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DNA editing using relatively long single-stranded DNA and CRISPR/Cas9 to … — Board Of Regents Of The University Of Nebraska (US11555208B2)

Board Of Regents Of The University Of Nebraska · Google Patents

Google Patents · Patents · License: Open Access

patent, google patents, intellectual property, US11555208B2, Board Of Regents Of The University Of Nebraska, Channabasavaiah B. Gurumurthy, en, 2023

ABSTRACT

Abstract

Disclosed are compositions, methods, and kits for modifying DNA within cells as well as compositions and methods for modifying gene expression in a cell. In particular, the invention generally relates to compositions, methods, and kits for DNA editing using single-stranded DNA. Compositions and methods for modifying gene expression using artificial microRNAs (amiRNA) are also contemplated.

Description

CROSS-REFERENCE TO RELATED PATENT APPLICATIONS

The present application is a continuation application under 35 U.S.C.Â§ 111(a), of U.S. patent application Ser. No. 15/828,979, filed on Dec. 1, 2017, which is a continuation-in-part application under 35 U.S.C. Â§ 365(c), of International Application No. PCT/US2016/035660, filed on Jun. 3, 2016, which claims the benefit of priority to U.S. Provisional Patent Application No. 62/170,306, filed on Jun. 3, 2015, the contents of which are incorporated herein by reference in their entireties.

SEQUENCE LISTING

This application includes an electronically submitted sequence listing in .txt format. The .txt file contains a sequence listing entitled â2018-02-07_6278-00006_Sequence_Listing_ST25.txtâ created on Jan. 17, 2018 and is 1,460 bytes in size. The Sequence Listing contained in this .txt file is part of the specification and is hereby incorporated by reference herein in its entirety. The Substitute Sequence Listing does not introduce new matter and otherwise is proper.

BACKGROUND

The field of the invention relates to compositions, methods, and kits for modifying DNA within cells as well as compositions and methods for modifying gene expression in a cell. In particular, the field of the invention relates to compositions, methods, and kits for DNA editing using single-stranded DNA (ssDNA). Compositions and methods for modifying gene expression using artificial microRNAs (amiRNA) are also contemplated.

To ensure overall genome stability and viability, cells have evolved complex mechanisms for the accurate and efficient repair of DNA damage. In eukaryotic cells, the repair of double-strand breaks (DSBs) occurs primarily by two pathways: Non-Homologous End-Joining (NHEJ) and Homology Directed Repair (HDR). In the NHEJ pathway, several factors act to re-ligate the two DNA ends created by the DSB. In the HDR pathway, a homologous DNA template is used to repair the DSB.

Exploiting the HDR pathway has become a powerful means of DNA editing, including the editing of genomes. Currently, there are several widely used systems to introduce targeted cuts such as DSBs into the genomes of cells including Zinc Finger Nucleases (ZFNs), Transcription activator-like effector nucleases (TALENs), CRISPR-Cas systems (Clustered, regularly interspaced short palindromic repeat (CRISPR)-CRISPR-associated proteins (Cas)), and Argonaute nuclease systems. See, e.g., Gaj et al., Trends in Biotechnology 31(7): 397-405 (2013); Gao et al., Nature Biotechnology , published online May 2, 2016. ZFNs and TALENs are generally chimeric nucleases composed of programmable sequence-specific DNA-binding sequences linked to nonspecific DNA cleavage domains. The sequence specificity of CRISPR-Cas and Argonaute nuclease systems, on the other hand, derive from guide polynucleotides (e.g., RNA or DNA) that direct the nuclease activity of Cas or Argonaute proteins to particular sequences. By introducing one of these targeted nuclease systems into a cell along with a repair template DNA encoding sequences or âarmsâ homologous to the upstream and downstream sequences near the nuclease cut site, the HDR pathway can be used to insert a DNA of interest (DOI) at nearly any location in the genome.

The repair-template DNA may be single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA). Single-stranded DNA repair templates have been typically about 100-200 bases long, consisting of a few bases of altered sequence (e.g., point mutations, recombinase recognition sequences, short deletions or insertions of a few bases) flanked by homology arms of about 40-80 bases. Double-stranded DNA repair-templates generally require long homology arms and typically are inserted with much lower efficiency than ssDNA repair templates. See Singh et al., Genetics 199:1-15 (2015); Yang et al., Nat Protoc 9:1956-1968 (2014); and Ran et al., Nat Protoc 8:2281-2308 (2013). Currently, ssDNA repair templates have not been used to insert long DOIs due to limitations in the overall length of ssDNA that can be synthesized and uncertainties of whether ssDNA repair templates harboring long DOIs would be properly incorporated into a target sequence using a cell's endogenous HDR machinery. Insertion of large DOIs (>100 bases) generally relies on the use of dsDNA with long homology arms, which are laborious to create and have poor insertion efficiencies. Thus, there is a need in the art for simpler, more efficient methods of inserting large DOIs (>100 bases) into target DNA sequences within a cell.

SUMMARY

Disclosed are compositions, methods, and kits for DNA editing using single-stranded DNA (ssDNA) as well as compositions and methods for modifying gene expression. The disclosed composition, methods, and kits may be used for modifying genomic DNA.

In one aspect, compositions for modifying a target DNA sequence in a cell are provided. The compositions may include single-stranded DNA (ssDNA). The compositions may also include (a) single-stranded DNA (ssDNA) and (b) a nuclease system capable of cutting the target DNA sequence. The ssDNA may include a 5â² homology arm having substantial sequence identity to the target DNA sequence, an exogenous sequence, and a 3â² homology arm having substantial sequence identity to the target DNA sequence. Also contemplated are delivery particles including such compositions for use in pharmaceutical compositions. Such delivery particles may include polymeric nanoparticles, liposomal nanoparticles, or nanoparticles including lipids and at least one type of polymer.

In a further aspect, methods for modifying a target DNA sequence in a cell are provided. The methods may include: (a) introducing a single-stranded DNA (ssDNA) in the cell and (b) introducing or expressing a nuclease system in the cell, wherein the nuclease system cuts the target DNA sequence.

In a still further aspect, the methods of the present invention may be performed to modify a target DNA sequence in a cell and may include contacting the cell with any one of the delivery particles described herein in an amount effective to allow delivery of the composition into the cell and modification of the target DNA sequence. The contacting may occur in vitro, in vivo, in situ, or ex vivo.

In another aspect, kits or systems for modifying a target DNA sequence in a cell also are contemplated. The kits or systems include components which may include one or more of an RNA polymerase, a reverse transcriptase, an RNA-degrading enzyme, and a nuclease system. Optionally, the kits or systems may include a DNA vector comprising from 5â² to 3â² a promoter, a cloning site, and a restriction enzyme site.

In still another aspect, the kits or systems of the present invention may include (a) single-stranded DNA (ssDNA) and (b) a nuclease system capable of cutting a target DNA sequence. The ssDNA of the kits may be relatively long (e.g., >100 bases).

In a further aspect, engineered eukaryotic cells including amiRNAs are also provided. The engineered eukaryotic cells may include an exogenous DNA construct encoding an amiRNA. The DNA construct may be inserted into an intron of a gene. In some embodiments, the DNA construct lacks a promoter, reporter sequence, and/or a polyA tail.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows ssDNA synthesis by the ivTRT (âin vitro Transcription and Reverse Transcriptionâ) strategy. Schematic of plasmid or PCR product templates showing elements such as T7 promoter (purple) and amiRNA fragment flanked by 3â² and 5â² homologous sequences to the target (55-bp each, green), used for in vitro transcription of RNA. Plasmid templates are linearized by digesting with a suitable restriction enzyme. In vitro transcription is performed using T7 promoter and T7 RNA polymerase. cDNA (ssDNA) is synthesized by reverse transcription and the RNA template is degraded by RNaseH.

FIG. 2 shows targeted insertion of ssDNA encoding anti-eGFP amiRNA by CRISPR/Cas9 system (Exp. 2). FIG. 2 ( a ) shows schematics of targeted integration of amiR-eGFP123/419 sequences into the intron 6 of eEF-2 gene (upper panel) and location of amiR-eGFP123 and -eGFP419 target sites on eGFP cDNA (lower panel). From the correctly targeted eEF-2 locus, amiRNAs get transcribed and subsequently bind to the target sites (amiR-eGFP123=pink line and amiR-eGFP419=purple line) on eGFP mRNA, leading to eGFP knockdown. Red arrows indicate the location of primer set (PP119/PP120) used for detection of fetuses with targeted insertion. FIG. 2 ( b ) shows eGFP fluorescence among E13.5 day fetuses observed under a fluorescent stereomicroscope showing successful knockdown in some fetuses. FIG. 2 ( c ) shows genotyping of fetuses by PCR using primer set shown in FIG. 2 ( a ) . The embryo numbers in FIG. 2 ( b ) and FIG. 2 ( c ) correspond with each other. Expected fragment sizes: wild-type=301-bp (black lower arrow), targeted insertion=625-bp (blue upper arrow). FIG. 2 ( d ) shows targeted insertion efficiency. Fetuses containing functional amiRNA sequence were considered as âembryos with targeted insertionsâ even though insertions were not fully accurate.

FIG. 3 shows targeted insertion of ssDNA encoding anti-Otx2 amiRNA by CRISPR/Cas9 system (Exp. 4). FIG. 3 ( a ) shows schematics of targeted integration of amiR-Otx2_546 into intron 6 of eEF-2 gene (upper panel) and Otx2 genomic region showing amiR-Otx2_546 binding site (lower panel). The exons of Otx2 are shown as boxes and the boxes with homeodomain region are shaded black. Red arrows indicate the location of primer set (PP119/PP120) used for detection of fetuses with targeted insertion. FIG. 3 ( b ) shows the resultant fetuses photographed at E14.5. FIG. 3 ( c ) shows genotyping of fetuses by PCR using primer set shown in FIG. 3 ( a ) . The embryo numbers in FIG. 3 ( b ) and FIG. 3 ( c ) correspond with each other. Expected fragment sizes: wild-type=301-bp (black upper arrow), targeted insertion=487-bp (blue lower arrow). FIG. 3 ( d ) shows targeted insertion efficiency. Fetuses containing functional amiRNA sequence were considered as âembryos with targeted insertionsâ even though insertions were not fully accurate.

FIG. 4 shows targeted insertion of ssDNA encoding Cre-activatable anti-eGFP amiRNA by CRISPR/Cas9 system (Exp. 5). FIG. 4 ( a ) shows schematics of targeted integration of reverse orientated âamiR-eGFP123/419â and mutant loxP sites (JT15 and JTZ17) into the intron 6 of eEF-2 gene and subsequent Cre-loxP recombination to switch the amiRNA cassette to the right orientation. Functional amiRNAs do not get produced from the targeted âamiRNA-offâ allele because of the opposite orientation of amiRNA with respect to the eEF-2 gene. After Cre recombination, the allele gets converted to âamiRNA-onâ that produces functional amiRNA. Red arrows indicate the primers (PP119, PP120 and M412) used for genotyping. FIG. 4 ( b ) shows genotyping of fetuses by PCR using primer set (PP119/PP120). Expected fragment sizes: wild-type=301-bp (black arrow), targeted insertion=705-bp (blue arrow). FIG. 4 ( c ) shows targeted insertion efficiency. FIG. 4 ( d ) shows dotplot of embryonic feeder cells, derived from Exp. 5 samples #4 (upper) and #6 (lower), nine days after transfection with (left) or without (right) the iCre plasmid. The cells showing weak eGFP fluorescence are partitioned within the box in each plot. FIG. 4 ( e ) shows genotyping of embryonic feeder cells used in the experiment FIG. 4 ( d ) by PCR with primer sets shown in FIG. 4 ( a ) .

FIG. 5 shows targeted insertion of ssDNA encoding anti-eGFP amiRNA by CRISPR/Cas9 system (Exp. 1). FIG. 5 ( a ) shows schematics of targeted integration of amiRNA-eGFP123/419 into the intron 1 of eEF-2 gene (upper panel) and location of amiRNA-eGFP123 and -eGFP419 target sites on eGFP cDNA (lower panel). From the correctly targeted eEF-2 locus, amiRNAs get transcribed and subsequently bind to the target sites (amiR-eGFP123=pink line and amiR-eGFP419=purple line) on eGFP mRNA, leading to eGFP knockdown. Red arrows indicate the location of primer set (PP113/M412) used for detection of fetuses with targeted insertion. FIG. 5 ( b ) shows eGFP fluorescence among E13.5 fetuses observed under a fluorescent stereomicroscope showing successful knockdown in some fetuses. FIG. 5 ( c ) shows genotyping of fetuses by PCR using primer set shown in FIG. 5 ( a ) . The embryo numbers in FIG. 5 ( b ) and FIG. 5 ( c ) correspond with each other. Expected fragment sizes: targeted insertion=562-bp (blue arrow). FIG. 5 ( d ) shows targeted insertion efficiency. Fetuses containing functional amiRNA sequence were considered as âembryos with targeted insertionsâ even though insertions were not fully accurate.

FIG. 6 shows targeted insertion of ssDNA encoding anti-Otx2 amiRNA by CRISPR/Cas9 system (Exp. 3). FIG. 6 ( a ) shows schematics of targeted integration of amiR-Otx2_518 into the intron 6 of eEF-2 gene (upper) and Otx2 genomic region showing amiRNA-Otx2_518 binding site (lower panel). The exons of Otx2 are shown as boxes and the boxes with homeodomain region are shaded black. Red arrows indicate the location of primer set (PP119/PP120) used for detection of fetuses with targeted insertion. FIG. 6 ( b ) shows the resultant fetuses photographed at E14.5. FIG. 6 ( c ) shows genotyping of fetuses by PCR using primer set shown in FIG. 6 ( a ) . The embryo numbers in FIG. 6 ( b ) and FIG. 6 ( c ) correspond with each other. Expected fragment sizes: wild-type=301-bp (black lower arrow), targeted insertion=487-bp (blue upper arrow). FIG. 6 ( d ) shows targeted insertion efficiency.

FIG. 7 shows comparison of insertion efficiencies of ssDNA or dsDNA repair templates (encoding anti-eGFP amiRNA) by the CRISPR/Cas9 system (Exp. 6 and 7). FIG. 7 ( a ) shows the genomic structure of eEF-2 locus with targeted integration of amiRNA-eGFP123/419. Red arrows indicate the location of primer sets (PP117/PP118 and PP119/M412) used for detection of blastocysts with targeted insertion by nested PCR. ssDNA (in Exp. 6) or dsDNA (in Exp. 7) containing amiR-eGFP123/419 and homology arms with 55-bases long on each side were prepared and used as repair DNAs. Each of the repair DNA (20 ng/Î¼l) was subjected to micro-injections together with Cas9 mRNA (10 ng/Î¼l) and sgRNAs for TS2 (10 ng/Î¼l). FIG. 7 ( b ) shows the genotyping of blastocysts by nested PCR using primer set shown in FIG. 7 ( a ) . Expected fragment size: 459-bp. FIG. 7 ( c ) shows targeted insertion efficiency.

FIG. 8 shows insertion of sequences in the

CROSS-REFERENCE TO RELATED PATENT APPLICATIONS

SEQUENCE LISTING

BACKGROUND

SUMMARY

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 8 shows insertion of sequences in the eEF-2 intron 6 does not affect its mRNA splicing. FIG. 8 ( a ) shows the genomic structure and expected splicing pattern of wild-type and âamiRNA-offâ alleles (containing reverse orientated âamiRNA-eGFP123/419â and mutant loxP sites) of eEF-2 gene. Red arrows indicate the location of primer set (PP164/PP118) used for reverse transcription PCR (RT-PCR). FIG. 8 ( b ) shows RT-PCR results using cDNAs prepared from embryonic feeder cells derived from the fetuses in Exp. 5 (see FIG. 4 ). The sample numbers in FIG. 8 ( b ) correspond with those in FIG. 4 ( b ) . Sample No. 6; wild-type allele, No. 4 and 9; heterozygotes for âamiRNA-offâ allele, No. 8; homozygote for âamiRNA-offâ allele. Expected fragment size: 500-bp (from cDNA). FIG. 8 ( c ) shows junctional regions between exon 6 and 7 (SEQ ID NO: 1).

FIG. 9 shows ssDNA synthesis by ivTRT strategy. Schematic of plasmid or PCR product templates showing elements such as rtTA/Cre/Egfp inserts (green) flanked by 3â and 5â² homologous sequences to the target (Ë60 bp each), used for in vitro transcription of RNA.

FIG. 10 shows a schematic illustrating that the ssDNA repair templates disclosed herein include significantly greater ratios between the length of the exogenous or insert sequence (Insert) and the sum of the length of the 5â² homology arm and the 3â² homology arm (Arms (total)) as compared to ssDNA repair templates previously used.

FIG. 11 shows insertion of over 1 kb ssDNA at Otoancorin and Fgf8 loci. FIG. 11 ( a, b ) Schematic showing Otoancorin FIG. 11 ( a ) and Fgf8 FIG. 11 ( b ) loci, ssDNA donor templates and targeted Knock-in alleles. The lengths of ssDNA, homology arms and the rtTA-polyA FIG. 11 ( a ) or P2A-FlpO FIG. 11 ( b ) cassettes are indicated. FIG. 11 ( c, d ) Genotyping G0 animals for detection of cassette insertion. Schematic of primer locations for 5â² and 3â² junction PCRs is shown along with the expected amplicon sizes. FIG. 11 ( c ) Samples

Otoa G0 pups

3, 7 and 8 are positive for the rtTA cassette insertion as seen by both the 5â² and 3â² junction PCRs. Note that the amplicons for the 3â² PCR are weak and are indicated by asterisks. FIG. 11 ( d ) Founder 4 is positive for the FlpO cassette insertion by both 5â² and 3â² PCRs. The gel on the right shows that this founder has a bi-allelic insertion of the cassette. Wt: wild type, M; 100 bp marker, kb: 1 kb Marker. FIG. 11 ( e, f ) Sequencing of Otoancorin founder 3 (SEQ ID NO: 2) and Fgf8 founder 4 (SEQ ID NO: 3). The guide RNA sequences (italics), along with the cut sites, PAM sequences (in red) and a few bases of flanking sequences are shown above. Sequence chromatograms showing correct insertion of cassette junctions.

FIG. 12 shows insertion of over 1 kb ssDNA into Slc26a5 and MafB. FIG. 12 ( a, b ) Schematic showing Slc26a5 FIG. 12 ( a ) and MafB FIG. 12 ( b ) , ssDNA donor templates and targeted knock-in alleles. The lengths of ssDNA, homology arms and the P2A-FlpO cassettes are indicated. FIGS. 12 ( b, d ) Genotyping G0 animals for detection of cassette insertion. Schematic of primer locations for 5â² and 3â² junction PCRs is shown along with the expected amplicon sizes. FIG. 12 ( c )

Founders 1 and 3 are positive for the P2A-FlpO cassette insertion using both 5â² and 3â² PCRs. Note that the 3â² junction PCR for founder # 1 is bigger than the expected size and it contains genomic DNA duplications (data not shown) FIG. 12 ( d ) Founder 4 is positive for the FlpO cassette insertion by both 5â² and 3â² PCRs. Wt: wild type, M; 100 bp marker. FIGS. 12 ( e, f ) Sequencing of Slc26a5 founder #1 (SEQ ID NO: 4) and Mafb founder #7 (SEQ ID NO: 5). The guide RNA sequences (italics), along with the cut sites, PAM sequences (in red) and a few bases of flanking sequences are shown above. Sequence chromatograms showing cassettes insertions junctions.

FIG. 13 shows a schematic of the Otoa-rtTA ssDNA. Various sequence elements are color coded. The primers used for 5â² and 3â² junction PCR and the amplicon sizes are shown above the schematic.

FIG. 14 shows a schematic of the Fgf8-P2A-Flpo-ssDNA. Various sequence elements are color coded. The primers used for 5â² and 3â² junction PCR and the amplicon sizes are shown above the schematic.

FIG. 15 shows a schematic of the slc26a5-Flpo-ssDNA. Various sequence elements are color coded. The primers used for 5â² and 3â² junction PCR and the amplicon sizes are shown above the schematic.

FIG. 16 shows a schematic and the sequence of the Mafb-Flpo-ssDNA. Various sequence elements are color coded. The primers used for 5â² and 3â² junction PCR and the amplicon sizes are shown above the schematic.

FIG. 17 shows germ line transmission of Easi-CRISPR knock-in mouse models. FIG. 17 ( a ) Genotyping of F1 pups derived from mating of the Fgf8-P2A- FlpO founder 4. Note that this founder is a homozygote and mating to a wild type mouse resulted in all pups heterozygous for the FlpO insertion. FIG. 17 ( b ) Genotyping of F1 pups from Slc25a5-P2A- FlpO founder # 3 showing that

F1 pups

2, 3 and 4 contain the knock-in cassette.

FIG. 18 shows endogenous gene tagging with ssDNA donors. FIG. 18 (A) Functional tagging at endogenous genomic loci. Tag (e.g. GFP) is introduced in an endogenous open-reading-frame (ORF) and the resulting fusion protein expressed from the endogenous ORF promoter. FIG. 18 (B) Endogenous GFP tagging of RAB11A (endosomal Rab protein), CLTA (clathrin light chain) and HISTH2BE (histone) in HEK293T using long ssDNA donors. Knock-in efficiency was measured by flow cytometry analysis Ë7 days after Cas9/sgRNA and donor electroporation. Confocal microscopy of GFP-sorted cells is shown (scale bars: 10 Î¼m). FIG. 18 (C) STORM super-resolution imaging of mEos3.2-CLTA in HEK293T cells. Scale bar: 1 Î¼m; grid size in insert: 100 nm.

FIG. 19 shows multiple methods to produce long ssDNA HDR templates. FIG. 19 (A) If a large enough amount of long single stranded DNA sequence could be produced for electroporation, off-target integrations could be reduced without overly compromising on-target efficiency. One method we developed involves a two step selective exonuclease digestion that specifically degrades one strand of a PCR product that has been labeled by 5â² phosphorylation, easily added onto a PCR primer prior to amplification. FIG. 19 (B) We also applied a second ssDNA production method based on sequential in-vitro transcription (IVT) and reverse transcription (RT) reaction. A PCR product with a short T7 promoter appended serves as an IVT template to produce a ssRNA product. Following annealing of an RT primer and reverse transcription, an RNA/DNA hybrid is formed which can be easily transformed into a long ssDNA template by incubation in sodium hydroxide (selectively degrades RNA strand). FIG. 19 (C) At 2 days post-electroporation, viability in CD3+ T cells electroporated with only a ssDNA template was higher than those electroporated with only a dsDNA template. FIG. 19 (D) A ssDNA RAB11A-GFP HDR template showed high efficiency GFP integration similar to dsDNA templates, and maintained high efficiency integrations at higher molar amounts of template, potentially due to increased viability as well as less mass per mole of DNA template. Individual points represent at least two healthy donors.

DESCRIPTION

Disclosed are compositions, methods, and kits for editing DNA, such as genomic DNA, using single-stranded DNA (ssDNA) as well as compositions and methods for modifying gene expression. The disclosed composition, methods, and kits may be further described as follows.

Unless otherwise specified or indicated by context, the terms âaâ, âanâ, and âtheâ mean âone or more.â In addition, singular nouns such as âssDNAâ and âamiRNA,â should be interpreted to mean âone or more ssDNAsâ and âone or more amiRNAs,â respectively, unless otherwise specified or indicated by context.

As used herein, âaboutâ and âapproximatelyâ will be understood by persons of ordinary skill in the art and will vary to some extent on the context in which they are used. If there are uses of the term which are not clear to persons of ordinary skill in the art given the context in which it is used, âaboutâ and âapproximatelyâ will mean plus or minus â¤10% of the particular term.

As used herein, the terms âincludeâ and âincludingâ have the same meaning as the terms âcompriseâ and âcomprising.â The terms âcompriseâ and âcomprisingâ should be interpreted as being âopenâ transitional terms that permit the inclusion of additional components further to those components recited in the claims. The terms âconsistâ and âconsisting ofâ should be interpreted as being âclosedâ transitional terms that do not permit the inclusion of additional components other than the components recited in the claims. The term âconsisting essentially ofâ should be interpreted to be partially closed and allowing the inclusion only of additional components that do not fundamentally alter the nature of the claimed subject matter.

Recitation of ranges of values herein are merely intended to serve as a shorthand method of referring individually to each separate value falling within the range, unless otherwise indicated herein, and each separate value is incorporated into the specification as if it were individually recited herein. For example, if a concentration range is stated as 1% to 50%, it is intended that values such as 2% to 40%, 10% to 30%, or 1% to 3%, etc., are expressly enumerated in this specification. These are only examples of what is specifically intended, and all possible combinations of numerical values between and including the lowest value and the highest value enumerated are to be considered to be expressly stated in this disclosure. Use of the word âaboutâ to describe a particular recited amount or range of amounts is meant to indicate that values very near to the recited amount are included in that amount, such as values that could or naturally would be accounted for due to manufacturing tolerances, instrument and human error in forming measurements, and the like. All percentages referring to amounts are by weight unless indicated otherwise.

Nuclease Editing Systems for DNA

Several nuclease systems, including the CRISPR/Cas system, have emerged as popular DNA and genome editing methods. These methods can be used not only for gene disruption, but also for targeted modification using a DNA repair template. Single-stranded DNA (ssDNA) repair templates, up to 200-bases long, are used as donors for insertion of short stretches. See, e.g., Harms et al., Curr Protoc Hum Genet 83:15(17) 11-15 (2014). However, because longer ssDNAs (>200-bases long) are not generally commercially available, longer insertions require the use of inefficient dsDNAs (plasmid-based constructs), which can be more laborious to create and generally have poor insertion efficiencies.

To overcome these limitations, the present inventors have, in part, developed a technique that can be used to synthesize ssDNA donors having more than 200 nucleotides. In one aspect, the present invention generally relates to the inventors' discovery that ssDNA having lengths above 200 nucleotides can serve as efficient donors for targeted modification in cells. Furthermore, the inventors discovered that relatively short homology arms are needed to insert longer DNA sequences of interest when ssDNAs having lengths over 200 nucleotides are used as repair templates. In another aspect, the present invention generally relates to the inventors' demonstration that amiRNAs targeted to introns can efficiently modify gene expression.

In the Examples, the inventors synthesized ssDNA donors greater than 200 nucleotides in length and then used them in CRISPR/Cas9-mediated targeted insertion experiments. The inventors observed up to 100% overall insertion efficiency, and up to 50% insertion efficiency in both alleles. Notably, the homology arm lengths in these samples ranged from approximately 55 bases-112 bases on each side demonstrating that ssDNA-based insertion is efficient even though the length of donors was greater than 200 nucleotides in length and that the DNA sequence of interest was significantly longer than the length of the homology arms.

In one aspect, the present invention comprises compositions, methods, and kits for DNA editing using single-stranded DNA (ssDNA). The disclosed compositions, methods, and kits may be utilized for DNA editing in vitro, in vivo, or ex vivo and may be used to insert DNA sequences of interest such as large expression cassettes and transgenes encoding, without limitation, artificial microRNA (amiRNA) constructs, reporters (e.g., EGFP/LacZ etc.), sequence tags (e.g., immune-affinity tags), and genes such as rtTA/tTA, Cre, Flpo and the like. The compositions, methods, and kits may also be used, for example, to introduce multiple point mutations into a genomic sequence, to generate conditional and nonconditional knock-in and knock-out constructs, to alter the expression of targeted genes, to generate transgenic animals and plants, and to develop human therapeutics.

Methods for Modifying a Target DNA Sequence

Methods for modifying a target DNA sequence in a cell are provided. The methods may include: (a) introducing a single-stranded DNA (ssDNA) in the cell and (b) introducing or expressing a nuclease system in the cell, wherein the nuclease system cuts the target DNA sequence. The ssDNA may include a 5â² homology arm having substantial sequence identity to the target DNA sequence, an exogenous sequence, and a 3â² homology arm having substantial sequence identity to the target DNA sequence.

The term âtarget DNA sequenceâ as used herein refers to any DNA nucleic acid residing in a cell. The target DNA sequence may be endogenous to the cell (e.g., genome or other self-replicating form of DNA such as a plasmid endogenously found in the cell) or exogenous to the cell (e.g., transgenes or plasmids introduced in the cell). The target DNA sequence may be within or around a gene.

In some embodiments, the target DNA sequence is in an intron of a gene. The gene may be constitutively expressed or may be expressed in a tissue-specific manner. As used herein, âconstitutively expressedâ refers to genes that are expressed in all cells of an organism. Common constitutively expressed genes include housekeeping genes that are required for the maintenance of basic cellular function. In the non-limiting Examples, the inventors target introns within the eEF2 housekeeping gene but other housekeeping genes may be used in accordance with the present invention.

As used herein, âintroducingâ describes a process by which exogenous polynucleotides (e.g., DNA or RNA) or protein is introduced into a recipient cell. Methods of introducing nucleic acids and proteins into a cell are known in the art and may include, without limitation, microinjection, transformation, and transfection methods. Transformation or transfection may occur under natural or artificial conditions according to various methods well known in the art, and may rely on any known method for the insertion of foreign nucleic acid sequences into a prokaryotic or eukaryotic host cell. The method for transformation or transfection is selected based on the type of host cell being transformed and may include, but is not limited to, bacteriophage or viral infection, electroporation, heat shock, lipofection, and particle bombardment. Microinjection of nucleic acids and/or proteins may also be used to introduce nucleic acids and/or proteins into cells as used, for example, with embryos when making transgenic animals.

Conventional viral and non-viral based gene transfer methods can be used to introduce nucleic acids into cells or target tissues. Non-viral vector delivery systems may include DNA plasmids or nucleic acid complexed with a delivery vehicle, such as a liposome. Delivery can be to cells (e.g. in vitro or ex vivo administration) or target tissues (e.g. in vivo administration).

Single-stranded DNA (ssDNA) of the present invention may be a single-stranded DNA polynucleotide. The terms âpolynucleotide,â âpolynucleotide sequence,â ânucleic acidâ and ânucleic acid sequenceâ refer to a nucleotide, oligonucleotide, polynucleotide (which terms may be used interchangeably), or any fragment thereof. These phrases also refer to DNA or RNA of genomic, natural, or synthetic origin (which may be single-stranded or double-stranded and may represent the sense or the antisense strand).

Regarding polynucleotide sequences, the terms âpercent identityâ and â% identityâ and âsequence identityâ refer to the percentage of residue matches between at least two polynucleotide sequences aligned using a standardized algorithm. Such an algorithm may insert, in a standardized and reproducible way, gaps in the sequences being compared in order to optimize alignment between two sequences, and therefore achieve a more meaningful comparison of the two sequences. Percent identity for a nucleic acid sequence may be determined as understood in the art. (See, e.g., U.S. Pat. No. 7,396,664). A suite of commonly used and freely available sequence comparison algorithms is provided by the National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST), which is available from several sources, including the NCBI, Bethesda, Md., at its website. The BLAST software suite includes various sequence analysis programs including âblastn,â that is used to align a known polynucleotide sequence with other polynucleotide sequences from a variety of databases. Also available is a tool called â BLAST 2 Sequencesâ that is used for direct pairwise comparison of two nucleotide sequences. â BLAST 2 Sequencesâ can be accessed and used interactively at the NCBI website. The â BLAST 2 Sequencesâ tool can be used for both blastn and blastp (discussed above).

Regarding polynucleotide sequences, percent identity may be measured over the length of an entire defined polynucleotide sequence, for example, as defined by a particular SEQ ID number, or may be measured over a shorter length, for example, over the length of a fragment taken from a larger, defined sequence, for instance, a fragment of at least 20, at least 30, at least 40, at least 50, at least 70, at least 100, or at least 200 contiguous nucleotides. Such lengths are exemplary only, and it is understood that any fragment length supported by the sequences shown herein, in the tables, figures, or Sequence Listing, may be used to describe a length over which percentage identity may be measured.

Regarding polynucleotide sequences, âvariant,â âmutant,â or âderivativeâ may be defined as a nucleic acid sequence having at least 50% sequence identity to the particular nucleic acid sequence over a certain length of one of the nucleic acid sequences using blastn with the â BLAST 2 Sequencesâ tool available at the National Center for Biotechnology Information's website. (See Tatiana A. Tatusova, Thomas L. Madden (1999), â Blast 2 sequencesâa new tool for comparing protein and nucleotide sequencesâ, FEMS Microbiol Lett. 174:247-250). Such a pair of nucleic acids may show, for example, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% or greater sequence identity over a certain defined length.

Single-stranded DNA (ssDNA) of the present invention is relatively long. In some embodiments, the ssDNA may have a length of at least about 200, 250, 300, 350, 400, 450, 500 and 1,500, 2,000, 5,000, 10,000, 15,000, 20,000, 30,000, or the ssDNA may have a length within a range bounded by any of these nucleotide lengths (e.g., a length of 200-1000 nucleotides). The ssDNA may be contain modified nucleotides well known in the art.

The ssDNA may include a 5â² homology arm having substantial sequence identity to the target DNA sequence, an exogenous sequence, and a 3â² homology arm having substantial sequence identity to a target DNA sequence. Preferably, the ssDNA is arranged in the 5â² to 3â² direction to include a 5â² homology arm having substantial sequence identity to a target DNA sequence, an exogenous sequence, and a 3â² homology arm having substantial sequence identity to a target DNA sequence.

In some embodiments, the 5â² homology arm and/or the 3â² homology arm of the ssDNA are substantially identical to at least about 15, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, or 110 nucleotides of the target DNA sequence. In some embodiments, the 5â² homology arm and 3â² homology arm of the ssDNA are substantially identical to no more than about 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, or 250 nucleotides of the target DNA sequence. Preferably, the 5â² homology arm and 3â² homology arm of the ssDNA are substantially identical to between 35 to 120 nucleotides of the target DNA sequence. In some embodiments, the 5â² homology arm is substantially identical to the target DNA sequence on one side of the cut created by a nuclease system and the 3â² homology arm is substantially identical to the target DNA sequence on the other side of the cut created by a nuclease system.

As used herein âsubstantially identical toâ or âsubstantial identityâ when referring to polynucleotide sequences of the 5â² homology arm and 3â² homology arm of the ssDNA of the present invention means polynucleotide sequence identity of at least 40%. Suitable polynucleotide identity can be any value between 40% and 100%. Preferably, polynucleotide identity of the 5â² homology arm and 3â² homology arm of the ssDNA is 100%.

Within the ssDNA of the present invention, the total length of the 5â² and 3â² homology arms may be significantly less than the length of the exogenous sequence. Prior to the work of the inventors, ssDNA repair templates were typically about 100-200 bases long. Such repair templates generally included exogenous sequences containing a few bases of altered sequence (e.g., point mutations, recombinase recognition sequences, short deletions or insertions of a few bases) which were flanked by homology arms of about 40-80 bases. See, e.g., FIG. 10 . The homology arms, therefore, made up a significant portion of the ssDNA repair template. The inventors, on the other hand, have discovered that ssDNA repair templates that include exogenous sequences over 200 bp could be inserted at high efficiencies even though the ssDNA repair templates only included relatively short 5â² and 3â² homology arms. See, e.g., FIG. 10 .

In view of this discovery, the ssDNA of the present invention may include certain ratios between the length of the exogenous sequence (ES) and the sum of the length of the 5â² homology arm (L5â²) and the 3â² homology arm (L3â²). The ratio (R) between the length of the exogenous sequence and the total lengths of the 5â² homology arm and the 3â² homology arm is determined by dividing the length of the exogenous sequence in nucleotides by the combined lengths of both the 5â² and 3â² homology arms in nucleotides as represented by the formula R=ES/(L5â²+L3â²). For example, if the ssDNA includes a 5â² homology arm that is 99 nucleotides in length, an exogenous sequence that is 1,368 nucleotides in length, and a 3â² homology arm this is 72 nucleotides in length, the ratio between the length of the exogenous sequence and the total lengths of the 5â² homology arm and the 3â² homology arm would be 1368/(99+72)=8:1. In some embodiments of ssDNA comtemplated herein, the ratio (R) of the length of the exogenous sequence to the total length of the 5â² homology arm and the 3â² homology arm (exogenous sequence length:homology arm length) may be about 1:1, 1.5:1, 2:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1, 10:1, 15:1, 20:1, 30:1, 40:1, 50:1, 60:1, 70:1, 80:1, 90:1, 100:1 or within a ratio range bounded by any two of these values (i.e., a ratio within a range of 5:1-50:1). In some embodiments, the ratio (R) of the length of the exogenous sequence to the total length of the 5â² homology arm and the 3â² homology arm (exogenous sequence length:homology arm length) may be between about 1.5:1 and 20:1.

The ssDNA may be synthesized using in vitro methods. In vitro methods contemplated for synthesizing ssDNA include a method including transcribing a DNA template encoding a promoter operably linked to nucleotide sequence including, preferably in the 5â² to 3â² direction, a 5â² homology arm having substantial sequence identity to the target DNA sequence, an exogenous sequence, and a 3â² homology arm having substantial sequence identity to the target DNA sequence to produce a RNA transcript, synthesizing a ssDNA/RNA duplex by reverse transcription of the RNA transcript, and degrading the RNA from the ssDNA/RNA duplex using an RNA-degrading enzyme to produce ssDNA. Optionally, the method may further comprise purifying the ssDNA. Purification of the ssDNA may be by gel purification or other DNA purification protocols well known in the art. Promoters appropriate for transcribing a DNA template in vitro are known in the art. Examples of suitable promoters include, without limitation, T7, T3, and SP6 promoters. Preferably, the promoter comprises a T7 promoter and transcription is performed using a T7 RNA polymerase.

Synthesis of the ssDNA/RNA duplex may be performed using a RNA-dependent DNA polymerase such as a reverse transcriptase. Suitable reverse transcriptase proteins for the present invention may be obtained from various retroviruses including, without limitation, Moloney Murine Leukemia virus, Human Immunodeficiency Virus (HIV), Simian Immunodeficiency Virus (SIV), and retrons isolated from various yeast and bacterial species. Preferably, the reverse transcriptase is from Moloney Murine Leukemia virus.

It will be appreciated by those skilled in the art that reverse transcriptases typically contain a domain conferring RNase H activity. In accordance with the present invention, the reverse transcriptase may or may not possess such RNase H activity. Thus, the RNA-degrading enzyme used in the present methods and kits may be an RNase H activity associated with the reverse transcriptase or may be a separate RNA-degrading enzyme known in the art to degrade RNA in a DNA/RNA duplex to produce ssDNA including, but not limited to, RNase H.

Additional in vitro methods may also be used to produce the ssDNA of the present invention. Suitable methods include: asymmetric PCR (See, e.g., U.S. Pat. No. 8,735,067), PCR using two oligonucleotide primers, one present in limiting concentration (See, e.g., U.S. Pat. No. 5,066,584), and use of ânickaseâ and/or restriction endonucleases enzymes to produce ssDNA from dsDNA molecules (See, e.g., LsODN Preparation KitâBiodynamics Laboratory Inc., Tokyo, Japan).

The efficiency of ssDNA-based insertion may also be affected by the secondary structure of the ssDNA. Such secondary structure may be prevented or minimized by using strategies that reduce the secondary structure present in ssDNA repair templates. Thus, the compositions, methods, and kits of the present invention may further include, without limitation, buffers (or use of buffers) that minimize secondary structure, proteins (or use of proteins) that reduce secondary structure such as ssDNA binding proteins, or modified nucleotides (or use of modified nucleotides) such as N4-ethyldeoxycytidine (d 4Et C).

The ssDNA of the present invention may include an exogenous sequence. As used herein, an âexogenous sequenceâ or âexogenous polynucleotideâ refers to polynucleotides that are introduced into a cell.

The exogenous sequence may have a length of at least about 200, 250, 300, 350, 400, 450, 500 and 1,500, 2,000, 5,000, 10,000, 15,000, 20,000, or 30,000, or the exogenous sequence may have a length within a range bounded by any of these nucleotide lengths (e.g., a length of 200-1000 nucleotides).

The exogenous sequence may include any given sequences including those that may be artificially designed or modified. The exogenous sequence may encode a protein product, an RNA product, a DNA regulatory element, a variant DNA sequence, or any combinations thereof.

Protein products may be full-length proteins, fragments of proteins such as exons, fusion proteins, polypeptides, or peptides. The protein products may be expressed (e.g., exogenous sequence is transcribed and translated to produce protein product) when the exogenous sequence is introduced into the cell and/or introduced into the target DNA sequence. The protein products may become part of a fusion protein that becomes expressed in the cell when the exogenous sequence is introduced into the target DNA sequence or may be expressed as individual proteins. Exemplary protein products include, without limitation, fluorescent proteins such as eGFP, Cre proteins, Flp proteins, reverse tetracycline-controlled transactivator (rtTA) proteins, tetracycline-controlled transactivator (tTA) proteins, or epitope tag proteins such as CBP, FLAG, GST, HA, HBH, MBP, Myc, poly His, S-tag, SUMO, TAP, TRX, or V5 tags.

As used herein, the terms âproteinâ or âpolypeptideâ or âpeptideâ may be used interchangeably to refer to a polymer of amino acids. A âpolypeptideâ as contemplated herein typically comprises a polymer of naturally occurring amino acids (e.g., alanine, arginine, asparagine, aspartic acid, cysteine, glutamine, glutamic acid, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, and valine). The proteins contemplated herein may be further modified in vitro or in vivo to include non-amino acid moieties. These modifications may include but are not limited to acylation (e.g., O-acylation (esters), N-acylation (amides), S-acylation (thioesters)), acetylation (e.g., the addition of an acetyl group, either at the N-terminus of the protein or at lysine residues), formylation, lipoylation (e.g., attachment of a lipoate, a C8 functional group), myristoylation (e.g., attachment of myristate, a C14 saturated acid), palmitoylation (e.g., attachment of palmitate, a C16 saturated acid), alkylation (e.g., the addition of an alkyl group, such as an methyl at a lysine or arginine residue), isoprenylation or prenylation (e.g., the addition of an isoprenoid group such as farnesol or geranylgeraniol), amidation at C-terminus, glycosylation (e.g., the addition of a glycosyl group to either asparagine, hydroxylysine, serine, or threonine, resulting in a glycoprotein). Distinct from glycation, which is regarded as a nonenzymatic attachment of sugars, polysialylation (e.g., the addition of polysialic acid), glypiation (e.g., glycosylphosphatidylinositol (GPI) anchor formation, hydroxylation, iodination (e.g., of thyroid hormones), and phosphorylation (e.g., the addition of a phosphate group, usually to serine, tyrosine, threonine or histidine).

The exogenous sequence may encode an RNA product. RNA products may be expressed (i.e., when the exogenous sequence is transcribed to produce RNA product) when the exogenous sequence is introduced into the cell and/or introduced into the target DNA sequence. The RNA products may include RNAs involved in protein synthesis, RNAs involved in post-transcriptional modification or DNA replication, or regulatory RNAs. RNAs involved in protein synthesis may include, without limitation, mRNAs, rRNAs, tRNAs, or SRP RNAs. RNAs involved in post-transcriptional modification may include, without limitation, snRNAs, snoRNAs, or Y RNAs. Regulatory RNAs may include, without limitation, antisense RNAs, CRISPR RNAs, guide RNAs, long noncoding RNAs, microRNAs, siRNAs, piRNAs, tasiRNAs, 5â²UTR sequences, 3â²UTR sequences, RNA splicing regulatory sequences, IRES sequences, or polyA signal sequences.

The exogenous sequence may encode DNA regulatory elements. DNA regulatory elements may be non-coding DNA sequences that regulate the transcription of genes or serve as recognition sequences for protein products or RNA products. Exemplary DNA regulatory elemen

CLAIMS

Claims ( 9 )

We claim:

1. A method for inserting an exogenous sequence encoding a protein product or an RNA product at a target DNA sequence in a mouse embryo and obtaining a transgenic mouse developed from the mouse embryo comprising the exogenous sequence, the method comprising:

(a) obtaining a mouse embryo,

(b) introducing a single-stranded DNA (ssDNA) donor molecule into the mouse embryo, the ssDNA donor molecule comprising a 5â² homology arm having 100% sequence identity to the target DNA sequence, the exogenous sequence encoding the protein product or the RNA product, and a 3â² homology arm having 100% sequence identity to the target DNA sequence, wherein the ssDNA donor molecule is between 200 and 2,000 nucleotides in length, and wherein the ratio of the length of the exogenous sequence to the total length of the 5â² homology arm and the 3â² homology arm (exogenous sequence length:homology arm length) is between 1.5:1 and 20:1,

(c) introducing or expressing a CRISPR/Cas9 system in the mouse embryo, under conditions wherein the CRISPR/Cas9 system cuts the target DNA sequence and the ssDNA donor molecule is recombined with the target DNA sequence, and

(d) transplanting the mouse embryo into the oviducts of a pseudo-pregnant female mouse and obtaining the transgenic mouse developed from the mouse embryo.

2. The method of claim 1 , wherein the ratio of the length of the exogenous sequence to the total length of the 5â² homology arm and the 3â² homology arm (exogenous sequence length:homology arm length) is between 2:1 and 5:1.

3. The method of claim 1 , wherein the exogenous sequence encodes an artificial microRNA (amiRNA).

4. The method of claim 1 , wherein the ssDNA is between 225 and 2,000 nucleotides in length.

5. A method for inserting an exogenous sequence at a target DNA sequence in a mouse embryo and obtaining a transgenic mouse developed from the mouse embryo comprising the exogenous sequence, the method comprising:

(a) transcribing a DNA template to provide an RNA transcript and isolating the RNA transcript, the DNA template comprising a promoter operably linked to a DNA donor sequence, the DNA donor sequence comprising a 5â² homology arm having 100% sequence identity to the target DNA sequence, the exogenous sequence, and a 3â² homology arm having 100% sequence identity to the target DNA, wherein the DNA donor sequence is between 200 and 10,000 nucleotides in length, and wherein the ratio of the length of the exogenous sequence to the total length of the 5â² homology arm and the 3â² homology arm (exogenous sequence length:homology arm length) is between 1.5:1 and 20:1,

(b) reverse transcribing the RNA transcript to synthesize a ssDNA/RNA duplex,

(c) degrading the RNA from the ssDNA/RNA duplex using an RNA-degrading enzyme to produce a donor DNA sample, wherein the donor DNA sample comprises a ssDNA donor molecule comprising the DNA donor sequence and the DNA donor sample does not comprise a single-stranded nucleic acid that is complementary to the ssDNA donor molecule,

(d) purifying the ssDNA donor molecule produced in step (c),

(e) introducing the ssDNA donor molecule into the mouse embryo, introducing or expressing a CRISPR/Cas9 system in the mouse embryo, under conditions wherein the nuclease system cuts the target DNA sequence and the ssDNA donor molecule is recombined with the target DNA sequence, and (g) transplanting the mouse embryo into the oviducts of a pseudo-pregnant female mouse and obtaining the transgenic mouse developed from the embryo.

6. The method of claim 5 , wherein the ssDNA donor molecule is between 225 and 10,000 nucleotides in length.

7. The method of claim 5 , wherein the exogenous sequence encodes a protein product, an RNA product, a DNA regulatory element, or a variant DNA sequence.

8. The method of claim 7 , wherein the ssDNA donor molecule is between 225 and 10,000 nucleotides in length.

9. A method for inserting an exogenous sequence, encoding a protein product or an RNA product, at a target DNA sequence in a mouse embryo and obtaining a transgenic mouse developed from the mouse embryo, the method comprising:

(a) obtaining a mouse embryo,

(b) introducing a single-stranded DNA (ssDNA) donor molecule into the mouse embryo, the ssDNA donor molecule comprising a 5â² homology arm having 100% sequence identity to the target DNA sequence, the exogenous sequence encoding the protein product or the RNA product, and a 3â² homology arm having 100% sequence identity to the target DNA sequence, wherein the ssDNA donor molecule is between 500 and 2,000 nucleotides in length and the 5â² homology arm and 3â² homology arm are between 50-150 nucleotides in length and wherein the ratio of the length of the exogenous sequence to the total length of the 5â² homology arm and the 3â² homology arm (exogenous sequence length:homology arm length) is between 1.5:1 and 20:1,

(c) introducing or expressing a CRISPR/Cas9 system in the mouse embryo, under conditions wherein the CRISPR/Cas9 system cuts the target DNA sequence and the ssDNA is recombined with the target DNA sequence, and

(d) transplanting the mouse embryo into the oviducts of a pseudo-pregnant female mouse and obtaining the transgenic mouse developed from the mouse embryo.

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