Engineered class 2 type v crispr systems

Abstract

Provided herein are engineered Class 2, Type V nucleases and guide RNAs useful for the editing of target nucleic acids. Also provided are methods of making and using such variants to modify nucleic acids.

What is claimed is: 
     
         1 . A guide RNA (gRNA) scaffold comprising a sequence having at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% sequence identity to any one of the sequences selected from the group consisting of SEQ ID NOS: 2292, 2291, 2307, 2281-2290, 2293-2306, 2308-2332 and 23530-2398. 
     
     
         2 . The gRNA scaffold of  claim 1 , comprising a sequence selected from the group consisting of SEQ ID NOS: 2292, 2291, 2307, 2281-2290, 2293-2306, 2308-2332 and 23530-2398. 
     
     
         3 . The gRNA scaffold of  claim 1 , comprising a sequence having one or more modifications relative to SEQ ID NO: 2238, wherein the one or more modifications result in an improved characteristic. 
     
     
         4 . The gRNA scaffold of  claim 3 , wherein the one or more modifications comprise one or more nucleotide substitutions, insertions, and/or deletions as set forth in Table 19. 
     
     
         5 . The gRNA scaffold of  claim 3  or  claim 4 , wherein the improved characteristic is one or more functional properties selected from the group consisting of increased editing activity, increased pseudoknot stem stability, increased triplex region stability, increased scaffold stem stability, extended stem stability, reduced off-target folding intermediates, and increased binding affinity to a Class 2, Type V CRISPR protein, optionally in an in vitro assay. 
     
     
         6 . The gRNA scaffold of any one of  claims 3 - 5 , wherein the gRNA scaffold exhibits an improved enrichment score (log 2) of at least about 2.0, at least about 2.5, at least about 3, or at least about 3.5 greater compared to the score of the gRNA scaffold of SEQ ID NO: 2238 in an in vitro assay. 
     
     
         7 . The gRNA scaffold of  claim 1 , comprising a sequence having one or more modifications relative to SEQ ID NO: 2239, wherein the one or more modifications result in an improved characteristic. 
     
     
         8 . The gRNA scaffold of  claim 7 , wherein the one or more modifications comprise one or more nucleotide substitutions, insertions, and/or deletions as set forth in Table 20. 
     
     
         9 . The gRNA scaffold of  claim 7  or  claim 8 , wherein the improved characteristic is one or more functional properties selected from the group consisting of increased editing activity, increased pseudoknot stem stability, increased triplex region stability, increased scaffold stem stability, extended stem stability, reduced off-target folding intermediates, and increased binding affinity to a Class 2, Type V CRISPR protein, optionally in an in vitro assay. 
     
     
         10 . The gRNA scaffold of any one of  claims 7 - 9 , wherein the gRNA scaffold exhibits an improved enrichment score (log 2) of at least about 1.2, at least about 1.5, at least about 2.0, at least about 2.5, at least about 3, or at least about 3.5 greater compared to the score of the gRNA scaffold of SEQ ID NO: 2239 in an in vitro assay. 
     
     
         11 . The gRNA scaffold of  claim 1 , comprising one or more modifications at positions relative to the sequence of SEQ ID NO: 2239 selected from the group consisting of C9, U11, C17, U24, A29, U54, G64, A88, and A95. 
     
     
         12 . The gRNA scaffold of  claim 11 , comprising one or more modifications relative to the sequence of SEQ ID NO: 2239 selected from the group consisting of C9U, U11C, C17G, U24C, A29C, an insertion of G at position 54, an insertion of C at position 64, A88G, and A95G. 
     
     
         13 . The gRNA scaffold of  claim 12 , comprising modifications relative to the sequence of SEQ ID NO: 2239 consisting of C9U, U11C, C17G, U24C, A29C, an insertion of G at position 54, an insertion of C at position 64, A88G, and A95G. 
     
     
         14 . The gRNA scaffold of any one of  claims 7 - 13 , wherein the improved characteristic is selected from the group consisting of pseudoknot stem stability, triplex region stability, scaffold bubble stability, extended stem stability, and binding affinity to a Class 2, Type V CRISPR protein. 
     
     
         15 . The gRNA scaffold of  claim 14 , wherein the insertion of C at position 64 and the A88G substitution relative to the sequence of SEQ ID NO: 2239 resolves an asymmetrical bulge element of the extended stem, enhancing the stability of the extended stem of the gRNA scaffold. 
     
     
         16 . The gRNA scaffold of  claim 14 , wherein the substitutions of U11C, U24C, and A95G increase the stability of the triplex region of the gRNA scaffold. 
     
     
         17 . The gRNA scaffold of  claim 14 , wherein the substitution of A29C increases the stability of the pseudoknot stem. 
     
     
         18 . The gRNA scaffold of  claim 1  or  claim 2 , wherein the gRNA scaffold comprises one or more heterologous RNA sequences in the extended stem. 
     
     
         19 . The gRNA scaffold of  claim 18 , wherein the heterologous RNA is selected from the group consisting of a MS2 hairpin, Qβ hairpin, U1 hairpin II, Uvsx hairpin, and a PP7 stem loop, or sequence variants thereof. 
     
     
         20 . The gRNA scaffold of  claim 18  or  claim 19 , wherein the heterologous RNA sequence increases the stability of the gRNA. 
     
     
         21 . The gRNA scaffold of  claim 18  or  claim 19 , wherein the heterologous RNA is capable of binding a protein, a RNA, a DNA, or a small molecule. 
     
     
         22 . The gRNA scaffold of any one of  claims 18 - 21 , wherein the gRNA scaffold comprises a Rev response element (RRE) or a portion thereof. 
     
     
         23 . The gRNA scaffold of  claim 22 , wherein the RRE or portion thereof is selected from the group consisting of Stem IIB of the RRE having sequence UGGGCGCAGCGUCAAUGACGCUGACGGUACA (SEQ ID NO: 1280), Stem II-V of the RRE having sequence CAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACAA UUAUUGUCUGGUAUAGUGCAGCAGCAGAACAAUUUGCUGAGGGCUAUUGAGG CGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCA AGAAUCCUG (SEQ ID NO: 1282), Stem II of the RRE having sequence GCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACAAUUAUUG UCUGGUAUAGUGC (SEQ ID NO: 1281), Rev-binding element (RBE) of Stem IIB having sequence GCUGACGGUACAGGC (SEQ ID NO: 1284), and full-length RRE having sequence AGGAGCUUUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCA GCGUCAAUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGC AGCAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCA ACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAAUCCUGGCUGUGGAAA GAUACCUAAAGGAUCAACAGCUCCU (SEQ ID NO: 1283). 
     
     
         24 . The gRNA of any one of  claims 1 - 23 , wherein the gRNA scaffold comprises one or more thymines (T). 
     
     
         25 . A gRNA comprising the gRNA scaffold of any one of  claims 1 - 24 , and a targeting sequence at the 3′ end of the gRNA scaffold that is complementary to a target nucleic acid sequence. 
     
     
         26 . The gRNA of  claim 25 , wherein the targeting sequence has 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. 
     
     
         27 . The gRNA of  claim 26 , wherein the targeting sequence has 18, 19, or 20 nucleotides. 
     
     
         28 . The gRNA of any one of  claims 25 - 27 , wherein the gRNA is capable of forming a ribonucleoprotein (RNP) complex with a Class 2, Type V CRISPR protein. 
     
     
         29 . An engineered Class 2, Type V CRISPR protein comprising:
 a. a NTSB domain comprising a sequence of QPASKKIDQNKLKPEMDEKGNLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFG RCNVAEHEKLILLAQLKPEKDSDEAVTYSLGKFGQ (SEQ ID NO: 2335), or a sequence having at least 80% at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identity thereto;   b. a helical I-II domain comprising a sequence of RALDFYSIHVTKESTHPVKPLAQIAGNRYASGPVGKALSDACMGTIASFLSKYQDIIIE HQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAYNEVIARVRMWV NLNLWQKLKLSRDDAKPLLRLKGFPSF (SEQ ID NO: 2336), or a sequence having at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identity thereto;   c. a helical II domain comprising a sequence of PLVERQANEVDWWDMVCNVKKLINEKKEDGKVFWQNLAGYKRQEALRPYLSSEE DRKKGKKFARYQLGDLLLHLEKKHGEDWGKVYDEAWERIDKKVEGLSKHIKLEEE RRSEDAQSKAALTDWLRAKASFVIEGLKEADKDEFCRCELKLQKWYGDLRGKPFAI EAE (SEQ ID NO: 2351), or a sequence having at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identity thereto; and   d. a RuvC-I domain comprising a sequence of SSNIKPMNLIGVDRGENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQ AKKEVEQRRAGGYSRKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFENLSRG FGRQGKRTFMAERQYTRMEDWLTAKLAYEGLPSKTYLSKTLAQYTSKTC (SEQ ID NO: 2352), or a sequence having at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identity thereto.   
     
     
         30 . The Class 2, Type V CRISPR protein of  claim 29 , wherein the CRISPR protein comprises an OBD-I domain comprising a sequence of QEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQ (SEQ ID NO: 2342), or a sequence having at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity thereto. 
     
     
         31 . The Class 2, Type V CRISPR protein of  claim 29  or  claim 30 , wherein the CRISPR protein comprises an OBD-II domain comprising a sequence of NSILDISGFSKQYNCAFIWQKDGVKKLNLYLIINYFKGGKLRFKKIKPEAFEANRFYT VINKKSGEIVPMEVNFNFDDPNLIILPLAFGKRQGREFIWNDLLSLETGSLKLANGRVI EKTLYNRRTRQDEPALFVALTFERREVLD (SEQ ID NO: 2347), or a sequence having at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity thereto. 
     
     
         32 . The Class 2, Type V CRISPR protein of any one of  claims 29 - 31 , wherein the CRISPR protein comprises a helical I-I domain comprising a sequence of PISNTSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVA (SEQ ID NO: 2343), or a sequence having at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity thereto. 
     
     
         33 . The Class 2, Type V CRISPR protein of any one of  claims 29 - 32 , wherein the CRISPR protein comprises a TSL domain comprising a sequence of SNCGFTITSADYDRVLEKLKKTATGWMTTINGKELKVEGQITYYNRYKRQNVVKDL SVELDRLSEESVNNDISSWTKGRSGEALSLLKKRFSHRPVQEKFVCLNCGFETH (SEQ ID NO: 2349), or a sequence having at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity thereto. 
     
     
         34 . The Class 2, Type V CRISPR protein of any one of  claims 29 - 33 , wherein the CRISPR protein comprises a RuvC-II domain comprising a sequence of ADEQAALNIARSWLFLRSQEYKKYQTNKTTGNTDKRAFVETWQSFYRKKLKEVWK PAV (SEQ ID NO: 2350), or a sequence having at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity thereto. 
     
     
         35 . The Class 2, Type V CRISPR protein of  claim 34 , comprising the sequence of SEQ ID NO: 416, or a sequence having at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity thereto. 
     
     
         36 . The Class 2, Type V CRISPR protein of any one of  claims 29 - 35 , wherein the Class 2, Type V CRISPR protein comprises at least one modification in one or more domains. 
     
     
         37 . The Class 2, Type V CRISPR protein of  claim 36 , wherein the at least one modification comprises:
 a. at least one amino acid substitution in a domain;   b. at least one amino acid deletion in a domain;   c. at least one amino acid insertion in a domain; or   d. any combination of (a)-(c).   
     
     
         38 . The Class 2, Type V CRISPR protein of  claim 36  or  claim 37 , comprising a modification at one or more amino acid positions in the NTSB domain relative to SEQ ID NO: 2335 selected from the group consisting of P2, S4, Q9, E15, G20, G33, L41, Y51, F55, L68, A70, E75, K88, and G90. 
     
     
         39 . The Class 2, Type V CRISPR protein of  claim 38 , wherein the one or more modifications at one or more amino acid positions in the NTSB domain are selected from the group consisting of an insertion of G at position 2, an insertion of I at position 4, an insertion of L at position 4, Q9P, E15S, G20D, a deletion of S at position 30, G33T, L41A, Y51T, F55V, L68D, L68E, L68K, A70Y, A70S, E75A, E75D, E75P, K88Q, and G90Q relative to SEQ ID NO: 2335. 
     
     
         40 . The Class 2, Type V CRISPR protein of any one of  claims 36 - 39 , comprising a modification at one or more amino acid positions in the helical I-II domain relative to SEQ ID NO: 2336 selected from the group consisting of 124, A25, Y29 G32, G44, S48, S51, Q54, 156, V63, S73, L74, K97, V100, M112, L116, G137, F138, and S140. 
     
     
         41 . The Class 2, Type V CRISPR protein of  claim 40 , wherein the one or more modifications at one or more amino acid positions in the helical I-II domain are selected from the group consisting of an insertion of T at position 24, an insertion of C at position 25, Y29F, G32Y, G32N, G32H, G32S, G32T, G32A, G32V, a deletion of G at position 32, G32S, G32T, G44L, G44H, S48H, S48T, S51T, Q54H, I56T, V63T, S73H, L74Y, K97G, K97S, K97D, K97E, V100L, M112T, M112W, M112R, M112K, L116K, G137R, G137K, G137N, an insertion of Q at position 138, and S140Q relative to SEQ ID NO: 2336. 
     
     
         42 . The Class 2, Type V CRISPR protein of any one of  claims 36 - 41 , comprising a modification at one or more amino acid positions in the helical II domain relative to SEQ ID NO: 2351 selected from the group consisting of L2, V3, E4, R5, Q6, A7, E9, V10, D11, W12, W13, D14, M15, V16, C17, N18, V19, K20, L22, I23, E25, K26, K31, Q35, L37, A38, K41, R 42, Q43, E44, L46, K57, Y65, G68, L70, L71, L72, E75, G79, D81, W82, K84, V85, Y86, D87, I93, K95, K96, E98, L100, K102, I104, K105, E109, R110, D114, K118, A120, L121, W124, L125, R126, A127, A129, I133, E134, G135, L136, E138, D140, K141, D142, E143, F144, C145, C147, E148, L149, K150, L151, Q152, K153, L158, E166, and A167. 
     
     
         43 . The Class 2, Type V CRISPR protein of  claim 42 , wherein the one or more modifications at one or more amino acid positions in the helical II domain are selected from the group consisting of an insertion of A at position 2, an insertion of H at position 2, a deletion of L at position 2 and a deletion of V at position 3, V3E, V3Q, V3F, a deletion of V at position 3, an insertion of D at position 3, V3P, E4P, a deletion of E at position 4, E4D, E4L, E4R, R5N, Q6V, an insertion of Q at position 6, an insertion of G at position 7, an insertion of H at position 9, an insertion of A at position 9, VD10, an insertion of T1 at position 0, a deletion of V at position 10, an insertion of F at position 10, an insertion of D at position 11, a deletion of D at position 11, D11S, a deletion of W at position 12, W12T, W12H, an insertion of P at position 12, an insertion of Q at position 13, an insertion of G at position 12, an insertion of R at position 13, W13P, W13D, an insertion of D at position 13, W13L, an insertion of P at position 14, an insertion of D at position 14, a deletion of D at position 14 and a deletion of M at position 15, a deletion of M at position 15, an insertion of T at position 16, an insertion of P at position 17, N18I, V19N, V19H, K20D, L22D, 123S, E25C, E25P, an insertion of G at position 25, K26T, K27E, K31L, K31Y, Q35D, Q35P, an insertion of S at position 37, a deletion of L at position 37 and a deletion of A at position 38, K41L, an insertion of R at position 42, a deletion of Q at position 43 and a deletion of E at position 44, L46N, K57Q, Y65T, G68M, L70V, L71C, L72D, L72N, L72W, L72Y, E75F, E75L, E75Y, G79P, an insertion of E at position 79, an insertion of T at position 81, an insertion of R at position 81, an insertion of W at position 81, an insertion of Y at position 81, an insertion of W at position 82, an insertion of Y at position 82, W82G, W82R, K84D, K84H, K84P, K84T, V85L, V85A, an insertion of L at position 85, Y86C, D87G, D87M, D87P, I93C, K95T, K96R, E98G, L100A, K102H, 1104T, 1104S, 1104Q, K105D, an insertion of K at position 109, E109L, R110D, a deletion of R at position 110, D114E, an insertion of D at position 114, K118P, A120R, L121T, W124L, L125C, R126D, A127E, A127L, A129T, A129K, 1133E, an insertion of C at position 133, an insertion of S at position 134, an insertion of G at position 134, an insertion of R at position 135, G135P, L136K, L136D, L136S, L136H, a deletion of E at position 138, D140R, an insertion of D at position 140, an insertion of P at position 141, an insertion of D at position 142, a deletion of E at position 143+a deletion of F at position 144, an insertion of Q at position 143, F144K, a deletion of F at position 144, a deletion of F at position 144 and a deletion of C at position 145, C145R, an insertion of G at position 145, C145K, C147D, an insertion of V at position 148, E148D, an insertion of H at position 149, L149R, K150R, L151H, Q152C, K153P, L158S, E166L, and an insertion of F at position 167 relative to SEQ ID NO: 2351. 
     
     
         44 . The Class 2, Type V CRISPR protein of any one of  claims 36 - 43 , comprising a modification at one or more amino acid positions in the RuvC-I domain relative to SEQ ID NO: 2352 selected from the group consisting of 14, K5, P6, M7, N8, L9, V12, G49, K63, K80, N83, R90, M125, and L146. 
     
     
         45 . The Class 2, Type V CRISPR protein of  claim 44 , wherein the one or more modifications at one or more amino acid positions in the RuvC-I domain are selected from the group consisting of an insertion of I at position 4, an insertion of S at position 5, an insertion of T at position 6, an insertion of N at position 6, an insertion of R at position 7, an insertion of K at position 7, an insertion of H at position 8, an insertion of S at position 8, V12L, G49W, G49R, S51R, S51K, K62S, K62T, K62E, V65A, K80E, N83G, R90H, R90G, M125S, M125A, L137Y, an insertion of P at position 137, a deletion of L at position 141, L141R, L141D, an insertion of Q at position 142, an insertion of R at position 143, an insertion of N at position 143, E144N, an insertion of P at position 146, L146F, P147A, K149Q, T150V, an insertion of R at position 152, an insertion of H153, T155Q, an insertion of H at position 155, an insertion of R at position 155, an insertion of L at position 156, a deletion of L at position 156, an insertion of W at position 156, an insertion of A at position 157, an insertion of F at position 157, A157S, Q158K, a deletion of Y at position 159, T160Y, T160F, an insertion of I at position 161, S161P, T163P, an insertion of N at position 163, C164K, and C164M relative to SEQ ID NO: 2351. 
     
     
         46 . The Class 2, Type V CRISPR protein of any one of  claims 36 - 45 , comprising a modification at one or more amino acid positions in the OBD-I domain relative to SEQ ID NO: 2342 selected from the group consisting of 13, K4, R5, I6, N7, K8, K15, D16, N18, P27, M28, V33, R34, M36, R41, L47, R48, E52, P55, and Q56. 
     
     
         47 . The Class 2, Type V CRISPR protein of  claim 46 , wherein the one or more modifications at one or more amino acid positions in the OBD-I domain are selected from the group consisting of an insertion of G at position 3, I3G, I3E, an insertion of G at position 4, K4G, K4P, K4S, K4W, K4W, R5P, an insertion of P at position 5, an insertion of G at position 5, RSS, an insertion of S at position 5, R5A, R5P, R5G, R5L, I6A, I6L, an insertion of G at position 6, N7Q, N7L, N7S, K8G, K15F, D16W, an insertion of F at position 16, an insertion of F18, an insertion of P at position 27, M28P, M28H, V33T, R34P, M36Y, R41P, L47P, an insertion of P at position 48, E52P, an insertion of P at position 55, a deletion of P at position 55 and a deletion of Q at position 56, Q56S, Q56P, an insertion of D at position 56, an insertion of T at position 56, and Q56P relative to SEQ ID NO: 2342. 
     
     
         48 . The Class 2, Type V CRISPR protein of any one of  claims 36 - 47 , comprising a modification at one or more amino acid positions in the OBD-II domain relative to SEQ ID NO: 2347 selected from the group consisting of S2, I3, L4, K11, V24, K37, R42, A53, T58, K63, M70, I82, Q92, G93, K110, L121, R124, R141, E143, V144, and L145. 
     
     
         49 . The Class 2, Type V CRISPR protein of  claim 48 , wherein the one or more modifications at one or more amino acid positions in the OBD-II domain are selected from the group consisting of a deletion of S at position 2, I3R, I3K, a deletion of I at position 3 and a deletion of L4, a deletion of L at position 4, K11T, an insertion of P at position 24, K37G, R42E, an insertion of S at position 53, an insertion of R at position 58, a deletion of K at position 63, M70T, I82T, Q92I, Q92F, Q92V, Q92A, an insertion of A at position 93, K110Q, R115Q, L121T, an insertion of A at position 124, an insertion of R at position 141, an insertion of D at position 143, an insertion of A at position 143, an insertion of W at position 144, and an insertion of A at position 145 relative to SEQ ID NO: 2342. 
     
     
         50 . The Class 2, Type V CRISPR protein of any one of  claims 36 - 49 , comprising a modification at one or more amino acid positions in the TSL domain relative to SEQ ID NO: 2349 selected from the group consisting of S1, N2, C3, G4, F5, I7, K18, V58, S67, T76, G78, S80, G81, E82, S85, V96, and E98. 
     
     
         51 . The Class 2, Type V CRISPR protein of  claim 50 , wherein the one or more modifications at one or more amino acid positions in the OBD-II domain are selected from the group consisting of an insertion of M at position 1, a deletion of N at position 2, an insertion of V at position 2, C3S, an insertion of G at position 4, an insertion of W at position 4, F5P, an insertion of W at position 7, K18G, V58D, an insertion of A at position 67, T76E, T76D, T76N, G78D, a deletion of S at position 80, a deletion of G at position 81, an insertion of E at position 82, an insertion of N at position 82, S85I, V96C, V96T, and E98D relative to SEQ ID NO: 2349. 
     
     
         52 . The Class 2, Type V CRISPR protein of any one of  claims 29 - 51 , exhibiting an improved characteristic relative to SEQ ID NO: 2, wherein the improved characteristic comprises increased binding affinity to a gRNA, increased binding affinity to the target nucleic acid, improved ability to utilize a greater spectrum of PAM sequences in the editing of the target nucleic acid, improved unwinding of the target nucleic acid, increased editing activity, improved editing efficiency, improved editing specificity for cleavage of the target nucleic acid, decreased off-target editing or cleavage of the target nucleic acid, increased percentage of a eukaryotic genome that can be edited, increased activity of the nuclease, increased target strand loading for double strand cleavage, decreased target strand loading for single strand nicking, increased binding of the non-target strand of DNA, improved protein stability, increased protein:gRNA (RNP) complex stability, and improved fusion characteristics. 
     
     
         53 . The Class 2, Type V CRISPR protein of  claim 52 , wherein the improved characteristic comprises increased cleavage activity at a target nucleic sequence comprising an TTC, ATC, GTC, or CTC PAM sequence. 
     
     
         54 . The Class 2, Type V CRISPR protein of  claim 53 , wherein the improved characteristic comprises increased cleavage activity at a target nucleic acid sequence comprising an ATC or CTC PAM sequence relative to cleavage activity of the sequence of SEQ ID NO: 416. 
     
     
         55 . The Class 2, Type V CRISPR protein of  claim 54 , wherein the improved cleavage activity is an enrichment score (log 2) of at least about 1.5, at least about 2.0, at least about 2.5, at least about 3, at least about 3.5, at least about 4, at least about 4.5, at least about 5, at least about 6, at least about 7, at least about 8 or more greater compared to score of the sequence of SEQ ID NO: 416 in an in vitro assay. 
     
     
         56 . The Class 2, Type V CRISPR protein of  claim 54 , wherein the improved characteristic comprises increased cleavage activity at a target nucleic acid sequence comprising an CTC PAM sequence relative to the sequence of SEQ ID NO: 416. 
     
     
         57 . The Class 2, Type V CRISPR protein of  claim 56 , wherein the improved cleavage activity is an enrichment score (log 2) of at least about 2, at least about 2.5, at least about 3, at least about 3.5, at least about 4, at least about 4.5, at least about 5, or at least about 6 or more greater compared to the score of the sequence of SEQ ID NO: 416 in an in vitro assay. 
     
     
         58 . The Class 2, Type V CRISPR protein of  claim 53 , wherein the improved characteristic comprises increased cleavage activity at a target nucleic acid sequence comprising an TTC PAM sequence relative to the sequence of SEQ ID NO: 416. 
     
     
         59 . The Class 2, Type V CRISPR protein of  claim 58 , wherein the improved cleavage activity is an enrichment score of at least about 1.5, at least about 2.0, at least about 2.5, at least about 3, at least about 3.5, at least about 4, at least about 4.5, at least about 5, or at least about 6 log 2 or more greater compared to the sequence of SEQ ID NO: 416 in an in vitro assay. 
     
     
         60 . The Class 2, Type V CRISPR protein of  claim 52 , wherein the improved characteristic comprises increased specificity for cleavage of the target nucleic acid sequence relative to the sequence of SEQ ID NO: 416. 
     
     
         61 . The Class 2, Type V CRISPR protein of  claim 60 , wherein the increased specificity is an enrichment score of at least about 2.0, at least about 2.5, at least about 3, at least about 3.5, at least about 4, at least about 4.5, at least about 5, or at least about 6 log 2 or more greater compared to the sequence of SEQ ID NO: 416 in an in vitro assay. 
     
     
         62 . The Class 2, Type V CRISPR protein of  claim 52 , wherein the improved characteristic comprises decreased off-target cleavage of the target nucleic acid sequence. 
     
     
         63 . The Class 2, Type V CRISPR protein of any one of  claims 29 - 62 , wherein the Class 2, Type V CRISPR protein has a sequence selected from the group consisting of the sequences of SEQ ID NOS: 415-592 and 1147-1231, as set forth in Table 3, or a sequence having at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, or at least about 95%, or at least about 96%, or at least about 97%, or at least about 98%, or at least about 99%, sequence identity thereto. 
     
     
         64 . The Class 2, Type V CRISPR protein of any one of  claims 29 - 62 , comprising a sequence selected from the group consisting of SEQ ID NOS: 415-592 and 1147-1231, as set forth in Table 3. 
     
     
         65 . The Class 2, Type V CRISPR protein of any one of  claims 29 - 64 , comprising one or more nuclear localization signals (NLS). 
     
     
         66 . The Class 2, Type V CRISPR protein of  claim 65 , wherein the one or more NLS are selected from the group of sequences consisting of PKKKRKV (SEQ ID NO: 352), KRPAATKKAGQAKKKK (SEQ ID NO: 353), PAAKRVKLD (SEQ ID NO: 354), RQRRNELKRSP (SEQ ID NO: 355), NQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGY (SEQ ID NO: 356), RMRIZFKNKGKDTAELRRRRVEVSVELRKAKKDEQILKRRNV (SEQ ID NO: 357), VSRKRPRP (SEQ ID NO: 358), PPKKARED (SEQ ID NO: (359), PQPKKKPL (SEQ ID NO: 360), SALIKKKKKMAP (SEQ ID NO: 361), DRLRR (SEQ ID NO: 362), PKQKKRK (SEQ ID NO: 363), RKLKKKIKKL (SEQ ID NO: 364), REKKKFLKRR (SEQ ID NO: 365), KRKGDEVDGVDEVAKKKSKK (SEQ ID NO: 366), RKCLQAGMNLEARKTKK (SEQ ID NO: 367), PRPRKIPR (SEQ ID NO: 368), PPRKKRTVV (SEQ ID NO: 369), NLSKKKKRKREK (SEQ ID NO: 370), RRPSRPFRKP (SEQ ID NO: 371), KRPRSPSS (SEQ ID NO: 372), KRGINDRNFWRGENERKTR (SEQ ID NO: 373), PRPPKMARYDN (SEQ ID NO: 374), KRSFSKAF (SEQ ID NO: 375), KLKIKRPVK (SEQ ID NO: 376), PKKKRKVPPPPAAKRVKLD (SEQ ID NO: 377), PKTRRRPRRSQRKRPPT (SEQ ID NO: 378), SRRRKANPTKLSENAKKLAKEVEN (SEQ ID NO: 379), KTRRRPRRSQRKRPPT (SEQ ID NO: 380), RRKKRRPRRKKRR (SEQ ID NO: 381), PKKKSRKPKKKSRK (SEQ ID NO: 382), HKKKHPDASVNFSEFSK (SEQ ID NO: 383), QRPGPYDRPQRPGPYDRP (SEQ ID NO: 384), LSPSLSPLLSPSLSPL (SEQ ID NO: 385), RGKGGKGLGKGGAKRHRK (SEQ ID NO: 386), PKRGRGRPKRGRGR (SEQ ID NO: 387), PKKKRKVPPPPKKKRKV (SEQ ID NO: 389), PAKRARRGYKC (SEQ ID NO: 63), KLGPRKATGRW (SEQ ID NO: 64), PRRKREE (SEQ ID NO: 65), PYRGRKE (SEQ ID NO: 66), PLRKRPRR (SEQ ID NO: 67), PLRKRPRRGSPLRKRPRR (SEQ ID NO:68), PAAKRVKLDGGKRTADGSEFESPKKKRKV (SEQ ID NO: 69), PAAKRVKLDGGKRTADGSEFESPKKKRKVGIHGVPAA (SEQ ID NO:70), PAAKRVKLDGGKRTADGSEFESPKKKRKVAEAAAKEAAAKEAAAKA (SEQ ID NO:71), PAAKRVKLDGGKRTADGSEFESPKKKRKVPG (SEQ ID NO:72), KRKGSPERGERKRHW (SEQ ID NO:73), KRTADSQHSTPPKTKRKVEFEPKKKRKV (SEQ ID NO:74), and PKKKRKVGGSKRTADSQHSTPPKTKRKVEFEPKKKRKV (SEQ ID NO:75), and, optionally, wherein the one or more NLS are linked to the Class 2, Type V CRISPR protein or to an adjacent NLS with a linker peptide wherein the linker peptide is selected from the group consisting of SR, RS, (G)n (SEQ ID NO: 1023), (GS)n (SEQ ID NO: 1024), (GSGGS)n (SEQ ID NO: 399), (GGSGGS)n (SEQ ID NO: 400), (GGGS)n (SEQ ID NO: 401), GGSG (SEQ ID NO: 402), GGSGG (SEQ ID NO: 403), GSGSG (SEQ ID NO: 404), GSGGG (SEQ ID NO: 405), GGGSG (SEQ ID NO: 406), GSSSG (SEQ ID NO: 407), GPGP (SEQ ID NO: 408), GGP, PPP, PPAPPA (SEQ ID NO: 409), PPPG (SEQ ID NO: 24), PPPGPPP (SEQ ID NO: 410), PPP(GGGS)n (SEQ ID NO: 25), (GGGS)nPPP (SEQ ID NO: 26), AEAAAKEAAAKEAAAKA (SEQ ID NO: 1025), and TPPKTKRKVEFE (SEQ ID NO: 27), wherein n is 1 to 5. 
     
     
         67 . The Class 2, Type V CRISPR protein of  claim 65  or  claim 66 , wherein the one or more NLS are positioned at or near the C-terminus of the protein. 
     
     
         68 . The Class 2, Type V CRISPR protein of  claim 65  or  claim 66 , wherein the one or more NLS are positioned at or near at the N-terminus of the protein. 
     
     
         69 . The Class 2, Type V CRISPR protein of  claim 65  or  claim 66 , comprising at least two NLS, wherein the at least two NLS are positioned at or near the N-terminus and at or near the C-terminus of the protein. 
     
     
         70 . The Class 2, Type V CRISPR protein of any one of  claims 29 - 69 , wherein the Class 2, Type V CRISPR protein is capable of forming a ribonuclear protein complex (RNP) with a gRNA. 
     
     
         71 . The Class 2, Type V CRISPR protein of  claim 70 , wherein the RNP exhibits at least one or more improved characteristics as compared to a an RNP of a reference protein of any one of SEQ ID NOS: 1-3 and a gRNA of SEQ ID NO: 4 or SEQ ID NO: 5. 
     
     
         72 . The Class 2, Type V CRISPR protein of 71, wherein the improved characteristic is selected from the group consisting of increased binding affinity to a guide nucleic acid (gRNA); increased binding affinity to a target nucleic acid; improved ability to utilize a greater spectrum of one or more PAM sequences, including ATC, CTC, GTC, or TTC, in the editing of target nucleic acid; increased unwinding of the target nucleic acid; increased editing activity; increased editing efficiency; increased editing specificity of the target nucleic acid; increased nuclease activity; increased target strand loading for double strand cleavage; decreased target strand loading for single strand nicking; decreased off-target cleavage of the target nucleic acid; increased binding of non-target nucleic acid strand; and increased protein:gRNA complex (RNP) stability. 
     
     
         73 . The Class 2, Type V CRISPR protein of  claim 71  or  claim 72 , wherein the improved characteristic of the RNP is at least about 1.1 to about 100,000-fold increased relative to the RNP of a reference protein of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3 and the gRNA of SEQ ID NO: 4 or SEQ ID NO: 5. 
     
     
         74 . The Class 2, Type V CRISPR protein of  claim 71  or  claim 72 , wherein the improved characteristic of the RNP is at least about 10-fold, at least about 100-fold, at least about 1,000-fold, or at least about 10,000-fold increased relative to the RNP of the reference protein of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3 and the gRNA of SEQ ID NOS: 4 or 5. 
     
     
         75 . The Class 2, Type V CRISPR protein of any one of  claims 71 - 74 , wherein the improved characteristic of the RNP comprises a 1.1 to 100-fold improvement in editing efficiency compared to the RNP of the reference protein of SEQ ID NO: 2 and the gRNA comprising of SEQ ID NOS: 4 or 5. 
     
     
         76 . A gene editing pair comprising a gRNA and a Class 2, Type V CRISPR protein, the pair comprising:
 a. a gRNA of any one of  claims 25 - 28 ; and   b. a Class 2, Type V CRISPR protein of any one of  claims 29 - 75 .   
     
     
         77 . The gene editing pair of  claim 76 , wherein the gRNA and the Class 2, Type V CRISPR protein are capable of forming a ribonuclear protein complex (RNP). 
     
     
         78 . The gene editing pair of  claim 76  or  claim 77 , wherein the gRNA and the Class 2, Type V CRISPR protein are associated together as a ribonuclear protein complex (RNP). 
     
     
         79 . The gene editing pair of  claim 77  or  claim 78 , wherein an RNP of the Class 2, Type V CRISPR protein and the gRNA exhibit at least one or more improved characteristics as compared to an RNP of a reference protein of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3 and a gRNA comprising a sequence of SEQ ID NO: 4 or SEQ ID NO: 5. 
     
     
         80 . The gene editing pair of  claim 79 , wherein the improved characteristic is selected from one or more of the group consisting of increased binding affinity of the Class 2, Type V CRISPR protein to the gRNA; increased binding affinity to a target nucleic acid; increased ability to utilize a greater spectrum of one or more PAM sequences, including ATC, CTC, GTC, or TTC, in the editing of target nucleic acid; increased unwinding of the target nucleic acid; increased editing activity; increased editing efficiency; increased editing specificity of the target nucleic acid; increased nuclease activity; increased target strand loading for double strand cleavage; decreased target strand loading for single strand nicking; decreased off-target cleavage of the target nucleic acid; increased binding of non-target nucleic acid strand; increased protein:gRNA complex (RNP) stability; and increased fusion characteristics. 
     
     
         81 . The gene editing pair of  claim 79  or  claim 80 , wherein the improved characteristic of the RNP of the Class 2, Type V CRISPR protein and the gRNA is at least about 1.1 to about 100-fold or more increased relative to the RNP of a reference protein of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3 and the gRNA comprising a sequence of SEQ ID NO: 4 or SEQ ID NO: 5 in a comparable in vitro assay system. 
     
     
         82 . The gene editing pair of  claim 79  or  claim 80 , wherein the improved characteristic of the Class 2, Type V CRISPR protein is at least about 1.1, at least about 2, at least about 10, at least about 100-fold or more increased relative to the reference protein of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3 and the gRNA comprising a sequence of SEQ ID NO: 4 or SEQ ID NO: 5 in a comparable in vitro assay system. 
     
     
         83 . The gene editing pair of any one of  claims 77 - 82 , wherein the RNP comprising the Class 2, Type V CRISPR protein and the gRNA exhibits greater editing efficiency and/or binding of a target nucleic acid sequence in the target nucleic acid when any one of the PAM sequences TTC, ATC, GTC, or CTC is located 1 nucleotide 5′ to the non-target strand of the protospacer having identity with the targeting sequence of the gRNA in a cellular assay system compared to the editing efficiency and/or binding of an RNP comprising a reference protein of SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3 and a reference gRNA in a comparable assay system. 
     
     
         84 . The gene editing pair of  claim 83 , wherein the PAM sequence is TTC. 
     
     
         85 . The gene editing pair of  claim 83 , wherein the PAM sequence is ATC. 
     
     
         86 . The gene editing pair of  claim 83 , wherein the PAM sequence is CTC. 
     
     
         87 . The gene editing pair of  claim 83 , wherein the PAM sequence is GTC. 
     
     
         88 . The gene editing pair of any one of  claims 83 - 87 , wherein the RNP comprising the Class 2, Type V CRISPR and the gRNA exhibits increased binding affinity for the one or more PAM sequences that is at least 1.5-fold, at least 2-fold, at least 4-fold, at least 10-fold, at least 20-fold, at least 30-fold, or at least 40-fold greater compared to the binding affinity of an RNP of any one of the reference proteins of SEQ ID NOS:1-3 and the gRNA of SEQ ID NO: 4 or SEQ ID NO: 5, when assessed in a comparable in vitro assay system. 
     
     
         89 . The gene editing pair of any one of  claims 77 - 88 , wherein the RNP of the Class 2, Type V CRISPR protein and the gRNA exhibits increased editing efficiency that is at least 1.5-fold, at least 2-fold, at least 4-fold, at least 10-fold, at least 20-fold, at least 30-fold, or at least 40-fold greater compared to the editing efficiency of an RNP of any one of the reference proteins of SEQ ID NOS:1-3 and the gRNA of SEQ ID NO: 4 or SEQ ID NO: 5, when assessed in a comparable in vitro assay system. 
     
     
         90 . The gene editing pair of any one of  claims 77 - 89 , wherein the Class 2, Type V CRISPR and the gRNA are able to form RNP having at least about a 5%, at least about a 10%, at least about a 15%, or at least about a 20% higher percentage of cleavage-competent conformation compared to an RNP of any one of the reference proteins of SEQ ID NOS: 1-3 and the gRNA of SEQ ID NO: 4 or SEQ ID NO: 5, when assessed in a comparable in vitro assay system. 
     
     
         91 . The gene editing pair of any one of  claims 77 - 90 , wherein the RNP comprising the Class 2, Type V CRISPR and the gRNA exhibit a cleavage rate for the target nucleic acid in a timed in vitro assay that is at least about 5-fold, at least about 10-fold, or at least about 20-fold higher compared to an RNP of any one of the reference proteins of SEQ ID NOS: 1-3 and the gRNA of SEQ ID NO: 4 or SEQ ID NO: 5, when assessed in a comparable in vitro assay system. 
     
     
         92 . The gene editing pair of any one of  claims 77 - 91 , wherein the RNP comprising the Class 2, Type V CRISPR and the gRNA exhibit higher percent editing of the target nucleic acid in a timed in vitro assay that is at least about 5-fold, at least about 10-fold, at least about 20-fold, or at least about 100-fold higher compared to an RNP of any one of the reference proteins of SEQ ID NOS: 1-3 and the gRNA of SEQ ID NO: 4 or SEQ ID NO:5, when assessed in a comparable in vitro assay system. 
     
     
         93 . A catalytically-dead Class 2, Type V CRISPR protein, comprising a sequence selected from the group consisting of SEQ NOs: 44-62 and 1232-1235, as set forth in Table 7, or a sequence having at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, at least 99% thereto. 
     
     
         94 . A catalytically-dead Class 2, Type V CRISPR protein, comprising a sequence selected from the group consisting of SEQ NOs: 44-62 and 1232-1235, as set forth in Table 7. 
     
     
         95 . The Class 2, Type V CRISPR protein of  claim 93  or  claim 94 , wherein and RNP of the catalytically-dead Class 2, Type V CRISPR protein and a gRNA of any one of  claims 25 - 28  retain the ability to bind target nucleic acid. 
     
     
         96 . A nucleic acid comprising a sequence that encodes the gRNA scaffold of any one of  claims 1 - 24 , or the gRNA of any one of  claims 25 - 28 . 
     
     
         97 . A nucleic acid comprising a sequence that encodes the Class 2, Type V CRISPR protein of any one of  claims 29 - 75 . 
     
     
         98 . The nucleic acid of  claim 97 , wherein the sequence that encodes the Class 2, Type V CRISPR protein is codon optimized for expression in a eukaryotic cell. 
     
     
         99 . A vector comprising the gRNA of any one of  claims 25 - 28 , the Class 2, Type V CRISPR protein of any one of  claims 29 - 75 , or the nucleic acid of any one of  claims 96 - 98 . 
     
     
         100 . The vector of  claim 99 , wherein the vector comprises a promoter. 
     
     
         101 . The vector of  claim 99  or  claim 100 , wherein the vector is selected from the group consisting of a retroviral vector, a lentiviral vector, an adenoviral vector, an adeno-associated viral (AAV) vector, a herpes simplex virus (HSV) vector, a CasX delivery particle (XDP), a plasmid, a minicircle, a nanoplasmid, a DNA vector, and an RNA vector. 
     
     
         102 . The vector of  claim 101 , wherein the vector is an AAV vector. 
     
     
         103 . The vector of  claim 102 , wherein the AAV vector is selected from AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11, AAV12, AAV-Rh74, or AAVRh10. 
     
     
         104 . The vector of  claim 101 , wherein the vector is a retroviral vector. 
     
     
         105 . The vector of  claim 101 , wherein the vector is a XDP comprising one or more components of a gag polyprotein. 
     
     
         106 . The vector of  claim 105 , wherein the one or more components of the gag polyprotein are selected from the group consisting of matrix protein (MA), a nucleocapsid protein (NC), a capsid protein (CA), a p1 peptide, a p6 peptide, a P2A peptide, a P2B peptide, a P10 peptide, a p12 peptide, a PP21/24 peptide, a P12/P3/P8 peptide, a P20 peptide, and a protease cleavage site. 
     
     
         107 . The vector of  claim 105  or  claim 106 , wherein the Class 2, Type V CRISPR protein and the gRNA are associated together in an RNP. 
     
     
         108 . The vector of any one of  claims 105 - 107 , comprising a glycoprotein tropism factor. 
     
     
         109 . The vector of  claim 108 , wherein the glycoprotein tropism factor has binding affinity for a cell surface marker of a target cell and facilitates entry of the XDP into the target cell. 
     
     
         110 . The vector of any one of  claims 99 - 109 , comprising the donor template. 
     
     
         111 . A host cell comprising the vector of any one of  claims 99 - 110 . 
     
     
         112 . The host cell of  claim 111 , wherein the host cell is selected from the group consisting of Baby Hamster Kidney fibroblast (BHK) cells, human embryonic kidney 293 (HEK293) cells, human embryonic kidney 293T (HEK293T) cells, NS0 cells, SP2/0 cells, YO myeloma cells, P3X63 mouse myeloma cells, PER cells, PER.C6 cells, hybridoma cells, NIH3T3 cells, CV-1 (simian) in Origin with SV40 genetic material (COS) cells, HeLa, Chinese hamster ovary (CHO) cells, or yeast cells. 
     
     
         113 . A method of modifying a target nucleic acid in a cell, comprising contacting the target nucleic acid of the cell with: i) the gene editing pair of any one of  claims 76 - 92 ; ii) the gene editing pair of any one of  claims 76 - 92  together with a donor template; iii) one or more nucleic acids encoding the gene editing pair of (i) or (ii); iv) a vector comprising the nucleic acid of (iii); v) an XDP comprising the gene editing pair of (i) or (ii); or vi) combinations of two or more of (i) to (v), wherein the contacting of the target nucleic acid modifies the target nucleic acid. 
     
     
         114 . The method of  claim 113 , comprising contacting the target with a plurality of gene editing pairs comprising a first and a second, or a plurality of gRNAs comprising targeting sequences complementary to different or overlapping regions of the target nucleic acid. 
     
     
         115 . The method of  claim 113 , comprising contacting the target with a plurality of nucleic acids encoding gene editing pairs comprising a first and a second, or a plurality of gRNAs comprising targeting sequences complementary to different or overlapping regions of the target nucleic acid. 
     
     
         116 . The method of  claim 113 , comprising contacting the target with a plurality of XDP comprising gene editing pairs comprising a first and a second, or a plurality of gRNAs comprising targeting sequences complementary to different or overlapping regions of the target nucleic acid. 
     
     
         117 . The method of any one of  claim 113 , wherein the contacting comprises binding the target nucleic acid with the gene editing pair and introducing one or more single-stranded breaks in the target nucleic acid, wherein the modifying comprises introducing a mutation, an insertion, or a deletion in the target nucleic acid. 
     
     
         118 . The method of any one of  claims 113 - 116  wherein the contacting comprises binding the target nucleic acid and introducing one or more double-stranded breaks in the target nucleic acid, wherein the modifying comprises introducing a mutation, an insertion, or a deletion in the target nucleic acid. 
     
     
         119 . The method of any one of  claims 113 - 118 , comprising contacting the target nucleic acid with a nucleotide sequence of a donor template nucleic acid wherein the donor template comprises a nucleotide sequence having homology to the target nucleic acid. 
     
     
         120 . The method of  claim 119 , wherein the donor template comprises homologous arms on the 5′ and 3′ ends of the donor template. 
     
     
         121 . The method of  claim 119  or  claim 120 , wherein the donor template is inserted in the target nucleic acid at the break site by homology-directed repair. 
     
     
         122 . The method of  claim 121 , wherein the donor template is inserted in the target nucleic acid at the break site by non-homologous end joining (NHEJ) or micro-homology end joining (MMEJ). 
     
     
         123 . The method of any one of  claims 113 - 122 , wherein the modifying of the cell occurs in vitro. 
     
     
         124 . The method of any one of  claims 113 - 122 , wherein modifying of the cell occurs in vivo. 
     
     
         125 . The method of any one of  claims 113 - 124 , wherein the cell is a eukaryotic cell. 
     
     
         126 . The method of  claim 125 , wherein the eukaryotic cell is selected from the group consisting of a rodent cell, a mouse cell, a rat cell, a primate cell, and a non-human primate cell. 
     
     
         127 . The method of  claim 125 , wherein the eukaryotic cell is a human cell. 
     
     
         128 . The method of any one of  claims 113 - 127 , wherein the cell is selected from the group consisting of an embryonic stem cell, an induced pluripotent stem cell, a germ cell, a fibroblast, an oligodendrocyte, a glial cell, a hematopoietic stem cell, a neuron progenitor cell, a neuron, a muscle cell, a bone cell, a hepatocyte, a pancreatic cell, a retinal cell, a cancer cell, a T-cell, a B-cell, an NK cell, a fetal cardiomyocyte, a myofibroblast, a mesenchymal stem cell, an autotransplanted expanded cardiomyocyte, an adipocyte, a totipotent cell, a pluripotent cell, a blood stem cell, a myoblast, an adult stem cell, a bone marrow cell, a mesenchymal cell, a parenchymal cell, an epithelial cell, an endothelial cell, a mesothelial cell, a fibroblast cell, an osteoblast cell, a chondrocyte cell, an exogenous cell, an endogenous cell, a stem cell, a hematopoietic stem cell, a bone-marrow derived progenitor cell, a myocardial cell, a skeletal cell, a fetal cell, an undifferentiated cell, a multi-potent progenitor cell, a unipotent progenitor cell, a monocyte, a cardiac myoblast, a skeletal myoblast, a macrophage, a capillary endothelial cell, a xenogenic cell, an allogenic cell, an autologous cell, and a post-natal stem cell. 
     
     
         129 . The method of any one of  claims 124 - 128 , wherein the cell is in a subject. 
     
     
         130 . The method of  claim 129 , wherein the modifying occurs in the cells of the subject having a mutation in an allele of a gene wherein the mutation causes a disease or disorder in the subject. 
     
     
         131 . The method of  claim 130 , wherein the modifying changes the mutation to a wild type allele of the gene or results in the expression of a functional gene product. 
     
     
         132 . The method of  claim 130 , wherein the modifying knocks down or knocks out the allele of the gene causing the disease or disorder in the subject. 
     
     
         133 . The method of any one of  claims 129 - 132 , wherein the cell is autologous with respect to the subject. 
     
     
         134 . The method of any one of  claims 129 - 132 , wherein the cell is allogeneic autologous with respect to the subject. 
     
     
         135 . The method of any one of  claims 113 - 134 , wherein the vector is an Adeno-Associated Viral (AAV) vector. 
     
     
         136 . The method of  claim 135 , wherein the AAV is AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV-Rh74, or AAVRh10. 
     
     
         137 . The method of  claim 113 , wherein the vector is a lentiviral vector. 
     
     
         138 . The method of any one of  claims 113 - 137 , wherein the vector is administered to a subject in need using a therapeutically effective dose. 
     
     
         139 . The method of  claim 138 , wherein the subject is selected from the group consisting of mouse, rat, pig, and non-human primate. 
     
     
         140 . The method of  claim 138 , wherein the subject is a human. 
     
     
         141 . The method of any one of  claims 138 - 140 , wherein the vector is administered to the subject at a dose of at least about 1×10 5  vector genomes/kg (vg/kg), at least about 1×10 6  vg/kg, at least about 1×10 7  vg/kg, at least about 1×10 8  vg/kg, at least about 1×10 9  vg/kg, at least about 1×10 10  vg/kg, at least about 1×10 11  vg/kg, at least about 1×10 12  vg/kg, at least about 1×10 13  vg/kg, at least about 1×10 14  vg/kg, at least about 1×10 15  vg/kg, or at least about 1×10 16  vg/kg. 
     
     
         142 . The method of any one of  claims 138 - 140 , wherein the vector is administered to the subject at a dose of at least about 1×10 5  vg/kg to about 1×10 16  vg/kg, at least about 1×10 6  vg/kg to about 1×10 15  vg/kg, or at least about 1×10 7  vg/kg to about 1×10 14  vg/kg. 
     
     
         143 . The method of  claim 113 , wherein the vector is an XDP. 
     
     
         144 . The method of  claim 143 , wherein the XDP is administered to the subject in need using a therapeutically effective dose. 
     
     
         145 . The method of  claim 144 , wherein the XDP is administered to the subject at a dose of at least about 1×10 5  particles/kg, at least about 1×10 6  particles/kg, at least about 1×10 7  particles/kg at least about 1×10 8  particles/kg, at least about 1×10 9  particles/kg, at least about 1×10 10  particles/kg, at least about 1×10 11  particles/kg, at least about 1×10 12  particles/kg, at least about 1×10 13  particles/kg, at least about 1×10 14  particles/kg, at least about 1×10 15  particles/kg, at least about 1×10 16  particles/kg. 
     
     
         146 . The method of  claim 143 , wherein the XDP is administered to the subject at a dose of at least about 1×10 5  particles/kg to about 1×10 16  particles/kg, or at least about 1×10 6  particles/kg to about 1×10 15  particles/kg, or at least about 1×10 7  particles/kg to about 1×10 14  particles/kg. 
     
     
         147 . The method of any one of  claims 138 - 146 , wherein the vector is administered by a route of administration selected from the group consisting of intraparenchymal, intravenous, intra-arterial, intracerebroventricular, intracisternal, intrathecal, intracranial, and intraperitoneal routes wherein the administering method is injection, transfusion, or implantation. 
     
     
         148 . The method of any one of  claims 141 - 147 , wherein the vector is administered to the subject according to a treatment regimen comprising one or more consecutive doses using a therapeutically effective dose of the vector. 
     
     
         149 . The method of  claim 148 , wherein the therapeutically effective dose is administered to the subject as two or more doses over a period of at least two weeks, or at least one month, or at least two months, or at least three months, or at least four months, or at least five months, or at least six months, or once a year, or every 2 or 3 years. 
     
     
         150 . A cell comprising a target nucleic acid modified by the gene editing pair of any one of  claims 76 - 92 . 
     
     
         151 . A cell edited by the method of any one of  claims 113 - 149 . 
     
     
         152 . The cell of  claim 150  or  151 , wherein the cell is a prokaryotic cell. 
     
     
         153 . The cell of  claim 150  or  151 , wherein the cell is a eukaryotic cell. 
     
     
         154 . The cell of  claim 153 , wherein the eukaryotic cell is selected from the group consisting of a rodent cell, a mouse cell, a rat cell, a primate cell, and a non-human primate cell. 
     
     
         155 . The cell of  claim 153 , wherein the eukaryotic cell is a human cell. 
     
     
         156 . A composition, comprising the Class 2, Type V CRISPR protein of any one of  claims 29 - 75 . 
     
     
         157 . The composition of  claim 156 , comprising the gRNA of any one of  claims 25 - 28 . 
     
     
         158 . The composition of  claim 157 , wherein the protein and the gRNA are associated together in a ribonuclear protein complex (RNP). 
     
     
         159 . The composition of any one of  claims 156 - 158 , comprising a donor template nucleic acid wherein the donor template comprises a nucleotide sequence having homology to a target nucleic acid. 
     
     
         160 . The composition of any one of  claims 156 - 159 , comprising a buffer, a nuclease inhibitor, a protease inhibitor, a liposome, a therapeutic agent, a label, a label visualization reagent, or any combination of the foregoing. 
     
     
         161 . A composition, comprising a gRNA scaffold of any one of  claims 1 - 24 , or a gRNA of any one of  claims 25 - 28 . 
     
     
         162 . The composition of  claim 161 , comprising the Class 2, Type V CRISPR protein of any one of  claims 29 - 75 . 
     
     
         163 . The composition of  claim 162 , wherein the Class 2, Type V CRISPR protein and the gRNA are associated together in a ribonuclear protein complex (RNP). 
     
     
         164 . The composition of any one of  claims 161 - 163 , comprising a donor template nucleic acid wherein the donor template comprises a nucleotide sequence having homology to a target nucleic acid. 
     
     
         165 . The composition of any one of  claims 161 - 164 , comprising a buffer, a nuclease inhibitor, a protease inhibitor, a liposome, a therapeutic agent, a label, a label visualization reagent, or any combination of the foregoing. 
     
     
         166 . A composition, comprising the gene editing pair of any one of  claims 76 - 92 . 
     
     
         167 . The composition of  claim 166 , comprising a donor template nucleic acid wherein the donor template comprises a nucleotide sequence having homology to a target nucleic acid. 
     
     
         168 . The composition of  claim 166  or  claim 167 , comprising a buffer, a nuclease inhibitor, a protease inhibitor, a liposome, a therapeutic agent, a label, a label visualization reagent, or any combination of the foregoing. 
     
     
         169 . A kit, comprising the Class 2, Type V CRISPR protein of any one of  claims 29 - 75  and a container. 
     
     
         170 . The kit of  claim 169 , comprising a gRNA scaffold of any one of  claims 1 - 24 , or a gRNA of any one of  claims 25 - 28 . 
     
     
         171 . The kit of  claim 169  or  claim 170 , comprising a donor template nucleic acid wherein the donor template comprises a nucleotide sequence having homology to a target nucleic acid sequence of a target nucleic acid. 
     
     
         172 . The kit of any one of  claims 169 - 171 , comprising a buffer, a nuclease inhibitor, a protease inhibitor, a liposome, a therapeutic agent, a label, a label visualization reagent, or any combination of the foregoing. 
     
     
         173 . A kit, comprising a gRNA scaffold of any one of  claims 1 - 24 , or a gRNA of any one of  claims 25 - 28 . 
     
     
         174 . The kit of  claim 173 , comprising the Class 2, Type V CRISPR protein of any one of  claims 29 - 75 . 
     
     
         175 . The kit of  claim 173  or  claim 174 , comprising a donor template nucleic acid wherein the donor template comprises a nucleotide sequence having homology to a target nucleic acid sequence of a target nucleic acid. 
     
     
         176 . The kit of any one of  claims 173 - 175 , comprising a buffer, a nuclease inhibitor, a protease inhibitor, a liposome, a therapeutic agent, a label, a label visualization reagent, or any combination of the foregoing. 
     
     
         177 . A kit, comprising the gene editing pair of any one of  claims 76 - 92 . 
     
     
         178 . The kit of  claim 177 , comprising a donor template nucleic acid wherein the donor template comprises a nucleotide sequence having homology to a target nucleic acid. 
     
     
         179 . The kit of  claim 177  or  claim 178 , comprising a buffer, a nuclease inhibitor, a protease inhibitor, a liposome, a therapeutic agent, a label, a label visualization reagent, or any combination of the foregoing. 
     
     
         180 . An engineered Class 2, Type V CRISPR protein comprising any one of the sequences listed in Table 3. 
     
     
         181 . A gRNA comprising any one of the gRNA scaffold variant sequences listed in Table 2. 
     
     
         182 . The gRNA of  claim 181 , wherein one or more uracils (U) of the gRNA scaffold variants of the Table 2 sequences are replaced with thymines (T). 
     
     
         183 . The gRNA of  claim 182 , comprising a targeting sequence of at least 10 to 30 nucleotides complementary to a target nucleic acid. 
     
     
         184 . The gRNA of  claim 183 , wherein the targeting sequence has 20 nucleotides. 
     
     
         185 . The gRNA of  claim 183 , wherein the targeting sequence has 19 nucleotides. 
     
     
         186 . The gRNA of  claim 183 , wherein the targeting sequence has 18 nucleotides. 
     
     
         187 . The gRNA of  claim 183 , wherein the targeting sequence has 17 nucleotides. 
     
     
         188 . The gRNA of  claim 183 , wherein the targeting sequence has 16 nucleotides. 
     
     
         189 . The gRNA of  claim 183 , wherein the targeting sequence has 15 nucleotides. 
     
     
         190 . A method of treating a disease in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of a composition comprising: (a) an engineered class 2, type V CRISPR protein of any one of  claims 29 - 75  and  180  and (b) a gRNA of any one of  claims 25 - 28  and  181 - 189 . 
     
     
         191 . A composition comprising: (a) an engineered class 2, type V CRISPR protein of any one of  claims 29 - 75  and  180  and (b) a gRNA of any one of  claims 25 - 28  and  181 - 189 , for use as a medicament for the treatment of a subject having a disease.