-03065038 | Aug 2003 | WO |
| WO-03066212 | Aug 2003 | WO |
| WO-03089605 | Oct 2003 | WO |
| WO-03093504 | Nov 2003 | WO |
| WO-03100012 | Dec 2003 | WO |
| WO-2004024886 | Mar 2004 | WO |
| WO-2004029220 | Apr 2004 | WO |
| WO-2004029586 | Apr 2004 | WO |
| WO-2004031351 | Apr 2004 | WO |
| WO-2004031399 | Apr 2004 | WO |
| WO-2004039953 | May 2004 | WO |
| WO-2004059556 | Jul 2004 | WO |
| WO-03060084 | Aug 2004 | WO |
| WO-2005014850 | Feb 2005 | WO |
| WO-2005051970 | Jun 2005 | WO |
| WO-2005059096 | Jun 2005 | WO |
| WO-2005059097 | Jun 2005 | WO |
| WO-2005093092 | Oct 2005 | WO |
| WO-2006023144 | Mar 2006 | WO |
| WO-2006044956 | Apr 2006 | WO |
| WO-2006076679 | Jul 2006 | WO |
| WO-2006116476 | Nov 2006 | WO |
| WO-2007073171 | Jun 2007 | WO |
| WO-2007109221 | Sep 2007 | WO |
| WO-2007118214 | Oct 2007 | WO |
| WO-2007120627 | Oct 2007 | WO |
| WO-2007137242 | Nov 2007 | WO |
| WO-2008006078 | Jan 2008 | WO |
| WO-2008027558 | Mar 2008 | WO |
| WO-2008045380 | Apr 2008 | WO |
| WO-2008054543 | May 2008 | WO |
| WO-2008063134 | May 2008 | WO |
| WO-2008063135 | May 2008 | WO |
| WO-2008068280 | Jun 2008 | WO |
| WO-2008103474 | Aug 2008 | WO |
| WO-2008109176 | Sep 2008 | WO |
| WO-2009132876 | Nov 2009 | WO |
| WO-2009126290 | Dec 2009 | WO |
| WO-2010001251 | Jan 2010 | WO |
| WO-2010025310 | Mar 2010 | WO |
| WO-2010025566 | Mar 2010 | WO |
| WO-2010027512 | Mar 2010 | WO |
| WO-2010053443 | May 2010 | WO |
| WO-2010089412 | Aug 2010 | WO |
| WO-2010141249 | Dec 2010 | WO |
| WO-2010141433 | Dec 2010 | WO |
| WO-2011020529 | Feb 2011 | WO |
| WO-2010141433 | Apr 2011 | WO |
| WO-2011053957 | May 2011 | WO |
| WO-2011056872 | May 2011 | WO |
| WO-2011066185 | Jun 2011 | WO |
| WO-2011066186 | Jun 2011 | WO |
| WO-2011085075 | Jul 2011 | WO |
| WO-2011103468 | Aug 2011 | WO |
| WO-2011109031 | Sep 2011 | WO |
| WO-2011143556 | Nov 2011 | WO |
| WO-2011150168 | Dec 2011 | WO |
| WO-2011161413 | Dec 2011 | WO |
| WO-2012013913 | Feb 2012 | WO |
| WO-2012061832 | May 2012 | WO |
| WO-2012078312 | Jun 2012 | WO |
| WO-2012149171 | Nov 2012 | WO |
| WO-2012154201 | Nov 2012 | WO |
| WO-2013010062 | Jan 2013 | WO |
| WO-2013030827 | Mar 2013 | WO |
| WO-2013032850 | Mar 2013 | WO |
| WO-2013036668 | Mar 2013 | WO |
| WO-2013049227 | Apr 2013 | WO |
| WO-2013101896 | Jul 2013 | WO |
| WO-2013134881 | Sep 2013 | WO |
| WO-2013154770 | Oct 2013 | WO |
| WO-2013170168 | Nov 2013 | WO |
| WO-2013177220 | Nov 2013 | WO |
| WO-2014004393 | Jan 2014 | WO |
| WO-2014008447 | Jan 2014 | WO |
| WO-2014021938 | Feb 2014 | WO |
| WO-2014035693 | Mar 2014 | WO |
| WO-2014088693 | Jun 2014 | WO |
| WO-2014089160 | Jun 2014 | WO |
| WO-2014093330 | Jun 2014 | WO |
| WO-2014093694 | Jun 2014 | WO |
| WO-2014151696 | Sep 2014 | WO |
| WO-2014160004 | Oct 2014 | WO |
| WO-2014160059 | Oct 2014 | WO |
| WO-2015017527 | Feb 2015 | WO |
| WO-2015021080 | Feb 2015 | WO |
| WO-2015021280 | Feb 2015 | WO |
| WO-2015040075 | Mar 2015 | WO |
| WO-2015054292 | Apr 2015 | WO |
| WO-2015081114 | Jun 2015 | WO |
| WO-2015081142 | Jun 2015 | WO |
| WO-2015081440 | Jun 2015 | WO |
| WO-2015090879 | Jun 2015 | WO |
| WO-2015120403 | Aug 2015 | WO |
| WO-2015136072 | Sep 2015 | WO |
| WO-2015160004 | Oct 2015 | WO |
| WO-2015175832 | Nov 2015 | WO |
| WO-2016007604 | Jan 2016 | WO |
| WO-2016011080 | Jan 2016 | WO |
| WO-2016022557 | Feb 2016 | WO |
| WO-2016053883 | Apr 2016 | WO |
| WO-2016055956 | Apr 2016 | WO |
| WO-2016065056 | Apr 2016 | WO |
| WO-2016126882 | Aug 2016 | WO |
| WO-2016126987 | Aug 2016 | WO |
| WO-2016130868 | Aug 2016 | WO |
| WO-2016161244 | Oct 2016 | WO |
| WO-2016164779 | Oct 2016 | WO |
| WO-2016172377 | Oct 2016 | WO |
| WO-2016173719 | Nov 2016 | WO |
| WO-2016183100 | Nov 2016 | WO |
| WO-2017049231 | Mar 2017 | WO |
| WO-2017053450 | Mar 2017 | WO |
| WO-2017059399 | Apr 2017 | WO |
| WO-2017095958 | Jun 2017 | WO |
| WO-2017100441 | Jun 2017 | WO |
| WO-2017118761 | Jul 2017 | WO |
| WO-2017158103 | Sep 2017 | WO |
| WO-2017214574 | Dec 2017 | WO |
| WO-2018026920 | Feb 2018 | WO |
| WO-2018038772 | Mar 2018 | WO |
| WO-2018057526 | Mar 2018 | WO |
| WO-2018094263 | May 2018 | WO |
| WO-2018112426 | Jun 2018 | WO |
| WO-2018119246 | Jun 2018 | WO |
| WO-2018156792 | Aug 2018 | WO |
| WO-2018170164 | Sep 2018 | WO |
| WO-2018170169 | Sep 2018 | WO |
| WO-2018170559 | Sep 2018 | WO |
| WO-2018200380 | Nov 2018 | WO |
| WO-2018231872 | Dec 2018 | WO |
| WO-2019014781 | Jan 2019 | WO |
| WO-2019051501 | Mar 2019 | WO |
| WO-2019079769 | Apr 2019 | WO |
| WO-2019084500 | May 2019 | WO |
| WO-2019136175 | Jul 2019 | WO |
| WO-2019222706 | Nov 2019 | WO |
| WO-2020139871 | Jul 2020 | WO |
| WO-2020176362 | Sep 2020 | WO |
| WO-2020176678 | Sep 2020 | WO |
| WO-2020176680 | Sep 2020 | WO |
| WO-2020257612 | Dec 2020 | WO |
| WO-2021046655 | Mar 2021 | WO |
| WO-2021119193 | Jun 2021 | WO |
| WO-2022010934 | Jan 2022 | WO |
| WO-2022046797 | Mar 2022 | WO |
| WO-2022046944 | Mar 2022 | WO |
| WO-2022047076 | Mar 2022 | WO |
| WO-2022076326 | Apr 2022 | WO |
| WO-2022086866 | Apr 2022 | WO |
| WO-2022087293 | Apr 2022 | WO |
| WO-2022098662 | May 2022 | WO |
| WO-2022159620 | Jul 2022 | WO |
| WO-2022178137 | Aug 2022 | WO |
| WO-2022204309 | Sep 2022 | WO |
| WO-2022204316 | Sep 2022 | WO |
| WO-2022217004 | Oct 2022 | WO |
| WO-2022235579 | Nov 2022 | WO |
| WO-2022235584 | Nov 2022 | WO |
| WO-2022271884 | Dec 2022 | WO |
| Entry |
|---|
| Momentive, Safety Data Sheet Version 4.0, 2019, 1-14 (Year: 2019). |
| Alberts et al.: Molecular Biology of the Cell. 4th edition. New York: Garland Science; 2002. The Generation of Antibody Diversity. https://www.ncbi.nlm.nih.gov/books/NBK26860/. |
| Carter and Friedman, DNA synthesis and Biosecurity: Lessons learned and options for the future. J. Craig Venter Institute, La Jolla, CA, 28 pages, Oct. 2015. |
| Chervin et al.: Design of T-cell receptor libraries with diverse binding properties to examine adoptive T-cell responses. Gene Therapy. 20(6):634-644 (2012). |
| Cui et al.: Information Security Technology Based on DNA Computing. International Workshop on Anti-Counterfeiting, Security and Identification (ASID); IEEE Xplore 4 pages (2007). |
| Gaytan et al.: Chemical synthesis of oligonucleotides using acetone as a washing solvent. BioTechniques 47:701-702 (2009). |
| Hopcroft et al.: What is the Young's Modulus of Silicon?. Journal of Microelectromechanical Systems. 19(2):229-238 (2010). |
| Jaiswal et al.: An architecture for creating collaborative semantically capable scientific data sharing infrastructures. Proceeding WIDM '06 Proceedings of the 8th annual ACM international workshop on Web information and data management. ACM Digital Library pp. 75-82 (2006). |
| Jang et al.: Characterization of T cell repertoire of blood, tumor, and ascites in ovarian cancer patients using next generation sequencing. Oncoimmunology, 4(11):e1030561:1-10 (2015). |
| Kosuri et al.: A scalable gene synthesis platform using high-fidelity DNA microchips Nat.Biotechnol. 28(12):1295-1299 (2010). |
| PCT/US2018/056783 International Preliminary Report on Patentability dated Apr. 30, 2020. |
| PCT/US2019/012218 International Preliminary Report on Patentability dated Jul. 16, 2020. |
| PCT/US2020/019371 International Search Report and Written Opinion dated Jun. 25, 2020. |
| PCT/US2020/019986 International Search Report and Written Opinion dated Jul. 29, 2020. |
| PCT/US2020/019986 Invitation to Pay Additional Fees dated Jun. 5, 2020. |
| PCT/US2020/019988 International Search Report and Written Opinion dated Jul. 29, 2020. |
| PCT/US2020/019988 Invitation to Pay Additional Fees dated Jun. 8, 2020. |
| Simonyan and Zisserman, Very Deep Convolutional Networks for Large-Scale Image Recognition, Published as a conference paper at Int. Conf. Learn. Represent., pp. 1-14, 2015. |
| U.S. Appl. No. 15/151,316 Final Office Action dated Jul. 9, 2020. |
| U.S. Appl. No. 15/272,004 Office Action dated Jun. 12, 2020. |
| U.S. Appl. No. 15/816,995 Office Action dated May 19, 2020. |
| U.S. Appl. No. 15/835,342 Final Office Action dated Sep. 8, 2020. |
| U.S. Appl. No. 15/921,479 Final Office Action dated Jun. 15, 2020. |
| U.S. Appl. No. 15/991,992 Office Action dated May 21, 2020. |
| U.S. Appl. No. 16/039,256 Office Action dated Aug. 20, 2020. |
| Van der Velde: Thesis. Finding the Strength of Glass. Delft University of Technology. 1-16 (2015). |
| Weiler et al.: Combining the Preparation of Oligonucleotide Arrays and Synthesis of High-Quality Primers. Analytical Biochemistry. 243:218-227 (1996) . |
| Yes HMDS vapor prime process application note Prepared by UC Berkeley and University of Texas at Dallas and re-printed by Yield Engineering Systems, Inc., 6 pages (http://www.yieldengineering.com/Portals/0/HMDS%20Application%20Note.pdf (Published online Aug. 23, 2013). |
| Abudayyeh et al.: C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science, available on line, Jun. 13, 2016, at: http://zlab.mit.edu/assets/reprints/Abudayyeh_OO_Science_2016.pdf , 17 pages. |
| Acevedo-Rocha et al.: Directed evolution of stereoselective enzymes based on genetic selection as opposed to screening systems. J. Biotechnol. 191:3-10 (2014). |
| Adessi et al.: Solid phase DNA amplification: characterisation of primer attachment and amplification mechanisms. Nucleic Acids Res. 28(20):E87, 2000. |
| Alexeyev, Mikhail F. et al.: Gene synthesis, bacterial expression and purification of the Rickettsia prowazekii ATP/ADP translocase, Biochimica et Biophysics Acta, 1419:299-306, 1999. |
| Ai-Housseiny et al.: Control of interfacial instabilities using flow geometry Nature Physics, 8:747-750, 2012. |
| Amblard, Francois et al.: A magnetic manipulator for studying local rheology and micromechanical properties of biological systems, Rev. Sci. Instrum., 67(3):18-827, 1996. |
| Andoni and Indyk, Near-Optimal Hashing Algorithms for Approximate Nearest Neighbor in High Dimensions, Communications of the ACM, 51(1):117-122, 2008. |
| Arand et al.: Structure of Rhodococcus erythropolis limonene-1,2-epoxide hydrolase reveals a novel active site. EMBO J. 22:2583-2592 (2003). |
| Arkles et al.: The Role of Polarity in the Structure of Silanes Employed in Surface Modification. Silanes and Other Coupling Agents. 5:51-64, 2009. |
| Arkles, Hydrophobicity, Hydrophilicity Reprinted with permission from the Oct. 2006 issue of Paint & Coatings Industry magazine, Retrieved on Mar. 19, 2016, 10 pages. |
| Assembly manual for the POSaM: The ISB Piezoelelctric Oligonucleotide Synthesizer and Microarrayer, The Institute for Systems Biology, May 28, 2004 (50 pages). |
| Assi et al.: Massive-parallel adhesion and reactivity—measurements using simple and inexpensive magnetic tweezers. J. Appl. Phys. 92(9):5584-5586 (2002). |
| ATDBio, Nucleic Acid Structure, Nucleic Acids Book, 9 pages, published on Jan. 22, 2005. from: http://www.atdbio.eom/content/5/Nucleic-acid-structure. |
| ATDBio, Solid-Phase Oligonucleotide Synthesis, Nucleic Acids Book, 20 pages, Published on Jul. 31, 2011. from: http://www.atdbio.com/content/17/Solid-phase-oligonucleotide-synthesis. |
| Au et al.: Gene synthesis by a LCR-based approach: high level production of Leptin-L54 using synthetic gene in Escherichia coli. Biochemical and Biophysical Research Communications 248:200-203 (1998). |
| Baedeker, Mathias et al.: Overexpression of a designed 2.2kb gene of eukaryotic phenylalanine ammonialyase in Escherichia coli⋅. FEBS Letters, 457:57-60, 1999. |
| Barbee et al.: Magnetic Assembly of High-Density DNA Arrays for Genomic Analyses. Anal Chem. 80(6):2149-2154, 2008. |
| Barton et al.: A desk electrohydrodynamic jet printing system. Mechatronics, 20:611-616, 2010. |
| Beaucage et al.: Advances in the synthesis of oligonucleotides by the phosphoramidite approach. Tetrahedron. 48:2223-2311, 1992. |
| Beaucage et al.: Deoxynucleoside phosphoramidites—A new class of key intermediates for deoxypolynucleotide synthesis. Tetrahedron Lett. 22(20):1859-1862, 1981. |
| Beaucage, Serge L. et al.: The Chemical synthesis of DNA/RNA Chapter 2 in: Encyclopedia of Cell Biology, 1:36-53, 2016. |
| Beaulieu, Martin et al.: PCR candidate region mismatch scanning adaptation to quantitative, high-throughput genotyping, Nucleic Acids Research, 29(5):1114-1124, 2001. |
| Beigelman et al.: Base-modified phosphoramidite analogs of pyrimidine ribonucleosides for RNA structure-activity studies. Methods Enzymol. 317:39-65, 2000. |
| Bethge et al.: Reverse synthesis and 3′-modification of RNA. Jan. 1, 2011, pp. 64-64, XP055353420. Retrieved from the Internet: URL:http://www.is3na.org/assets/events/Category%202-Medicinal %20Chemistry%20of%2001igonucleotides%20%2864-108%29.pdf. |
| Binkowski et al.: Correcting errors in synthetic DNA through consensus shuffling. Nucleic Acids Research, 33(6):e55, 8 pages, 2005. |
| Biswas, Indranil et al.: Identification and characterization of a thermostable MutS homolog from Thennus aquaticus, The Journal of Biological Chemistry, 271(9):5040-5048, 1996. |
| Biswas, Indranil et al.: Interaction of MutS protein with the major and minor grooves of a heteroduplex DNA, The Journal of Biological Chemistry, 272(20):13355-13364, 1997. |
| Bjornson, Keith P. et al.: Differential and simultaneous adenosine Di- and Triphosphate binding by MutS, The Journal of Biological Chemistry, 278(20):18557-18562, 2003. |
| Blanchard et al.: High-Density Oligonucleotide Arrays, Biosensors & Bioelectronics, 11(6/7):687-690, 1996. |
| Blanchard, in: Genetic Engineering, Principles and Methods, vol. 20, Ed. J. Sedlow, New York: Plenum Press, p. 111-124, 1979. |
| Blawat et al.: Forward error correction for DNA data storage. Procedia Computer Science, 80:1011-1022, 2016. |
| Bonini and Mondino, Adoptive T-cell therapy for cancer: The era of engineered T cells. European Journal of Immunology, 45:2457-2469, 2015. |
| Bornholt et al.: A DNA-Based Archival Storage System, in International Conference on Architectural Support for Programming Languages and Operating Systems (ASPLOS), Apr. 2-6, 2016, Atlanta, GA, 2016, 637-649. |
| Borovkov et al.: High-quality gene assembly directly from unpurified mixtures of microassay-synthesized oligonucleotides. Nucleic Acid Research, 38(19):e180, 10 pages, 2010. |
| Brunet, Aims and methods of biosteganography. Journal of Biotechnology, 226:56-64, 2016. |
| Buermans et al.: Next Generation sequencing technology: Advances and applications, Biochimica et Biophysica Acta (BBA)—Molecular Basis of Disease, 1842:1931-1941, 2014. |
| Butler et al.: In situ synthesis of oligonucleotide arrays by using surface tension. J Am Chem Soc. 123(37):8887-94, 2001. |
| Calvert, Lithographically patterned self-assembled films. In: Organic Thin Films and Surfaces: Directions for The Nineties, vol. 20, p. 109, ed. By Abraham Ulman, San Diego: Academic Press, 1995. |
| Cardelli. Two-Domain DNA Strand Displacement, Electron. Proc. Theor. Comput. Sci., 26:47-61, 2010. |
| Carlson. Time for New DNA Synthesis and Sequencing Cost Curves, 2014. [Online]. Available: http://www.synthesis.cc/synthesis/2014/02/time_for_new_cost_curves_2014. 10 pages. |
| Carr et al.: Protein-mediated error correction for de novo DNA synthesis. Nucleic Acids Res. 32(20):e162, 9 pages, 2004. |
| Caruthers. Chemical synthesis of deoxyoligonucleotides by the phosphoramidite method. In Methods in Enzymology, Chapter 15, 154:287-313, 1987. |
| Caruthers. The Chemical Synthesis of DNA/RNA: Our Gift to Science. J. Biol. Chem., 288(2):1420-1427, 2013. |
| Caruthers. Gene synthesis machines: DNA chemistry and its uses. Science 230(4723):281-285 (1985). |
| Casmiro et al.: PCR-based gene synthesis and protein NMR spectroscopy, Structure, 5(11):1407-1412, 1997. |
| CeGaT. Tech Note available at https://www.cegat.de/web/wp-content/uploads/2018/06/Twist-Exome-Tech-Note.pdf (4 pgs.) (2018). |
| Cello et al.: Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template. Science. 297(5583):1016-8, 2000. |
| Chalmers et al.: Scaling up the ligase chain reaction-based approach to gene synthesis. Biotechniques. 30(2):249-52, 2001. |
| Chan et al.: Natural and engineered nicking endonucleases—from cleavage mechanism to engineering of strand-specificity. Nucleic Acids Res. 39(1):1-18, 2011. |
| Chen et al.: Chemical modification of gene silencing oligonucleotides fordrug discovery and development. Drug Discov Today. 10(8):587-93 2005. |
| Chen et al.: Programmable chemical controllers made from DNA, Nat. Nanotechnol., 8(10):755-762, 2013. |
| Cheng et al.: High throughput parallel synthesis of oligonucleotides with 1536 channel synthesizer. Nucleic Acids Res. 30(18):e93, 2002. |
| Chilamakuri et al.: Performance comparison of four exome capture systems for deep sequencing. BMC Genomics 15(1):449 (2014). |
| Cho et al.: Capillary passive valve in microfluidic systems. NSTI-Nanotech. 2004; 1:263-266. |
| Chrisey et al.: Fabrication of patterned DNA surfaces Nucleic Acids Research, 24(15):3040-3047 (1996). |
| Chung et al.: One-step preparation of competent Escherichia coli: Transformation and storage of bacterial cells in the same solution. Proc Natl Acad Sci U S A. Apr. 1989;86(7):2172-2175. |
| Church et al.: Next-generation digital information storage in DNA. Science, 337:6102, 1628-1629, 2012. |
| Cleary et al.: Production of complex nucleic acid libraries using highly parallel in situ oligonucleotide synthesis. Nat Methods 1(3):241-248 (2004). |
| Cohen et al.: Human population: The next half century. Science, 302:1172-1175, 2003. |
| Crick. On protein synthesis. Symp Soc Exp Biol12:138-163, 1958. |
| Cruse et al.: Atlas of Immunology, Third Edition. Boca Raton:CRC Press (pp. 282-283) (2010). |
| Cutler et al.: High-throughput variation detection and genotyping using microarrays, Genome Research, vol. 11, 1913-19 (2001). |
| Dahl et al.: Circle-to-circle amplification for precise and sensitive DNA analysis. Proc Natl Acad Sci U S A. Mar. 30, 2004;101(13):4548-53. Epub Mar. 15, 2004. |
| De Mesmaeker et al.: Backbone modifications in oligonucleotides and peptide nucleic acid systems. Curr Opin Struct Biol. Jun. 1995;5(3):343-55. |
| De Silva et al.: New Trends of Digital Data Storage in DNA. BioMed Res Int. 2016:8072463 (2016). |
| Deamer et al.: Characterization of nucleic acids by nanopore analysis, Ace. Cham. Res., vol. 35, No. 10, 817-825 (2002). |
| Deaven. The Human Genome Project: Recombinant clones for mapping and sequencing DNA. Los Alamos Science, 20:218-249, 1992. |
| Deng et al.: Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming Nature Biotechnology, 27:352-360 (2009). |
| Dietrich et al.: Gene assembly based on blunt-ended double-stranded DNA-modules, Biotechnology Techniques, vol. 12, No. 1, 49-54 (Jan. 1998). |
| Dillon et al.: Exome sequencing has higher diagnostic yield compared to simulated disease-specific panels in children with suspected monogenic disorders. Eur J Hum Genet 26(5):644-651 (2018). |
| Dormitzer et al.: Synthetic generation of influenza vaccine viruses for rapid response to pandemics. Sci Translational Medicine, 5(185):185ra68, 14 pages, 2013. |
| Doudna et al.: Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science 346(6213):1258096-1 -1258096-9, 2014. |
| Douthwaite et al.: Affinity maturation of a novel antagonistic human monoclonal antibody with a long VH CDR3 targeting the Class A GPCR formyl-peptide receptor 1; mAbs, vol. 7, Iss. 1, pp. 152-166 (Jan. 1, 2015). |
| Dower et al.: High efficiency transformation of E.coli by high voltage electroporation. Nucleic Acids Res. 16(13):6127-45 (1988). |
| Dressman et al.: Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations. Proc Natl Acad Sci U S A. Jul. 22, 2003;100(15):8817-22. Epub Jul. 11, 2003. |
| Drmanac et al.: Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science. Jan. 1, 2010;327(5961):78-81. doi: 10.1126/science.1181498. Epub Nov. 5, 2009. |
| Droege and Hill. The Genome Sequencer FLXTM System-Longer reads, more applications, straight forward bioinformatics and more complete data sets Journal of Biotechnology, 136:3-10, 2008. |
| Duffy et al.: Rapid Prototyping of Microfluidic Systems in Poly(dimethylsiloxane). Anal Chem. Dec. 1, 1998;70(23):4974-84. doi: 10.1021/ac980656z. |
| Duggan et al.: Expression profiling using cDNA microarrays. Nat Genet. Jan. 1999; 21(1 Suppl):10-4. |
| Dvorsky. Living Bacteria Can Now Store Data. GIZMODO internet publication. Retrieved from https://gizmodo.com/living-bacteria-can-now-store-data-1781773517 (4 pgs) (Jun. 10, 2016). |
| Eadie et al.: Guanine modification during chemical DNA synthesis. Nucleic Acids Res. Oct. 26, 1987;15(20):8333-49. |
| Eisen, Jonathan A.: A phylogenomic study of the MutS family of proteins, Nucleic Acids Research, vol. 26, No. 18, 4291-4300 (1998). |
| Ellis et al.: DNA assembly for synthetic biology: from parts to pathways and beyond. Integr Biol (Camb). Feb. 2011;3(2):109-18. doi: 10.1039/c0ib00070a. Epub Jan. 19, 2011. |
| El-Sagheer et al.: Biocompatible artificial DNA linker that is read through by DNA polymerases and is functional in Escherichia coli. Proc Natl Acad Sci U S A. Jul. 12, 2011;108(28):11338-43. doi: 10.1073/pnas.1101519108. Epub Jun. 27, 2011. |
| Elsik et al.: The Genome sequence of taurine cattle: A window of ruminant biology and evolution. Science, 324:522-528, 2009. |
| Elsner et al.: 172 nm excimer VUV-triggered photodegradation and micropatterning of aminosilane films, Thin Solid Films, 517:6772-6776 (2009). |
| Engler et al.: A one pot, one step, precision cloning method with high throughput capability. PLoS One. 2008;3(11):e3647. doi: 10.1371/journal.pone.0003647. Epub Nov. 5, 2008. |
| Engler et al.: Golden gate shuffling: a one-pot DNA shuffling method based on type IIs restriction enzymes. PLoS One. 2009;4(5):e5553. doi: 10.1371/journal.pone.0005553. Epub May 14, 2009. |
| Erlich and Zielinski. DNA fountain enables a robust and efficient storage architecture. Science, 355(6328):950-054, 2017. |
| Eroshenko et al.: Gene Assembly from Chip-Synthesized Oligonucleotides; Current Protocols in Chemical biology 4: 1-17 (2012). |
| European Patent Application No. 12827479.2 Extended European Search Report dated May 18, 2015. |
| European Patent Application No. 12827479.2 Partial European Search Report dated Jan. 29, 2015. |
| European Patent Application No. 14834665.3 Communication dated Jan. 16, 2018. |
| European Patent Application No. 14834665.3 extended European Search Report dated Apr. 28, 2017. |
| European Patent Application No. 14834665.3 Further Examination Report dated Nov. 28, 2018. |
| European Patent Application No. 14834665.3 Office Action dated May 2, 2018. |
| European Patent Application No. 16847497.1 Extended European Search Report dated Jan. 9, 2019. |
| European Patent Application No. 16871446.7 European Search Report dated Apr. 10, 2019. |
| European Patent Application No. 16871446.7 First Official Action dated Nov. 13, 2019. |
| Evans et al.: DNA Repair Enzymes. Current Protocols in Molecular Biology 84:III:3.9:3.9.1-3.9.12 http://www.ncbi.nlm.nih.gov/pubmed/18972391 (Published online Oct. 1, 2008 Abstract only provided). |
| Fahy et al.: Self-sustained sequence replication (3SR): an isothermal transcription-based amplification system alternative to PCR. PCR Methods Appl. Aug. 1991;1(1):25-33. |
| Fedoryak et al.: Brominated hydroxyquinoline as a photolabile protecting group with sensitivity to multiphoton excitation, Org. Lett., vol. 4, No. 2 , 3419-3422 (2002). |
| Ferretti et al.: Total synthesis of a gene for bovine rhodopsin. PNAS, 83:599-603 (1986). |
| Finger et al.: The wonders of Flap Endonucleases: Structure, function, mechanism and regulation. Subcell Biochem., 62:301-326, 2012. |
| Fodor et al.: Light-directed, spatially addressable parallel chemical synthesis. Science. 251(4995):767-773 (1991). |
| Fogg et al.: Structural basis for uracil recognition by archaeal family B DNA polymerases. Nature Structural Biology, 9(12):922-927, 2002. |
| Foldesi et al.: The synthesis of deuterionucleosides. Nucleosides Nucleotides Nucleic Acids. Oct.-Dec. 2000;19(10-12):1615-56. |
| Frandsen et al.: Efficient four fragment cloning for the construction of vectors for targeted gene replacement in filamentous fungi. BMC Molecular Biology 2008, 9:70. |
| Frandsen. Experimental setup. Dec. 7, 2010, 3 pages. http://www.rasmusfrandsen.dk/experimental_setup.htm. |
| Frandsen. The USER Friendly technology. USER cloning. Oct. 7, 2010, 2 pages. http://www.rasmusfrandsen.dk/user_cloning.htm. |
| Fullwood et al.: Next-generation DNA sequencing of paired-end tags [PET] for transcriptome and genome analysis Genome Research, 19:521-532, 2009. |
| Galka et al.: QuickLib, a method for building fully synthetic plasmid libraries by seamless cloning of degenerate oligonucleotides. Plos One, 12, e0175146:1-9 (2017). |
| Galka et al.: QuickLib, a method for building fully synthetic plasmid libraries by seamless cloning of degenerate oligonucleotides. Plos One, 12, e0175146:S1 figure (2017). |
| Galka et al.: QuickLib, a method for building fully synthetic plasmid libraries by seamless cloning of degenerate oligonucleotides. Plos One, 12, e0175146:S1 Table (2017). |
| Galka et al.: QuickLib, a method for building fully synthetic plasmid libraries by seamless cloning of degenerate oligonucleotides. Plos One, 12, e0175146:S2 figure (2017). |
| Galneder et al.: Microelectrophoresis of a bilayer-coated silica bead in an optical trap: application to enzymology. Biophysical Journal, vol. 80, No. 5, 2298-2309 (May 2001). |
| Gao et al.: A flexible light-directed DNA chip synthesis gated by deprotection using solution photogenerated acids. Nucleic Acids Res. Nov. 15, 2001;29(22):4744-50. |
| Gao et al.: A method for the generation of combinatorial antibody libraries using pIX phage display. PNAS 99(20):12612-12616 (2002). |
| Gao et al.: Thermodynamically balanced inside-out (TBIO) PCR-based gene synthesis: a novel method of primer design for high-fidelity assembly of longer gene sequences. Nucleic Acids Res. Nov. 15, 2003;31(22):e143. |
| Garaj et al.: Graphene as a subnanometre trans-electrode membrane. Nature. Sep. 9, 2010;467(7312):190-3. doi: 10.1038/nature09379. |
| Garbow et al.: Optical tweezing electrophoresisof isolated, highly charged colloidal spheres, Colloids and Surfaces A: Physiochem. Eng. Aspects, vol. 195, 227-241 (2001). |
| GeneArt Seamless Cloning and Assembly Kits. Life Technologies Synthetic Biology. 8 pages, available online Jun. 15, 2012. |
| Genomics 101. An Introduction to the Genomic Workflow. 2016 edition, 64 pages. Available at: http://www.frontlinegenomics.com/magazine/6757/genomics-101/. |
| Geu-Flores et al.: USER fusion: a rapid and efficient method for simultaneous fusion and cloning of multiple PCR products. Nucleic Acids Res. 2007;35(7):e55. Epub Mar. 27, 2007. |
| Gibson Assembly. Product Listing. Application Overview. 2 pages, available online Dec. 16, 2014. |
| Gibson et al.: Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science. Feb. 29, 2008;319(5867):1215-20. doi: 10.1126/science.1151721. Epub Jan. 24, 2008. |
| Gibson et al.: Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome. Science 329(5989):52-56 (2010). |
| Goldfeder et al.: Medical implications of technical accuracy in genome sequencing. Genome Med 8(1):24 (2016). |
| Goldman et al.: Towards practical, high-capacity, low-maintenance information storage in synthesized DNA, Nature, 494(7435):77-80, 2013. |
| Gosse et al.: Magnetic tweezers: micromanipulation and force measurement at the molecular level, Biophysical Journal, vol. 8, 3314-3329 (Jun. 2002). |
| Grass et al.: Robust chemical preservation of digital information on DNA in silica with error-correcting codes, Angew. Chemie—Int. Ed., 54(8):2552-2555, 2015. |
| Greagg et al.: A read-ahead function in archaeal DNA polymerases detects promutagenic template-strand uracil. Proc. Nat. Acad. Sci. USA, 96:9045-9050, 1999. |
| Grovenor. Microelectronic materials. Graduate Student Series in Materials Science and Engineering. Bristol, England: Adam Hilger, 1989; p. 113-123. |
| Gu et al.: Depletion of abundant sequences by hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications. Genome Biology, 17:41, 13 pages, 2016. |
| Haber, Charbel et al.: Magnetic tweezers for DNA micromanipulation, Rev. Sci. Instrum., vol. 71, No. 12, 4561-4570 (Dec. 2000). |
| Han et al.: Linking T-cell receptor sequence to functional phenotype at the single-cell level. Nat Biotechnol 32(7):684-692 (2014). |
| Hanahan and Cold Spring Harbor Laboratory, Studies on transformation of Escherichia coli with plasmids J. Mol. Biol. 166:557-580 (1983). |
| Hanahan et al.: Plasmid transformation of Escherichia coli and other bacteria. Methods Enzymol, vol. 204, p. 63-113 (1991). |
| Harada et al.: Unexpected substrate specificity of T4 DNA ligase revealed by in vitro selection. Nucleic Acids Res. May 25, 1993;21(10):2287-91. |
| Heckers et al.: Error analysis of chemically synthesized polynucleotides, BioTechniques, vol. 24, No. 2, 256-260 (1998). |
| Herzer et al.: Fabrication of patterned silane based self-assembled monolayers by photolithography and surface reactions on silicon-oxide substrates Chem. Commun., 46:5634-5652 (2010). |
| Hoover et al.: DNAWorks: an automated method for designing oligonucleotides for PCR-based gene synthesis, Nucleic Acids Research, vol. 30, No. 10, e43, 7 pages (2002). |
| Hosu et al.: Magnetic tweezers for intracellular applications⋅, Rev. Sci. Instrum., vol. 74, No. 9, 4158-4163 (Sep. 2003). |
| Huang et al.: Three-dimensional cellular deformation analysis with a two-photon magnetic manipulator workstation, Biophysical Journal, vol. 8 2, No. 4, 2211-2223 (Apr. 2002). |
| Hughes et al.: Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer Nat Biotech 4:342-347 (2001). |
| Hughes et al.: Principles of early drug discovery. Br J Pharmacol 162(2):1239-1249, 2011. |
| Hutchison et al.: Cell-free cloning using phi29 DNA polymerase. Proc Natl Acad Sci U S A. Nov. 29, 2005;102(48):17332-6. Epub Nov. 14, 2005. |
| IMGUR: The magic of the internet. Uploaded May 10, 2012, 2 pages, retrieved from: https://imgur.com/mEWuW. |
| In-Fusion Cloning: Accuracy, Not Background. Cloning & Competent Cells, ClonTech Laboratories, 3 pages, available online Jul. 6, 2014. |
| International Application No. PCT/US2017/026232 International Preliminary Report on Patentability dated Feb. 26, 2019. |
| International Application No. PCT/US2017/045105 International Preliminary Report on Patentability dated Feb. 5, 2019. |
| International Application No. PCT/US2017/052305 International Preliminary Report on Patentability dated Apr. 30, 2019. |
| International Application No. PCT/US2017/062391 International Preliminary Report on Patentability dated May 21, 2019. |
| International Application No. PCT/US2018/019268 International Preliminary Report on Patentability dated Sep. 6, 2019. |
| International Application No. PCT/US2018/050511 International Search Report and Written Opinion dated Jan. 11, 2019. |
| International Application No. PCT/US2018/057857 International Search Report and Written Opinion dated Mar. 18, 2019. |
| International Application No. PCT/US2019/012218 International Search Report and Written Opinion dated Mar. 21, 2019. |
| International Application No. PCT/US2019/032992 International Search Report and Written Opinion dated Oct. 28, 2019. |
| International Application No. PCT/US2019/032992 Invitation to Pay Additional Fees dated Sep. 6, 2019. |
| Jackson et al.: Recognition of DNA base mismatches by a rhodium intercalator, J. Am. Chem. Soc., vol. 19, 12986-12987 (1997). |
| Jacobs et al.: DNA glycosylases: In DNA repairand beyond. Chromosoma 121:1-20 (2012)—http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3260424/. |
| Jacobus et al.: Optimal cloning of PCR fragments by homologous recombination in Escherichia soli. PLoS One 10(3):e0119221 (2015). |
| Jager et al.: Simultaneous Humoral and Cellular: Immune Response against Cancer—Testis Antigen NY-ES0-1: Definition of Human Histocompatibility Leukocyte Antigen (HLA)-A2—binding Peptide Epitopes. J. Exp. Med. 187(2):265-270 (1998). |
| Jinek et al.: A Programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science, 337:816-821, 2012. |
| Jo et al.: Engineering therapeutic antibodies targeting G-protein-coupled receptors; Experimental & Molecular Medicine; 48; 9 pages (2016). |
| Karagiannis and EI-OSTA. RNA interference and potential therapeutic applications of short interfering RNAs Cancer Gene Therapy, 12:787-795, 2005. |
| Ke et al.: Influence of neighboring base pairs on the stability of single base bulges and base pairs in a DNA fragment, Biochemistry, Vo. 34, 4593-4600 (1995). |
| Kelley, Shana et al.: Single-base mismatch detection based on charge transduction through DNA, Nucleic Acids Research, vol. 27, No. 24, 4830-4837 (1999). |
| Kim et al.: High-resolution patterns of quantum dots formed by electrohydrodynamic jet printing for light-emitting diodes. Nano Letters, 15:969-973, 2015. |
| Kim et al.: Site specific cleavage of DNA-RNA hybrids by zinc finger/Fok I cleavage domain fusions Gene, vol. 203, 43-49 (1997). |
| Kim et al.: Chimeric restriction endonuclease, Proc. Natl. Acad. Sci. USA, vol. 91,883-887 (Feb. 1994). |
| Kim. The interaction between Z-ONA and the Zab domain of double-stranded RNA adenosine deaminase characterized using fusion nucleases, The Journal of Biological Chemistry, vol. 274, No. 27, 19081-19086 (1999). |
| Kinde et al.: Detection and quantification of rare mutations with massively parallel sequencing. Proc Natl Acad Sci U S A. Jun. 7, 2011;108(23):9530-5. Epub May 17, 2011. |
| Kodumal et al.: Total synthesis of long DNA sequences: synthesis of a contiguous 32-kb polyketide synthase gene cluster. Proc Natl Acad Sci U S A. Nov. 2, 2004;101(44):15573-8. Epub Oct. 20, 2004. |
| Koike-Yusa et al.: Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library. Nature Biotechnology, 32:267-273, 2014 (with three pages of supplemental Online Methods). |
| Kong et al.: Parallel gene synthesis in a microfluidic device. Nucleic Acids Res., 35(8):e61 (2007). |
| Kong. Microfluidic Gene Synthesis. MIT Thesis. Submitted to the program in Media Arts and Sciences, School of Architecture and Planning, in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Media Arts and Sciences at the Massachusetts Institute of Technology. 143 pages Jun. 2008. |
| Kopp et al.: Chemical amplification: continuous-flow PCR on a chip, Science, vol. 280, 1046-1048 (May 15, 1998). |
| Kosuri and Church. Large-scale de novo DNA synthesis: technologies and applications, Nature Methods, 11:499-507, 2014. Available at: http://www.nature.com/nmeth/journal/v11/n5/full/nmeth.2918.html. |
| Kosuri et al.: A scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips. Nature Biotechnology. 2010; 28:1295-1299. |
| Krayden, Inc.: A Guide to Silane Solutions. Silane coupling agents. 7 pages. Published on May 31, 2005 at: http://krayden.com/pdf/xia_silane_chemistry.pdf. |
| Lagally et al.: Single-Molecule DNA Amplification and Analysis in an Integrated Microfluidic Device. Analytical Chemistry. 2001;73(3): 565-570. |
| Lahue et al.: DNA mismatch correction in a defined system, Science, vol. 425; No. 4914, 160-164 (Jul. 14, 1989). |
| Lambrinakos et al.: Reactivity of potassium permanganate and tetraethylammonium chloride with mismatched bases and a simple mutation detection protocol,Nucleic Acids Research, vol. 27, No. 8, 1866-1874 (1999). |
| Landegren et al.: A ligase-mediated gene detection technique. Science. Aug. 26, 1988;241(4869):1077-80. |
| Lang et al.: An automated two-dimensional optical force clamp for single molecule studies, Biophysical Journal, vol. 83, 491-501 (Jul. 2002). |
| Lashkari et al.: An automated multiplex oligonucleotide synthesizer: development of high-throughput, low-cost DNA synthesis. Proc Natl Acad Sci U S A. Aug. 15, 1995;92(17):7912-5. |
| Lausted et al.: POSaM: a fast, flexible, open-source, inkjet oligonucleotide synthesizer and microarrayer, Genome Biology, 5:R58, 17 pages, 2004. available at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC507883/. |
| Leamon et al.: A massively parallel PicoTiterPlate based platform for discrete picoliter-scale polymerase chain reactions. Electrophoresis. Nov. 2003;24(21):3769-77. |
| Lee et al.: A microfluidic oligonucleotide synthesizer. Nucleic Acids Research 2010 vol. 38(8):2514-2521. DOI: 10.1093/nar/gkq092. |
| Lee et al.: Microelectromagnets for the control of magnetic nanoparticles, Appl. Phys. Lett., vol. 79, No. 20, 3308-3310 (Nov. 12, 2001). |
| Lee: Covalent End-Immobilization of Oligonucleotides onto Solid Surfaces; Thesis, Massachusetts Institute of Technology, Aug. 2001 (315 pages). |
| Leproust et al.: Agilent's Microarray Platform: How High-Fidelity DNA Synthesis Maximizes the Dynamic Range of Gene Expression Measurements. 2008; 1-12. http://www.miltenyibiotec.com/˜/media/Files/Navigation/Genomic%20Services/Agilent_DNA_Microarray_Platform.ashx. |
| Leproust et al.: Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process. Nucleic Acids Research. 2010; 38(8):2522-2540. |
| Lesnikowski et al.: Nucleic acids and nucleosides containing carboranes. J. Organometallic Chem. 1999; 581:156-169. |
| Leumann. Dna analogues: from supramolecular principles to biological properties. Bioorg Med Chem. Apr. 2002;10(4):841-54. |
| Levene et al.: Zero-mode waveguides for single-molecule analysis at high concentrations. Science. Jan. 31, 2003;299(5607):682-6. |
| Lewontin and Harti. Population genetics in forensic DNA typing. Science, 254:1745-1750, 1991. |
| Li et al.: Beating bias in the directed evolution of proteins: Combining high-fidelity on-chip solid-phase gene synthesis with efficient gene assembly for combinatorial library construction. First published Nov. 24, 2017, 2 pages. retrieved from: https://doi.org/10.1002/cbic.201700540. |
| Li et al.: Beating Bias in the Directed Evolution of Proteins: Combining High-Fidelity on-Chip Solid-Phase Gene Synthesis with Efficient Gene Assembly for Combinatorial Library Construction. ChemBioChem 19:221-228 (2018). |
| Light source unit for printable patterning VUV-Aligner / USHIO Inc., Link here: https://www.ushio.co.jp/en/products/1005.html, published Apr. 25, 2016, printed from the internet on Aug. 2, 2016, 3 pages. |
| Limbachiya et al.: Natural data storage: A review on sending information from now to then via Nature. ACM Journal on Emerging Technologies in Computing Systems, V(N):Article A, May 19, 2015, 17 pages. |
| Link Technologies. Product Guide 2010. Nov. 27, 2009, 136 pages. XP055353191. Retrieved from the Internet: URL:http://www.linktech.co.uk/documents/517/517.pdf. |
| Lipshutz et al.: High density synthetic oligonucleotide arrays, Nature Genetics Supplement, vol. 21, 20-24 (Jan. 1999). |
| Lishanski et al.: Mutation detection by mismatch binding protein, MutS, in amplified DNA: application to the cystic fibrosis gene, Proc. Natl. Acad. Sci. USA, vol. 91, 2674-2678 (Mar. 1994). |
| Liu et al.: Comparison of Next-Generation Sequencing Systems. J Biomed Biotechnol 2012: 251364 (2012). |
| Liu et al.: Enhanced Signals and Fast Nucleic Acid Hybridization by Microfluidic Chaotic Mixing. Angew. Chem. Int. Ed. 2006; 45:3618-3623. |
| Liu et al.: Rational design of CXCR4 specific antibodies with elongated CDRs. JACS, 136:10557-10560, 2014. |
| Lizardi et al.: Mutation detection and single-molecule counting using isothermal rolling-circle amplification. Nat Genet. Jul. 1998;19(3):225-32. |
| Li et al.: Functional domains in Fok I restriction endonuclease, Proc. Natl. Acad. Sci. USA, 89:4275-4279, 1992. |
| Lu et al.: Methyl-directed repair of DNA base-pair mismatches in vitro, Proc. Natl. Acad. Sci. USA, 80:4639-4643, 1983. |
| Lund et al.: A validated system for ligation-free uracilexcision based assembly of expression vectors for mammalian cell engineering. DTU Systems of Biology. 2011. 1 page. http://www.lepublicsystemepco.com/files/modules/gestion_rubriques/REF-B036-Lund_Anne%20Mathilde.pdf. |
| Ma et al.: DNA synthesis, assembly and application in synthetic biology. Current Opinion in Chemical Biology. 16:260-267, 2012. |
| Ma et al.: Versatile surface functionalization of cyclic olefin copolymer (COC) with sputtered SiO2 thin film for potential BioMEMS applications. Journal of Materials Chemistry, 11 pages, 2009. |
| Mahato et al.: Modulation of gene expression by antisense and antigene oligodeoxynucleotides and small interfering RNA Expert Opin. Drug Delivery, 2(1):3-28, 2005. |
| Margulies et al.: Genome sequencing in open microfabricated high-density picolitre reactors. Nature. 437(7057):376-80, 2005. |
| Martinez-Torrecuadrada et al.: Targeting the Extracellular Domain of Fibroblast Growth Factor Receptor 3 with Human Single-Chain Fv Antibodies Inhibits Bladder Carcinoma Cell Line Proliferation; Clinical Cancer Research; vol. 11; pp. 6282-6290 (2005). |
| Matteucci et al.: Synthesis of deoxyoligonucleotides on a polymer support. J. Am. Chem. Soc. 103(11):3185-3191, 1981. |
| Matzas et al.: Next generation gene synthesis by targeted retrieval of bead-immobilized, sequence verified DNA clones from a high throughput pyrosequencing device. Nat. Biotechnol., 28(12):1291-1294, 2010. |
| Mazor et al.: Isolation of Full-Length IgG Antibodies from Combinatorial Libraries Expressed in Escherichia coli; Antony S. Dimitrov (ed.), Therapeutic Antibodies: Methods and Protocols, vol. 525, Chapter 11, pp. 217-239 (2009). |
| McBride & Caruthers. An investigation of several deoxynucleoside phosphoramidites useful for synthesizing deoxyoligonucleotides. Tetrahedron Lett. 24: 245-248, 1983. |
| McGall et al.: Light-directed synthesis of high-density oligonucleotide arrays using semiconductor photoresists. Proc Natl Acad Sci U S A. 93(24):13555-60, 1996. |
| McGall et al.: The Efficiency of Light-Directed Synthesis of DNA Arrays on Glass Substrates. J. Am. Chem. Soc. 119(22):5081-5090, 1997. |
| Mei et al.: Cell-free protein synthesis in microfluidic array devices Biotechnol. Prog., 23(6):1305-1311, 2007. |
| Mendel-Hartvig. Padlock probes and rolling circle amplification. New possibilities for sensitive gene detection. Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine 1175. Uppsala University. 2002, 39 pages, http://www.diva-portal.org/smash/get/diva2:161926/FULLTEXT01.pdf. |
| Meyers and Friedland, Knowledge-based simulation of genetic regulation in bacteriophage lambda. Nucl. Acids Research, 12(1):1-16, 1984. |
| Meynert et al.: Quantifying single nucleotide variant detection sensitivity in exome sequencing. BMC Bioinformatics 14:195 (2013). |
| Meynert et al.: Variant detection sensitivity and biases in whole genome and exome sequencing. BMC Bioinformatics 15:247 (2014). |
| Milo and Phillips. Numbers here reflect the No. of protein coding genes and excludes tRNA and non-coding RNA. Cell Biology by the Numbers, p. 286, 2015. |
| Mitra et al.: In situ localized amplification and contact replication of many individual DNA molecules. Nucleic Acids Res. 27(24):e34, 1999. |
| Morin et al.: Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. Biotechniques, 45:81-94, 2008. |
| Morris and Stauss. Optimizing T-cell receptor gene therapy for hematologic malignancies. Blood, 127(26):3305-3311, 2016. |
| Muller et al.: Protection and labelling of thymidine by a fluorescent photolabile group, Helvetica Chimica Acta, vol. 84, 3735-3741 (2001). |
| Mulligan. Commercial Gene Synthesis Technology PowerPoint presentation. BlueHeron® Biotechnology. Apr. 5, 2006 (48 pgs). |
| Nakatani et al.: Recognition of a single guanine bulge by 2-Acylamino-1 ,8-naphthyridine, J. Am. Chem. Soc., vol. 122, 2172-2177 (2000). |
| Neiman M.S.: Negentropy principle in information processing systems. Radiotekhnika, 1966, No. 11, p. 2-9. |
| Neiman M.S.: On the bases of the theory of information retrieval. Radiotekhnika, 1967, No. 5, p. 2-10. |
| Neiman M.S.: On the molecular memory systems and the directed mutations. Radiotekhnika, 1965, No. 6, pp. 1-8. |
| Neiman M.S.: On the relationships between the reliability, performance and degree of microminiaturization at the molecular-atomic level. Radiotekhnika, 1965, No. 1, pp. 1-9. |
| Neiman M.S.: Some fundamental issues of microminiaturization. Radiotekhnika, 1964, No. 1, pp. 3-12. |
| Nishikura. A short primer on RNAi: RNA-directed RNA polymerase acts as a key catalyst Cell, 107:415-418, 2001. |
| Nour-Eldin et al.: USER Cloning and USER Fusion: The Ideal Cloning Techniques for Small and Big Laboratories. Plant Secondary Metabolism Engineering. Methods in Molecular Biology vol. 643, 2010, pp. 185-200. |
| Ochman et al.: Genetic applications of an inverse polymerase chain reaction. Genetics. Nov. 1988;120(3):621-3. |
| Organick et al.: Random access in large-scale DNA data storage. Nature Biotechnology, Advance Online Publication, 8 pages, 2018. |
| Organick et al.: Scaling up DNA data storage and random access retrieval, bioRxiv, preprint first posted online Mar. 7, 2017, 14 pages. |
| Pan et al.: An approach for global scanning of single nucleotide variations. Proc Natl Acad Sci U S A. Jul. 9, 2002;99(14):9346-51. |
| Pankiewicz. Fluorinated nucleosides. Carbohydr Res. Jul. 10, 2000;327(1-2):87-105. |
| Paul et al.: Acid binding and detritylation during oligonucleotide synthesis. Nucleic Acids Research. 15. pp. 3048-3052 (1996). |
| PCT/IL2012/000326 International Preliminary Report on Patentability dated Dec. 5, 2013. |
| PCT/IL2012/000326 International Search Report dated Jan. 29, 2013. |
| PCT/US2014/049834 International Preliminary Report on Patentability dated Feb. 18, 2016. |
| PCT/US2014/049834 International Search Report and Written Opinion dated Mar. 19, 2015. |
| PCT/US2014/049834, Invitation to Pay Additional Fees and, where applicable, protest fee, mailed Jan. 5, 2015. |
| PCT/US2015/043605 International Preliminary Report on Patentability dated Feb. 16, 2017. |
| PCT/US2015/043605 International Search Report and Written Opinion dated Jan. 6, 2016. |
| PCT/US2015/043605 Invitation to Pay Additional Fees dated Oct. 28, 2015. |
| PCT/US2016/016459 International Preliminary Report on Patentability dated Aug. 17, 2017. |
| PCT/US2016/016459 International Search Report and Written Opinion dated Apr. 13, 2016. |
| PCT/US2016/016636 International Preliminary Report on Patentability dated Aug. 17, 2017. |
| PCT/US2016/016636 International Search Report and Written Opinion dated May 2, 2016. |
| PCT/US2016/028699 International Preliminary Report on Patentability dated Nov. 2, 2017. |
| PCT/US2016/028699 International Search Report and Written Opinion dated Jul. 29, 2016. |
| PCT/US2016/031674 International Preliminary Report on Patentability dated Nov. 23, 2017. |
| PCT/US2016/031674 International Search Report and Written Opinion dated Aug. 11, 2016. |
| PCT/US2016/052336 International Preliminary Report on Patentability dated Mar. 29, 2018. |
| PCT/US2016/052336 International Search Report and Written Opinion dated Dec. 7, 2016. |
| PCT/US2016/052916 International Preliminary Report on Patentability dated Apr. 5, 2018. |
| PCT/US2016/052916 International Search Report and Written Opinion dated Dec. 30, 2016. |
| PCT/US2016/064270 International Preliminary Report on Patentability dated Jun. 14, 2018. |
| PCT/US2016/064270 International Search Report and Written Opinion dated Apr. 28, 2017. |
| PCT/US2017/026232 International Search Report and Written Opinion dated Aug. 28, 2017. |
| PCT/US2017/036868 International Search Report and Written Opinion dated Aug. 11, 2017. |
| PCT/US2017/045105 International Search Report and Written Opinion dated Oct. 20, 2017. |
| PCT/US2017/052305 International Search Report and Written Opinion dated Feb. 2, 2018. |
| PCT/US2017/062391 International Search Report and Written Opinion dated Mar. 28, 2018. |
| PCT/US2017/066847 International Search Report and Written Opinion dated May 4, 2018. |
| PCT/US2018/022487 International Search Report and Written Opinion dated Aug. 1, 2018. |
| PCT/US2018/022493 International Search Report and Written Opinion dated Aug. 1, 2018. |
| PCT/US2018/037152 International Preliminary Report on Patentability dated Dec. 26, 2019. |
| PCT/US2018/037152 International Search Report and Written Opinion dated Aug. 28, 2018. |
| PCT/US2018/037161 International Preliminary Report on Patentability dated Dec. 17, 2019. |
| PCT/US2018/037161 International Search Report and Written Opinion dated Oct. 22, 2018. |
| PCT/US2018/037161 Invitation to Pay Additional Fees dated Aug. 27, 2018. |
| PCT/US2018/050511 International Preliminary Report on Patentability dated Mar. 26, 2020. |
| PCT/US2018/056783 International Search Report and Written Opinion of the International Searching Authority dated Dec. 20, 2018. |
| PCT/US2018/19268 International Search Report and Written Opinion dated Jun. 26, 2018. |
| PCT/US2018/19268 Invitation to Pay Additional Fees and, where applicable, protest fee dated May 2, 2018. |
| PCT/US2018/22487 Invitation to Pay Additional Fees and, where applicable, protest fee dated May 31, 2018. |
| PCT/US2018/22493 Invitation to Pay Additional Fees and, where applicable, protest fee dated May 31, 2018. |
| PCT/US2019/068435 International Search Report and Written Opinion dated Apr. 23, 2020. |
| Pease et al.: Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc Natl Acad Sci U S A. May 24, 1994;91(11):5022-6. |
| Peisajovich et al.: BBF RFC 28: A method for combinatorial multi-part assembly based on the type-lis restriction enzyme aarl. Sep. 16, 2009, 7 pages. |
| Pellois et al.: Individually addressable parallel peptide synthesis on microchips, Nature Biotechnology, vol. 20 , 922-926 (Sep. 2002). |
| Petersen et al.: LNA: a versatile tool for therapeutics and genomics. Trends Biotechnol. Feb. 2003;21(2):74-81. |
| Pierce and Wangh. Linear-after-the-exponential polymerase chain reaction and allied technologies Real-time detection strategies for rapid, reliable diagnosis from single cells Methods Mol. Med. 132:65-85 (2007) (Abstract only). |
| Pierce et al.: Linear-after-the-exponential polymerase chain reaction and allied technologies. Real-time detection strategies for rapid, reliable diagnosis from single cells. Methods Mol Med. 2007;132:65-85. |
| Pirrung. How to make a DNA chip. Angew. Chem. Int. Ed., 41:1276-1289, 2002. |
| Plesa et al.: Multiplexed gene synthesis in emulsions for exploring protein functional landscapes. Science, 10.1126/science.aao5167, 10 pages, 2018. |
| Pon. Solid-phase supports for oligonucleotide synthesis. Methods Mol Biol. 1993;20:465-96. |
| Poster. Reimagine Genome Scale Research. 2016, 1 page. Available at http://www2.twistbioscience.com/Oligo_Pools_CRISPR_poster. |
| Powers et al.: Optimal strategies for the chemical and enzymatic synthesis of bihelical deoxyribonucleic acids. J Am Chem Soc., 97(4):875-884, 1975. |
| Pray. Discovery of DNA Structure and Function: Watson and Crick, Nature Education, 2008, 6 pages, available at: http://www.nature.com/scitable/topicpage/discovery-of-dna-structure-and-function-watson-397. |
| Prodromou et al.: Recursive PCR: a novel technique for total gene synthesis. Protein Eng. Dec. 1992;5(8):827-9. |
| PubChem Data Sheet Acetonitrile. Printed from website https://pubchem.ncbi.nlm.nig.gov/ pp. 1-124 (2020). |
| PubChem Data Sheet Methylene Chloride. Printed from website https://pubchem.ncbi.nlm.nih.gov/ pp. 1-140 (2020). |
| Puigbo. Optimizer: a web server for optimizing the codon usage of DNA sequences. Nucleic Acid Research, 35(14):126-131, 2007. |
| Qian and Winfree. Scaling up digital circuit computation with DNA strand displacement cascades. Science, 332(6034):196-1201, 2011. |
| Qian et al.: Neural network computation with DNA strand displacement cascades, Nature, 475(7356):368-372, 2011. |
| Quan et al.: Parallel on-chip gene synthesis and application to optimization of protein expression. Nature Biotechnology. 2011; 29:449-452. |
| Rafalski and Morgante. Corn and humans: recombination and linkage disequilibrium in two genomes of similar size. Trends in Genetics, 20(2):103-111, 2004. |
| Raje and Murma. A Review of electrohydrodynamic-inkjet printing technology. International Journal of Emerging Technology and Advanced Engineering, 4(5):174-183, 2014. |
| Rajpal et al.: A general method for greatly improving the affinity of antibodies by using combinatorial libraries. Proc. Natl. Acad. Sci. 102(24):8466-8471 (2005). |
| Rastegari et al.: XNOR-Net: ImageNet Classification Using Binary Convolutional Neural Networks, in ECCV 2016, Part IV, LNCS 9908, p. 525-542, 2016. |
| Reimagine SequenceSpace. Reimagine Research, Twist Bioscience, Product Brochure, Published Apr. 6, 2016 online at: www2.twistbioscience.com/TB_Product_Brochure_04.2016, 8 pages. |
| RF Electric discharge type excimer lamp. Products Catalog. Excimer lamp light source flat excimer, 16 pages dated Jan. 2016. From: http://www.hamamatsu.com/jp/en/product/category/1001/3026/index.html. |
| Richmond et al.: Amplification and assembly ofchip-eluted DNA (AACED): a method for high-throughput gene synthesis. Nucleic Acids Res. Sep. 24, 2004;32(17):5011-8. Print 2004. |
| Roche. Restriction Enzymes from Roche Applied Science—A Tradition of Premium Quality and Scientific Support. FAQS and Ordering Guide. Roche Applied Science. Accessed Jan. 12, 2015, 37 pages. |
| Rogozin et al.: Origin and evolution of spliceosomal introns. Biology Direct, 7:11, 2012. |
| Ruminy et al.: Long-range identification of hepatocyte nuclear factor-3 (FoxA) high and low-affinity binding Sites with a chimeric nuclease, J. Mol. Bioi., vol. 310, 523-535 (2001). |
| Saaem et al.: In situ synthesis of DNA microarray on functionalized cyclic olefin copolymer substrate ACS Applied Materials & Interfaces, 2(2):491-497, 2010. |
| Saboulard et al.: High-throughput site-directed mutagenesis using oligonucleotides synthesized on DNA chips. Biotechniques. Sep. 2005;39(3):363-8. |
| Sacconi et al.: Three-dimensional magneto-optic trap for micro-object manipulation, Optics Letters, vol. 26, No. 17, 1359-1361 (1 Sep. 2001). |
| Saiki et al.: Analysis of enzymatically amplified beta-globin and HLA-DQ alpha DNA with allelespecific oligonucleotide probes. Nature 324:163-166 (1986). |
| Sandhu et al.: Dual asymmetric PCR: one-step construction of synthetic genes. Biotechniques. Jan. 1992;12(1):14-6. |
| Sargolzaei et al.: Extent of linkage disequilibrium in Holstein cattle in North America. J.Dairy Science, 91:2106-2117, 2007. |
| Schaller et al.: Studies on Polynucleotides. XXV.1 The Stepwise Synthesis of Specific Deoxyribopolynucleotides (5). Further Studies on the Synthesis of Internucleotide Bond by the Carbodiimide Method. The Synthesis of Suitably Protected Dinucleotides as Intermediates in the Synthesis of Higher Oligonucleotides. J. Am. Chem. Soc. 1963; 85(23):3828-3835. |
| Schmalzing et al.: Microchip electrophoresis: a method for high-speed SNP detection. Nucleic Acids Res 28(9):E43 (2000). |
| Schmitt et al.: New strategies in engineering T-cell receptor gene-modified T cells to more effectively target malignancies. Clinical Cancer Research, 21(23):5191-5197, 2015. |
| Seelig et al.: Enzyme-Free Nucleic Acid Logic Circuits, Science 314(5805):1585-1588, 2006. |
| Sharan et al.: Recombineering: a homologous recombination-based method of genetic engineering. Nat Profile 4(2):1-37 (originally pp. 206-223) (2009). |
| Sharpe and Mount. Genetically modified T cells in cancer therapy: opportunities and challenges. Disease Models and Mechanisms, 8:337-350, 2015. |
| Sierzchala, Agnieszka B et al.: Solid-phase oligodeoxynucleotide synthesis : a two-step cycle using peroxy anion deprotection, J. Am. Chem. Soc., vol. 125, No. 44, 13427-13441 (2003). |
| Singh-Gasson et al.: Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array, Nature Biotechnology, vol. 17, 974-978 (Oct. 1999). |
| Skerra. Phosphorothioate primers improve the amplification of DNA sequences by DNA polymerases with proofreading activity. Nucleic Acids Res. Jul. 25, 1992; 20(14):3551-4. |
| Smith et al.: Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides. Proc Natl Acad Sci U S A. Dec. 23, 2003;100(26):15440-5. Epub Dec. 2, 2003. |
| Smith et al.: Generation of cohesive ends on PCR products by UDG-mediated excision of dU, and application for cloning into restriction digest-linearized vectors. PCR Methods Appl. May 1993;2(4):328-32. |
| Smith et al.: Removal of Polymerase-Produced mutant sequences from PCR products, Proc. Natl. Acad. Sci. USA, vol. 94, 6847-6850 (Jun. 1997). |
| Smith et al.: Mutation detection with MutH, MutL, and MutS mismatch repair proteins, Proc. Natl. Acad. Sci. USA, vol. 93, 4374-4379 (Apr. 1996). |
| Smith et al.: Direct mechanical measurements of the elasticity of single DNA molecules using magnetic beads, Science, vol. 258, 1122-1126 (Nov. 13, 1992). |
| Solomon et al.: Genomics at Agilent: Driving Value in DNA Sequencing.https://www.agilent.com/labs/features/2010_genomics.html, 8 pages (Aug. 5, 2010). |
| Soni et al.: Progress toward ultrafast DNA sequencing using solid-state nanopores. Clin Chem. Nov. 2007;53(11):1996-2001. Epub Sep. 21, 2007. |
| Southern et al.: Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: evaluation using experimental models. Genomics. Aug. 1992;13(4):1008-17. |
| Sproat et al.: An efficient method for the isolation and purification of oligoribonucleotides. Nucleosides & Nucleotides. 1995; 14(1&2):255-273. |
| Srivannavit et al.: Design and fabrication of microwell array chips for a solution-based, photogenerated acid-catalyzed parallel oligonuclotide DNA synthesis. Sensors and Actuators A, 116:150-160, 2004. |
| Srivastava et al.: RNA synthesis: phosphoramidites for RNA synthesis in the reverse direction. Highly efficient synthesis and application to convenient introduction of ligands, chromophores and modifications of synthetic RNA at the 3′-end, Nucleic Acids Symposium Series, 52(1):103-104, 2008. |
| Steel. The Flow-Thru Chip a Three-dimensional biochip platform. In: Schena, Microarray Biochip Technology, Chapter 5, Natick, MA: Eaton Publishing, 2000, 33 pages. |
| Stemmer et al.: Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides. Gene. Oct. 16, 1995;164(1):49-53. |
| Stryer. DNA Probes and genes can be synthesized by automated solid-phase methods. Biochemistry, 3rd edition, New York: W.H. Freeman and Company, 1988; 123-125. |
| Stutz et al.: Novel fluoride-labile nucleobase-protecting groups for the synthesis of 3′(2′)-O-amino-acylated RNA sequences. Helv. Chim. Acta. 2000; 83(9):2477-2503. |
| Sullivan et al.: Library construction and evaluation for site saturation mutagenesis. Enzyme Microb. Technol. 53:70-77 (2013). |
| Sun et al.: Structure-Guided Triple-Code Saturation Mutagenesis: Efficient Tuning of the Stereoselectivity of an Epoxide Hydrolase. ACS Catal. 6:1590-1597 (2016). |
| Takahashi. Cell-free cloning using multiply-primed rolling circle amplification with modified RNA primers. Biotechniques. Jul. 2009;47(1):609-15. doi: 10.2144/000113155. |
| Tanase et al.: Magnetic trapping of multicomponent nanowires, The Johns Hopkins University, Baltimore, Maryland, p. 1-3 (Jun. 25, 2001). |
| Taylor et al.: Impact of surface chemistry and blocking strategies on DNA microarrays. Nucleic Acids Research, 31(16):e87, 19 pages, 2003. |
| The Hood Laboratory. Beta Group. Assembly Manual for the POSaM: The ISB Piezoelelctric Oligonucleotide Synthesizer and Microarrayer, Inkjet Microarrayer Manual Version 1.2, 50 pages, May 28, 2004. |
| The SLIC. Gibson, CPEC and SLiCE assembly methods (and GeneArt Seamless, In-Fusion Cloning). 5 pages, available online Sep. 2, 2010. |
| Tian et al.: Accurate multiplex gene synthesis from programmable DNA microchips. Nature. Dec. 23, 2004;432(7020):1050-4. |
| Tsai et al.: Dimeric CRISPR RNA-guided Fokl nucleases for highly specific genome editing Nat. Biotechnol., 32(6):569-576, 2014. |
| Twist Bioscience | White Paper. DNA-Based Digital Storage. Retrieved from the internet, Twistbioscience.com, Mar. 27, 2018, 5 pages. |
| U.S. Appl. No. 14/241,874 Final Office Action dated Jan. 28, 2019. |
| U.S. Appl. No. 14/241,874 Office Action dated Feb. 27, 2017. |
| U.S. Appl. No. 14/241,874 Office Action dated Jul. 14, 2016. |
| U.S. Appl. No. 14/241,874 Office Action dated May 4, 2018. |
| U.S. Appl. No. 14/452,429 Notice of Allowance dated Jun. 7, 2016. |
| U.S. Appl. No. 14/452,429 Office Action dated Oct. 21, 2015. |
| U.S. Appl. No. 14/452,429 Restriction Requirement dated Dec. 12, 2014. |
| U.S. Appl. No. 14/885,962 Notice of Allowance dated Nov. 8, 2017 and Sep. 29, 2017. |
| U.S. Appl. No. 14/885,962 Office Action dated Dec. 16, 2016. |
| U.S. Appl. No. 14/885,962 Office Action dated Sep. 8, 2016. |
| U.S. Appl. No. 14/885,962 Restriction Requirement dated Mar. 1, 2016. |
| U.S. Appl. No. 14/885,963 Notice of Allowance dated May 24, 2016. |
| U.S. Appl. No. 14/885,963 Office Action dated Feb. 5, 2016. |
| U.S. Appl. No. 14/885,965 Office Action dated Aug. 28, 2018. |
| U.S. Appl. No. 14/885,965 Office Action dated Aug. 30, 2017. |
| U.S. Appl. No. 14/885,965 Office Action dated Feb. 10, 2017. |
| U.S. Appl. No. 14/885,965 Office Action dated Feb. 18, 2016. |
| U.S. Appl. No. 14/885,965 Office Action dated Jan. 4, 2018. |
| U.S. Appl. No. 14/885,965 Office Action dated Jul. 7, 2016. |
| U.S. Appl. No. 15/015,059 Final Office Action dated Jul. 17, 2019. |
| U.S. Appl. No. 15/015,059 Office Action dated Aug. 19, 2019. |
| U.S. Appl. No. 15/015,059 Office Action dated Feb. 7, 2019. |
| U.S. Appl. No. 15/135,434 Notice of Allowance dated Feb. 9, 2018. |
| U.S. Appl. No. 15/135,434 Office Action dated Nov. 30, 2017. |
| U.S. Appl. No. 15/135,434 Restriction Requirement dated Jul. 12, 2017. |
| U.S. Appl. No. 15/151,316 Office Action dated Jun. 7, 2018. |
| U.S. Appl. No. 15/151,316 Office Action dated Oct. 4, 2019. |
| U.S. Appl. No. 15/151,316 Final Office Action dated Feb. 21, 2019. |
| U.S. Appl. No. 15/154,879 Notice of Allowance dated Feb. 1, 2017. |
| U.S. Appl. No. 15/156,134 Final Office Action dated Jan. 3, 2020. |
| U.S. Appl. No. 15/156,134 Office Action dated Apr. 4, 2019. |
| U.S. Appl. No. 15/187,714 Final Office Action dated Sep. 17, 2019. |
| U.S. Appl. No. 15/187,714 Office Action dated Apr. 4, 2019. |
| U.S. Appl. No. 15/187,714 Restriction Requirement dated Sep. 17, 2018. |
| U.S. Appl. No. 15/187,721 Notice of Allowance dated Dec. 7, 2016. |
| U.S. Appl. No. 15/187,721 Office Action dated Oct. 14, 2016. |
| U.S. Appl. No. 15/233,835 Notice of Allowance dated Oct. 4, 2017. |
| U.S. Appl. No. 15/233,835 Office Action dated Feb. 8, 2017. |
| U.S. Appl. No. 15/233,835 Office Action dated Jul. 26, 2017. |
| U.S. Appl. No. 15/233,835 Restriction Requirement dated Nov. 4, 2016. |
| U.S. Appl. No. 15/245,054 Office Action dated Mar. 21, 2017. |
| U.S. Appl. No. 15/245,054 Office Action dated Oct. 19, 2016. |
| U.S. Appl. No. 15/268,422 Final Office Action dated Oct. 3, 2019. |
| U.S. Appl. No. 15/268,422 Office Action dated Mar. 1, 2019. |
| U.S. Appl. No. 15/268,422 Restriction Requirement dated Oct. 4, 2018. |
| U.S. Appl. No. 15/377,547 Final Office Action dated Feb. 8, 2019. |
| U.S. Appl. No. 15/377,547 Office Action dated Jul. 27, 2018. |
| U.S. Appl. No. 15/377,547 Office Action dated Mar. 24, 2017. |
| U.S. Appl. No. 15/377,547 Office Action dated Nov. 30, 2017. |
| U.S. Appl. No. 15/433,909 Non-Final Office Action dated Feb. 8, 2019. |
| U.S. Appl. No. 15/433,909 Restriction Requirement dated Sep. 17, 2018. |
| U.S. Appl. No. 15/602,991 Final Office Action dated Dec. 13, 2018. |
| U.S. Appl. No. 15/602,991 Notice of Allowance dated Oct. 25, 2017. |
| U.S. Appl. No. 15/602,991 Office Action dated May 31, 2018. |
| U.S. Appl. No. 15/602,991 Office Action dated May 31, 2019. |
| U.S. Appl. No. 15/602,991 Office Action dated Sep. 21, 2017. |
| U.S. Appl. No. 15/603,013 Final Office Action dated Nov. 6, 2019. |
| U.S. Appl. No. 15/603,013 Office Action dated Jan. 30, 2018. |
| U.S. Appl. No. 15/603,013 Office Action dated Jul. 10, 2018. |
| U.S. Appl. No. 15/603,013 Office Action dated Oct. 20, 2017. |
| U.S. Appl. No. 15/619,322 Final Office Action dated Mar. 30, 2020. |
| U.S. Appl. No. 15/619,322 Office Action dated Aug. 14, 2019. |
| U.S. Appl. No. 15/682,100 Office Action dated Jan. 2, 2018. |
| U.S. Appl. No. 15/682,100 Restriction Requirement dated Nov. 8, 2017. |
| U.S. Appl. No. 15/709,274 Notice of Allowance dated Apr. 3, 2019. |
| U.S. Appl. No. 15/729,564 Final Office Action dated Dec. 13, 2018. |
| U.S. Appl. No. 15/729,564 Office Action dated Jan. 8, 2018. |
| U.S. Appl. No. 15/729,564 Office Action dated Jun. 6, 2018. |
| U.S. Appl. No. 15/729,564 Office Action dated May 30, 2019. |
| U.S. Appl. No. 15/816,995 Office Action dated Sep. 20, 2019. |
| U.S. Appl. No. 15/816,995 Restriction Requirement dated Apr. 4, 2019. |
| U.S. Appl. No. 15/835,342 Office Action dated Dec. 2, 2019. |
| U.S. Appl. No. 15/835,342 Restriction Requirement dated Sep. 10, 2019. |
| U.S. Appl. No. 15/844,395 Office Action dated Jan. 24, 2020. |
| U.S. Appl. No. 15/844,395 Restriction Requirement dated May 17, 2019. |
| U.S. Appl. No. 15/860,445 Final Office Action dated Dec. 13, 2018. |
| U.S. Appl. No. 15/860,445 Office Action dated May 30, 2018. |
| U.S. Appl. No. 15/921,479 Office Action dated Nov. 12, 2019. |
| U.S. Appl. No. 15/921,479 Restriction Requirement dated May 24, 2019. |
| U.S. Appl. No. 15/921,537 Office Action dated Apr. 1, 2020. |
| U.S. Appl. No. 15/960,319 Office Action dated Aug. 16, 2019. |
| U.S. Appl. No. 15/991,992 Restriction Requirement dated Mar. 10, 2020. |
| U.S. Appl. No. 16/006,581 Office Action dated Sep. 25, 2019. |
| U.S. Appl. No. 16/031,784 Office Action dated May 12, 2020. |
| U.S. Appl. No. 16/039,256 Restriction Requirement dated May 18, 2020. |
| U.S. Appl. No. 16/165,952 Office Action dated Mar. 12, 2020. |
| U.S. Appl. No. 16/239,453 Office Action dated Nov. 7, 2019. |
| U.S. Appl. No. 16/239,453 Office Action dated May 11, 2020. |
| U.S. Appl. No. 16/384,678 Office Action dated Jan. 21, 2020. |
| U.S. Appl. No. 16/409,608 Office Action dated Sep. 9, 2019. |
| U.S. Appl. No. 16/530,717 Final Office Action dated Apr. 15, 2020. |
| U.S. Appl. No. 16/530,717 Office Action dated Sep. 6, 2019. |
| U.S. Appl. No. 16/535,777 Office Action dated Jan. 23, 2020. |
| U.S. Appl. No. 16/535,779 First Action Interview dated Feb. 10, 2020. |
| U.S. Appl. No. 14/452,429 Office Action dated Apr. 9, 2015. |
| U.S. Appl. No. 15/603,013 Office Action dated Jun. 26, 2019. |
| Unger et al.: Monolithic microfabricated valves and pumps by multilayer soft lithography. Science. Apr. 7, 2000;288(5463):113-6. |
| Vaijayanthi et al.: Recent advances in oligonucleotide synthesis and their applications. Indian J Biochem Biophys. Dec. 2003;40(6):377-91. |
| Van Den Brulle et al.: A novel solid phase technology for high-throughput gene synthesis. Biotechniques. 2008; 45(3):340-343. |
| Van Der Werf et al.: Limonene-1,2-epoxide hydrolase from Rhodococcus erythropolis DCL14 belongs to a novel class of epoxide hydrolases. J. Bacteriol. 180:5052-5057 (1998). |
| Van Tassell et al.: SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nature Methods, 5:247-252, 2008. |
| Vargeese et al.: Efficient activation of nucleoside phosphoramidites with 4,5-dicyanoimidazole during oligonucleotide synthesis. Nucleic Acids Res. Feb. 15, 1998;26(4):1046-50. |
| Verma et al.: Modified oligonucleotides: synthesis and strategy for users. Annu Rev Biochem 67:99-134 (1998). |
| Vincent et al.: Helicase-dependent isothermal DNA amplification. EMBO Rep. Aug. 2004;5(8):795-800. |
| Visscher et al.: Construction of multiple-beam optical traps with nanometer-resolution position sensing, IEEE Journal of Selected Topics in Quantum Electronics, vol. 2, No. 4, 1066-1076 (Dec. 1996). |
| Voldmans Joel et al.: Holding forces of single-particle dielectrophoretic traps. Biophysical Journal, vol. 80, No. 1, 531-541 (Jan. 2001). |
| Vos et al.: AFLP:A new technique for DNA fingerprinting. Nucleic Acids Res. Nov. 11, 1995;23(21):4407-14. |
| Wagner et al.: Nucleotides, Part LXV, Synthesis of 2′-Deoxyribonucleoside 5′-Phosphoramidites: New Building Blocks for the Inverse (5′-3′)-Oligonucleotide Approach. Helvetica Chimica Acta, 83(8):2023-2035, 2000. |
| Wah et al.: Structure of Fok I has implications for DNA cleavage, Proc. Natl. Acad. Sci. USA, vol. 95, 10564-10569 (Sep. 1998). |
| Wah et al.: Structure of the multimodular endonuclease Fok I bound to DNA, Nature, vol. 388, 97-100 (Jul. 1997). |
| Walker et al.: Strand displacement amplification—an isothermal, in vitro DNA amplification technique. Nucleic Acids Res. Apr. 11, 1992;20(7):1691-6. |
| Wan et al.: Deep Learning for Content-Based Image Retrieval: A comprehensive study. in Proceedings of the 22nd ACM International Conference on Multimedia—Nov. 3-7, 2014, Orlando, FL, p. 157-166, 2014. |
| Warr et al.: Exome Sequencing: current and future perspectives. G3: (Bethesda) 5(8):1543-1550 (2015). |
| Weber et al.: A modular cloning system for standardized assembly of multigene constructs. PLoS One. Feb. 18, 2011;6(2):e16765. doi: 10.1371/journal.pone.0016765. |
| Welz et al.: 5-(Benzylmercapto)-1H-tetrazole as activator for 2′-O-TBDMS phosphoramidite building blocks in RNA synthesis. Tetrahedron Lett. 2002; 43(5):795-797. |
| Westin et al.: Anchored multiplex amplification on a microelectronic chip array Nature Biotechnology, 18:199-202 (2000) (abstract only). |
| Whitehouse, Adrian et al.: Analysis of the mismatch and insertion/deletion binding properties of Thermus thermophilus, HB8, MutS, Biochemical and Biophysical Research Communications, vol. 233, 834-837 (1997). |
| Wiedenheft et al.: RNA-guided genetic silencing systems in bacteria and archaea. Nature 482:331-338 (2012). |
| Wijshoff. Structure and fluid-dynamics in Piezo inkjet printheads. Thesis. Venio, The Netherlands, published 2008, p. 1-185. |
| Wirtz. Direct measurement of the transport properties of a single DNA molecule, Physical Review Letters, vol. 75, No. 12, 2436-2439 (Sep. 18, 1995). |
| Withers-Martinez et al.: PCR-based gene synthesis as an efficient approach for expression of the A+ T-rich malaria genome, Protein Engineering, vol. 12, No. 12, 1113-1120 (1999). |
| Wood et al.: Human DNA repair genes, Science, vol. 291, 1284-1289 (Feb. 16, 2001). |
| Wosnick et al.: Rapid construction of large synthetic genes: total chemical synthesis of two different versions of the bovine prochymosin gene. Gene. 1987;60(1):115-27. |
| Wright and Church. An open-source oligomicroarray standard for human and mouse. Nature Biotechnology, 20:1082-1083, 2002. |
| Wu et al.: RNA-mediated gene assembly from DNA arrays. Angew Chem Int Ed Engl. May 7, 2012;51(19):4628-32. doi: 10.1002/anie.201109058. |
| Wu et al.: Sequence-Specific Capture of Protein-DNA Complexes for Mass Spectrometric Protein Identification PLoS ONE. Oct. 20, 2011, vol. 6, No. 10. |
| Wu et al.: Specificity of the nick-closing activity of bacteriophage T4 DNA ligase. Gene. 1989;76(2):245-54. |
| Wu et al.: An improvement of the on-line electrophoretic concentration method for capillary electrophoresis of proteins an experimental factors affecting he concentration effect, Analytical Sciences, vol. 16, 329-331 (Mar. 2000). |
| Xiong et al.: A simple, rapid, high-fidelity and cost-effective PCR-based two-step DNA synthesis method for long gene sequences. Nucleic Acids Res. 2004, 32(12):e98. |
| Xiong et al.: Chemical gene synthesis: Strategies, softwares, error corrections, and applications. FEMS Microbiol. Rev., 32:522-540, 2008. |
| Xiong et al.: Non-polymerase-cycling-assembly-based chemical gene synthesis: Strategies, methods, and progress. Biotechnology Advances. 26(2):121-134, 2008. |
| Xu et al.: Design of 240,000 orthogonal 25mer DNA barcode probes. PNAS, 106(7):2289-2294, 2009. |
| Yang et al.: Purification, cloning, and characterization of the CEL I nuclease, Biochemistry, 39(13):3533-35, 2000. |
| Yazdi et al.: A Rewritable, Random-Access DNA-Based Storage System, Scientific Reports, 5, Article No. 14138, 27 pages, 2015. |
| Yehezkel et al.: De novo DNA synthesis using single molecule PCR Nucleic Acids Research, 36(17):e107, 2008. |
| Youil et al.: Detection of 81 of 81 known mouse Beta-Globin promoter mutations with T4 Endonuclease VII⋅ The EMC Method. Genomics, 32:431-435, 1996. |
| Young et al.: Two-step total gene synthesis method. Nucleic Acids Res. 32(7):e59, 2004. |
| Zhang and Seelig. Dynamic DNA nanotechnology using strand-displacement reactions, Nat. Chem., 3(2):103-113, 2011. |
| Zheleznaya et al.: Nicking endonucleases. Biochemistry (Mosc). 74(13):1457-66, 2009. |
| Zheng et al.: Manipulating the Stereoselectivity of Limonene Epoxide Hydrolase by Directed Evolution Based on Iterative Saturation Mutagenesis. J. Am. Chem. Soc. 132:15744-15751 (2010). |
| Zhirnov et al.: Nucleic acid memory. Nature Materials, 15:366, 2016. |
| Zhou et al.: Establishment and application of a loop-mediated isothermal amplification (LAMP) system for detection of cry1Ac transgenic sugarcane Scientific Reports May 9, 2014, vol. 4, No. 4912. |
| Zhou et al.: Microfluidic PicoArray synthesis of oligodeoxynucleotides and simultaneous assembling of multiple DNA sequences Nucleic Acids Research, 32(18):5409-5417, 2004. |
| Bai. A Novel Human scFv Library with Non-Combinatorial Synthetic CDR Diversity. PLoS One. 10(10):1-18 (2015). |
| Berg: Biochemistry. 5th ED. New York (2002) 148-149. |
| Borda et al.: Secret writing by DNA hybridization. Acta Technica Napocensis Electronics and Telecommunications. 50(2):21-24 (2008). |
| Fernández-Quintero et al.: Characterizing the Diversity of the CDR-H3 Loop Conformational Ensembles in Relationship to Antibody Binding Properties. Front. Immunol. 9:1-11 (2019). |
| GE Healthcare. AKTA oligopilot plus. Data File 18-114-66 ADC. 8 pages (2006). |
| GE Healthcare. Robust and cost-efficient oligonucleotide synthesis. Application Note 28-4058-08 AA. 4 pages (2005). |
| Geetha et al.: Survey on Security Mechanisms for Public Cloud Data. 2016 International Conference on Emerging Trends in Engineering, Technology and Science (ICETETS). 8 pages (2016). |
| Hudson: Matrix Assisted Synthetic Transformations: A Mosaic of Diverse Contributions. Journal of Combinatorial Chemistry. 1(6):403-457 (1999). |
| Kalva et al.: Gibson Deletion: a novel application of isothermal in vitro recombination. Biological Procedures Online. 20(1):1-10 (2018). |
| Lebl et al.: Economical Parallel Oligonucleotide and Peptide Synthesizer—Pet Oligator. Int. J. Peptide Res. Ther. 13(1-2):367-376 (2007). |
| Mlab 2321 Molecular Diagnostics for Clinical Laboratory Science. Mar. 6, 2015. |
| Momentiv. Technical Data Sheet. Silquest A-1100. Momentiv. 1-6 (2020). |
| Nucleic acid thermodynamics. Wikipedia. Feb. 4, 2021. |
| O'Driscoll et al.: Synthetic DNA: The next generation of big data storage. Bioengineered. 4(3):123-125 (2013). |
| Opposition to European Patent No. 3030682 filed Mar. 3, 2021. |
| PCT/US2019/032992 International Preliminary Report on Patentability dated Nov. 24, 2020. |
| PCT/US2019/068435 International Preliminary Report on Patentability dated Jul. 8, 2021. |
| PCT/US2020/019371 International Preliminary Report on Patentability dated Sep. 2, 2021. |
| PCT/US2020/019986 International Preliminary Report on Patentability dated Sep. 10, 2021. |
| PCT/US2020/019988 International Preliminary Report on Patentability dated Sep. 10, 2021. |
| PCT/US2020/038679 International Search Report and Written Opinion dated Oct. 28, 2020. |
| PCT/US2020/052291 International Search Report and Written Opinion dated Mar. 10, 2021. |
| PCT/US2020/052291 Invitation to Pay Additional Fees dated Dec. 31, 2020. |
| PCT/US2020/052306 International Search Report and Written Opinion dated Mar. 2, 2021. |
| PCT/US2020/052306 Invitation to Pay Additional Fees dated Dec. 18, 2020. |
| PCT/US2020/064106 International Search Report and Written Opinion dated Jun. 3, 2021. |
| PCT/US2020/064106 Invitation to Pay Additional Fees dated Apr. 9, 2021. |
| Pigott et al.: The Use of a Novel Discovery Platform to Identify Peptide-Grafted Antibodies that Activate GLP-1 Receptor Signaling. Innovative Targeting Solutions Inc. (2013) XP055327428 retrieved from the internet: http://www.innovativetargeting.com/wo-content/uploads/2013/12/Pigott-et-al-Antibody-Engineering-2013.pdf. |
| Ponsel. High Affinity, Developability and Functional Size: The Holy Grail of Combinatorial Antibody Library Generation. Molecules. 16:3675-3700 (2011). |
| PubChem Data Sheet Dichloromethane. Printed from website https://pubchem.ncbi.nlm.nih.gov/compound/Dichloromethane (2020). |
| Regep et al.: The H3 loop of antibodies shows unique structural characteristics. Proteins. 85(7):1311-1318 (2017). |
| Shipman et al.: Molecular recordings by directed CRISPR spacer acquisition. Science. 353(6298):1-16 (2016). |
| U.S. Appl. No. 15/156,134 Final Office Action dated Aug. 18, 2021. |
| U.S. Appl. No. 15/156,134 Office Action dated Nov. 25, 2020. |
| U.S. Appl. No. 15/245,054 Notice of Allowance dated Dec. 14, 2017. |
| U.S. Appl. No. 15/272,004 Final Office Action dated Mar. 18, 2021. |
| U.S. Appl. No. 15/619,322 Final Office Action dated Jul. 9, 2021. |
| U.S. Appl. No. 15/619,322 Office Action dated Nov. 4, 2020. |
| U.S. Appl. No. 15/835,342 Office Action dated Apr. 16, 2021. |
| U.S. Appl. No. 15/902,855 Restriction Requirement dated Apr. 6, 2021. |
| U.S. Appl. No. 15/921,479 Office Action dated Apr. 27, 2021. |
| U.S. Appl. No. 16/039,256 Final Office Action dated Mar. 30, 2021. |
| U.S. Appl. No. 16/128,372 Final Office Action dated Mar. 18, 2021. |
| U.S. Appl. No. 16/128,372 Office Action dated Oct. 8, 2020. |
| U.S. Appl. No. 16/384,678 Final Office Action dated Oct. 15, 2020. |
| U.S. Appl. No. 16/535,777 Final Office Action dated Oct. 20, 2020. |
| U.S. Appl. No. 16/535,777 Office Action dated Feb. 8, 2021. |
| U.S. Appl. No. 16/712,678 Restriction Requirement dated Aug. 25, 2021. |
| U.S. Appl. No. 16/798,275 Office Action dated Feb. 10, 2021. |
| U.S. Appl. No. 16/802,439 Restriction Requirement dated Oct. 1, 2021. |
| U.S. Appl. No. 16/879,705 Office Action dated Sep. 9, 2021. |
| U.S. Appl. No. 16/906,555 Office Action dated Aug. 17, 2021. |
| U.S. Appl. No. 17/154,906 Restriction Requirement dated Jul. 26, 2021. |
| U.S. Appl. No. 16/798,275 Final Office Action dated Aug. 30, 2021. |
| Xu et al.: Coordination between the Polymerase and 5′-Nuclease Components of DNA Polymerase I of Escherichia coli. The Journal of Biological Chemistry. 275(27):20949-20955 (2000). |
| Yazdi et al.: DNA-Based Storage: Trends and Methods. IEEE Transactions on Molecular, Biological and Multi-Scale Communications. IEEE. 1(3):230-248 (2016). |
| Agbavwe et al.: Efficiency, Error and Yield in Light-Directed Maskless Synthesis of DNA Microarrays. Journal of Nanobiotechnology. 9(57):1-17 (2011). |
| De Graff et al.: Glucagon-Like Peptide-1 and its Class B G Protein-Coupled Receptors: A Long March to Therapeutic Successes. Pharmacol Rev. 68(4):954-1013 (2016). |
| Diehl et al.: BEAMING: single-molecule PCR on microparticles in water-in-oil emulsions. Nature Methods. 3(7):551-559 (2006). |
| Hood et al.: The digital code of DNA. Nature 421.6921:444-448 (2003). |
| U.S. Appl. No. 15/921,479 Final Office Action dated Dec. 20, 2021. |
| U.S. Appl. No. 15/902,855 Office Action dated Dec. 9, 2021. |
| U.S. Appl. No. 16/128,372 Office Action dated Dec. 13, 2021. |
| U.S. Appl. No. 16/712,678 Office Action dated Nov. 26, 2021. |
| U.S. Appl. No. 16/737,401 Office Action dated Jan. 5, 2022. |
| U.S. Appl. No. 16/737,401 Restriction Requirement dated Nov. 15, 2021. |
| U.S. Appl. No. 16/802,423 Restriction Requirement dated Dec. 29, 2021. |
| U.S. Appl. No. 16/802,439 Office Action dated Mar. 17, 2022. |
| U.S. Appl. No. 17/154,906 Office Action dated Nov. 10, 2021. |
| Wikipedia. Central dogma of molecular biology. URL: https://en.wikipedia.org/wiki/Central_dogma_of_molecular_biology. 9 pages (2021). |
| Williams et al.: Amplification of complex gene libraries by emulsion PCR. Nature Methods. 3(7):545-550(2006). |
| Altshuler et al.: Generation of Recombinant Antibodies and Means for Increasing Their Affinity. Biochemistry (Moscow). 75(13:1584-1605 (2010). |
| Damha et al.: An improved procedure forderivatization of controlled-pore glass beads for solid-phase oligonucleotide synthesis. Nucleic Acids Research. 18(13):3813-3821 (1990). |
| PCT/US2020/052291 International Preliminary Report on Patentability dated Apr. 7, 2022. |
| PCT/US2020/052306 International Preliminary Report on Patentability dated Mar. 15, 2022. |
| PCT/US2022/023936 International Search Report and Written Opinion dated Jul. 14, 2022. |
| Smith et al.: Changing the peptide specificity of a human T-cell receptor by directed evolution. Nature Communications. 5:1-13 (2014). |
| Sommermeyer et al.: Minimal Amino Acid Exchange in Human TCR Constant Regions Fosters Improved Function of TCR Gene-Modified T Cells. Journal of Immunology. 184:6223-6231 (2010). |
| U.S. Appl. No. 16/737,401 Final Office Action dated Jun. 13, 2022. |
| U.S. Appl. No. 15/272,004 Office Action dated Apr. 13, 2022. |
| U.S. Appl. No. 15/835,342 Office Action dated Jun. 17, 2022. |
| U.S. Appl. No. 15/902,855 Final Office Action dated Aug. 11, 2022. |
| U.S. Appl. No. 15/921,479 Office Action dated Apr. 28, 2022. |
| U.S. Appl. No. 16/039,256 Office Action dated May 10, 2022. |
| U.S. Appl. No. 16/417,023 Final Office Action dated Aug. 2, 2022. |
| U.S. Appl. No. 16/417,023 Office Action dated Feb. 22, 2022. |
| U.S. Appl. No. 16/590,301 Office Action dated Jul. 20, 2022. |
| U.S. Appl. No. 16/590,301 Restriction Requirement dated Apr. 28, 2022. |
| U.S. Appl. No. 16/726,073 Office Action dated Jun. 30, 2022. |
| U.S. Appl. No. 16/802,423 Notice of Allowance dated Jul. 25, 2022. |
| U.S. Appl. No. 17/154,906 Office Action dated May 17, 2022. |
| Frederickson et al.: A rationally designed agonist antibody fragment that funxtionally mimics thrombopoietin. Proceedings of the National Academy of Sciences. National Academy of Sciences. 103(39):14307-14312 (2006). |
| Legault-Demare et al.: Studies on Hybrid Molecules of Nucleic Acids. Biochemical and Biophysical Research Communications. 28(4):1-16 (1967). |
| Liu et al.: Functional GLP-1R antibodies identified from a synthetic GPCR-focused library demonstrate potent blood glucose control. MABS. 13(1):15 pages (2021). |
| U.S. Appl. No. 15/156,134 Office Action dated Dec. 8, 2022. |
| U.S. Appl. No. 15/619,322 Office Action dated Nov. 10, 2022. |
| U.S. Appl. No. 15/902,855 Office Action dated Oct. 5, 2022. |
| U.S. Appl. No. 15/921,479 Final Office Action dated Jan. 9, 2023. |
| U.S. Appl. No. 16/590,301 Office Action dated Dec. 5, 2022. |
| U.S. Appl. No. 16/726,073 Final Office Action dated Dec. 16, 2022. |
| U.S. Appl. No. 16/921,712 Non-Final Office Action dated Nov. 25, 2022. |
| U.S. Appl. No. 17/030,216 Restriction Requirement dated Dec. 23, 2022. |
| U.S. Appl. No. 17/030,232 Restriction Requirement dated Jan. 26, 2023. |
| U.S. Appl. No. 17/068,551 Restriction Requirement dated Dec. 23, 2022. |
| U.S. Appl. No. 17/116,939 Restriction Requirement dated Dec. 27, 2022. |
| U.S. Appl. No. 17/154,906 Office Action dated Jan. 20, 2023. |
| U.S. Appl. No. 17/180,614 Office Action dated Oct. 5, 2022. |
| U.S. Appl. No. 17/578,356 Notice of Allowance dated Dec. 5, 2022. |
| Number | Date | Country | |
|---|---|---|---|
| 20200299322 A1 | Sep 2020 | US |
| Number | Date | Country | |
|---|---|---|---|
| 62112083 | Feb 2015 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 15015059 | Feb 2016 | US |
| Child | 16854719 | US |
