Patent Application
20230054204
The present disclosure relates generally to analytical chemistry and biology, and has specific applicability to flow cells used for analytical methods such as nucleic acid sequence analyses.
Flow cells are a convenient vessel for multi-step reactions in the modern analytical chemistry or biology laboratory. Flow cells can contain target analytes (e.g., cells, proteins, or nucleic acids) fixed within a chamber, wherein different liquid reagents can be flowed through the chamber and wherein the chamber is configured to facilitate detection of the target analytes. Flowing different reagents in ordered sequence through the flow cell to contact the fixed targets controls the nature of the biochemical reactions that may take place.
Certain next-generation nucleic acid sequencing technologies have been automated to employ flow cells, wherein flow of reagents across a surface attached array of immobilized nucleic acids allows for convenient and efficient reagent exchange in a cyclic fashion. The flow cell is observed, for example, via luminescence microscopy techniques to detect changes in the immobilized nucleic acid features that are indicative of their sequences. Flow cells are typically disposable since they are in direct contact with the analytes that are to be detected, and even a small level of analyte carry-over from a previous procedure can lead to erroneous results. For many procedures, nucleic acid sequencing being exemplary, the flow cell is configured for high precision detection. Even relatively small aberrations in flow cell manufacturing or design can adversely impact the quality of analytical results.
There exists a need for flow cells and methods for their manufacture that are precise enough to support high precision detection yet efficient enough to restrain costs at a level that supports disposable use. The present invention satisfies this need and provides related advantages as well.
The present disclosure provides a flow cell that optionally includes (a) a gasket interposed between a first substrate and a second substrate, wherein the gasket, the first substrate and the second substrate are impermeable to aqueous liquid and liquid adhesive, wherein the gasket has a footprint on the first substrate that delineates a channel for containing the aqueous liquid; (b) a via in the gasket, the via containing a solidified liquid adhesive that bonds the first substrate to the second substrate, wherein the solidified liquid adhesive in the via is separated from the channel by the gasket; and (c) a channel port connecting the channel to the exterior of the flow cell, wherein the channel port is permeable to the aqueous liquid.
The present disclosure also provides a method of making a flow cell. The method can include steps of (a) interposing a gasket between a first substrate and a second substrate to delineate a channel for containing an aqueous liquid, wherein the gasket, the first substrate and the second substrate are impermeable to aqueous liquid and liquid adhesive; (b) delivering a liquid adhesive to a via in the gasket; and (c) allowing the liquid adhesive to bond the first substrate to the second substrate, wherein the liquid adhesive is separated from the channel by the gasket.
The details of one or more variations of the subject matter described herein are set forth in the accompanying drawings and the description below. Other features and advantages of the subject matter described herein will be apparent from the description and drawings, and from the claims.
This disclosure provides flow cells that are useful for any of a variety of analytical or preparative processes. The flow cells provide high accuracy detection and processing of analytes. High accuracy detection is supported by precise dimensions of the flow cell such as uniform planarity and thickness of the surfaces through which analytes in the flow cell are detected. High accuracy processing of analytes can be achieved due to robust mechanical properties including, for example, ability to withstand high internal fluid pressure and ability to conveniently and reliably connect to fluidic components that deliver reagents to the flow cell.
The present disclosure also provides methods for making flow cells. For example, a method is provided for bonding a gasket between two substrates using a liquid adhesive that adheres to both substrates. Two substrates (e.g. optically transparent glass or plastic) are brought into contact with an interposing gasket layer (e.g. a pressure sensitive adhesive or rubber film). The gasket layer delineates a channel for analytes and the gasket layer can also include one or more vias that pass through the gasket. These vias can be filled with a liquid adhesive by injecting through a via port in one or both of the substrates or directly into the gasket material. In some configurations, a gasket is bonded to substrates due to a combination of liquid adhesive in a via and adhesive at the interfaces of the gasket and the substrates.
Liquid adhesive bonding of flow cells provides a modular method for bonding two substrates especially when creating a microfluidic channel. This modular approach to bonding provides the advantage of separating the geometric properties of flow cell design from the mechanical properties of the flow cell. The gasket layer can define channel geometry (e.g. channel length, width and height), and the liquid adhesive can provide mechanical strength. This modularity allows rapid prototyping and simple manufacturing.
Liquid adhesive bonding of flow cells also allows multiple layers to be bonded together, including dissimilar materials (e.g., glass and plastic). Moreover, fiducials can be created by configuring vias in the gasket to contain a detectable liquid adhesive or other detectable material. For example, one or more vias can contain a luminescent adhesive or other luminescent material. Efficient manufacturing techniques can be used to precisely control the shape of the vias and the placement of the vias relative to sites in the channel where analytes are to be detected. Accordingly, the vias provide a fiducial that can be relied upon during analytical procedures to register analyte sites in the channel. Flow cell fiducials having luminescent vias can be conveniently detected using the same detection hardware used to detect luminescent analytes in the detection channel of the flow cell. For example, luminescence of the material in the via and luminescence of analytes in the detection channel can be achieved using the same excitation wavelengths and the same emission wavelength. More specifically, the same excitation source can be used for the fiducial and the analyte. Alternatively or additionally, the same emission detector can be used for the fiducial and the analyte.
Terms used herein will be understood to take on their ordinary meaning in the relevant art unless specified otherwise. Several terms used herein, and their meanings, are set forth below.
As used herein, the term “array” refers to a population of molecules attached to one or more solid support such that the molecules at one site can be distinguished from molecules at other sites. An array can include different molecules that are each located at different addressable sites on a solid support. Alternatively, an array can include separate solid supports each functioning as a site that bears a different molecule, wherein the different molecules can be identified according to the locations of the solid supports on a surface to which the solid supports are attached, or according to the locations of the solid supports in a liquid such as a fluid stream. The molecules of the array can be, for example, proteins, nucleotides, nucleic acids, nucleic acid primers, nucleic acid templates, primed template nucleic acids, or nucleic acid enzymes such as polymerases, ligases, exonucleases or combinations thereof.
As used herein, the term “attached” refers to the state of two things being joined, fastened, adhered, connected, bonded or bound to each other. For example, a nucleic acid can be attached to a solid support by a covalent or non-covalent bond. Similarly, two nucleic acids can be attached to each other by a covalent (e.g. phosphodiester) bond or by a non-covalent bond (e.g. hydrogen bonding between bases of the two nucleic acids). A covalent bond is characterized by the sharing of pairs of electrons between atoms. A non-covalent bond is a chemical bond that does not involve the sharing of pairs of electrons and can include, for example, hydrogen bonds, ionic bonds, van der Waals forces, hydrophilic interactions and hydrophobic interactions.
As used herein, the term “blocking moiety,” when used in reference to a nucleotide, means a part of the nucleotide that inhibits or prevents the 3′ oxygen of the nucleotide from forming a covalent linkage to a next correct nucleotide during a nucleic acid polymerization reaction. An exemplary blocking moiety is a reversible terminator moiety. The blocking moiety of a “reversible terminator” nucleotide can be removed from the nucleotide analog, or otherwise modified, to allow the 3′-oxygen of the nucleotide to covalently link to a next correct nucleotide. This process is referred to as “deblocking” the nucleotide analog. Such a blocking moiety is referred to herein as a “reversible terminator moiety.” Exemplary reversible terminator moieties are set forth in U.S. Pat Nos. 7,427,673; 7,414,116; 7,057,026; 7,544,794 or 8,034,923; or PCT publications WO 91/06678 or WO 07/123744, each of which is incorporated herein by reference. A nucleotide that has a blocking moiety or reversible terminator moiety can be at the 3′ end of a nucleic acid, such as a primer, or can be a monomer that is not covalently attached to a nucleic acid.
As used herein, the term “bond,” when used in reference to an adhesive, means the process or result of attaching the adhesive to a substrate. Attachment can occur via mechanical means or a chemical means. An exemplary mechanical means of attachment includes, but is not limited to, the adhesive infiltrating small pores of the substrate. Exemplary chemical means include the formation of covalent bonds between adhesive and substrate, electrostatic forces between adhesive and substrate, van der Waals forces between adhesive and substrate, and hydrogen bonds between adhesive and substrate.
As used herein, the term “catalytic metal ion” refers to a metal ion that facilitates phosphodiester bond formation between the 3′-oxygen of a nucleic acid (e.g., a primer) and the phosphate of an incoming nucleotide by a polymerase. A “divalent catalytic metal cation” is a catalytic metal ion having a valence of two. Catalytic metal ions can be present at concentrations that stabilize formation of a complex between a polymerase, nucleotide, and primed template nucleic acid, referred to as non-catalytic concentrations of a metal ion insofar as phosphodiester bond formation does not occur. Catalytic concentrations of a metal ion refer to the amount of a metal ion sufficient for polymerases to catalyze the reaction between the 3′-oxygen of a nucleic acid (e.g., a primer) and the phosphate moiety of an incoming nucleotide. Exemplary catalytic metal ions include Mg2+ and Mn2+.
As used herein, the term “channel” means a passage, in or on a substrate, that directs the flow of a fluid. A channel can have the form of a tube within a substrate. Alternatively, a channel can have the form of a furrow or groove on a substrate.
The term “comprising” is intended herein to be open-ended, including not only the recited elements, but further encompassing any additional elements.
As used herein, the term “contiguous,” when used in reference to an adhesive that bonds two substrates together, means that an uninterrupted path of adhesive is present between the two substrates. An adhesive will be considered to form a contiguous bond between two substrates so long as at least one uninterrupted path of adhesive occurs between the substrates.
As used herein, the term “each,” when used in reference to a collection of items, is intended to identify an individual item in the collection but does not necessarily refer to every item in the collection. Exceptions can occur if explicit disclosure or context clearly dictates otherwise.
As used herein, “equilibrium” refers to a state of balance due to the equal action of opposing forces. For example, a ternary complex formed between a primed template nucleic acid, polymerase, and cognate nucleotide is in equilibrium with non-bound polymerase and non-bound nucleotide when the rate of formation of the ternary complex is balanced by the rate of its dissociation. Under this condition, the reversible binding reaction ceases to change its net ratio of products (e.g. ternary complex) to reactants (e.g. polymerase, nucleotide and nucleic acid). If the rate of a forward reaction (e.g., ternary complex formation) is balanced by the rate of a reverse reaction (e.g., ternary complex dissociation), then there is no net change in the ratio of products to reactants.
As used herein, the term “exogenous,” when used in reference to a moiety of a molecule, means a chemical moiety that is not present in a natural analog of the molecule. For example, an exogenous label of a nucleotide is a label that is not present on a naturally occurring nucleotide. Similarly, an exogenous label that is present on a polymerase is not found on the polymerase in its native milieu.
As used herein, the term “extension,” when used in reference to a nucleic acid, means a process of adding at least one nucleotide to the 3′ end of the nucleic acid. The term “polymerase extension,” when used in reference to a nucleic acid, refers to a polymerase catalyzed process of adding at least one nucleotide to the 3′ end of the nucleic acid. A nucleotide or oligonucleotide that is added to a nucleic acid by extension is said to be incorporated into the nucleic acid. Accordingly, the term “incorporating” can be used to refer to the process of joining a nucleotide or oligonucleotide to the 3′ end of a nucleic acid by formation of a phosphodiester bond.
As used herein, the term “extendable,” when used in reference to a nucleotide, means that the nucleotide has an oxygen or hydroxyl moiety at the 3′ position, and is capable of forming a covalent linkage to a next correct nucleotide if and when incorporated into a nucleic acid. An extendable nucleotide can be at the 3′ position of a primer or it can be a monomeric nucleotide. A nucleotide that is extendable will lack blocking moieties such as reversible terminator moieties.
As used herein, the terms “free” or “non-bound,” when used in reference to components that are capable of forming a complex in a binding reaction, refers to components that are not in a bound state. By way of example, an equilibrium binding reaction can include a product (e.g. a ternary complex) and reactants that are not bound up in the product (e.g. free polymerases, free nucleic acids or free nucleotides).
As used herein, a “flow cell” is a reaction chamber that includes one or more channels that direct fluid to a detection zone or reaction zone. The detection zone can be coupled to a detector such that a reaction occurring in the reaction chamber can be observed. For example, a flow cell can contain primed template nucleic acid molecules tethered to a solid phase support, to which nucleotides and ancillary reagents are iteratively applied and washed away. The flow cell can include a transparent material that permits the sample to be imaged after a desired reaction occurs. For example, a flow cell can include a glass or plastic slide containing small fluidic channels through which polymerases, dNTPs and buffers can be pumped. The glass or plastic inside the channels can be decorated with one or more primed template nucleic acid molecules to be sequenced.
As used herein, the term “fluid” refers to a liquid or a gas, that is capable of flowing and that changes its shape to fill a vessel. In many conditions, a fluid will change shape at a steady rate when acted upon by a force tending to change its shape.
As used herein, the term “inhibitory metal ion” refers to a metal ion that, when in the presence of a polymerase enzyme, inhibits phosphodiester bond formation needed for chemical incorporation of a nucleotide into a primer. An inhibitory metal ion may interact with a polymerase, for example, via competitive binding compared to catalytic metal ions. A “divalent inhibitory metal ion” is an inhibitory metal ion having a valence of two. Examples of divalent inhibitory metal ions include, but are not limited to, Ca2+, Zn2+, Ni2+, and Sr2+. The trivalent Eu3+ and Tb3+ ions are inhibitory metal ions having a valence of three.
As used herein, the term “label” refers to a molecule or moiety thereof that provides a detectable characteristic. The detectable characteristic can be, for example, an optical signal such as absorbance of radiation, luminescence or fluorescence emission, luminescence or fluorescence lifetime, luminescence or fluorescence polarization, or the like; Rayleigh and/or Mie scattering; binding affinity for a ligand or receptor; magnetic properties; electrical properties; charge; mass; radioactivity or the like. Exemplary labels include, without limitation, a fluorophore, luminophore, chromophore, nanoparticle (e.g., gold, silver, carbon nanotubes), heavy atom, radioactive isotope, mass label, charge label, spin label, receptor, ligand, or the like.
As used herein, the term “liquid adhesive” means a substance that bonds to a substrate, the substance being in a fluid state when applied to the substrate. The substance need not remain in a fluid state after being activated to adhere to the substrate. Accordingly, a liquid adhesive can be in a non-fluid state (e.g. a “hardened liquid adhesive” or “solidified liquid adhesive”) after reacting to bond to a substrate.
As used herein, the term “next correct nucleotide” refers to the nucleotide type that will bind and/or incorporate at the 3′ end of a primer to complement a base in a template strand to which the primer is hybridized. The base in the template strand is referred to as the “next base” and is immediately 5′ of the base in the template that is hybridized to the 3′ end of the primer. The next correct nucleotide can be referred to as the “cognate” of the next base and vice versa. Cognate nucleotides that interact specifically with each other in a ternary complex or in a double stranded nucleic acid are said to “pair” with each other. A nucleotide having a base that is not complementary to the next template base is referred to as an “incorrect”, “mismatch” or “non-cognate” nucleotide.
As used herein, the term “nucleotide” can be used to refer to a native nucleotide or analog thereof. Examples include, but are not limited to, nucleotide triphosphates (NTPs) such as ribonucleotide triphosphates (rNTPs), deoxyribonucleotide triphosphates (dNTPs), exogenously labelled nucleotides, or non-natural analogs thereof such as dideoxyribonucleotide triphosphates (ddNTPs) or reversibly terminated nucleotide triphosphates (rtNTPs).
As used herein, the term “polymerase” can be used to refer to a nucleic acid synthesizing enzyme, including but not limited to, DNA polymerase, RNA polymerase, reverse transcriptase, primase and transferase. Typically, the polymerase has one or more active sites at which nucleotide binding and/or catalysis of nucleotide polymerization may occur. The polymerase may catalyze the polymerization of nucleotides to the 3′ end of the first strand of the double stranded nucleic acid molecule. For example, a polymerase catalyzes the addition of a next correct nucleotide to the 3′ oxygen group of the first strand of the double stranded nucleic acid molecule via a phosphodiester bond, thereby covalently incorporating the nucleotide to the first strand of the double stranded nucleic acid molecule. Optionally, a polymerase need not be capable of nucleotide incorporation under one or more conditions used in a method set forth herein. For example, a mutant polymerase may be capable of forming a ternary complex but incapable of catalyzing nucleotide incorporation. The amount of polymerase in a fluid can be quantified in activity units. For example, a unit of polymerase can be equal to the amount of enzyme catalyzing the incorporation of 10 nmol of dNTP into DNA in 30 min at a particular temperature. For example, thermostable polymerases can be measured at 75° C., whereas thermolabile polymerases can be measured at 37° C.
As used herein, the term “primed template nucleic acid” refers to a nucleic acid hybrid having a double stranded region such that one of the strands has a 3′-end that can be extended by a polymerase. The two strands can be parts of a contiguous nucleic acid molecule (e.g. a hairpin structure) or the two strands can be separable molecules that are not covalently attached to each other.
As used herein, the term “primer” refers to a nucleic acid having a sequence that binds to a nucleic acid sequence at or near a template sequence. Generally, the primer binds in a configuration that allows replication of the template, for example, via polymerase extension of the primer. The primer can be a first portion of a nucleic acid molecule that binds to a second portion of the nucleic acid molecule, the first portion being a primer sequence and the second portion being a primer binding sequence (e.g. a hairpin primer). Alternatively, the primer can be a first nucleic acid molecule that binds to a second nucleic acid molecule having the template sequence (e.g. a dissociable primer). A primer can consist of DNA, RNA or analogs thereof. A primer can be blocked at the 3′ end or it can be extendable.
As used herein, the term “site,” when used in reference to an array, means a location in an array where a particular molecule is present. A site can contain only a single molecule or it can contain a population of several molecules of the same species (i.e. an ensemble of the molecules). Alternatively, a site can include a population of molecules that are different species (e.g. a population of different template sequences). Sites of an array are typically discrete. The discrete sites can be contiguous or they can have spaces between each other.
As used herein, the term “substrate” refers to a solid support that is insoluble in aqueous liquid. The solid support can be non-porous or porous. The solid support can optionally be capable of taking up a liquid (e.g. due to porosity) but will typically be sufficiently rigid that the solid support does not swell substantially when taking up the liquid and does not contract substantially when the liquid is removed by drying. A nonporous substrate is generally impermeable to liquids or gases. Exemplary substrates include, but are not limited to, glass and modified or functionalized glass, plastics (including acrylics, polystyrene and copolymers of styrene and other materials, polypropylene, polyethylene, polybutylene, polyurethanes, Teflon™, cyclic olefins, polyimides etc.), nylon, ceramics, resins, Zeonor, silica or silica-based materials including silicon and modified silicon, carbon, metals, inorganic glasses, optical fiber bundles, and polymers.
As used herein, the term “surface” refers to a portion of a solid support that contacts a fluid or another solid support. The fluid can be gas or liquid. The surface can be substantially flat or planar. Alternatively, the surface can be rounded or contoured. Exemplary contours that can be included on a surface are wells, depressions, pillars, ridges, channels or the like.
As used herein, the term “ternary complex” refers to an intermolecular association between a polymerase, a double stranded nucleic acid and a nucleotide. Typically, the polymerase facilitates interaction between a next correct nucleotide and a template strand of the primed nucleic acid. A next correct nucleotide can interact with the template strand via Watson-Crick hydrogen bonding. The term “stabilized ternary complex” means a ternary complex having promoted or prolonged existence or a ternary complex for which disruption has been inhibited. Generally, stabilization of the ternary complex prevents covalent incorporation of the nucleotide component of the ternary complex into the primed nucleic acid component of the ternary complex.
As used herein, the term “type” or “species” is used to identify molecules that share the same chemical structure. For example, a mixture of nucleotides can include several dCTP molecules. The dCTP molecules will be understood to be the same type (or species) of nucleotide as each other, but a different type (or species) of nucleotide compared to dATP, dGTP, dTTP etc. Similarly, individual DNA molecules that have the same sequence of nucleotides are the same type (or species) of DNA, whereas DNA molecules with different sequences are different types (or species) of DNA. The term “type” or “species” can also identify moieties that share the same chemical structure. For example, the cytosine bases in a template nucleic acid will be understood to have the same type (or species) of base as each other independent of their position in the template sequence.
As used herein, the term “via,” when used in reference to a gasket or other substrate, means a void in or through the substrate. A void that passes through a substrate can have a cross-section that is round, oblong, elliptical, oval, triangular, square, rectangular or polygonal (e.g. wherein the number of sides is greater than 4). The cross-section can be symmetric (e.g. rotationally, reflectionally or translationally symmetric), asymmetric, or elongated (e.g. forming a channel). A via can provide a contiguous passage from a substrate on one side of a gasket to a substrate on another side (e.g. the opposite side) of the gasket.
The embodiments set forth below and recited in the claims can be understood in view of the above definitions.
The present disclosure provides flow cells that can be used for any of a variety of analytical or preparative uses. Characteristics of a flow cell set forth herein can be modified to suit a particular use. Several characteristics of flow cells will be exemplified herein in the context of particular uses. However, those skilled in the art will understand that the exemplified flow cells, and more specifically the exemplified characteristics, can be used for purposes other than those that are explicitly exemplified.
Some useful characteristics for a flow cell are demonstrated by the flow cell shown in perspective view in
The flow cell also includes two wings 130 and 131 which are located in a different z-plane than the channels 101 and 102. The wings include holes 132 and 133, respectively, the holes being configured to engage posts on a sliding rack of an optical detection device (see
A flow cell of the present disclosure can have one or more openings for transfer of fluids into a channel. In particular configurations, a first opening can function as an ingress for the fluids and a second opening can function as an egress for the fluids. This is exemplified by channel ports 120 and 121 which can function as ingress or egress ports for channel 101. Alternatively, a flow cell can have a single opening that functions as both an ingress and egress. The fluid can be a liquid, gas or mixed-phase fluid (e.g. foam, emulsion or particle slurry). Exemplary apparatus and methods that can be used for producing and manipulating mixed-phase fluids are set forth in U.S. patent application Ser. No. 16/700,422, which is incorporated herein by reference.
An analytical reaction can occur in bulk solution within a flow cell of the present disclosure. For example, two solutions can be mixed and the product of the mixture can be observed in a detection channel. Alternatively, an analytical reaction can occur on a solid support within the detection channel. For example, a solid support that is attached to analytes of interest can be present in channel 101 or 102, a reagent solution can be flowed over the solid support, and a resulting reaction can be observed on the solid support. A flow cell allows convenient fluidic manipulation by passing solutions through a channel port that functions as an ingress, into the detection channel and out of the interior via a channel port that functions as an egress opening. The detection channel also has an observation region (e.g. an observation area or observation volume), for example, being visible through an optically transparent window (e.g. optically transparent substrates 110 and 111). A particularly useful flow cell has a window that is transparent to excitation radiation and emission radiation used for luminescence detection in the UV, VIS or IR regions of the electromagnetic spectrum.
As exemplified in
Flow cell 200 (
Flow cell 300 (
As exemplified by
The xy cross-sectional area of a detection channel in a flow cell of the present disclosure can be at least about 1 μm2, 10 μm2, 100 μm2, 1 mm2, 10 mm2, or 100 mm2 or larger. Alternatively or additionally, the xy cross-sectional area of a detection channel can be at most about 100 mm2, 10 mm2, 1 mm2, 100 μm2, 10 μm2, 1 μm2, or smaller. The volume of a detection channel in a flow cell can be at least about 1 nL, 10 nL, 100 nL, 1 μL, 10 μL, 100 μL, 1 mL or more. Alternatively or additionally, the volume of a detection channel in a flow cell can be at most about 1 mL, 100 μL, 10 μL, 1 μL, 100 nL, 10 nL, 1 nL or less. The length of a flow cell channel can be selected to provide a desired volume, surface area etc. For example, the length of a flow cell channel can be at least 1 mm, 1 cm, 10 cm or longer. Alternatively or additionally, the length of a flow cell channel can be at most 10 cm, 1 cm or 1 mm.
The detection channels exemplified in
A flow cell channel can further include a region where analytes are detected. A fluid can flow into the flow cell via the ingress, then through the region and then out the egress to exit the flow cell. By way of illustrative example, the region can be examined or detected through a window in the flow cell. For example, an external optical detector can observe an interior region of a flow cell through an optically transparent window of the flow cell such as the windows formed by substrates 110, 111, 210, 211, 310 or 311. One or more regions of a flow cell channel can be examined or observed by techniques other than optical techniques including, for example, detection techniques set forth herein. Accordingly, the flow cell can have a transmission surface that transmits signals from the region of the flow cell to the appropriate detector apparatus. It will be understood that a flow cell need not be configured for detection of analytes. For example, the flow cell can provide a chamber for a reaction to occur and a product of the reaction can flow out of the flow cell for subsequent use or detection. Accordingly, a flow cell need not have an optically transparent window or other surface that is configured for transmitting analytical signals.
The present disclosure provides a flow cell that optionally includes (a) a gasket interposed between a first substrate and a second substrate, wherein the gasket, the first substrate and the second substrate are impermeable to aqueous liquid and liquid adhesive, wherein the gasket has a footprint on the first substrate that delineates a channel for containing the aqueous liquid; (b) a via in the gasket, the via containing a solidified liquid adhesive that bonds the first substrate to the second substrate, wherein the solidified liquid adhesive in the via is separated from the channel by the gasket; and (c) a channel port connecting the channel to the exterior of the flow cell, wherein the channel port is permeable to the aqueous liquid.
The present disclosure also provides a method of making a flow cell. The method can include steps of (a) interposing a gasket between a first substrate and a second substrate to delineate a channel for containing an aqueous liquid, wherein the gasket, the first substrate and the second substrate are impermeable to aqueous liquid and liquid adhesive; (b) delivering a liquid adhesive to a via in the gasket; and (c) allowing the liquid adhesive to bond the first substrate to the second substrate, wherein the liquid adhesive is separated from the channel by the gasket.
An exemplary flow cell that is made using liquid adhesive is shown in
Assembled flow cell 500 includes a via 550 that contains a solidified liquid adhesive that bonds substrate 510 to substrate 511. As shown in the view of
Wings 530 and 531 are attached to the outer surface of substrate 510 (i.e. opposite the inner surface of substrate 510). Wing 530 is attached to substrate 510 via gasket 570 and solidified liquid adhesive in via 571. Wing 531 is attached to substrate 510 via gasket 560 and solidified liquid adhesive in via 561. Wings 530 and 531 include holes 532 and 533, respectively, for attaching to a rack on a scanning apparatus. Wing 530 includes receptacle 525 which houses channel ports 520 and 525. Channel 501 can be accessed through a path that includes port 520, hole 572 in gasket 570, and hole 515 in substrate 510, and channel 501 can also be accessed through a path that includes port 521, hole 562 in gasket 560, and hole 512 in substrate 510. Channel 502 can be accessed through a path that includes port 524, hole 573 in gasket 570, and hole 514 in substrate 510, and channel 502 can also be accessed through a path that includes port 523, hole 563 in gasket 560, and hole 513 in substrate 510. Via 571 forms a moat surrounding holes 572 and 573 in gasket 570, to form a fluid tight seal between wing 530 and substrate 510. Similarly, via 561 forms a moat surrounding holes 562 and 563 in gasket 560, to form a fluid tight seal between wing 531 and substrate 510.
As demonstrated by
Any of a variety of substrates can be used for a flow cell. Rigid materials can be particularly useful, for example, when a flow cell is likely to be subjected to mechanical stresses. Optionally, the polymeric material is shaped into a substantially rigid configuration. For example, the material can be shaped to have a thickness that resists flexing when used as a planar surface for a flow cell. Planar substrates are useful as exemplified by the figures of the present application. However, the substrates need not be planar and can instead have other shapes that are complemented by a gasket and/or other substrate(s) to form a flow cell channel. In particular configurations, the substrate is made from a material that facilitates transmission of optical signals, for example, in the UV, VIS, and/or IR region of the spectrum. A material can also be selected for its inertness to fluids that will be used in a flow cell. However, in some cases it may be desirable for at least a portion of the surface of the substrate to be reactive to a particular chemical linking procedure. Such procedures are exemplified herein with respect to attaching analytes or arrays of analytes to a substrate.
Exemplary materials that can be useful for the substrates of a flow cell include, but are not limited to, glass, borosilicate glass, silanized glass (e.g. aminosilane, glycidoxysilane or mercaptosilane), silicon, silicon dioxide, metal, carbon fiber, silicon nitride, fused silica, quartz, ceramic, acrylic, plastic or polymer. Particularly useful plastics or polymers include, but are not limited to, polyimide, polybutylene, polybutylene terephthalate (PBT); styrene-butadiene copolymer (SBC); polypropylene, polyethylene, cyclic olefin copolymer (COC); cyclo-olefin polymer (COP); styrene methyl methacrylate (SMMA); polystyrene (PS); polycarbonate (PC); copolyester; polysulfone; nylon; polyether ether ketone (PEEK); acrylonitrile butadiene styrene (ABS); Kapton, and poly(methyl methacrylate) (PMMA).
For flow cells that use two substrates, the first and second substrates can be made from the same material. For example, both substrates can be glass, or both can be the same plastic (e.g. both substrates can be COP). Alternatively, the material for the two substrates can differ from each other. For example, one substrate can be glass and the other can be COP. Generally, it is preferable to select materials having similar coefficients of thermal expansion (CTE) to avoid warpage if the bonded flow cell experiences substantial temperature changes. However, materials having different CTE from each other can be accommodated by use of a thermal expansion joint as set forth in further detail below for example in connection with
A gasket or spacer used for a flow cell can be made from any of a variety of materials. Useful materials can be inert to the fluids that will be used in the flow cell. The materials used for a gasket can be transparent to optical signals, but need not be transparent for certain uses of a flow cell. For many uses, the material used for a gasket or spacer will be non-compressible or non-elastic, whereby the gasket maintains a fixed distance between two substrates when used as a spacer. The material used for a gasket can advantageously have a similar CTE as materials used for one or more other substrates in a flow cell. This can be beneficial to avoid warpage or breakage when the flow cell is subjected to substantial temperature changes. A gasket or spacer can include an adhesive surface, for example, to adhere to a substrate used in a flow cell herein. For example, a gasket can have a pressure sensitive adhesive on a surface that interfaces with one or more substrates to which the gasket bonds.
Exemplary materials for use in a gasket or spacer include, but are not limited to, the materials set forth above for substrates. Particularly useful materials include, for example, rubber, polytetrafluoroethylene (e.g. Teflon), polyethylene terephthalate (PET), polyimide, acrylic-based adhesives, silicon-based adhesives, polydimethylsiloxane (PDMS), glass, latex. Elastomers are useful, for example, as gaskets for creating a tight seal with relatively rigid materials. The gasket used for a particular flow cell may be the same material as one or both substrates or, alternatively, the gasket can be a different material from the substrates.
A liquid adhesive can be selected for its ability to bind to the materials used as substrates in a flow cell. For flow cell configurations in which liquid adhesive is present in a via that connects two substrates, the adhesive can bond to the two substrates to assemble the flow cell. In this configuration, the adhesive need not bond to the gasket. However, a liquid adhesive can be selected for its ability to bond to the substrates and to the gasket if desired. A liquid adhesive can be selected based on the method of curing or solidifying the adhesive. For example, a UV cure adhesive can be useful when the materials or contents of a flow cell are adversely impacted by chemical-based or heat-based curing techniques used for other adhesives. Low outgassing or even absence of outgassing can be a desirable characteristic of a liquid adhesive, for example, when vacuum is used to draw adhesive into a via, or when venting is not convenient. A liquid adhesive can also be selected based on compatibility of the adhesive, or compatibility of the carrier solvent, with regard to the structural or chemical integrity of the flow cell or its contents. In some cases, it is desirable to use a liquid adhesive that does not expand or contract upon curing. For example, an adhesive that experiences less than 10% or even less than 1% expansion or contraction can be particularly useful. However, in other cases, expansion may be desirable, for example, to help the adhesive invade contours of a surface. Contraction may be desirable to draw substrates together upon curing or to avoid warping substrates due to the volume of the liquid adhesive. In some configurations, low viscosity is desirable for the liquid adhesive since this will facilitate delivery of the adhesive by allowing it to flow into vias or other physical features of substrates that are to be adhered.
Useful liquid adhesives include, but are not limited to epoxy, light-cure adhesive (e.g. UV cure adhesives), and heat cure adhesives. Optionally, the liquid adhesive can be bonded by heat treatment, for example in an oven, exposure to UV light, or other treatment appropriate to bonding the adhesive.
As demonstrated by the flow cells of
A liquid adhesive rivet need not adhere to all materials that are to be attached to each other. Rather, a liquid adhesive can be solidified to form a solid material that holds two or more materials together using mechanical means.
A further example of an adhesive bond that provides mechanical means for bonding two components is provided by the dual port component 980 shown in
Adhesion of the dual port component 980 to the surface of a flow cell is facilitated by wells 986 and 997 that are formed in base 987. Wells 986 and 997 surround ports 983 and 993, respectively. Wells 986 and 997 can be filled with an adhesive that bonds to the flow cell surface. The adhesive can bond to the flow cell surface and to the inner surface of wells 986 and 997 in order to adhere the dual port component to the flow cell surface. As shown in
Any of a variety of analytes can be present in a flow cell set forth herein. Exemplary analytes include, but are not limited to, the analytes exemplified herein or in references cited herein. Particularly useful analytes participate in nucleic acid sequencing processes. Accordingly, a flow cell can contain one or more nucleic acids, polymerases, polymerase inhibitors, polymerase cofactors (e.g. catalytic metal ions), ternary complex stabilizing agents (e.g. inhibitory metal ions), nucleotides, nucleic acid binding proteins, nucleotide deblocking reagents, or the like.
Other analytes that can be present in a flow cell include, for example, biological tissues, biological cells; organelles; protein-based enzymes; protein-based receptors such as antibodies, lectins, or streptavidin; peptides; RNA molecules; aptamers or the like. Exemplary protein-based enzymes that can be used include, but are not limited to, polymerase, transposase, ligase, recombinase, kinase, phosphatase, exonuclease, endonuclease, sulfurylase, apyrase, luciferase, green fluorescent protein (GFP), or phycobiliprotein (e.g. phycocyanin, allophycocyanin, or phycoerythrin).
In some configurations, a flow cell includes a ternary complex (e.g. a stabilized ternary complex) immobilized inside the flow cell, wherein the ternary complex (e.g. stabilized ternary complex) includes a polymerase, a primed template nucleic acid and a next correct nucleotide for the template.
A flow cell can include an array of nucleic acids, proteins or other analytes. In particular configurations, ternary complexes (e.g. stabilized ternary complexes) are present at one or more sites of an array. Arrays provide an advantage of multiplex processing of analytes, whereby the multiple different types of analytes are manipulated or detected in parallel. An array can include at least 2, 10, 100, 1×103, 1×104, 1×105, 1×106, 1×109, or more different analyte sites. Alternatively or additionally, an array can include at most 1×109, 1×106, 1×105, 1×104, 1×103, 100, 10, 2 or fewer, different analyte sites.
An array useful herein can have, for example, sites that are separated by less than 100 microns, 50 microns, 10 microns, 5 microns, 1 micron, or 0.5 micron. Alternatively or additionally, an array can have sites that are separated by greater than 0.5 micron, 1 micron, 5 microns, 10 microns, 50 microns or 100 microns. The sites can each have an area of less than 1 square millimeter, 500 square microns, 100 square microns, 25 square microns, 1 square micron or less. The density of sites of sites in an array can be, for example, at least about 10 sites/cm2, 100 sites/cm2, 1×103 sites/cm2, 1×104 sites/cm2, 1×105 sites/cm2, 1×106 sites/cm2, or higher.
An array can be attached to an inner surface of a flow cell wall or to a solid support inside of a flow cell. The flow cell or solid support can be made from any of a variety of materials used for analytical biochemistry. Suitable materials may include glass, polymeric materials, silicon, quartz (fused silica), borofloat glass, silica, silica-based materials, carbon, metals, an optical fiber or bundle of optical fibers, sapphire, or plastic materials. The material can be selected based on properties desired for a particular use. For example, materials that are transparent to a desired wavelength of radiation are useful for analytical techniques that will utilize radiation at that wavelength. Conversely, it may be desirable to select a material that does not pass radiation of a certain wavelength (e.g. being opaque, absorptive or reflective). Other properties of a material that can be exploited are inertness or reactivity to certain reagents used in a downstream process, such as those set forth herein, or ease of manipulation, or low cost of manufacture.
A particularly useful solid support for use in a flow cell or other vessel is a particle such as a bead or microsphere. Populations of beads can be used for attachment of populations of analytes such as stabilized ternary complexes or components capable of forming the complexes (e.g. polymerases, templates, primers or nucleotides). In some configurations, each bead has a single type of stabilized ternary complex or a single type of component capable of forming the complex or a single type of some other analyte set forth herein or in references cited herein. For example, an individual bead can be attached to a single type of ternary complex, a single type of template allele, a single type of template locus, a single type of primer, or a single type of nucleotide. Alternatively, different types of components need not be separated on a bead-by-bead basis. As such, a single bead can bear multiple different types of ternary complexes, template nucleic acids, primers, primed template nucleic acids and/or nucleotides. The composition of a bead can vary, depending for example, on the format, chemistry and/or method of attachment to be used. Exemplary bead compositions include, for example, plastics, ceramics, glass, polystyrene, melamine, methyl styrene, acrylic polymers, paramagnetic materials, thoria sol, carbon graphite, titanium dioxide, controlled pore glass (CPG), latex or cross-linked dextrans such as Sepharose™, cellulose, nylon, cross-linked micelles and Teflon™, as well as other materials set forth in “Microsphere Detection Guide” from Bangs Laboratories, Fishers Ind., which is incorporated herein by reference.
Beads can have a symmetrical shape, such as spherical, polyhedral, cylindrical or the like. Alternatively, beads can have an irregular or non-symmetric shape. Exemplary sizes for beads used herein can have average diameter that is at least about 10 nm, 100 nm, 1 μm, 5 μm, 10 μm, 100 μm, 1 mm or larger. Alternatively or additionally, beads used herein can have average diameter that is at most about 1 mm, 100 μm, 10 μm, 5 μm, 1 μm, 100 nm, 10 nm, 1 nm or smaller. Beads in these size ranges can be used as array features or as particles in a fluid slurry.
Exemplary compositions and techniques that can be used to make an array of beads include, without limitation, those used for BeadChip™ Arrays available from Illumina, Inc. (San Diego, Calif.) or those described in U.S. Pat. Nos. 6,266,459; 6,355,431; 6,770,441; 6,859,570; or 7,622,294; or PCT Publication No. WO 00/63437, each of which is incorporated herein by reference. Beads can be located at discrete locations, such as wells, on a solid support, whereby each location accommodates a single bead. Alternatively, discrete locations where beads reside can each include a plurality of beads as described, for example, in U.S. Pat. App. Pub. Nos. 2004/0263923 A1, 2004/0233485 A1, 2004/0132205 A1, or 2004/0125424 A1, each of which is incorporated herein by reference.
Other useful arrays include those that are used in nucleic acid sequencing applications. For example, arrays that are used to immobilize amplicons of genomic fragments (often referred to as clusters) can be particularly useful. Examples of nucleic acid sequencing arrays that can be used herein include those described in Bentley et al., Nature 456:53-59 (2008), PCT Pub. Nos. WO 91/06678; WO 04/018497 or WO 07/123744; U.S. Pat. Nos. 7,057,026; 7,211,414; 7,315,019; 7,329,492 or 7,405,281; or U.S. Pat. App. Pub. No. 2008/0108082, each of which is incorporated herein by reference.
Nucleic acids or other analytes can be attached to an array in a way that provides detection at a single molecule level or at an ensemble level. For example, a plurality of different nucleic acids can be attached to an array in a way that an individual stabilized ternary complex that forms on one nucleic acid molecule in the array can be distinguished from all neighboring ternary complexes that form in the array. Alternatively, an array of the present disclosure can include a plurality of ensembles, an ensemble being a population of analytes of the same type such as a population of nucleic acids having a common template sequence. An array can have a plurality of ensembles, each of the ensembles being formed using methods known in the art such as bridge amplification, emulsion PCR or other methods set forth herein.
A flow cell of the present disclosure, for example, a flow cell that is bonded using a solidified liquid adhesive can provide advantages of withstanding high positive pressures. This can be beneficial when using positive pressure to drive a fluid through the flow cell. Positive pressure is particularly useful for driving a mixed-phase fluid (e.g. foam, emulsion or particle slurry) through a flow cell. Exemplary mixed phase fluids and methods that employ such fluids in flow cells are set forth in U.S. patent application Ser. No. 16/700,422, which is incorporated herein by reference. A flow cell of the present disclosure can be configured to withstand pressures that are greater than 5 PSI, 10 PSI, 50 PSI, 90 PSI or higher.
A flow cell of the present disclosure can be configured for use in any of a variety of analytical systems. An analytical system of the present disclosure can optionally include an optical detection system configured to detect the inside of a flow cell such as the inside of a detection channel in a flow cell. Particularly useful optical detection systems include those that are found in sub-systems or components of nucleic acid sequencing systems. Several such detection apparatus are configured for optical detection, for example, detection of luminescence signals. Accordingly, an optical detection system can include an excitation system configured to irradiate the inside of a flow cell channel. The optical detection system can further include an emission system configured to detect luminescence from the inside of the flow cell channel. Detection of luminescence can be carried out using methods known in the art pertaining to nucleic acid arrays or nucleic acid sequencing. A luminophore can be detected based on any of a variety of luminescence properties including, for example, emission wavelength, excitation wavelength, fluorescence resonance energy transfer (FRET) intensity, quenching, anisotropy or lifetime.
Examples of nucleic acid sequencing systems and components thereof that can be used with a flow cell of the present disclosure are described, for example, in US Pat. App. Pub. No. 2010/0111768 A1 or U.S. Pat. Nos. 7,329,860; 8,951,781 or 9,193,996, each of which is incorporated herein by reference. Other nucleic acid sequencing systems include those commercialized for nucleic acid sequencing such as those provided by Illumina™, Inc. (e.g. HiSeq™, MiSeq™, NextSeq™, or NovaSeq™ systems), Life Technologies™ (e.g. ION TORRENT™, or SOLiD™ systems), Pacific Biosciences (e.g. systems using SMRT™ Technology such as the Sequel™ or RS II™ systems), or BGI (e.g. DNBSEQ™ systems). Other useful detectors that can be used with a flow cell of the present disclosure are described in U.S. Pat. Nos. 5,888,737; 6,175,002; 5,695,934; 6,140,489; or 5,863,722; or US Pat. Pub. Nos. 2007/007991 A1, 2009/0247414 A1, or 2010/0111768; or WO2007/123744, each of which is incorporated herein by reference in its entirety.
Although the system and methods of the present disclosure are illustrated in the context of optical detection in several exemplary embodiments herein, it will be understood that other detection modalities can be used in addition or instead. For example, the detector can be an electronic detector used for detection of protons or pyrophosphate (see, for example, US Pat. App. Pub. Nos. 2009/0026082 A1; 2009/0127589 A1; 2010/0137143 A1; or 2010/0282617 A1, each of which is incorporated herein by reference in its entirety, or the Ion Torrent™ systems commercially available from ThermoFisher, Waltham, Mass.) or as used in detection of nanopores such as those commercialized by Oxford Nanopore™, Oxford UK (e.g. MinION™ or PromethION™ systems) or set forth in U.S. Pat. No. 7,001,792; Soni & Meller, Clin. Chem. 53, 1996-2001 (2007); Healy, Nanomed. 2, 459-481 (2007); or Cockroft, et al. J. Am. Chem. Soc. 130, 818-820 (2008), each of which is incorporated herein by reference. A FET detector can be used such as one or more of those described in U.S. Pat. App. Ser. No. 62/767,712; US Pat. App. Pub. Nos. 2017/0240962 A1, 2018/0051316 A1, 2018/0112265 A1, 2018/0155773 A1 or 2018/0305727 A1; or U.S. Pat. Nos. 9,164,053, 9,829,456, 10,036,064, or 10,125,391, each of which is incorporated herein by reference.
As demonstrated by the example of
The pipette adapter 1105 includes a pipette fluid inlet 1110 and a fluid outlet 1115. The pipette fluid inlet 1110 aligns with the port 121 (
When the retainer 1215 is coupled to the substrate 1210, the retainer exerts a force on the septum 1230 and wick 1225 to maintain a seal. The retainer also may have a snap fit with the wing 131. The septum 1230 acts as a seal for a pipette inserted into the pipette fluid inlet 1240 so as to inhibit or prevent the leaking of reagent. The wick 1225 is configured to soak or otherwise capture a reagent dispensed by a user.
The overmolds 1235 also form a seal with any tubing positioned therein. A first overmold co-axially aligns with the pipette fluid inlet 1240 and a second overmold co-axially aligns with the fluid outlet 1245. The overmolds can facilitate proper alignment of a pipette insertion into the pipette fluid inlet 1240 and can also securely maintain or fix positioning of the pipette therein. The overmolds 1235 are tubular in shape each with an internal lumen sized and shaped to receive a tube or other structure such as a pipette.
One or more overmolds can also be used in combination with the adapter or fluidic connector 1000 that was previously described with reference to
A flow cell of the present disclosure can be used to sequence nucleic acids. Particularly useful sequencing processes are cyclical processes that employ repeated cycles of reagent delivery and flow cell detection. Each cycle can include one step or multiple steps. For example, each cycle can include all steps needed to detect a single nucleotide position in a template nucleic acid. Some sequencing processes employ cyclical reversible terminator (CRT) chemistry in which each cycle includes steps for (i) adding a single reversibly terminated nucleotide to increment a nascent primer to a nucleotide position that is to be detected; (ii) detecting the nucleotide at the single nucleotide position, and (iii) deblocking the nascent primer to allow a return to step (i) to start a subsequent cycle.
A specific example of a useful CRT nucleic acid sequencing process is a Sequencing By Binding™ (SBB™) reaction, for example, as described in commonly owned US Pat. App. Pub. Nos. 2017/0022553 A1; 2018/0044727 A1; 2018/0187245 A1; or 2018/0208983 A1, each of which is incorporated herein by reference. Generally, SBB™ methods for determining the sequence of a template nucleic acid molecule can be based on formation of a stabilized ternary complex (between polymerase, primed nucleic acid and cognate nucleotide) under specified conditions. The method can include an examination phase followed by a nucleotide incorporation phase.
The examination phase of an SBB™ process can be carried out in a flow cell, the flow cell containing at least one template nucleic acid molecule primed with a primer by delivering to the flow cell reagents to form a first reaction mixture. The reaction mixture can include the primed template nucleic acid, a polymerase and at least one nucleotide type. Interaction of polymerase and a nucleotide with the primed template nucleic acid molecule(s) can be observed under conditions where the nucleotide is not covalently added to the primer(s); and the next base in each template nucleic acid can be identified using the observed interaction of the polymerase and nucleotide with the primed template nucleic acid molecule(s). The interaction between the primed template, polymerase and nucleotide can be detected in a variety of schemes. For example, the nucleotides can contain a detectable label. Each nucleotide can have a distinguishable label with respect to other nucleotides. Alternatively, some or all of the different nucleotide types can have the same label and the nucleotide types can be distinguished based on separate deliveries of different nucleotide types to the flow cell. In some embodiments, the polymerase can be labeled. Polymerases that are associated with different nucleotide types can have unique labels that distinguish the type of nucleotide to which they are associated. Alternatively, polymerases can have similar labels and the different nucleotide types can be distinguished based on separate deliveries of different nucleotide types to the flow cell. Detection can be carried out by scanning the flow cell using an apparatus or method set forth herein or in reference cited herein.
During the examination phase of an SBB™ process, discrimination between correct and incorrect nucleotides can be facilitated by ternary complex stabilization. A variety of conditions and reagents can be useful. For example, the primer can contain a reversible blocking moiety that prevents covalent attachment of nucleotide; and/or cofactors that are required for extension, such as divalent metal ions, can be absent; and/or inhibitory divalent cations that inhibit polymerase-based primer extension can be present; and/or the polymerase that is present in the examination phase can have a chemical modification and/or mutation that inhibits primer extension; and/or the nucleotides can have chemical modifications that inhibit incorporation, such as 5′ modifications that remove or alter the native triphosphate moiety. The examination phase can include scanning of the flow cell using apparatus and methods set forth herein.
The extension phase can then be carried out by creating conditions in the flow cell where a nucleotide can be added to the primer on each template nucleic acid molecule. In some embodiments, this involves removal of reagents used in the examination phase and replacing them with reagents that facilitate extension. For example, examination reagents can be replaced with a polymerase and nucleotide(s) that are capable of extension. Alternatively, one or more reagents can be added to the examination phase reaction to create extension conditions. For example, catalytic divalent cations can be added to an examination mixture that was deficient in the cations, and/or polymerase inhibitors can be removed or disabled, and/or extension competent nucleotides can be added, and/or a deblocking reagent can be added to render primer(s) extension competent, and/or extension competent polymerase can be added.
Another useful CRT sequencing process is sequencing-by-synthesis (SBS). SBS generally involves the enzymatic extension of a nascent primer through the iterative addition of nucleotides against a template strand to which the primer is hybridized. Briefly, SBS can be initiated by contacting target nucleic acids, for example, attached to sites in a flow cell, with one or more labeled nucleotides, DNA polymerase, etc. Those sites where a primer is extended using the target nucleic acid as template will incorporate a labeled nucleotide that can be detected. Detection can include scanning using an apparatus or method set forth herein. Optionally, the labeled nucleotides can further include a reversible terminator that prevents further primer extension once a nucleotide has been added to a primer. For example, a nucleotide analog having a reversible terminator moiety can be added to a primer such that subsequent extension cannot occur until a deblocking agent is delivered to remove the moiety. Thus, for embodiments that use reversible termination, a deblocking reagent can be delivered to the vessel (before or after detection occurs). Washes can be carried out between the various delivery steps. The cycle can be performed n times to extend the primer by n nucleotides, thereby detecting a sequence of length n. Exemplary SBS procedures, reagents and detection components that can be readily adapted for use with a method, system or apparatus of the present disclosure are described, for example, in Bentley et al., Nature 456:53-59 (2008), WO 04/018497; WO 91/06678; WO 07/123744; U.S. Pat. Nos. 7,057,026; 7,329,492; 7,211,414; 7,315,019 or 7,405,281, and US Pat. App. Pub. No. 2008/0108082 A1, each of which is incorporated herein by reference. Also useful are SBS methods that are commercially available from Illumina, Inc. (San Diego, Calif.).
Some SBS embodiments are cyclical but need not employ reversible terminator nucleotides. A particularly useful method includes detection of a proton released upon incorporation of a nucleotide into an extension product. For example, sequencing based on detection of released protons can use reagents and an electrical detector that are commercially available from Thermo Fisher (Waltham, Mass.) or described in US Pat. App. Pub. Nos. 2009/0026082 A1; 2009/0127589 A1; 2010/0137143 A1; or 2010/0282617 A1, each of which is incorporated herein by reference.
Other cyclical sequencing processes can be used, such as pyrosequencing. Pyrosequencing detects the release of inorganic pyrophosphate (PPi) as nucleotides are incorporated into a nascent primer hybridized to a template nucleic acid strand (Ronaghi, et al., Analytical Biochemistry 242 (1), 84-9 (1996); Ronaghi, Genome Res. 11 (1), 3-11 (2001); Ronaghi et al. Science 281 (5375), 363 (1998); U.S. Pat. Nos. 6,210,891; 6,258,568 and 6,274,320, each of which is incorporated herein by reference). In pyrosequencing, released PPi can be detected by being converted to adenosine triphosphate (ATP) by ATP sulfurylase, and the resulting ATP can be detected via luciferase-produced photons.
Sequencing-by-ligation reactions are also useful including, for example, those described in Shendure et al. Science 309:1728-1732 (2005); U.S. Pat. No. 5,599,675; or U.S. Pat. No. 5,750,341, each of which is incorporated herein by reference. Some embodiments can include sequencing-by-hybridization procedures as described, for example, in Bains et al., Journal of Theoretical Biology 135 (3), 303-7 (1988); Drmanac et al., Nature Biotechnology 16, 54-58 (1998); Fodor et al., Science 251 (4995), 767-773 (1995); or WO 1989/10977, each of which is incorporated herein by reference. In both sequencing-by-ligation and sequencing-by-hybridization procedures, primers that are hybridized to nucleic acid templates are subjected to repeated cycles of extension by oligonucleotide ligation. Typically, the oligonucleotides are luminescently labeled and can be detected to determine the sequence of the template, for example, using a system or method set forth herein.
Steps for the above sequencing methods can be carried out cyclically. For example, examination and extension steps of an SBB™ method can be repeated such that in each cycle a single next correct nucleotide is examined (i.e. the next correct nucleotide being a nucleotide that correctly binds to the nucleotide in a template nucleic acid that is located immediately 5′ of the base in the template that is hybridized to the 3′-end of the hybridized primer) and, subsequently, a single next correct nucleotide is added to the primer. Any number of cycles of a sequencing method set forth herein can be carried out including, for example, at least 1, 2, 10, 100, 250, 500 or more cycles. Alternatively or additionally, no more than 500, 250, 100, 10, 2 or 1 cycles are carried out.
Some embodiments can utilize methods involving real-time monitoring of DNA polymerase activity. For example, nucleotide incorporations can be detected through fluorescence resonance energy transfer (FRET) interactions between a fluorophore-bearing polymerase and gamma-phosphate-labeled nucleotides, or with zero-mode waveguides (ZMW). Techniques and reagents for sequencing via FRET and or ZMW detection that can be modified for use in an apparatus or method set forth herein are described, for example, in Levene et al. Science 299, 682-686 (2003); Lundquist et al. Opt. Lett. 33, 1026-1028 (2008); Korlach et al. Proc. Natl. Acad. Sci. USA 105, 1176-1181 (2008); or U.S. Pat. Nos. 7,315,019; 8,252,911 or 8,530,164, the disclosures of which are incorporated herein by reference.
Any of a variety of nucleic acid amplification techniques can be used to copy nucleic acids in a flow cell. Exemplary techniques that can be used include, but are not limited to, polymerase chain reaction (PCR), rolling circle amplification (RCA), multiple displacement amplification (MDA), bridge amplification, random prime amplification (RPA) or others known in the art of molecular biology. In particular configurations, one or more primers used for amplification can be attached to a surface in a flow cell. In such embodiments, extension of the surface-attached primer(s) along template nucleic acids will result in copies of the templates being attached to the surface. Such amplification methods can be used for analytical purposes such as real time PCR or quantitative PCR. Alternatively, amplification can be used to prepare nucleic acids for downstream applications such as nucleic acid sequencing. Preparative amplification methods that result in one or more sites on a solid support, where each site is attached to multiple copies of a particular nucleic acid template, are referred to as “clustering” methods.
In PCR techniques, one or both primers used for amplification can be attached to a surface. Formats that utilize two species of attached primer are often referred to as bridge amplification because double stranded amplicons form a bridge-like structure between the two attached primers that flank the template sequence that has been copied. Exemplary reagents and conditions that can be used for bridge amplification are described, for example, in U.S. Pat. Nos. 5,641,658 or 7,115,400; U.S. Patent Pub. Nos. 2002/0055100 A1, 2004/0096853 A1, 2004/0002090 A1, 2007/0128624 A1 or 2008/0009420 A1, each of which is incorporated herein by reference. PCR amplification can also be carried out with one of the amplification primers attached to the surface and the second primer in solution. An exemplary format that uses a combination of one solid phase-attached primer and a solution phase primer is known as primer walking and can be carried out as described in U.S. Pat. No. 9,476,080, which is incorporated herein by reference. Another example is emulsion PCR which can be carried out as described, for example, in Dressman et al., Proc. Natl. Acad. Sci. USA 100:8817-8822 (2003), WO 05/010145, or U.S. Patent Pub. Nos. 2005/0130173 A1 or 2005/0064460 A1, each of which is incorporated herein by reference.
RCA techniques can be used in a method set forth herein. Exemplary reagents that can be used in an RCA reaction and principles by which RCA produces amplicons are described, for example, in Lizardi et al., Nat. Genet. 19:225-232 (1998) or US Pat. App. Pub. No. 2007/0099208 A1, each of which is incorporated herein by reference. Primers used for RCA can be in solution or attached to a surface in a flow cell.
MDA techniques can also be used in a method of the present disclosure. Some reagents and useful conditions for MDA are described, for example, in Dean et al., Proc Natl. Acad. Sci. USA 99:5261-66 (2002); Lage et al., Genome Research 13:294-307 (2003); Walker et al., Molecular Methods for Virus Detection, Academic Press, Inc., 1995; Walker et al., Nucl. Acids Res. 20:1691-96 (1992); or U.S. Pat. Nos. 5,455,166; 5,130,238; or 6,214,587, each of which is incorporated herein by reference. Primers used for MDA can be in solution or attached to a surface in a flow cell.
Nucleic acid templates that are used in a method or composition herein can be DNA such as genomic DNA, synthetic DNA, amplified DNA, complementary DNA (cDNA) or the like. RNA can also be used such as mRNA, ribosomal RNA, tRNA or the like. Nucleic acid analogs can also be used as templates herein. Primers used herein can be DNA, RNA or analogs thereof.
A channel of a flow cell can run straight from ingress to egress as exemplified in
A flow cell of the present disclosure can include one or more fiducials that are useful for 2-dimensional registration of the flow cell in the x and y dimensions. As shown in
An advantage of incorporating a fiducial 881 into the gasket material is that using routine manufacturing processes can be used to accurately position the gasket with respect to the channels and to accurately place the fiducial in the gasket, resulting in a high confidence spatial relationship between the fiducial and an array present in the channel. Although the fiducial in
Various other fiducials and techniques for producing the fiducials are demonstrated by
Exemplary luminophores that can be used as a dopant for a fiducial or as a label for an analyte include, but are not limited to, fluorescent nanocrystals; quantum dots; green fluorescent protein and color shifted mutants thereof, phycobiliproteins such as phycocyanin and phycoerythrin, d-Rhodamine acceptor dyes including dichloro[R110], dichloro[R6G], dichloro[TAMRA], dichloro[ROX] or the like; fluorescein donor dye including fluorescein, 6-FAM, or the like; Cyanine dyes such as Cy3B; Alexa dyes, SETA dyes, Atto dyes such as atto 647N which forms a FRET pair with Cy3B and the like. Others include, but are not limited to, MDCC (7-diethylamino-3-[([(2-maleimidyl)ethyl]amino)carbonyl]coumarin), TET, HEX, Cy3, TMR, ROX, Texas Red, Cy5, LC red 705 and LC red 640. Other luminophores known in the art such as those described in Principles of Fluorescence Spectroscopy, Joseph R. Lakowicz (Editor), Plenum Pub Corp, 2nd edition (July 1999) and the 6th Edition of Molecular Probes Handbook by Richard P. Hoagland (each of which is incorporated herein by reference, can be useful. In particular embodiments, a luminophore that is used herein or a luminescent material can have a fluorescence quantum yield that is at least 0.2, 0.5, 0.8 or higher.
In an example embodiment, there is disclosed a flow cell comprising: (a) a gasket interposed between a first substrate and a second substrate, wherein the gasket, the first substrate and the second substrate are impermeable to aqueous liquid and liquid adhesive, wherein the gasket has a footprint on the first substrate that delineates a channel for containing the aqueous liquid; (b) a via in the gasket, the via containing a solidified liquid adhesive that bonds the first substrate to the second substrate, wherein the solidified liquid adhesive in the via is separated from the channel by the gasket; and (c) a first channel port connecting the channel to the exterior of the flow cell, wherein the first channel port is permeable to the aqueous liquid. In an example variation of any embodiment, there is disclosed the flow cell of any disclosed embodiment, further comprising a via port connecting the via to the exterior of the flow cell. In an example variation of any embodiment, there is disclosed the flow cell of any disclosed embodiment, further comprising a second via port connecting the via to the exterior of the flow cell. In an example variation of any embodiment, there is disclosed the flow cell of any disclosed embodiment, wherein the gasket comprises a plurality of vias, the vias each containing a solidified liquid adhesive that bonds the first substrate to the second substrate, wherein the solidified liquid adhesive in the vias is separated from the channel by the gasket. In an example variation of any embodiment, there is disclosed the flow cell of any disclosed embodiment, wherein the channel comprises an array of analytes. In an example variation of any embodiment, the array of analytes is attached to the first substrate in the channel. In an example variation of any embodiment, a second array of analytes is attached to the second substrate in the channel. In an example variation of any embodiment, the analytes comprise nucleic acids, different nucleic acids being attached to respective sites of the array. In an example variation of any embodiment, the array comprises at least 100 of the sites per mm2. In an example variation of any embodiment, the gasket has a footprint on the second substrate that delineates a channel for containing the aqueous liquid. In an example variation of any embodiment, the footprint on the first substrate is the same shape as the footprint on the second substrate. In an example variation of any embodiment, the first substrate comprises a planar surface that forms a first side of the channel and the second substrate comprise a planar surface that forms a second side of the channel. In an example variation of any embodiment, there is disclosed a second channel port connecting the channel to the exterior of the flow cell, wherein the second channel port is permeable to the aqueous liquid. In an example variation of any embodiment, the aqueous liquid is present in the channel. In an example variation of any embodiment, the aqueous liquid exerts a positive pressure of at least 10 PSI on the channel. In an example variation of any embodiment, the gasket comprises pressure sensitive adhesive, the pressure sensitive adhesive being in contact with one or both of the first and second substrates. In an example variation of any embodiment, the first substrate and the second substrate comprise the same material. In an example variation of any embodiment, the material comprises glass or plastic. In an example variation of any embodiment, the glass comprises a silane or organosilane coating. In an example variation of any embodiment, the first substrate comprises a different material from the material of the second substrate. In an example variation of any embodiment, the first substrate comprises glass and the second substrate comprises plastic. In an example variation of any embodiment, the first substrate comprises a transparent material and a thermal expansion joint. In an example variation of any embodiment, the via contiguously encircles the channel. In an example variation of any embodiment, the via contiguously encircles individual channels of a plurality of channels in the flow cell. In an example variation of any embodiment, the gasket delineates the distance between the first and second substrate in the channel. In an example variation of any embodiment, the distance is greater than 0.1 mm and less than 1 cm. In an example variation of any embodiment, the volume of the channel is greater than 10 μl and less than 10 ml. In an example variation of any embodiment, one or both of the first and second substrates is transparent to UV, VIS or IR radiation. In an example variation of any embodiment, the solidified liquid adhesive comprises a luminescent material. In an example variation of any embodiment, the gasket comprises a luminescent material. In an example variation of any embodiment, the channel comprises a turn of at least ninety degrees, wherein the turn has an inner wall and an outer wall, the inner wall having substantially the same length as the outer wall.
In another example embodiment, there is disclosed a method of making a flow cell comprising (a) interposing a gasket between a first substrate and a second substrate to delineate a channel for containing an aqueous liquid, wherein the gasket, the first substrate and the second substrate are impermeable to aqueous liquid and liquid adhesive; (b) delivering a liquid adhesive to a via in the gasket; and (c) allowing the liquid adhesive to bond the first substrate to the second substrate, wherein the liquid adhesive is separated from the channel by the gasket. In an example variation of any embodiment, step (b) is performed prior to step (a). In an example variation of any embodiment, the liquid adhesive is delivered through a via ingress port in the first substrate, in the second substrate or in the gasket. In an example variation of any embodiment, the flow cell comprises a via egress port through which air is vented when the liquid adhesive is delivered through the via ingress port. In an example variation of any embodiment, step (c) comprises applying heat or light to allow the liquid adhesive to bond the first substrate to the second substrate and the gasket. In an example variation of any embodiment, there is further disclosed creating an array of analytes in the channel. In an example variation of any embodiment, the analytes comprise nucleic acids, different nucleic acids being attached to respective sites of the array. In an example variation of any embodiment, the array is created by attaching the analytes to the first substrate in the channel. In an example variation of any embodiment, there is disclosed adhering the gasket to the first substrate using a pressure sensitive adhesive. In an example variation of any embodiment, there is disclosed adhering the gasket to the second substrate using a pressure sensitive adhesive. In an example variation of any embodiment, the first substrate and the second substrate comprise the same material. In an example variation of any embodiment, the material comprises glass or plastic. In an example variation of any embodiment, the glass comprises a silane or organosilane coating. In an example variation of any embodiment, the first substrate comprises a different material from the material of the second substrate. In an example variation of any embodiment, the first substrate comprises glass and the second substrate comprises plastic. In an example variation of any embodiment, there is disclosed a receptacle that houses at least the first channel port, wherein the receptacle defines a basin. In an example variation of any embodiment, the receptacle is configured to mate with a pipette adapter wherein the pipette adapter is configured to facilitate introduction of a nucleic acid library starting materials into the flow cell. In an example variation of any embodiment, there is disclosed a pipette adapter wherein the pipette adapter mates with the basin of the receptacle. In an example variation of any embodiment, the pipette adapter includes a pipette fluid inlet that aligns with the first channel port, the pipette fluid inlet configured to receive a pipette. In an example variation of any embodiment, the pipette adapter includes an overmold that aligns with the with the first channel port when the pipette adapter mates with the receptacle. In an example variation of any embodiment, the receptacle is configured to mate with an adapter that connects the flow cell channels to a fluidic delivery apparatus. In an example variation of any embodiment, the fluidic delivery apparatus comprises at least one fluid line fluidly coupled to a fluidics system such that reagents and other fluids can be delivered to the channels of the flow cell. In an example variation of any embodiment, the adapter includes an overmold that mates with the at least one fluid line. In an example variation of any embodiment, the overmold enables high pressure fluid flow through the at least one fluid line and inhibits leaking of fluid from the at least one fluid line. In an example variation of any embodiment, the overmold enables high pressure fluid flow through the at least one fluid line and inhibits leaking of fluid from the at least one fluid line at an interface between the at least one fluid line and a flow cell.
In another example embodiment, there is disclosed an adapter device for facilitating ingress or egress of fluid relative to a flow cell, the adapter comprising: an outer housing configured to mate with the flow cell, the housing including a first port that aligns with an ingress or egress of the flow cell, the port configured to receive a tube that delivers or receives fluid relative to the flow cell; and a first overmold positioned inside the housing and aligned with the first port, the first overmold configured to secure the tube relative to the flow cell. In an example variation of any embodiment, the tube is a pipette. In an example variation of any embodiment, the tube is coupled to a fluidics system such that reagents and other fluids can be delivered to the channels of the flow cell. In an example variation of any embodiment, the first overmold is made of silicone. In an example variation of any embodiment, the first port aligns with an ingress of the flow cell. In an example variation of any embodiment, the housing further comprises a second port that aligns with an egress of the flow cell, and further comprising a second overmold positioned inside the housing and aligned with the second port. In an example variation of any embodiment, the overmold enables high pressure fluid flow through the tube and inhibits leaking of fluid from the tube.
Throughout this application various publications, patents and/or patent applications have been referenced. The disclosures of these documents in their entireties are hereby incorporated by reference in this application. A number of embodiments have been described. Nevertheless, it will be understood that various modifications may be made. Accordingly, other embodiments are within the scope of the following claims.
While this specification contains many specifics, these should not be construed as limitations on the scope of an invention that is claimed or of what may be claimed, but rather as descriptions of features specific to particular embodiments. Certain features that are described in this specification in the context of separate embodiments can also be implemented in combination in a single embodiment. Conversely, various features that are described in the context of a single embodiment can also be implemented in multiple embodiments separately or in any suitable sub-combination. Moreover, although features may be described above as acting in certain combinations and even initially claimed as such, one or more features from a claimed combination can in some cases be excised from the combination, and the claimed combination may be directed to a sub-combination or a variation of a sub-combination. Similarly, while operations are depicted in the drawings in a particular order, this should not be understood as requiring that such operations be performed in the particular order shown or in sequential order, or that all illustrated operations be performed, to achieve desirable results. Only a few examples and implementations are disclosed. Variations, modifications and enhancements to the described examples and implementations and other implementations may be made based on what is disclosed.
This application is based on, and claims the benefit of, U.S. Provisional Application No. 62/969,845, filed Feb. 4, 2020, which is incorporated herein by reference.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US2021/016152 | 2/2/2021 | WO |
| Number | Date | Country | |
|---|---|---|---|
| 62969845 | Feb 2020 | US |
