Patent Application
20240067960
Incorporated by reference in its entirety is a computer-readable nucleotide/amino acid sequence listing submitted concurrently herewith and identified as follows: 1,055 kilobytes xml file named “920006-391462_SL.xml,” created on Sep. 7, 2023.
The invention relates to barcoded nucleic acid nanostructure delivery compositions for in vivo screening for subsequent use in vivo therapeutic delivery, and methods therefor. More particularly, the invention relates to nucleic acid nanostructure delivery compositions, such as DNA origami structures, associated with barcodes for high throughput in vivo screening of the nucleic acid nanostructure delivery compositions for subsequent use in drug delivery, and methods therefor.
Genetic medicines (including gene therapy, gene silencing, splicing regulators, and nuclease based gene editors) are poised to produce revolutionary treatments, including vaccines, infectious disease treatments, antimicrobial treatments, antiviral treatments, and most notably, genetic disease treatments. However, the in vivo delivery of these genetic medicine payloads to the specific tissues and cells that need to be treated, while avoiding tissues and cells that can reduce the efficacy or safety of the genetic medicine, poses a significant challenge. Additional challenges include the ability to deliver large genetic payloads or multiple payloads. Adeno-associated viruses (AAVs) are the most widely used tool for genetic medicine delivery, but AAVs are not able to deliver large genetic payloads or multiple payloads (such as the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system), and they sometimes trigger unwanted immune responses, including the generation of anti-AAV antibodies, a cell mediated response. Some of the immune responses caused by AAV in patients are potentially fatal immune responses.
Therapeutics based on the CRISPR/Cas9 system have an exceptional potential to treat a number of genetic diseases due to the capability of this system for precise and programmable gene editing. Gene editing and repair using the CRISPR/Cas9 system has two main mechanisms, including non-homologous end joining (NHEJ) which repairs the site of cut by inducing random indel mutation, and homology-directed repair (HDR), which repairs the cut site based on a pre-existing template. Because a pre-designed template can be used for HDR-directed repair, therapies based on this mechanism can be tailored to cure a large number of different genetic diseases. However, the main challenge is that HDR repair requires the delivery of CRISPR/Cas9, small guide RNA (sgRNA) and a donor DNA strand at the same time to a particular location. This requirement becomes particularly limiting for in vivo applications because ensuring co-delivery of multiple large molecules to the same targeted location is currently not feasible. For example, the Cas9 enzyme sequence and guide RNA complex is too large to fit into AAVs.
There is a need for effective non-viral delivery systems, not only for genetic delivery systems, but also for delivery of small molecule therapeutics. The current state-of-the-art non-viral gene delivery systems, such as liposomes, have many drawbacks such as poor biocompatibility and the inability to easily engineer or functionalize them. Additional concerns are that such non-viral gene delivery systems are easily degraded by various enzymes as they pass through intracellular or intercellular compartments, and these systems have not been able to package multiple large payloads.
The inventors have designed nucleice acid nanostructure delivery compositions (e.g., DNA origami nanostructures). These compositions have the advantage of being biocompatible, non-toxic, and can be programmed in many ways. For example, the nucleice acid nanostructure delivery compositions can be programmed to have functional groups that enable them to evade early degradation, that enable them to evade immune responses, and that enable intracellular imaging and targeted and controlled delivery of therapeutic genes and small molecule therapeutics. Thus, these non-viral delivery compositions can enhance the stability, safety, and/or efficacy of payloads by providing immune evasion, tissue-directed intracellular delivery, and the ability to deliver large genetic payloads or multiple payloads, or other genetic medicine payloads, or small molecule therapeutics.
The rate limiting step for development of such drug delivery vehicles is in vivo testing of the drug delivery vehicles leading to slow or un-optimized final products and a lack of new drug delivery vehicle candidates. The inventors have demonstrated the utility of a nucleic acid nanostructure delivery composition (e.g., a DNA origami nanostructure composition) for in vivo delivery, and the inventors have also developed novel methods for labeling the nucleic acid nanostructure delivery compositions with unique barcodes, administering them to an animal, and then extracting them from animal tissues for detection. This method will allow for in vivo high throughput screening of a diverse set of drug delivery nanoparticles, including DNA origami structures, for use in the delivery of large genetic payloads, multiple payloads, other genetic medicine payloads, or small molecule therapeutics.
The following clauses, and combinations thereof, provide various additional illustrative aspects of the invention described herein. The various embodiments described in any other section of this patent application, including the section titled “DETAILED DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS” and the “EXAMPLES” are applicable to any of the following embodiments of the invention described in the numbered clauses below.
The invention relates to barcoded nucleic acid nanostructure delivery compositions for in vivo screening for subsequent use in vivo therapeutic delivery, and methods therefor. More particularly, the invention relates to nucleic acid nanostructure delivery compositions, such as DNA origami structures, associated with barcodes for high throughput in vivo screening of the nucleic acid nanostructure delivery compositions for subsequent use of the nucleic acid nanostructure delivery compositions in drug delivery, and methods therefor.
The invention also relates to nucleic acid nanostructure delivery compositions for non-viral delivery, and methods therefor. More particularly, the invention relates to single-stranded or double-stranded DNA or RNA nanostructure delivery compositions, such as DNA origami compositions, for the delivery of more than one payload, a nucleic acid construct payload of 3 kB or more, other genetic medicine payloads, or small molecule therapeutics.
The following clauses, and combinations thereof, provide various additional illustrative aspects of the invention described herein. The various embodiments described in any other section of this patent application, including the summary portion of the section titled “BACKGROUND AND SUMMARY”, the “EXAMPLES”, and this “DETAILED DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS” section of the application are applicable to any of the following embodiments of the invention described in the numbered clauses below.
In various embodiments, the nucleic acid nanostructure delivery compositions described herein may comprise any non-viral composition for in vivo delivery of the payloads. By way of example, the nucleic acid nanostructure delivery compositions described herein may be selected from the group comprising synthetic virus-like particles, carbon nanotubes, emulsions, and any nucleic acid nanostructure delivery composition, such as DNA origami structures.
In these embodiments, the nucleic acid nanostructure delivery compositions have a high degree of tunability in structure and function, opportunities to protect payloads from adverse reactions or degradation by the immune system, and cell targeting via surface charge, particle size, or conjugation with various aptamers. These delivery systems also lend themselves to computer aided design, and they have suitable pathways to robust, commercial scale manufacturing processes with higher yields and fewer purification steps than viral manufacturing processes.
A nucleic acid nanostructure delivery composition (e.g., a DNA origami structure), as a delivery platform, is programmable and offers an opportunity for precise scale-up and manufacturing. In this embodiment, the biologic and non-viral nature of the nucleic acid nanostructure delivery composition reduces the chance of adverse immune reactions. In this embodiment, control of each nucleotide that forms a part of the nucleic acid nanostructure delivery composition (e.g., DNA origami nanostructure) allows for the precise design and modification of the structure, including suitable chemical moieties which can make in vivo delivery and endosomal escape possible. In other embodiments, the nucleic acid nanostructure delivery composition can comprise RNA. In various embodiments, the nucleic acid nanostructure delivery composition can be single-stranded or double-stranded, and can comprise DNA or RNA.
In this embodiment, the nucleic acid nanostructure delivery composition can undergo self-base pairing (i.e., a DNA origami structure) to fold into structures that can form the single-stranded or double-stranded scaffold that can encapsulate a payload.
In this embodiment, the nucleic acid nanostructure delivery composition can comprise overhangs that bind through complementary base paring with payload nucleic acids or with the nucleic acid barcode constructs described herein. In this embodiment, the overhangs can be located within a cavity within the nucleic acid nanostructure delivery composition scaffold, and the cavity can be covered by a lid and a hinge allowing the payloads or the nucleic acid barcode constructs to be completely enclosed within the cavity when the lid is shut. In this embodiment, the lid can further comprise oligonucleotide strands that bind through complementary base pairing with other oligonucleotide strands attached to the nucleic acid nanostructure delivery composition scaffold when the lid is in the closed position. DNA nanostructure delivery compositions (e.g., DNA origami structures) are described in U.S. Pat. No. 9,765,341, incorporated herein by reference.
As used herein, the term “complementary base pairing” refers to the ability of purine and pyrimidine nucleotide sequences to associate through hydrogen bonding to form double-stranded nucleic acid molecules. Guanine and cytosine, adenine and thymine, and adenine and uracil are complementary and can associate through hydrogen bonding resulting in the formation of double-stranded nucleic acid molecules when two nucleic acid molecules have “complementary” sequences. The complementary sequences can be DNA or RNA sequences. The complementary DNA or RNA sequences are referred to as a “complement.”
In one aspect, the nucleic acid nanostructure delivery composition of the invention can comprise more than one payload for delivery to target cells, or a nucleic acid payload of 3 kB or more, or another genetic payload, or a small molecule therapeutic for delivery to target cells. In these embodiments, the nucleic acid payload can have a size of 3 kB or more and can be DNA or RNA. In any of the nucleic acid nanostructure delivery composition embodiments described herein, the nucleic acid nanostructure can comprise M13 bacteriophage DNA.
In one illustrative embodiment, the nucleic acid nanostructure delivery composition further comprises a targeting component for targeting to cells. In one aspect, the targeting component can be a nucleotide that is an RNA that forms a ‘stem-and-loop’ structure. In this aspect, the nucleic acid nanostructure delivery composition can be designed so that the polynucleotide strands fold into three-dimensional structures via a series of highly tuned ‘stem-and-loop’ configurations. In this embodiment, the nucleic acid nanostructure delivery composition can have a high affinity for protein receptors expressed on specific cells resulting in targeting of the nucleic acid nanostructure delivery composition and the payload to the specific cells. In this embodiment, the polynucleotide that binds to the target cell receptor can bind in conjunction with a peptide aptamer. In another aspect, the nucleic acid nanostructure delivery composition can be folded so that, in the presence of certain biomarkers such as cell receptors, microRNA, DNA, RNA or an antigen, the self-base pairs are disrupted and the nucleic acid nanostructure delivery composition can unfold, resulting in the triggered release of the payload only in the presence of the specific biomarker. For example, a lock-and-key mechanism for triggered opening of a nucleic acid nanostructure delivery composition (e.g., a DNA origami construct) has been demonstrated previously (Andersen, et al., Nature, Vol. 459, pages 73-76(2009), incorporated by reference herein). In these embodiments, the use of the nucleic acid nanostructure delivery composition to create three-dimensional structures that target cells and tissues allows for more efficient delivery of payloads with fewer side effects, since the nucleic acid nanostructure delivery composition can have low immunogenicity, and the payload will be released only in the presence of RNA or peptide biomarkers, for example, that exist in the cytosol of target cells and tissues.
In another embodiment, a cell-targeting peptide can be conjugated to a charge neutral peptide nucleic acid, PNA, oligonucleotide instead of a DNA oligonucleotide. PNAs are synthetic polymers of repeating peptide-like amide units (N-(2-aminoethyl) glycine) that mimic nucleic acids in their hybridization affinity and specificity via base-pairing. Their uncharged backbones lead to higher binding affinity with DNA than DNA:DNA so these molecules are suitable for binding to proteins and peptides.
In the embodiment where a nucleic acid nanostructure delivery composition is used, computer aided design tools can predict the nucleotide sequence necessary to produce highly engineered nucleic acid nanostructure delivery compositions. For gene delivery, these nucleic acid nanostructure delivery compositions offer the advantages of encapsulation efficiency, as the size and shape of the structure can be tailored to fit the cargo. In another aspect, loading efficiency can be increased by incorporating payloads into the encapsulating nucleic acid nanostructure delivery composition itself.
In another illustrative embodiment, any of the nucleic acid nanostructure delivery compositions described herein can be coated with one or more polymers to protect the compositions from immune responses or to enhance endosomal escape. In one embodiment, the one or more polymers comprise polyethylene glycol. In another embodiment, the one or more polymers comprise polyethylene glycol poly-L-lysine. In yet another embodiment, the one or more polymers comprise polyethylenimine. In an additional embodiment, the one or more polymers comprise polyethylene glycol poly-L-lysine and polyethylenimine.
In various embodiments, payloads may be combined with the nucleic acid nanostructure delivery compositions using any or all of covalent bonds, electrostatic interactions, and ligand affinity interactions. In one aspect, covalent bonding methods include the use of EDC/NHS to form stable amide bonds between the payload and the nucleic acid nanostructure delivery compositions for improved stability (both “on the shelf” and in vivo), ease of separation and extraction, and sensitive detection. In another illustrative aspect, electrostatic bonding methods include the use of cationic nucleic acid nanostructure delivery compositions that electrostatically complex with the payload. In another embodiment, ligand affinity bonding includes the use of ligands such as avidin and biotin, both covalently bonded to the nucleic acid nanostructure delivery compositions and the payload via EDC/NHS chemistry to yield the stable combination of the payload and the nucleic acid nanostructure delivery compositions. In another embodiment, methods for bonding the payload, including the nucleic acid barcode construct, to the nucleic acid nanostructure delivery composition are provided, including the use of cleavable linkers that can reverse the bond with high specificity, such as the inclusion of nuclease specific oligonucleic acid sequences, allowing the payload, including the nucleic acid barcode construct, to be cleaved and extracted as desired. In another embodiment, cleavable linker and enzyme pairs include amide bonds and amidase enzymes.
In one embodiment, a composition comprising a non-viral delivery vehicle comprising a nucleic acid nanostructure delivery composition, and a nucleic acid barcode construct is provided. In embodiments where the nucleic acid nanostructure delivery composition is barcoded, the nucleic acid barcode construct can be associated with the nucleic acid nanostructure delivery composition via base-pairing. In this embodiment, the base-pairing can occur between a sequence of a single-stranded overhang on the nucleic acid nanostructure delivery composition and a complementary sequence appended to the nucleic acid barcode construct. In other embodiments, the nucleic acid nanostructure delivery composition can comprise staples that self-assemble to form the nucleic acid nanostructure delivery composition, and exemplary stapes are described in Example 1.
In other embodiments, the nucleic acid barcode construct can be associated with the nucleic acid nanostructure delivery composition by a high affinity, non-covalent bond interaction between a biotin molecule on the 5′ and/or the 3′ end of the nucleic acid barcode construct and a molecule that binds to biotin on the nucleic acid nanostructure delivery composition. In this embodiment, the molecule that binds to biotin can be bound to the nucleic acid nanostructure delivery composition by a covalent phosphoramidate bond formed via an EDC-NHS coupling reaction between a terminal phosphate group of a 5′ end of an overhang on the nucleic acid nanostructure delivery composition and an amine group on the molecule that binds to biotin. In this embodiment, the biotin can be bound to the nucleic acid barcode construct by a covalent bond.
In another illustrative embodiment, the nucleic acid barcode construct can be bound to the nucleic acid nanostructure delivery composition by a covalent bond. In this embodiment, the covalent bond can be formed via an EDC-NHS coupling reaction between a terminal phosphate group of the 5′ end of an overhang on the nucleic acid nanostructure delivery composition and an amine group on an amino terminal nucleotide of the nucleic acid barcode construct. In another embodiment, the covalent bond can be formed via a click chemistry coupling reaction between an azide group on the nucleic acid nanostructure delivery composition and an alkyne group on the nucleic acid barcode construct. In yet another embodiment, the covalent bond can be formed via a click chemistry coupling reaction between an azide group on the nucleic acid barcode construct and an alkyne group on the nucleic acid nanostructure delivery composition. In still another embodiment, the nucleic acid barcode construct can be associated with the nucleic acid nanostructure delivery composition by a covalent bond between a carboxy terminated molecule on the nucleic acid nanostructure delivery composition and a primary amine on the nucleic acid barcode construct at the 5′ and/or the 3′ end.
In one aspect, the nucleic acid barcode construct can comprise a polynucleotide barcode and the barcode comprises a unique sequence not present in any known genome for identification of the polynucleotide barcode. In another embodiment, a set of different nucleic acid barcode constructs with different polynucleotide barcodes (e.g., 88 or 96 different polynucleotide barcodes) can be used to allow for multiplexing of samples on one sequencing run.
In various embodiments, the barcodes can be from about 5 to about 100 base pairs in length, from about 5 to about 90 base pairs in length, from about 5 to about 80 base pairs in length, from about 5 to about 70 base pairs in length, from about 5 to about 60 base pairs in length, from about 5 to about 50 base pairs in length, from about 5 to about 40 base pairs in length, from about 5 to about 35 base pairs in length, about 5 to about 34 base pairs in length, about 5 to about 33 base pairs in length, about 5 to about 32 base pairs in length, about 5 to about 31 base pairs in length, about 5 to about 30 base pairs in length, about 5 to about 29 base pairs in length, about 5 to about 28 base pairs in length, about 5 to about 27 base pairs in length, about 5 to about 26 base pairs in length, about 5 to about 25 base pairs in length, about 5 to about 24 base pairs in length, about 5 to about 23 base pairs in length, about 5 to about 22 base pairs in length, about 5 to about 21 base pairs in length, about 5 to about 20 base pairs in length, about 5 to about 19 base pairs in length, about 5 to about 18 base pairs in length, about 5 to about 17 base pairs in length, about 5 to about 16 base pairs in length, about 5 to about 15 base pairs in length, about 5 to 14 base pairs in length, about 5 to 13 base pairs in length, about 5 to 12 base pairs in length, about 5 to 11 base pairs in length, about 5 to 10 base pairs in length, about 5 to 9 base pairs in length, about 5 to 8 base pairs in length, about 6 to 10 base pairs in length, about 7 to 10 base pairs in length, about 8 to 10 base pairs in length, or about 6 to about 20 base pairs in length.
Various embodiments of barcodes are shown below in Table 1 (labeled “Polynucleotide Barcodes”). These barcodes can be used in the nucleic acid barcode constructs alone or in combinations of, for example, two or more barcodes, three or more barcodes, four or more barcodes, etc. In the embodiment where more than one barcode is used, the hamming distance between the barcodes can be about 2 to about 6 nucleotides, or any suitable number of nucleotides can form a hamming distance, or no nucleotides are present between the polynucleotide barcodes.
In another embodiment, a random sequence fragment can be linked to the 5′ and/or the 3′ end of the barcode and the random sequence fragment can, for example, be used for bioinformatic removal of PCR duplicates. The random sequence fragment can also be used to add length to the nucleic acid construct and can serve as a marker for bioinformatic analysis to identify the beginning or the end of the barcode after sequencing. In another embodiment, the nucleic acid barcode construct comprises at least a first and a second random sequence fragment, and the first random sequence fragment can be linked to the 5′ end of the barcode and the second random sequence fragment can be linked to the 3′ end of the barcode. In another embodiment, one or at least one random sequence fragment is linked to the 5′ and/or the 3′ end of the barcode. In one aspect, the random sequence fragments can be extended as needed to make the nucleic acid barcode construct longer for different applications such as whole genome sequencing where short inserts may be lost.
In various embodiments, the random sequence fragments can be from about 5 to about 20 base pairs in length, about 5 to about 19 base pairs in length, about 5 to about 18 base pairs in length, about 5 to about 17 base pairs in length, about 5 to about 16 base pairs in length, about 5 to about 15 base pairs in length, about 5 to about 14 base pairs in length, about 5 to about 13 base pairs in length, about 5 to about 12 base pairs in length, about 5 to about 11 base pairs in length, about 5 to about 10 base pairs in length, about 5 to about 9 base pairs in length, about 5 to about 8 base pairs in length, about 6 to about 10 base pairs in length, about 7 to about 10 base pairs in length, or about 8 to about 10 base pairs in length.
In another illustrative aspect, the barcode may be flanked by primer binding segments (i.e., directly or indirectly linked to the barcode) so that the nucleic acid barcode construct comprising the barcode can be amplified during a polymerase chain reaction (PCR) and/or sequencing protocol. In one aspect, the primer binding segments can be useful for binding to one or more universal primers or a universal primer set. In one illustrative embodiment, the universal primers can contain overhang sequences that enable attachment of index adapters for sequencing. In one embodiment, the adapters can be NGS adapters (e.g. Illumina) positioned internally but towards the end of either the 5′ or the 3′ primer, not as the terminating structure, to avoid the formation of primer dimers. In this aspect, the primers can be any primers of interest. In this embodiment, the first primer binding segment can be linked at its 3′ end to the 5′ end of a first random sequence fragment and the second primer binding segment can be linked at its 5′ end to the 3′ end of a second random sequence fragment with the barcode between the random sequence fragments. In another embodiment, the first primer binding segment can be linked at its 3′ end to the 5′ end of the barcode and the second primer binding segment can be linked at its 5′ end to the 3′ end of a random sequence fragment linked to the 3′ end of the barcode. In another embodiment, the first primer binding segment can be linked at its 3′ end to the 5′ end of a random sequence fragment and the second primer binding segment can be linked at its 5′ end to the 3′ end of the barcode where the barcode is linked at its 5′ end to the 3′ end of the random sequence fragment. In yet another embodiment, the first primer binding segment can be linked at its 3′ end to the 5′ end of the barcode and the second primer binding segment can be linked at its 5′ end to the 3′ end of the barcode.
In embodiments where primer binding segments are included in the nucleic acid barcode construct, the primer binding segments can range in length from about 15 base pairs to about 30, from about 15 base pairs to about 29 base pairs, from about 15 base pairs to about 28 base pairs, from about 15 base pairs to about 26 base pairs, from about 15 base pairs to about 24 base pairs, from about 15 base pairs to about 22 base pairs, from about 15 base pairs to about 20 base pairs, 16 base pairs to about 28 base pairs, from about 16 base pairs to about 26 base pairs, from about 16 base pairs to about 24 base pairs, from about 16 base pairs to about 22 base pairs, from about 16 base pairs to about 20 base pairs, 17 base pairs to about 28 base pairs, from about 17 base pairs to about 26 base pairs, from about 17 base pairs to about 24 base pairs, from about 17 base pairs to about 22 base pairs, from about 17 base pairs to about 20 base pairs, 18 base pairs to about 28 base pairs, from about 18 base pairs to about 26 base pairs, from about 18 base pairs to about 24 base pairs, from about 18 base pairs to about 22 base pairs, or from about 18 base pairs to about 20 base pairs.
An exemplary sequence of a nucleic acid barcode construct is shown below. The /5AmMC6/s a 5′ amine modification for attachment to the nucleic acid nanostructure delivery composition. The *'s are phosphorothioate bond modifications for stability. The A*G*A*CGTGTGCTCTTCCGATCT sequence (SEQ ID NO: 1001) is the 5′ primer binding segment sequence. The GCTACATAAT (SEQ ID NO: 1) is an exemplary barcode sequence. The N's represent the random sequence fragment. The AGATCGGAAGAGCGTCG*T*G*T (SEQ ID NO: 1002) is the 3′ primer binding segment sequence.
In all of the various embodiments described above, the entire nucleic acid barcode construct can range in length from about 30 base pairs to about 350 base pairs, from about 30 base pairs to about 300 base pairs, from about 30 base pairs to about 270 base pairs, about 30 base pairs to about 240 base pairs, about 30 base pairs to about 230 base pairs, about 30 base pairs to about 220 base pairs, about 30 base pairs to about 210 base pairs, about 30 base pairs to about 200 base pairs, about 30 base pairs to about 190 base pairs, about 30 base pairs to about 180 base pairs, about 30 base pairs to about 170 base pairs, about 30 base pairs to about 160 base pairs, about 30 base pairs to about 150 base pairs, about 30 base pairs to about 140 base pairs, about 30 base pairs to about 130 base pairs, about 30 base pairs to about 120 base pairs, from about 30 base pairs to about 110 base pairs, from about 30 base pairs to about 100 base pairs, from about 30 base pairs to about 90 base pairs, from about 30 base pairs to about 80 base pairs, from about 30 base pairs to about 70 base pairs, from about 30 base pairs to about 60 base pairs, from about 30 base pairs to about 50 base pairs, from about 30 base pairs to about 40 base pairs, 40 base pairs to about 120 base pairs, from about 40 base pairs to about 110 base pairs, from about 40 base pairs to about 100 base pairs, from about 40 base pairs to about 90 base pairs, from about 40 base pairs to about 80 base pairs, from about 40 base pairs to about 70 base pairs, from about 40 base pairs to about 60 base pairs, from about 40 base pairs to about 50 base pairs, 50 base pairs to about 120 base pairs, from about 50 base pairs to about 110 base pairs, from about 50 base pairs to about 100 base pairs, from about 50 base pairs to about 90 base pairs, from about 50 base pairs to about 80 base pairs, from about 50 base pairs to about 70 base pairs, from about 50 base pairs to about 60 base pairs, or about 42 base pairs to about 210 base pairs.
In another embodiment, a method of in vivo screening for a desired nucleic acid nanostructure delivery composition is provided. The method comprises (a) preparing a library comprising two or more types of nucleic acid nanostructure delivery compositions, wherein each nucleic acid nanostructure delivery composition is associated with a nucleic acid barcode construct comprising a different unique barcode sequence, (b) administering the library to an animal, (c) removing cells or tissues from the animal, (d) isolating the nucleic acid barcode constructs from the cells or the tissues of the animal, (e) detecting the nucleic acid barcode constructs in the cells or the tissues of the animal, and (f) identifying the desired nucleic acid nanostructure delivery composition for use as a delivery vehicle. In this embodiment, any of the nucleic acid nanostructure delivery compositions can be used and any of the nucleic acid barcode constructs described herein can be used.
In various embodiments, any suitable route for administration of the library of nucleic acid nanostructure delivery compositions associated with nucleic acid barcode constructs for the method of in vivo screening for the nucleic acid nanostructure delivery compositions associated with a nucleic acid barcode construct, or for the method of treatment described below can be used including parenteral administration. Suitable routes for such parenteral administration include intravenous, intraarterial, intraperitoneal, intrathecal, epidural, intracerebroventricular, intraurethral, intrasternal, intracranial, intratumoral, intramuscular and subcutaneous delivery. In one embodiment, means for parenteral administration include needle (including microneedle) injectors, needle-free injectors and infusion techniques. In other embodiments, oral or pulmonary routes of administration can be used.
In one aspect, libraries of nucleic acid nanostructure delivery compositions can be pooled and concentrated before administration to the animal of the nucleic acid barcode constructs associated with the nucleic acid nanostructure delivery compositions. Methods for library preparation and for sequencing are described in Green and Sambrook, “Molecular Cloning: A Laboratory Manual”, 4th Edition, Cold Spring Harbor Laboratory Press, (2012), incorporated herein by reference.
In various embodiments, cell or tissue samples may be analyzed for the presence of the nucleic acid nanostructure delivery compositions associated with the nucleic acid barcode constructs described herein. The samples can be any tissue, cell, or fluid sample from an animal, for example, selected from the group consisting of urine, nasal secretions, nasal washes, inner ear fluids, bronchial lavages, bronchial washes, alveolar lavages, spinal fluid, bone marrow aspirates, sputum, pleural fluids, synovial fluids, pericardial fluids, peritoneal fluids, saliva, tears, gastric secretions, stool, reproductive tract secretions, lymph fluid, whole blood, serum, plasma, or any tissue or cell sample from an animal. Exemplary tissue or cell samples include brain tissue or cells, muscle tissue or cells, skin tissue or cells, heart tissue or cells, kidney tissue or cells, stomach tissue or cells, liver tissue or cells, urinary tract tissue or cells, gastrointestinal tract tissue or cells, head or neck tissue or cells, lung tissue or cells, reproductive tract tissue or cells, pancreatic tissue or cells, or any other tissue or cell type from an animal.
In one illustrative aspect for removing cells or tissues from the animal and isolating the nucleic acid barcode constructs from the cells or tissues of the animal, the nucleic acid barcode constructs are removed from cells or tissues of the animal. In various embodiments, nucleic acid barcode constructs (e.g., DNA or RNA) obtained from the tissues or cells of the animal can be removed by rupturing the cells and isolating the nucleic acid barcode constructs from the lysate. Techniques for rupturing cells and for isolation of nucleic acids are well-known in the art, and removal techniques include homogenization, such as by using a bead-beating technique. In other embodiments, the nucleic acid barcode constructs may be isolated by rupturing cells using a detergent or a solvent, such as phenol-chloroform. In another aspect, the nucleic acid barcode constructs may be separated from the lysate by physical methods including, but not limited to, centrifugation, dialysis, diafiltration, filtration, size exclusion, pressure techniques, digestion of proteins with Proteinase K, or by using a substance with an affinity for nucleic acids such as, for example, beads that bind nucleic acids.
In one illustrative embodiment, the nucleic acid barcode constructs are removed from cells or tissues by treating with a mixture of an organic phase (e.g., phenol chloroform) and an aqueous phase (e.g., water). The organic phase (e.g., phenol chloroform) is isolated and the nucleic acid barcode construct can be precipitated by raising the pH, for example, to pH 7.4. The organic phase (e.g., phenol chloroform) can be evaporated and the nucleic acid barcode constructs can be suspended in water and diluted to appropriate concentrations for PCR and/or sequencing. In one embodiment, the isolated nucleic acid barcode constructs are suspended in either water or a buffer after sufficient washing.
In other embodiments, commercial kits are available for isolation of the nucleic acid barcode constructs, such as Qiagen™, Nuclisensm™, Wizard™ (Promega), QiaAmp 96 DNA Extraction Kit™ and a Qiacube HT™ instrument, and Promegam™. Methods for preparing nucleic acids for PCR and/or sequencing are also described in Green and Sambrook, “Molecular Cloning: A Laboratory Manual”, 4th Edition, Cold Spring Harbor Laboratory Press, (2012), incorporated herein by reference.
The nucleic acid barcode constructs can be detected by using, for example, the polymerase chain reaction (PCR), isothermic amplification, sequencing, and/or imaging. The polymerase chain reaction (PCR) has been developed to analyze nucleic acids in a laboratory. PCR evolved over the last decade into a new generation of devices and methods known as Next Generation Sequencing (NGS). NGS provides faster detection and amplification of nucleic acids at a cheaper price. The NGS devices and methods allow for rapid sequencing as the nucleic acids are amplified in massively parallel, high-throughput platforms.
In one illustrative aspect, the nucleic acid barcode constructs can be sequenced, to detect the polynucleotide barcodes using any suitable sequencing method including Next Generation Sequencing (e.g., using Illumina, ThermoFisher, or PacBio or Oxford Nanopore Technologies sequencing platforms), sequencing by synthesis, pyrosequencing, nanopore sequencing, or modifications or combinations thereof can be used. In one embodiment, the sequencing can be amplicon sequencing. In another embodiment, the sequencing can be whole genome sequencing. In another embodiment, the sequencing can be exome/targeted hybridization sequencing. Methods for sequencing nucleic acids are also well-known in the art and are described in Sambrook et al., “Molecular Cloning: A Laboratory Manual”, Cold Spring Harbor Laboratory Press, incorporated herein by reference.
In another embodiment, a method of treating a patient with a disease is provided. The method comprises administering to the patient the nucleic acid nanostructure delivery composition identified in the in vivo screening method described herein, or administering to the patient any of the nucleic acid nanostructure delivery compositions described herein, wherein the nucleic acid nanostructure delivery compositions comprises a payload, and treating the disease in the patient.
Illustrative payloads for the nucleic acid nanostructure delivery compositions described herein can include any one or a combination of compositions selected from the group comprising: nucleic acids (e.g., DNA or RNA), pDNA, oligodeoxyribonucleic acids (ODNs), dsDNA, ssDNA, antisense oligonucleotides, antisense RNA, siRNA, messenger RNA, guide RNA (e.g., small guide RNA), ribonucleoproteins, donor DNA strands used in the CRISPR/Cas9 system, and enzymes, such as CRISPR-associated enzymes, e.g., Cas9, enzymes used in other gene editing systems, such as ZFNs, custom designed homing endonucleases, TALENS systems, other gene editing endonucleases, and reverse transcriptase.
Other illustrative payloads include DNA constructs such as chimeric antigen receptor (CAR) constructs. CAR-T cells are T cells expressing chimeric antigen receptors (CARs). The CAR is a genetically engineered receptor that is designed to target a specific antigen, for example, a tumor antigen. This targeting can result in cytotoxicity against the tumor, for example, such that CAR-T cells expressing CARs can target and kill tumors via the specific tumor antigens. CARs can comprise a recognition region, e.g., a single chain fragment variable (scFv) region derived from an antibody for recognition and binding to the antigen expressed by the tumor, an activation signaling domain, e.g., the CD3 chain of T cells can serve as a T cell activation signal in CARs, and a co-stimulation domain (e.g., CD137, CD28 or CD134) to achieve prolonged activation of T cells in vivo. In some aspects, CARs are large DNA constructs.
In another embodiment, the payload can be a nucleic acid (e.g., DNA or RNA) with a size selected from the group consisting of 3 kB or more, 3.1 kB or more, 3.2 kB or more, 3.3 kB or more, 3.4 kB or more, 3.5 kB or more, 3.6 kB or more, 3.7 kB or more, 3.8 kB or more, 3.9 kB or more, 4 kB or more, 4.1 kB or more, 4.2 kB or more, 4.3 kB or more, 4.4 kB or more, 4.5 kB or more, 4.6 kB or more, 4.7 kB or more, 4.8 kB or more, 4.9 kB or more, 5 kB or more, 5.1 kB or more, 5.2 kB or more, 5.3 kB or more, 5.4 kB or more, 5.5 kB or more, 5.6 kB or more, 5.7 kB or more, 5.8 kB or more, 5.9 kB or more, 6 kB or more, 6.1 kB or more, 6.2 kB or more, 6.3 kB or more, 6.4 kB or more, 6.5 kB or more, 6.6 kB or more, 6.7 kB or more, 6.8 kB or more, 6.9 kB or more, 7 kB or more, 7.1 kB or more, 7.2 kB or more, 7.3 kB or more, 7.4 kB or more, 7.5 kB or more, 7.6 kB or more, 7.7 kB or more, 7.8 kB or more, 7.9 kB or more, 8 kB or more, 8.1 kB or more, 8.2 kB or more, 8.3 kB or more, 8.4 kB or more, and 8.5 kB or more.
In various embodiments, the payload can be any one or more of the components of the CRISPR RNP system including a CRISPR-associated enzyme (e.g., Cas9), a short guide RNA (sgRNA), and a donor DNA strand. In an embodiment where the payload comprises Cas9, Cas9 can be fused to a deaminase. In yet another embodiment, the payload can comprise an sgRNA used for targeting an enzyme to a specific genomic sequence. In another aspect, the targeted enzyme can be a CRISPR-associated enzyme. In another illustrative aspect, the payload can comprise one molecule each of CRISPR/Cas9, an sgRNA, and a donor DNA strand in the nucleic acid nanostructure delivery compositions described herein. In another embodiment, the payloads can be nucleic acids used for homology directed repair or as transposable elements. In yet another embodiment, the payloads can be any of the payloads described herein in the form of a plasmid construct.
In one aspect, the nucleic acid nanostructure delivery composition described herein can encapsulate a payload that is used for gene editing. In one aspect, the CRISPR/Cas9 system can be the payload and can be used for gene editing. In another embodiment, another gene editing system can be the payload, such as ZFNs, custom designed homing endonucleases, and TALENS systems. In the embodiment where the CRISPR/Cas9 system is the payload, the Cas9 endonuclease is capable of introducing a double strand break into a DNA target sequence. In this aspect, the Cas9 endonuclease is guided by the guide polynucleotide (e.g., sgRNA) to recognize and optionally introduce a double strand break at a specific target site into the genome of a cell. In this illustrative embodiment, the Cas9 endonuclease can unwind the DNA duplex in close proximity to the genomic target site and can cleave both target DNA strands upon recognition of a target sequence by a guide polynucleotide (e.g., sgRNA), but only if the correct protospacer-adjacent motif (PAM) is approximately oriented at the 3′ end of the target. In this embodiment, the donor DNA strand can then be incorporated into the genomic target site. The CRISPR/Cas9 system for gene editing is well-known in the art.
In another illustrative embodiment, the payload may include DNA segments that serve as nuclear localization signals, enhancing nuclear delivery of the nucleic acid nanostructure delivery compositions upon endosomal escape. In another aspect, the payload may include a nucleotide sequence designed to bind as an aptamer to endosomal receptors, enhancing intracellular trafficking of the nucleic acid nanostructure delivery compositions.
In one illustrative aspect, a nucleic acid nanostructure delivery composition (e.g., DNA origami) is provided to package the Cas9 protein, the sgRNA and the single stranded donor DNA strand together in one nanostructure to ensure co-delivery of all the components to a particular location at the same time. In this embodiment, the single stranded nature of the sgRNA and the donor DNA strand can be used to convert these components into constitutive parts of the nucleic acid nanostructure delivery composition (e.g., the DNA origami structure) such that they get delivered together and dissociate at the same time from the DNA nanostructure delivery composition upon reaching the target site (e.g., a target cell). In this embodiment, the DNA nanostructure delivery composition can deliver either a plasmid or the ribonucleoprotein (RNP) form of CRISPR/Cas 9.
In one embodiment, a method for gene therapy is provided. In one aspect, the method comprises administering to a patient a nucleic acid nanostructure delivery composition described herein.
In one embodiment, the nucleic acid nanostructure delivery compositions described herein may be formulated as pharmaceutical compositions for parenteral or topical administration. Such pharmaceutical compositions and processes for making the same are known in the art for both humans and non-human mammals. See, e.g., REMINGTON: THE SCIENCE AND PRACTICE OF PHARMACY, (1995) A. Gennaro, et al., eds., 19th ed., Mack Publishing Co. Additional active ingredients may be included in the compositions.
In one aspect, the nucleic acid nanostructure delivery composition may be administered, for example, directly into the blood stream of a patient, into muscle, into an internal organ, or can be administered in a topical formulation. In various embodiments, suitable routes for such parenteral administration include intravenous, intraarterial, intraperitoneal, intrathecal, epidural, intracerebroventricular, intraurethral, intrasternal, intracranial, intratumoral, intramuscular and subcutaneous delivery. In one embodiment, means for parenteral administration include needle (including microneedle) injectors, needle-free injectors and infusion techniques.
In one illustrative aspect, parenteral formulations are typically aqueous solutions which may contain carriers or excipients such as salts, carbohydrates and buffering agents (preferably at a pH of from 3 to 9), but they may be more suitably formulated as a sterile non-aqueous solution or as a dried form to be used in conjunction with a suitable vehicle such as sterile, pyrogen-free water or sterile saline. The preparation under sterile conditions, by lyophilization to produce a sterile lyophilized powder for a parenteral formulation, may readily be accomplished using standard pharmaceutical techniques well-known to those skilled in the art. In one embodiment, the solubility of the composition used in the preparation of a parenteral formulation may be increased by the use of appropriate formulation techniques, such as the incorporation of solubility-enhancing agents.
In one illustrative embodiment, pharmaceutical compositions for parenteral administration comprise: a) a pharmaceutically active amount of the nucleic acid nanostructure delivery composition; b) a pharmaceutically acceptable pH buffering agent to provide a pH in the range of about pH 4.5 to about pH 9; c) an ionic strength modifying agent in the concentration range of about 0 to about 300 millimolar; and d) water soluble viscosity modifying agent in the concentration range of about 0.25% to about 10% total formula weight or any combinations of a), b), c) and d) are provided.
In various illustrative embodiments, the pH buffering agents for use in the compositions and methods described herein are those agents known to the skilled artisan and include, for example, acetate, borate, carbonate, citrate, and phosphate buffers, as well as hydrochloric acid, sodium hydroxide, magnesium oxide, monopotassium phosphate, bicarbonate, ammonia, carbonic acid, hydrochloric acid, sodium citrate, citric acid, acetic acid, disodium hydrogen phosphate, borax, boric acid, sodium hydroxide, diethyl barbituric acid, and proteins, as well as various biological buffers, for example, TAPS, Bicine, Tris, Tricine, HEPES, TES, MOPS, PIPES, cacodylate, or MES.
In another illustrative embodiment, the ionic strength modulating agents include those agents known in the art, for example, glycerin, propylene glycol, mannitol, glucose, dextrose, sorbitol, sodium chloride, potassium chloride, and other electrolytes.
Useful viscosity modulating agents include but are not limited to, ionic and nonionic water soluble polymers; crosslinked acrylic acid polymers such as the “carbomer” family of polymers, e.g., carboxypolyalkylenes that may be obtained commercially under the Carbopol® trademark; hydrophilic polymers such as polyethylene oxides, polyoxyethylene-polyoxypropylene copolymers, and polyvinylalcohol; cellulosic polymers and cellulosic polymer derivatives such as hydroxypropyl cellulose, hydroxyethyl cellulose, hydroxypropyl methylcellulose, hydroxypropyl methylcellulose phthalate, methyl cellulose, carboxymethyl cellulose, and etherified cellulose; gums such as tragacanth and xanthan gum; sodium alginate; gelatin, hyaluronic acid and salts thereof, chitosans, gellans or any combination thereof. Typically, non-acidic viscosity enhancing agents, such as a neutral or a basic agent are employed in order to facilitate achieving the desired pH of the formulation.
In one embodiment, the solubility of the compositions described herein used in the preparation of a parenteral formulation may be increased by the use of appropriate formulation techniques, such as the incorporation of solubility-enhancing agents.
In other embodiments, the compositions described herein may be administered topically. A variety of dose forms and bases can be applied to the topical preparations, such as an ointment, cream, gel, gel ointment, plaster (e.g. cataplasm, poultice), solution, powders, and the like. These preparations may be prepared by any conventional method with conventional pharmaceutically acceptable carriers or diluents as described below.
For example, vaseline, higher alcohols, beeswax, vegetable oils, polyethylene glycol, etc. can be used. In the preparation of a cream formulation, fats and oils, waxes, higher fatty acids, higher alcohols, fatty acid esters, purified water, emulsifying agents etc. can be used. In the preparation of gel formulations, conventional gelling materials such as polyacrylates (e.g. sodium polyacrylate), hydroxypropyl cellulose, hydroxypropyl methyl cellulose, polyvinyl alcohol, polyvinylpyrrolidone, purified water, lower alcohols, polyhydric alcohols, polyethylene glycol, and the like are used. In the preparation of a gel ointment, an emulsifying agent (preferably nonionic surfactants), an oily substance (e.g. liquid paraffin, triglycerides, and the like), etc. are used in addition to the gelling materials as mentioned above. A plaster such as cataplasm or poultice can be prepared by spreading a gel preparation as mentioned above onto a support (e.g. fabrics, non-woven fabrics). In addition to the above-mentioned ingredients, paraffins, squalane, lanolin, cholesterol esters, higher fatty acid esters, and the like may optionally be used. Moreover, antioxidants such as BHA, BHT, propyl gallate, pyrogallol, tocopherol, etc. may also be incorporated. In addition to the above-mentioned preparations and components, there may optionally be used any other conventional formulations for incorporation with any other additives.
In various embodiments, the dosage of the nucleic acid nanostructure delivery composition can vary significantly depending on the patient condition, or the disease state being treated, the route of administration and tissue distribution, and the possibility of co-usage of other therapeutic treatments. The effective amount to be administered to a patient is based on body surface area, patient weight or mass, and physician assessment of patient condition. In various embodiments, the nucleic acid nanostructure delivery composition can be administered to a patient with a disease or a disorder selected from the group consisting of cancer, a muscular disorder, a pulmonary disorder, a skin disorder, a neurological disease, neurofibromatosis 1 (NF1), and a hemoglobinopathy. In one embodiment, the cancer is selected from the group consisting of lung cancer, bone cancer, pancreatic cancer, skin cancer, uterine cancer, ovarian cancer, endometrial cancer, rectal cancer, stomach cancer, colon cancer, breast cancer, cancer of the esophagus, cancer of the endocrine system, prostate cancer, leukemia, lymphoma, mesothelioma, cancer of the bladder, cancer of the kidney, neoplasms of the central nervous system, brain cancer, and adenocarcinoma. In another embodiment, the skin disorder is a Staphlococcus aureus infection. In yet another embodiment, the muscular disorder is muscular dystrophy (e.g., Duchenne Muscular Dystrophy). In still another embodiment, the nucleic acid nanostructure delivery composition are not cytotoxic to the cells of the patient. In another embodiment, the gene therapy may result in the inactivation of a pathogen (i.e., a microorganism) rather than altering the genome of the patient.
In another embodiment, a method is provided comprising synthesizing a diverse set of non-viral gene delivery compositions, wherein each non-viral gene delivery composition differs from each other non-viral gene delivery composition of the diverse set with respect to at least one of a set of composition characteristics, simultaneously testing one or more quality attributes of each of the non-viral gene delivery composition of the diverse set, and creating from results of the testing, a predictive model that correlates the composition characteristics with the quality attributes. In this embodiment, the composition characteristics can comprise one or more of molecular weight, degree of branching, number of ionizable groups, core-to-corona molecular weight ratio, hydrophilicity, hydrophobicity, propensity for aggregation, size, pKa, logP, and surface charge. In this embodiment, the quality attributes can comprise one or more of cytotoxicity, immunogenicity, transfection efficiency, zeta potential, size, pKa, logP, and loading efficiency. In this embodiment, the diverse set can comprises hundreds or thousands of non-viral gene delivery compositions. In this embodiment, each of the non-viral gene delivery compositions of the diverse set can be a nucleic acid nanostructure delivery composition according to any one of clauses described above. In one embodiment of this method, high-throughput testing, and machine learning data analysis can accelerate the design-build-test-learn (DBTL) cycle for development of CRISPR-based therapeutics.
In some embodiments, the nucleic acid nanostructure delivery composition may be labelled to enhance downstream separation. For example, this may include covalently bonding the nucleic acid nanostructure delivery composition to a magnetic nanoparticle (e.g., superparamagnetic iron oxide), to polyhistidine tags for metal ion chromatography, and/or to fluorescent labels for fluorescent assisted separation (such as with FACS). The labels may be used to track the nucleic acid delivery composition in vivo. Possible “endpoints” include, but are not limited to, quantitative presence in various physiological tissue, post administration, measured via, for example, fluorescence.
In the embodiment where labels are used, the labels allow for rapid in vivo screening of many non-viral delivery vehicle variants with parallel determination of quantitative bio-distribution, and rapid in vitro screening of many variants for stability, cytotoxicity, immunogenicity, and efficacy. This embodiment allows for the construction of a large library of non-viral delivery vehicles that can be drawn from for use as delivery vehicles for genetic medicines, including gene therapies, genetic vaccines, gene editing, gene regulators, and small molecule therapeutics.
In some illustrative embodiments, a large library of similar, but unique nucleic acid nanostructure delivery compositions may be constructed for use in a high-throughput screening process to identify targeting components that bind to specific targets. This rapid screening platform can quickly determine an effective targeting molecule that can be used for targeted delivery to a specific cell or tissue, or for use as a neutralizing molecule for a pathogen.
References in the specification to “one embodiment,” “an embodiment,” “an illustrative embodiment,” etc., indicate that the embodiment described may include a particular feature, structure, or characteristic, but every embodiment may or may not necessarily include that particular feature, structure, or characteristic. Moreover, such phrases are not necessarily referring to the same embodiment. Further, when a particular feature, structure, or characteristic is described in connection with an embodiment, it is submitted that it is within the knowledge of one skilled in the art to effect such feature, structure, or characteristic in connection with other embodiments whether or not explicitly described. Additionally, it should be appreciated that items included in a list in the form of “at least one A, B, and C” can mean (A); (B); (C); (A and B); (A and C); (B and C); or (A, B, and C). Similarly, items listed in the form of “at least one of A, B, or C” can mean (A); (B); (C); (A and B); (A and C); (B and C); or (A, B, and C).
In the drawings, some structural or method features may be shown in specific arrangements and/or orderings. However, it should be appreciated that such specific arrangements and/or orderings may not be required. Rather, in some embodiments, such features may be arranged in a different manner and/or order than shown in the illustrative figures. Additionally, the inclusion of a structural or method feature in a particular figure is not meant to imply that such feature is required in all embodiments and, in some embodiments, may not be included or may be combined with other features.
While certain illustrative embodiments have been described in detail in the drawings and the foregoing description, such an illustration and description is to be considered as exemplary and not restrictive in character, it being understood that only illustrative embodiments have been shown and described and that all changes and modifications that come within the spirit of the disclosure are desired to be protected. There exist a plurality of advantages of the present disclosure arising from the various features of the apparatus, systems, and methods described herein. It will be noted that alternative embodiments of the apparatus, systems, and methods of the present disclosure may not include all of the features described, yet still benefit from at least some of the advantages of such features. Those of ordinary skill in the art may readily devise their own implementations of the apparatus, systems, and methods that incorporate one or more of the features of the present disclosure.
While the concepts of the present disclosure are susceptible to various modifications and alternative forms, specific embodiments thereof have been shown by way of example in the appended drawings and will be described herein in detail. It should be understood, however, that there is no intent to limit the concepts of the present disclosure to the particular forms disclosed, but on the contrary, the intention is to cover all modifications, equivalents, and alternatives consistent with the present disclosure.
The materials and methods below describe an example in which a DNA origami (DNAO) nanostructure is a cuboid structure and the nucleic acid barcode constructs are attached to the DNAO via complementary base pairing of the barcodes with one of the oligonucleotide staples within the DNAO.
The barcodes used in this example comprise a unique portion comprising 8 to 10 nucleotides in the center of the polynucleotide, the unique portion further characterized by a hamming distance of at least 3 bases from any other barcodes to be pooled. Directly on the 3′ end of the barcode, 7 to 10 random bases are included for bioinformatic removal of PCR duplicates. This central sequence is flanked by universal primer annealing sites containing overhangs for the addition of index adapters during sequencing library preparation. The polynucleotide barcodes in this example were designed with a biotin functional group on the 5′ end.
The DNA origami scaffold is a single stranded DNA (ssDNA) isolated from the M13 bacteriophage. The oligonucleotide staples are short single stranded DNA with sequences described in Table 2. The barcode is a single stranded DNA segment as described under barcode design above.
A reaction mixture was prepared comprising the DNA scaffold, the oligonucleotide staples and magnesium together in TE buffer in a reaction vessel in the following amounts: 160 uL all oligonucleotide staples (described in Table 2) pooled at a total concentration of 500 nM, 80 uL scaffold (100 nM), 80 uL water, 40 uL of TE buffer (1.46 g EDTA, 3.03 g Tris Base, 1.46 g NaCl, 500 mL water), 40 uL of 200 mM MgCl2. The reaction vessel was placed in a thermocycler with thermal ramp starting at ˜65° C. and descending to 24° C. over the course of ˜67 hours. The product was purified using a precipitation with a PEG purification protocol using a PEG solution made with the following recipe: 75 g PEG8000, 50 mL of the TE buffer described above, and 62.5 mL of 4 M NaCl, brought up to 500 mL with water, yielding a DNAO nanostructure in water. The concentration was measured via nanodrop and then the barcodes were added to the product at a molar ratio of 4:1 (polynucleotide barcodes to DNAO nanostructure). This mixture was incubated at 37° C. for 2 to 3 hours. The product was purified with another PEG purification process as described above, yielding a final product of DNA barcoded DNAO in water. Transmission electron microscopy images were captured on formvar/carbon coated nickel grids with a negative stain with 1% phophotungstic acid (PTA) using an FEI Tecnai G2 Bio Twin TEM (see
Dilutions of the DNA barcoded DNAO nanostructure described above were prepared at the following concentrations: 13.5, 1.35, 0.135 and 0.0135 nM. A Master Mix was created with: Kapa HiFi 2×Master mix, Reverse barcode primer, forward barcode primer, DMSO, and nuclease free water. Master Mix (15 μL) was loaded into each well. Each of the dilutions of DNA barcoded DNAO was loaded (5 μL) into each well of a 96 well plate. Nuclease free water (5 μL) was loaded into the designated NTC wells. Positive control (5 μL) was loaded into the designated positive control wells where the positive control comprised a solution of polymer nanoparticles in phosphate buffered saline consisting of dimethylaminoethylmethacrylate, polyacylate, and butyl methacrylate, labelled with the same barcode as that used to label the DNAO, as described in US patent application 17/715784. Each well was covered, either with a strip cap or adhesive seal, and centrifuged for approx. 1 min at 1,000×g. Amplification of the barcodes was conducted by incubating in a thermocycler under typical PCR conditions.
The gel electrophoresis was done on a 4% 12-well Ethidium Bromide gel, using 15 μL of 1 kb E-gel Ladder in the first well. DNA barcoded DNAO dilutions (10 μL) from the multiwell plate above were added to each well of the 12-well gel. E-gel buffer (100 μL) was added to each well. Nuclease free water (15 μL) was added to any remaining empty wells as the no test control (NTC). The gel doe was powered on to run current through the gel for about 20 to 25 mins. or until the sample buffer line reached the end of the gel. The gel was removed from the base and analyzes in a Gel Imager (see
The materials and methods below describe an example in which a DNA origami (DNAO) nanostructure is a cuboid structure and the nucleic acid barcode constructs are attached to the DNAO via complementary base pairing of the barcodes with one of the oligonucleotide staples within the DNAO.
The barcodes used in this example comprise a unique portion comprising 8 to 10 nucleotides in the center of the polynucleotide, the unique portion further characterized by a hamming distance of at least 3 bases from any other barcodes to be pooled. Directly on the 3′ end of the barcode, 7 to 10 random bases are included for bioinformatic removal of PCR duplicates. This central sequence is flanked by universal primer annealing sites containing overhangs for the addition of index adapters during sequencing library preparation. The polynucleotide barcodes in this example were designed with a biotin functional group on the 5′ end.
The DNA origami scaffold is a single stranded DNA (ssDNA) isolated from the M13 bacteriophage. The oligonucleotide staples are short single stranded DNA with sequences described in Table 2. The barcode is a single stranded DNA segment as described under barcode design above.
A reaction mixture was prepared comprising the DNA scaffold, the oligonucleotide staples and magnesium together in TE buffer in a reaction vessel in the following amounts: 160 uL all oligonucleotide staples (described in Table 2) pooled at a total concentration of 500 nM, 80 uL scaffold (100 nM), 80 uL water, 40 uL of TE buffer (1.46 g EDTA, 3.03 g Tris Base, 1.46 g NaCl, 500 mL water), 40 uL of 200 mM MgCl2. The reaction vessel was placed in a thermocycler with thermal ramp starting at ˜65∇C and descending to 24∇C over the course of ˜67 hours. The product was purified using a precipitation with a PEG purification protocol using a PEG solution made with the following recipe: 75 g PEG8000, 50 mL of the TE buffer described above, and 62.5 mL of 4 M NaCl, brought up to 500 mL with water, yielding a DNAO nanostructure in water. The concentration was measured via nanodrop and then the barcodes were added to the product at a molar ratio of 4:1 (polynucleotide barcodes to DNAO nanostructure). This mixture was incubated at 37∇C for 2 to 3 hours. The product was purified with another PEG purification process as described above, yielding a final product of DNA barcoded DNAO in water. Transmission electron microscopy images were captured on formvar/carbon coated nickel grids with a negative stain with 1% phophotungstic acid (PTA) using an FEI Tecnai G2 Bio Twin TEM (see
HEK 293 cells were plated in a 48 well plate at 75,000 cells/well with 200 uL of complete growth media 24 hours prior to transfection. Complete growth media consisted of DMEM supplemented with 10% FBS and 1% Pen-Strep. Cells were dosed with DNAO at a final concentration of 10 nM, 5 nM and 2.5 nM DNAO with and without barcode in triplicate for a total of 16 wells. Three (3) wells were used for controls. After 16 hours the cells were trypsinized and replicate wells pooled together. DNA from the cells was extracted using a Qiagen DNA Extraction Kit. These cell extracts were used for PCR amplification.
A Master Mix was created with: Kapa HiFi 2×Master mix, Reverse barcode primer, forward barcode primer, DMSO, and nuclease free water. Master Mix (15 μL) was loaded into each well. Each of the cell extracts was loaded (5 μL) in duplicate into each well of a 96 well plate. Nuclease free water (5 μL) was loaded into the designated NTC wells. Positive control (5 μL) was loaded into the designated positive control wells. The positive control comprised a solution of polymer nanoparticles in phosphate buffered saline consisting of dimethylaminoethylmethacrylate, polyacylate, and butyl methacrylate, chemically conjugated with the same barcode as that used to label the DNAO, as described here before. Each well was covered, either with a strip cap or adhesive seal, and centrifuged for approx. 1 min at 1,000×g. Amplification of the barcodes was conducted by incubating in a thermocycler under typical PCR conditions.
The gel electrophoresis was done on a 4% 48-well Ethidium Bromide gel, using 15 μL of 1 kb E-gel Ladder in the first well. DNAO and DNA barcoded. DNAO cell extracts and controls (10 μL) were added to each well of the gel. E-gel buffer (5 μL) was added to each well. Negative controls from cells were extracts without any barcoded DNAO that underwent amplification. Negative controls in the last 2 wells were water. Nuclease free water (15 μL) was added to any remaining empty wells. The gel doe was powered on to run current through the gel for about 20 to 25 mins, or until the sample buffer line reached the end of the gel. The gel was removed from the base and analyzed in a Gel Imager (see
This non-provisional application claims the benefit and priority, under 35 U.S.C. § 119(e) and any other applicable laws and statutes, to U.S. Provisional Application Ser. No. 63/350,688 filed on Jun. 9, 2022, the entire disclosure of which is incorporated herein by reference.
| Number | Date | Country | |
|---|---|---|---|
| 63350688 | Jun 2022 | US |
