WO2015070083A1

WO2015070083A1 - CRISPR-RELATED METHODS AND COMPOSITIONS WITH GOVERNING gRNAS

Info

Publication number: WO2015070083A1
Application number: PCT/US2014/064663
Authority: WO
Inventors: Alexandra Glucksmann; Deborah PALESTRANT; Louis Anthony Tartaglia; Jordi MATA-FINK; Agnieszka Dorota CZECHOWICZ; Alexis Borisy
Original assignee: Editas Medicine,Inc.
Priority date: 2013-11-07
Filing date: 2014-11-07
Publication date: 2015-05-14
Also published as: US20150232881A1; US9834791B2; US10190137B2; AU2020250254B2; EP4372090A3; US10640788B2; EP3363903B1; KR20220044611A; EP3066201A1; JP7537707B2; KR20230054509A; JP2016536021A; AU2014346559B2; AU2020250254A1; NO3123224T3; LT3066201T; DK3066201T3; CA2930015A1; US20180127783A1; PT3066201T

Abstract

Disclosed herein are methods and compositions useful in targeting a payload to, or editing a target nucleic acid, where a governing gRNA molecule is used to target, optionally inactivate, a Cas9 molecule or a Cas9 molecule/gRNA complex.

Description

CRISPR-RELATED METHODS AND COMPOSITIONS WITH GOVERNING gRNAS

CROSS-REFERENCE TO RELATED APPLICATIONS

The present application claims the benefit of U.S. Provisional Application No.

61/901,215, filed November 7, 2013, the contents of which are hereby incorporated by reference in their entirety.

FIELD OF THE INVENTION

The invention relates to CRISPR-related methods and components for editing of, or delivery of a payload to, a target nucleic acid sequence.

BACKGROUND OF THE INVENTION CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats) evolved in bacteria as an adaptive immune system to defend against viral attack. Upon exposure to a virus, short segments of viral DNA are integrated into the CRISPR locus. RNA is transcribed from a portion of the CRISPR locus that includes the viral sequence. That RNA, which contains sequence complimentary to the viral genome, mediates targeting of a Cas9 protein to to a target sequence in the viral genome. The Cas9 protein cleaves and thereby silences the viral target.

Recently, the CRISPR/Cas system has been adapted for genome editing in eukaryotic cells. The introduction of site-specific double strand breaks (DSBs) allows for target sequence alteration through one of two endogenous DNA repair mechanisms— either non-homologous end-joining (NHEJ) or homology-directed repair (HDR). The CRISPR/Cas system has also been used for gene regulation including transcription repression and activation without altering the target sequence. Targeted gene regulation based on the CRISPR/Cas system uses an

enzymatically inactive Cas9 (also known as a catalytically dead Cas9).

Despite the recent advances adapting the CRISPR/Cas system for genome editing in eukaryotic cells, there remains a need for improved regulation and control of these systems for use in eukaryotic cells. SUMMARY OF THE INVENTION

Disclosed herein are methods and compositions, e.g., a Cas9 molecule complexed with a gRNA molecule, that can be used to target a specific location in a target DNA. Depending on the Cas9 molecule/gRNA molecule complex used in the disclosed methods and compositions, specific editing of a target nucleic acid, or the delivery of a payload, can be effected.

Methods and compositions that use, or include, a nucleic acid, e.g., a DNA, that encodes a Cas9 molecule or a gRNA molecule, can, in addition, use or include a "governing gRNA molecule." The governing gRNA molecule can complex with the Cas9 molecule to inactivate or silence a component of a Cas9 system. In one aspect, the disclosure features a gRNA molecule, referred to herein as a governing gRNA molecule, comprises a targeting domain which targets a component of the Cas9 system. In an embodiment, the governing gRNA molecule targets and silences (1) a nucleic acid that encodes a Cas9 molecule (i.e., a Cas9-targeting gRNA molecule), (2) a nucleic acid that encodes a gRNA molecule (i.e., a gRNA-targeting gRNA molecule), or (3) a nucleic acid sequence engineered into the Cas9 components that is designed with minimal homology to other nucleic acid sequences in the cell to minimize off-target cleavage (i.e., an engineered control sequence-targeting gRNA molecule).

The targeting sequence for the governing gRNA can be selected to increase regulation or control of the Cas9 system and/or to reduce or minimize off-target effects of the system. For example, a governing gRNA can minimize undesirable cleavage, e.g., "recleavage" after Cas9 mediated alteration of a target nucleic acid or off-target cutting of Cas9, by inactivating (e.g., cleaving) a nucleic acid that encodes a Cas9 molecule. In an embodiment, a governing gRNA places temporal or other limit(s) on the level of expression or activity of the Cas9

molecule/gRNA molecule complex. In an embodiment, the governing gRNA reduces off-target or other unwanted activity.

A target sequence for the governing gRNA can be disposed in the control or coding region of the Cas9 encoding sequence. This can be a Cas9 sequence or a non-Cas9 sequence, e.g., a sequence which is selected for, or which results in, reduced or minimized off target effect. The silencing, or inactivation, can be effected by cleaving the targeted nucleic acid sequence or by binding a Cas9 molecule/governing gRNA molecule complex to the targeted nucleic acid sequence. In an aspect, the disclosure features a gRNA molecule that targets, optionally inactivates, a Cas9 molecule. In an embodiment, the gRNA molecule targets a nucleic acid sequence that encodes the Cas9 molecule. For example, a sequence that encodes the Cas9 molecule can comprise one or more of: a sequence encoding the amino acid sequence of the Cas9 molecule, a sequence encoding the amino acid sequence of the Cas9 molecule comprising non-translated sequence, or a sequence encoding the amino acid sequence of the Cas9 molecule comprising non-transcribed sequence.

In an embodiment, the Cas9 molecule is an eaCas9 molecule. In another embodiment, the Cas9 molecule is an eiCas9 molecule.

In an embodiment, the gRNA is configured to provide a Cas9 molecule-mediated cleavage event in the nucleic acid sequence that encodes the Cas9 molecule. In an embodiment, the gRNA molecule comprises a targeting domain configured to provide a Cas9 molecule- mediated cleavage event in the nucleic acid sequence that encodes the Cas9 molecule.

In an embodiment, the gRNA molecule:

targets the Cas9 molecule-amino acid coding sequence of the nucleic acid sequence; is configured to provide a Cas9 molecule-mediated cleavage event in the Cas 9 molecule- amino acid coding sequence of the nucleic acid sequence; or

comprises a targeting domain configured to provide a Cas9 molecule-mediated cleavage event in the Cas9 molecule-amino acid coding sequence of the nucleic acid sequence.

In an embodiment, the gRNA molecule:

targets a non-coding sequence of the nucleic acid sequence;

is configured to provide a Cas9 molecule-mediated cleavage event in a non-coding sequence of the nucleic acid sequence; or

comprises a targeting domain configured to provide a Cas9 molecule-mediated cleavage event in a non-coding sequence of the nucleic acid sequence.

In an embodiment, the gRNA molecule:

targets an untranslated sequence of the nucleic acid sequence;

is configured to provide a Cas9 molecule-mediated cleavage event in an untranslated sequence of the nucleic acid sequence; or

comprises a targeting domain configured to provide a Cas9 moleucle-mediated cleavage event in an untranslated sequence of the nucleic acid sequence. In an embodiment, the gRNA molecule:

targets the nucleic acid sequence 5' of the Cas 9 molecule- amino acid coding region; is configured to provide a Cas9 molecule-mediated cleavage event in the nucleic acid sequence 5' of the Cas9 molecule-coding region; or

comprises a targeting domain configured to provide a Cas9 molecule-mediated cleavage event 5' of the Cas9 molecule-coding region of the nucleic acid sequence.

In an embodiment, the gRNA molecule:

targets the nucleic acid sequence that encodes the Cas9 molecule 3' of the Cas9 molecule-coding region;

is configured to provide a Cas9 molecule-mediated cleavage event in the nucleic acid sequence 3' of the Cas9 molecule-coding region; or

comprises a targeting domain configured to provide a Cas9 molecule-mediated cleavage event 3' of the Cas9 molecule-coding region of the nucleic acid sequence.

In an embodiment, the gRNA molecule:

targets the promoter region of the nucleic acid sequence,

is configured to provide a Cas9 molecule-mediated cleavage event in the promoter region of nucleic acid sequence; or

comprises a targeting domain configured to provide a Cas9 molecule-mediated cleavage event in the promoter region of the nucleic acid sequence,

wherein the promoter region is functionally linked to the Cas9 molecule amino acid coding region.

In an embodiment, the gRNA molecule:

targets Cas9 molecule intronic sequence of the nucleic acid sequence;

is configured to provide a Cas9 molecule-mediated cleavage event in Cas9 molecule intronic sequence of the nucleic acid sequence; or

comprises a targeting domain configured to provide a Cas9 molecule-mediated cleavage event in Cas9 molecule intronic sequence of the nucleic acid sequence.

In an embodiment, the Cas9 molecule is a S. pyogenes Cas9 molecule. In another embodiment, the Cas9 molecule is a S. aureus Cas9 molecule.

In an embodiment, the gRNA molecule is selected from Tables E1-E6. In another embodiment, the gRNA molecule is selected from Tables E7-E12. In an embodiment, the gRNA is a chimeric gRNA. In another embodiment, the gRNA is a modular gRNA.

In an embodiment, the governing gRNA molecule targets the coding sequence, or a control region, e.g., a promoter, for the Cas9 system component to be negatively regulated. For example, the gRNA can target the coding sequence for Cas9, or a control region, e.g., a promoter, that regulates the expression of the Cas9 coding sequence. In an embodiment, the governing gRNA, e.g., a Cas9-targeting gRNA molecule, or a nucleic acid that encodes it, is introduced separately, e.g., later than the Cas9 molecule or a nucleic acid that encodes it. For example, a first vector, e.g., a viral vector, e.g., an AAV vecvtor, can introduce nucleic acid encoding a Cas9 and one or more gRNAs and a second vector, e.g., a viral vector, e.g., an AAV vecvtor, can introduce a nucleic acid encoding a governing gRNA molecule, e.g., a Cas9- targeting gRNA molecule. The second vector can be introduced after the first. In an

embodiment, the governing gRNA, e.g., a Cas9-targeting gRNA molecule, or a nucleic acid that encodes it, can be introduced together, e.g., at the same time or in the same vector, with the Cas9 molecule or a nucleic acid that encodes it, but, e.g., under transcriptional control elements, e.g., a promoter or an enhancer, that are activated at a later time, e.g., such that after a period of time the transcription of Cas9 is silenced. In an embodiment, the transcriptional control element is activated intrinsically. In an embodiment, the transcriptional element is activated via the introduction of an external trigger.

In an aspect, the disclosure features a nucleic acid comprising a sequence that encodes a governing gRNA molecule. In an embodiment, the governing gRNA molecule comprises a Cas9 molecule-targeting gRNA molecule. In an embodiment, the nucleic acid comprises a sequence that encodes a gRNA molecule described herein. In an embodiment, the nucleic acid is purified.

In another aspect, the disclosure features a nucleic acid, e.g., one or more vectors, e.g., one or more viral vectors, e.g., one or more AAV vectors, comprising:

a) a first nucleic acid sequence that encodes a governing gRNA molecule, e.g., a Cas9 molecule-targeting gRNA molecule or a gRNA molecule-targeting gRNA molecule; and

b) a second nucleic acid sequence that encodes a Cas9 molecule, e.g., an eaCas9 or an eiCas9 molecule. In an embodiment, the governing gRNA molecule comprises a Cas9 molecule-targeting gRNA molecule. In another embodiment, the governing gRNA molecule comprises a gRNA molecule-targeting gRNA molecule.

In an embodiment, the governing gRNA molecule comprises a Cas9 molecule-targeting gRNA molecule and the Cas9 molecule-targeting gRNA molecule targets the second nucleic acid sequence that encodes the Cas9 molecule.

In an embodiment, the gRNA molecule is configured to provide a Cas9 molecule- mediated cleavage event in the second nucleic acid sequence. In an embodiment, the gRNA molecule comprises a targeting domain configured to provide a Cas9 molecule-mediated cleavage event in the second nucleic acid sequence. In an embodiment, the gRNA molecule is a gRNA molecule described herein and targets the second nucleic acid sequence.

In an embodiment, the nucleic acid is purified.

In an embodiment, component a) and component b) are provided on the same nucleic acid, e.g., the same vector, e.g., the same viral vector, e.g., the same AAV vector. In another embodiment, component a) and component b) are provided on different nucleic acids, e.g., different vectors, e.g., different viral vectors, e.g., different AAV vectors.

In an embodiment, the nucleic acid is configured such that a Cas9 molecule-targeting gRNA transcribed from said nucleic acid forms a complex with a Cas9 molecule produced from said nucleic acid.

In an embodiment, said complex is capable of inactivating or silencing, e.g., by cleaving, the nucleic acid sequence that comprises or encodes said Cas9 molecule sequence. In an embodiment, the inactivating comprises cleaving.

In an embodiment, said first nucleic acid sequence is under the control of a first control region, e.g., promoter, and said second nucleic acid sequence is under the control of a second control region, e.g., promoter, and said first and second control regions, e.g., promoters, are different, e.g., one is a constitutive promoter and one is an inducible promoter. In an

embodiment, one of the first and second control regions is a constitutive promoter and one is an inducible promoter. In an embodiment, said first nucleic acid sequence and said second nucleic acid sequence are differentially expressed, e.g., differentially expressed in terms of level of expression or temporally, e.g., the first sequence is expressed laterthan said second sequence, or the first sequence is expressed at a lower level than said second sequence.

In an embodiment, the nucleic acid further comprises:

c) a third nucleic acid sequence that encodes a gRNA molecule, e.g., a second gRNA molecule, comprising a targeting domain which is complementary with a target nucleic acid, e.g., wherein the second gRNA does not target b).

In an embodiment, the target nucleic acid is disclosed herein, e.g., a sequence from:

a gene or pathway described herein, e.g., in Section VIIB, e.g., in Table VII-13, VII-14,

VII-15, VII-16, VII-17, VII-18, VII-19, VII-20, VII, 21, VII-22, VII-23, VII-24, IX-1, IX- 1A, IX-3, or XII-1, or in Section VIII.

In an embodiment, said first nucleic acid sequence is under the control of a first control region, e.g., promoter,

said second nucleic acid sequence is under the control of said second control region, e.g., promoter, or a third control region, e.g., promoter,

said third nucleic acid sequence is under the control of said second control region, e.g., promoter, or said third control region, e.g., promoter, and

said first control region, e.g., promoter, is different from said second and/or said third control region, e.g., promoter.

In an embodiment, said first nucleic acid sequence and said third nucleic acid sequence are differentially expressed, e.g., differentially expressed in terms of level of expression or temporally, e.g., the first sequence is expressed laterthan said third sequence, or the first sequence is expressed at a lower level than said third sequence.

In an embodiment, the nucleic acid further comprises a template nucleic acid (referred to interchangeably herein as a swap nucleic acid sequence), e.g., having 5' and 3' flanking region sequences recognized by one or more governing gRNAs.

In an embodiment, the nucleic acid sequence that comprises or encodes the Cas9 molecule sequence or the gRNA molecule sequence (e.g., targeted by the governing gRNA as described herein) further comprises a nucleic acid sequence that is capable of being used as a template nucleic acid, e.g., after being cleaved or excised (e.g., by the method described herein) from the nucleic acid sequence that comprises or encodes the Cas9 molecule sequence or the gRNA molecule sequence, e.g., as a donor DNA for homologous recombination. In an embodiment, a first governing gRNA molecule targets a region 5' of a nucleic acid sequence comprising the template nucleic acid sequence and a second governing gRNA molecule targets a region 3' of the nucleic acid sequence comprising the template nucleic acid sequence. For example, at least two (e.g., two, three, four, five or more) governing gRNAs can be used to produce one or more (e.g., two, three, four or more) template nucleic acids. In another embodiment, a single governing gRNA molecule targets both the regions 5' and 3' of the nucleic acid sequence comprising the template nucleic acid sequence. For example, the region (e.g., targeted by the governing gRNA molecule) 5' of the nucleic acid sequence comprising the template nucleic acid sequence can be the same or substantially the same as the region (e.g., targeted by the governing gRNA molecule) 3' of the nucleic acid sequence comprising the template nucleic acid sequence. In an embodiment, the nucleic acid sequence comprising the template nucleic acid sequence is in a vector, e.g., a vector described herein. In an embodiment, the vector is a viral vector, e.g., an AAV vector.

In an aspect, the disclosure features a vector comprising a nucleic acid described herein. In an embodiment, the vector is a viral vector. In an embodiment, the viral vector, is an AAV rector.

In an aspect, the disclosure features a composition, e.g., a pharmaceutical composition, comprising:

a) a governing gRNA molecule, e.g., a governing gRNA molecule described herein, or a nucleic acid that encodes a governing gRNA molecule, e.g., a nucleic acid described herein.

In an embodiment, the composition comprises one or more (e.g., 2 or all) of;

b) a Cas9 molecule, e.g., a Cas9 molecule described herein, or a nucleic acid sequence that encodes the Cas 9 molecule, e.g., a nucleic acid sequence described herein;

c) a second gRNA molecule or a nucleic acid encoding the second gRNA molecule; or d) a template nucleic acid. In an embodiment, the governing gRNA molecule comprises a Cas9 molecule-targeting gRNA molecule. In an embodiment, the Cas 9 molecule-targeting gRNA comprises a gRNA molecule described herein.

In an embodiment, the gRNA molecule is configured to provide a Cas 9 molecule- mediated cleavage event in the nucleic acid sequence that encodes the Cas 9 molecule.

In an embodiment, the composition comprises a Cas9 molecule-targeting gRNA molecule and a nucleic acid encoding the Cas9 molecule. In another embodiment, the composition comprises a Cas9 molecule-targeting gRNA molecule and the Cas9 molecule.

In an embodiment, the composition further comprises:

c) a second gRNA molecule or a nucleic acid encoding the second gRNA molecule. In an embodiment, the second gRNA targets a Cas 9 molecule to a target nucleic acid. In an embodiment, the composition further comprises:

d) a template nucleic acid.

In an embodiment, the composition comprises a second gRNA or a nucleic acid encoding the second gRNA.

In an embodiment, the template nucleic acid is configured to mediate repair of a break positioned by the second gRNA.

In an embodiment, each of a), b), c) and d) is present as a nucleic acid and are encoded on the same nucleic acid molecule. In an embodiment, a first sequence selected from a), b), c) and d) is encoded on a first nucleic acid molecule and a second sequence selected from a), b), c), and d) is encoded on a second nucleic acid molecule.

In another aspect, the disclosure features a composition, e.g., a pharmaceutical composition, comprising the nucleic acid described herein. For example, the nucleic acid, e.g., one or more vectors, e.g., one or more viral vectors, e.g., one or more AAV vectors, can comprise:

a) a first nucleic acid sequence that encodes a governing gRNA molecule, e.g., a Cas9- targeting gRNA molecule or a gRNA-targeting gRNA molecule; and

b) a second nucleic acid sequence that encodes a Cas9 molecule, e.g., an eaCas9 or an eiCas9 molecule.

In an embodiment, said nucleic acid comprises an AAV vector. In an aspect, the disclosure features a composition, e.g., a pharmaceutical composition, comprising nucleic acid sequence, e.g., a DNA, that encodes a governing gRNA molecule, e.g., a Cas9-targeting gRNA molecule or a gRNA-targeting gRNA molecule, and one or more of

a) a Cas9 molecule,

b) a second Cas9 molecule,

c) a gRNA molecule, and

d) a second gRNA molecule.

In an embodiment, each of a), b), c) and d) present are encoded on the same nucleic acid molecule. In an embodiment, a first sequence selected from a, b, c and d is encoded on a first nucleic acid molecule and a second sequence selected from a, b, c, and d is encoded on a second nucleic acid molecule. In an embodiment, said nucleic acid encodes: a and c; a, c, and d; or a, b, c, and d.

In an aspect, the disclosure features a pharmaceutical preparation comprising:

a gRNA molecule described herein;

a nucleic acid described herein;

a vector described herein; or

a composition described herein.

In an aspect, the disclosure features a cell comprising:

a gRNA molecule described herein;

a nucleic acid described herein;

a vector described herein; or

a composition described herein.

In an embodiment, the cell comprises:

a nucleic acid sequence encoding a Cas 9 molecule, wherein a sequence that encodes the Cas9 molecule can comprise one or more of: a sequence encoding the amino acid sequence of the Cas9 molecule, a sequence encoding the amino acid sequence of the Cas9 molecule comprising non-translated sequence, and a sequence encoding the amino acid sequence of the Cas9 molecule comprising non-transcribed sequence; and

a governing gRNA molecule. In an embodiment, the governing gRNA molecule comprises a gRNA molecule that targets the nucleic acid sequence that encodes the Cas 9 molecule. In an embodiment, the gRNA molecule is a gRNA molecule described herein.

In an embodiment, the cell further comprises a Cas 9 molecule.

In an embodiment, the cell further comprises a second gRNA molecule or a nucleic acid encoding the second gRNA molecule. In an embodiment, the second gRNA targets a Cas9 molecule to a target nucleic acid.

In an embodiment, the cell further comprises a template nucleic acid. In an embodiment, the template nucleic acid is configured to mediate repair of a break in the target nucleic acid positioned by the second gRNA molecule.

In an embodiment, the cell comprises target nucleic acid cleaved by second gRNA molecule mediated targeting of the Cas9 molecule.

In an embodiment, the cell comprises the target nucleic acid that has been cleaved and repaired. In an embodiment, the repair comprises template nucleic acid mediated repair.

In an embodiment, the nucleic acid sequence encoding the Cas9 molecule has not been cleaved. In an embodiment, the nucleic acid sequence encoding the Cas9 molecule can express Cas 9 molecule.

In an embodiment, the nucleic acid sequence encoding the Cas9 molecule has been cleaved by gRNA mediated targeting of Cas 9 molecule. In an embodiment, the cleaved nucleic acid sequence encoding the Cas9 molecule has reduced ability to express Cas9 molecule, as compared to the same molecule not having been cleaved. In an embodiment, the cleaved nucleic acid sequence encoding the Cas9 molecule is substantially incapable of expressing Cas 9 molecule.

In an embodiment, the cell comprises one or both of:

a cleaved nucleic acid sequence encoding the Cas9 molecule; or

a target nucleic acid having a repaired Cas9 molecule-mediated cleavage event.

In an embodiment, the cell is a vertebrate, mammalian, rodent, goat, pig, bird, chicken, turkey, cow, horse, sheep, fish, primate, or human cell.

In another embodiment, the cell is a plant cell. In an embodiment, the plant cell is a monocot or a dicot. In an embodiment, the cell is a human cell. In an embodiment, the cell is a somatic cell, germ cell, or prenatal cell. In an embodiment, the cell is a zygotic, blastocyst or embryonic cell, a stem cell, a mitotically competent cell, a meiotically competent cell. In an aspect, the disclosure features a method of altering a cell, e.g., altering the structure, e.g., sequence, of a target nucleic acid of a cell, comprising contacting said cell with the nucleic acid described herein. For example, the nucleic acid, e.g., one or more vectors, e.g., one or more viral vectors, e.g., one or more AAV vectors, can comprise:

In an embodiment, the cell is a mammalian, primate, or human cell. In an embodiment, the cell is a human cell, e.g., a cell described herein, e.g., in Section VIIA. In an embodiment, the cell is: a somatic cell, germ cell, prenatal cell, e.g., zygotic, blastocyst or embryonic cell, , a stem cell, a mitotically competent cell, or a meiotically competent cell. In an embodiment, the target nucleic acid is a chromosomal nucleic acid.

In another aspect, the disclosure features a method of altering a cell, e.g., altering the structure, e.g., sequence, of a target nucleic acid of a cell, comprising contacting the cell with an effective amount of:

a gRNA molecule described herein;

a nucleic acid described herein;

a vector described herein; or

a composition described herein.

In another embodiment, the cell is a plant cell. In an embodiment, the plant cell is a monocot or a dicot.

In an embodiment, the cell is a human cell. In an embodiment, the cell is a somatic cell, germ cell, or prenatal cell. In an embodiment, the cell is a zygotic, blastocyst or embryonic cell, a stem cell, a mitotically competent cell, a meiotically competent cell. In an embodiment, the subject is a mammal, primate, or human.

In an embodiment, the target nucleic acid is a chromosomal nucleic acid.

In another aspect, the disclosure features a method of treating a subject, e.g., by altering the structure, e.g., altering the sequence, of a target nucleic acid, comprising administering to the subject, an effective amount of the nucleic acid described herein. For example, the nucleic acid, e.g., one or more vectors, e.g., one or more viral vectors, e.g., one or more AAV vectors, can comprise:

In an embodiment, the subject is a mammalian, primate, or human. In an embodiment, the target nucleic acid is the nucleic acid of a human cell, e.g., a cell described herein, e.g., in Section VIIA. In an embodiment, the target nucleic acid is the nucleic acid of: a somatic cell, germ cell, prenatal cell, e.g., zygotic, blastocyst or embryonic cell, a stem cell, a mitotically competent cell, or a meiotically competent cell. In an embodiment, the target nucleic acid is a chromosomal nucleic acid.

In another aspect, the disclosure features a method of treating a subject, e.g., by altering the structure, e.g., altering the sequence, of a target nucleic acid, in a cell of the subject, comprising contacting the cell or the subject, with an effective amount of the nucleic acid of: a gRNA molecule described herein;

a nucleic acid described herein;

a vector described herein; or

a composition described herein.

In another embodiment, the cell is a plant cell. In an embodiment, the plant cell is a monocot or a dicot. In an embodiment, the cell is a human cell. In an embodiment, the cell is a somatic cell, germ cell, or prenatal cell. In an embodiment, the cell is a zygotic, blastocyst or embryonic cell, a stem cell, a mitotically competent cell, a meiotically competent cell.

In an embodiment, the subject is a mammal, primate, or human.

In an embodiment, the target nucleic acid is a chromosomal nucleic acid.

In an aspect, the disclosure features a reaction mixture comprising a cell and:

a gRNA molecule described herein;

a nucleic acid described herein;

a vector described herein; or

a composition described herein.

In another aspect, the disclosure features a reaction mixture comprising a composition described herein and a cell, e.g., a cell described herein.

In an aspect, the disclosure features a kit comprising:

a gRNA molecule described herein;

a nucleic acid described herein;

a vector described herein; or

a composition described herein.

In an embodiment, the kit comprises an instruction for using the gRNA molecule, the nucleic acid, the vector, or the composition, in a method described herein.

In another aspect, the disclosure features a composition, e.g., pharmaceutical

composition, comprising a governing gRNA molecule described herein.

In an embodiment, the composition further comprises a Cas9 molecule, e.g., an eaCas9 or an eiCas9 molecule. In an embodiment, said Cas9 molecule is an eaCas9 molecule. In an embodiment, said Cas9 molecule is an eiCas9 molecule.

In an embodiment, the composition further comprises a gRNA molecule comprising a targeting domain which is complementary with a target sequence from a target nucleic acid disclosed herein, e.g., a sequence from: a gene or pathway described herein, e.g., in Section VIIB, e.g., in Table VII-13, VII-14, VII-15, VII-16, VII-17, VII-18, VII-19, VII-20, VII-21, VII-22, VII-23, VII-24, IX-1, IX- 1A, IX-3, or XII-1, or in Section VIII.

In another aspect, the disclosure features a composition, e.g., pharmaceutical

composition, comprising a gRNA molecule described herein.

In an embodiment, the composition further comprises a Cas9 molecule, e.g., an eaCas9 or an eiCas9 molecule. In an embodiment, said Cas9 molecule is an eaCas9 molecule. In another embodiment, said Cas9 molecule is an eiCas9 molecule.

In an embodiment, said composition comprises a payload, e.g., a payload described herein, e.g., in Section VI, e.g., in Table VI-1, VI-2, VI-3, VI-4, VI-5, or VI-6.

In an embodiment, the payload comprises: an epigenetic modifier, e.g., a molecule that modifies DNA or chromatin; component, e.g., a molecule that modifies a histone, e.g., an epigenetic modifier described herein, e.g., in Section VI; a transcription factor, e.g., a

transcription factor described herein, e.g., in Section VI; a transcriptional activator domain; an inhibitor of a transcription factor, e.g., an anti-transcription factor antibody, or other inhibitors; a small molecule; an antibody; an enzyme; an enzyme that interacts with DNA, e.g., a helicase, restriction enzyme, ligase, or polymerase; and/or a nucleic acid, e.g., an enzymatically active nucleic acid, e.g., a ribozyme, or an mRNA, siRNA, of antisense oligonucleotide. In an embodiment, the composition further comprises a Cas9 molecule, e.g., an eiCas9, molecule.

In an embodiment, said payload is coupled, e.g., covalently or noncovalently, to a Cas9 molecule, e.g., an eiCas9 molecule. In an embodiment, said payload is coupled to said Cas9 molecule by a linker. In an embodiment, said linker is or comprises a bond that is cleavable under physiological, e.g., nuclear, conditions. In an embodiment, said linker is, or comprises, a bond described herein, e.g., in Section XL In an embodiment, said linker is, or comprises, an ester bond. In an embodiment, said payload comprises a fusion partner fused to a Cas9 molecule, e.g., an eaCas9 molecule or an eiCas9 molecule.

In an embodiment, said payload is coupled, e.g., covalently or noncovalently, to the gRNA molecule. In an embodiment, said payload is coupled to said gRNA molecule by a linker. In an embodiment, said linker is or comprises a bond that is cleavable under physiological, e.g., nuclear, conditions. In an embodiment, said linker is, or comprises, a bond described herein, e.g., in Section XL In an embodiment, said linker is, or comprises, an ester bond. In an embodiment, the composition comprises an eaCas9 molecule. In an embodiment, the composition comprises an eaCas9 molecule which forms a double stranded break in the target nucleic acid.

In an embodiment, the composition comprises an eaCas9 molecule which forms a single stranded break in the target nucleic acid. In an embodiment, said single stranded break is formed in the complementary strand of the target nucleic acid. In an embodiment, said single stranded break is formed in the strand which is not the complementary strand of the target nucleic acid.

In an embodiment, the composition comprises HNH-like domain cleavage activity but having no, or no significant, N-terminal RuvC-like domain cleavage activity. In an embodiment, the composition comprises N-terminal RuvC-like domain cleavage activity but having no, or no significant, HNH-like domain cleavage activity.

In an embodiment, said double stranded break is within 10, 20, 30, 40, 50, 100, 150 or 200 nucleotides of a nucleotide of the target position. In an embodiment, said single stranded break is within 10, 20, 30, 40, 50, 100, 150 or 200 nucleotides of a nucleotide of the target position.

In an embodiment, the composition further comprises a template nucleic acid, e.g., a template nucleic acid described herein, e.g., in Section IV. In an embodiment, the template nucleic acid comprises a nucleotide that corresponds to a nucleotide of the target position.

In an embodiment, said template nucleic acid comprises a nucleotide that corresponds to a nucleotide of the target position from a sequence of: a gene, or a gene from a pathway, described herein, e.g., in Section VIIB, e.g., in Table VII-13, VII-14, VII-15, VII-16, VII-17, VII-18, VII-19, VII-20, VII-21, VII-22, VII-23, VII-24, IX-1, IX-1A, IX-3, or XII-1, or in Section VIII.

In an embodiment, the template nucleic acid is or comprises a fragment of 10 to 500, 10 to 400, 10 to 300, 10 to 200 nucleotides in length from a sequence in: a gene, or a gene from a pathway, described herein, e.g., in Section VIIB, e.g., in Table VII-13, VII-14, VII-15, VII-16, VII-17, VII-18, VII-19, VII-20, VII-21, VII-22, VII-23, VII-24, IX-1, IX-1A, IX-3, or XII-1, or in Section VIII.

In an embodiment, the template nucleic acid is or comprises a fragment of 10 to 500, 10 to 400, 10 to 300, 10 to 200 nucleotides in length, which differs at at least 1 nucleotide, but not more than 5, 10, 20 or 30% of its nucleotides, from a corresponding sequence in: a gene, or a gene from a pathway, described herein, e.g., in Section VIIB, e.g., in Table VII-13, VII-14, VII- 15, VII-16, VII-17, VII-18, VII-19, VII-20, VII-21, VII-22, VII-23, VII-24, IX-1, IX- 1A, IX- 3, or XII-1, or in Section VIII.

In an embodiment, the composition further comprises a second gRNA molecule, e.g., a second gRNA molecule described herein.

In an embodiment, said gRNA molecule and said second gRNA molecule mediate breaks at different sites in the target nucleic acid, e.g., flanking a target position. In an embodiment, said gRNA molecule and said second gRNA molecule are complementary to the same strand of the target. In an embodiment, said gRNA molecule and said second gRNA molecule are complementary to the different strands of the target.

In an embodiment, said Cas9 molecule mediates a double stranded break.

In an embodiment, said gRNA molecule and said second gRNA molecule are configured such that first and second break made by the Cas9 molecule flank a target position. In an embodiment, said double stranded break is within 10, 20, 30, 40, 50, 100, 150 or 200 nucleotides of a nucleotide of the target position.

In an embodiment, the composition further comprises a template nucleic acid. In an embodiment, the template nucleic acid comprises a nucleotide that corresponds to a nucleotide of the target position.

In an embodiment, said template nucleic acid comprises a nucleotide that corresponds to a nucleotide of a target position from a sequence of: a gene, or a gene from a pathway, described herein, e.g., in Section VIIB, e.g., in Table VII-13, VII-14, VII-15, VII-16, VII-17, VII-18, VII-19, VII-20, VII-21, VII-22, VII-23, VII-24, IX-1, IX- 1A, IX-3, or XII-1, or in Section VIII.

In an embodiment, the template nucleic acid is a fragment of 10 to 500, 10 to 400, 10 to 300, 10 to 200 nucleotides in length from a sequence in: a gene, or a gene from a pathway, described herein, e.g., in Section VIIB, e.g., in Table VII-13, VII-14, VII-15, VII-16, VII-17, VII-18, VII-19, VII-20, VII-21, VII-22, VII-23, VII-24, IX-1, IX-1A, IX-3, or XII-1, or in Section VIII.

In an embodiment, the template nucleic acid is a fragment of 10 to 500, 10 to 400, 10 to 300, 10 to 200 nucleotides in length, which differs at at least 1 nucleotide, but not more than 5, 10, 20 or 30% of its nucleotides, from a corresponding sequence in: a gene, or a gene from a pathway, described herein, e.g., in Section VIIB, e.g., in Table VII-13, VII-14, VII-15, VII-16, VII-17, VII-18, VII-19, VII-20, VII-21, VII-22, VII-23, VII-24, IX-1, IX-1A, IX-3, or XII-1, or in Section VIII.

In an embodiment, said Cas9 molecule mediates a single stranded break.

In an embodiment, said gRNA molecule and said second gRNA molecule are configured such that a first and second break are formed in the same strand of the nucleic acid target, e.g., in the case of transcribed sequence, the template strand or the non-template strand.

In an embodiment, said first and second break flank a target position.

In an embodiment, one of said first and second single stranded breaks, or both are independently, within 10, 20, 30, 40, 50, 100, 150 or 200 nucleotides of a nucleotide of the target position.

In an embodiment, the composition further comprises a template nucleic acid. In an embodiment, the template nucleic acid comprises a nucleotide that corresponds to a nucleotide of the target position. In an embodiment, said template nucleic acid comprises a nucleotide that corresponds to a nucleotide of the target position from a sequence of: a gene, or a gene from a pathway, described herein, e.g., in Section VIIB, e.g., in Table VII-13, VII-14, VII-15, VII-16, VII-17, VII-18, VII-19, VII-20, VII-21, VII-22, VII-23, VII-24, IX-1, IX-1A, IX-3, or XII-1, or in Section VIII.

In an embodiment, the template nucleic acid is or comprises a fragment of 10 to 500, 10 to 400, 10 to 300, 10 to 200 nucleotides in length from a sequence in: a gene, or a gene from a pathway, described herein, e.g., in Table VII-13, VII-14, VII-15, VII-16, VII-17, VII-18, VII- 19, VII-20, VII-21, VII-22, VII-23, VII-24, IX-1, IX-1A, IX-3, or XII-1, or in Section VIII.

In an embodiment, said gRNA molecule and said second gRNA molecule are configured such that a first and a second breaks are formed in different strands of the target. In an embodiment, said first and second break flank a target position. In an embodiment, one of said first and second single stranded breaks, or both are independently, within 10, 20, 30, 40, 50, 100, 150 or 200 nucleotides of a nucleotide of the target position.

In an embodiment, the composition comprises a second Cas9 molecule.

In an embodiment, one or both of said Cas9 molecule and said second Cas9 molecule are eiCas9 molecules. In an embodiment, said eiCas9 molecule is coupled to a payload by a linker and said second eiCas9 molecules is coupled to a second payload by a second linker.

In an embodiment, said payload and said second payload are the same. In an

embodiment, said payload and said second payload are different. In an embodiment, said linker and said second linker are the same. In an embodiment, said linker and said second linker are different, e.g., have different release properties, e.g., different release rates. In an embodiment, said payload and said second payload are each described herein, e.g., in Section VI, e.g., in Table VI-1, VI-2, VI-3, VI-4, VI-5, or VI-6. In an embodiment, said payload and said second payload can interact, e.g., they are subunits of a protein.

In an embodiment, one of both of said Cas9 molecule and said second Cas9 molecule are eaCas9 molecules.

In an embodiment, said eaCas9 molecule comprises a first cleavage activity and said second eaCas9 molecule comprises a second cleavage activity. In an embodiment, said cleavage activity and said second cleavage activity are the same, e.g., both are N-terminal RuvC-like domain activity or are both HNH-like domain activity. In an embodiment, said cleavage activity and said second cleavage activity are different, e.g., one is N-terminal RuvC-like domain activity and one is HNH-like domain activity.

In an embodiment, said Cas9 molecule and said second Cas9 molecule are specific for different PAMs, e.g., one is specific for NGG and the other is specific for, e.g., NGGNG, NNAGAAW (W = A or T), or NAAR (R = A or G). In an embodiment, said Cas9 molecule of S. aureus recognizes the sequence motif NNGRR (R = A or G) and directs cleavage of a target nucleic acid sequence 1 to 10, e.g., 3 to 5, base pairs upstream from that sequence. In an embodiment, one of said Cas 9 molecule and said second Cas 9 molecule recognizes an S. aureus PAM. In an embodiment, said Cas9 molecule of N. meningitidis recognizes the sequence motif NNNNGATT and directs cleavage of a target nucleic acid sequence 1 to 10, e.g., 3 to 5, base pairs upstream from that sequence. In an embodiment, one of said Cas 9 molecule and said second Cas 9 molecule recognizes an N. meningitidis PAM.

In an embodiment, said Cas9 molecule and said second Cas9 molecule both mediate double stranded breaks.

In an embodiment, said Cas9 molecule and said second Cas9 molecule are specific for different PAMs, e.g., one is specific for NGG and the other is specific for another PAM, e.g., another PAM described herein. In an embodiment, said gRNA molecule and said second gRNA molecule are configured such that first and second break flank a target position. In an embodiment, one of said first and second double stranded breaks, or both are independently, within 10, 20, 30, 40, 50, 100, 150 or 200 nucleotides of a nucleotide of the target position. In an embodiment, the composition further comprises a template nucleic acid. In an embodiment, the template nucleic acid comprises a nucleotide that corresponds to a nucleotide of the target position.

In an embodiment, said template nucleic acid comprises a nucleotide that corresponds to a nucleotide of the target position from a sequence of: a gene, or a gene from a pathway, described herein, e.g., in Section VIIB, e.g., in Table VII-13, VII-14, VII-15, VII-16, VII-17, VII-18, VII-19, VII-20, VII-21, VII-22, VII-23, VII-24, IX-1, IX-1A, IX-3, XII-1, or Section VIII.

In an embodiment, one of said Cas9 molecule and said second Cas9 molecule mediates a double stranded break and the other mediates a single stranded break.

In an embodiment, said Cas9 molecule and said second Cas9 molecule are specific for different PAMs, e.g., one is specific for NGG and the other is specific for another PAM, e.g., another PAM described herein. In an embodiment, said gRNA molecule and said second gRNA molecule are configured such that a first and second break flank a target position. In an embodiment, said first and second break flank a target position. In an embodiment, one of said first and second breaks, or both are independently, within 10, 20, 30, 40, 50, 100, 150 or 200 nucleotides of a nucleotide of the target position.

In an embodiment, said Cas9 molecule and said second Cas9 molecule both mediate single stranded breaks.

In an embodiment, said Cas9 molecule and said second Cas9 molecule are specific for different PAMs, e.g., one is specific for NGG and the other is specific for another PAM, e.g., another PAM described herein. In an embodiment, said first and second break flank a target position.

In an embodiment, said template nucleic acid comprises a nucleotide that corresponds to a nucleotide of the target position from a sequence of: a gene, or a gene from a pathway, described herein, e.g., in Section VIIB, e.g., in Table VII-13, VII-14, VII-15, VII-16, VII-17, VII-18, VII-19, VII-20, VII-21, VII-22, VII-23, VII-24, IX-1, IX-1A, IX-3, or XII-1, or in

Section VIII.

In an embodiment, said gRNA molecule, said second gRNA molecule are configured such that a first and second break are in the same strand.

In an embodiment, said Cas9 molecule and said second Cas9 molecule are specific for different PAMs, e.g., one is specific for NGG and the other is specific for another PAM, e.g., another PAM described herein. In an embodiment, said gRNA molecule, said second gRNA molecule are configured such that a first and second break flank a target position. In an embodiment, one of said first and second single stranded breaks, or both are independently, within 10, 20, 30, 40, 50, 100, 150 or 200 nucleotides of a nucleotide of the target position.

In an embodiment, said first and second break are on the different strands.

In an embodiment, said Cas9 molecule and said second Cas9 molecule are specific for different PAMs, e.g., one is specific for NGG and the other is specific for another PAM, e.g., another PAM described herein. In an embodiment, said gRNA molecule, said second gRNA molecule are configured such that a first and second break are on different strands.

In an embodiment, said gRNA molecule, said second gRNA molecule are configured such that a first and second break flank a target position. In an embodiment, said first and second break flank a target position.

In an embodiment, the template nucleic acid is or comprises a fragment of 10 to 500, 10 to 400, 10 to 300, 10 to 200 nucleotides in length, which differs at at least 1 nucleotide, but not more than 5, 10, 20 or 30% of its nucleotides, from a corresponding sequence in: a gene, or a gene from a pathway, described herein, e.g., in Section VIIB, e.g., in Table VII-13, VII-14, VII- 15, VII-16, VII-17, VII-18, VII-19, VII-20, VII-21, VII-22, VII-23, VII-24, IX-1, IX- 1A, IX- 3, or XII-1, or Section VIII.

In yet another aspect, the disclosure features a composition, e.g., a pharmaceutical composition, comprising governing gRNA molecule, e.g., a Cas9-targeting gRNA molecule or a gRNA-targeting gRNA molecule, a gRNA molecule and a second gRNA molecule described herein.

In an embodiment, the composition further comprises a nucleic acid, e.g., a DNA or mRNA, that encodes a Cas9 molecule described herein. In an embodiment, the composition further comprises a nucleic acid, e.g., a DNA or RNA, that encodes a second Cas9 molecule described herein. In an embodiment, the composition further comprises a template nucleic acid described herein.

In one aspect, the disclosure features a composition, e.g., a pharmaceutical composition, comprising, nucleic acid sequence, e.g., a DNA, that encodes a governing gRNA molecule, e.g., a Cas9-targeting gRNA molecule or a gRNA-targeting gRNA molecule, and one or more gRNA molecules described herein.

In an embodiment, said nucleic acid comprises a promoter operably linked to the sequence that encodes a gRNA molecule, e.g., a promoter described herein.

In an embodiment, said nucleic acid comprises a second promoter operably linked to the sequence that encodes a second gRNA molecule, e.g., a promoter described herein. In an embodiment, the promoter and second promoter are different promoters. In an embodiment, the promoter and second promoter are the same.

In an embodiment, the nucleic acid further encodes a Cas9 molecule described herein. In an embodiment, the nucleic acid further encodes a second Cas9 molecule described herein.

In an embodiment, said nucleic acid comprises a promoter operably linked to the sequence that encodes a Cas9 molecule, e.g., a promoter described herein. In an embodiment, said nucleic acid comprises a second promoter operably linked to the sequence that encodes a second Cas9 molecule, e.g., a promoter described herein. In an embodiment, the promoter and second promoter are different promoters. In an embodiment, the promoter and second promoter are the same.

In an embodiment, the composition further comprises a template nucleic acid e.g., a template nucleic acid described herein, e.g., in Section IV.

In another aspect, the disclosure features a composition, e.g., a pharmaceutical composition, comprising nucleic acid sequence that encodes one or more of: a) a Cas9 molecule, b) a second Cas9 molecule, c) a gRNA molecule, d) a second gRNA molecule, and e) a governing gRNA molecule, e.g., a Cas9-targeting gRNA molecule or a gRNA-targeting gRNA molecule.

In an embodiment, each of a), b), c) d) and e) present are encoded on the same nucleic acid molecule.

In an embodiment, a first sequence selected from of a), b), c), d) and e) is encoded on a first nucleic acid molecule and a second sequence selected from a), b), c), d) and e) is encoded on a second nucleic acid molecule.

In an embodiment, said nucleic acid encodes: a), c) and e); a), c), d) and e); or a), b), c), d) and e).

In an embodiment, the composition further comprises a Cas9 molecule, e.g., comprising one or more of the Cas9 molecules wherein said nucleic acid does not encode a Cas9 molecule.

In an embodiment, the composition further comprises an mRNA encoding Cas9 molecule, e.g., comprising one or more mRNAs encoding one or more of the Cas9 molecules wherein said nucleic acid does not encode a Cas9 molecule.

In yet another aspect, the disclosure features a nucleic acid described herein.

In one aspect, the disclosure features a composition comprising: a) a gRNA molecule (or combination of gRNA molecules, e.g., a gRNA molecule and a second gRNA molecule); b) an eaCas9 molecule (or combination of eaCas9 molecules, e.g., an eaCas9 molecule; and a second eaCas9 molecule); and c) optionally, a template nucleic acid e.g., a template nucleic acid described herein, e.g., in Section IV. In another aspect, the disclosure features a composition comprising: a) a gRNA molecule (or combination of gRNA molecules, e.g., a gRNA molecule and a second gRNA molecule); b) a nucleic acid, e.g. a DNA or mRNA encoding an eaCas9 molecule (or combination of eaCas9 molecules, e.g., an eaCas9 molecule and a second eaCas9 molecule); c) optionally, a template nucleic acid, e.g., a template nucleic acid described herein, e.g., in Section IV; and d) a governing gRNA molecule, e.g., a Cas9-targeting gRNA molecule.

In yet another aspect, the disclosure features a composition comprising: a) a nucleic acid, e.g., a DNA, which encodes a gRNA molecule (or combination of gRNA molecules, e.g., a gRNA molecule and a second gRNA molecule); b) an eaCas9 molecule (or combination of eaCas9 molecules, e.g., an eaCas9 molecule and a second eaCas9 molecule); c) optionally, a template nucleic acid, e.g., a template nucleic acid described herein, e.g., in Section IV; and d) a governing gRNA molecule, e.g., a gRNA-targeting gRNA molecule.

In still another aspect, the disclosure features a composition comprising: a) nucleic acid, e.g., a DNA, which encodes a gRNA molecule or (or combination of gRNA molecules, e.g., a gRNA molecule and a second gRNA molecule); b) nucleic acid, e.g. a DNA or mRNA encoding eaCas9 molecule or (or combination of eaCas9 molecules, e.g., an eaCas9 molecule and a second eaCas9 molecule) (wherein the gRNA molecule encoding nucleic acid and the eaCas9 molecule encoding nucleic acid can be on the same or different molecules); c) optionally, a template nucleic acid, e.g., a template nucleic acid described herein, e.g., in Section IV; and d) a governing gRNA molecule, e.g., a Cas9-targeting gRNA molecule or a gRNA-targeting gRNA molecule.

In one aspect, the disclosure features a method of altering a cell, e.g., altering the structure, e.g., sequence, of a target nucleic acid of a cell, comprising contacting said cell with:

1) a composition comprising:

a) a gRNA molecule (or combination of gRNA molecules, e.g., a gRNA molecule and a second gRNA molecule); b) an eaCas9 molecule (or combination of eaCas9 molecules, e.g., an eaCas9 molecule; and a second eaCas9 molecule); and

c) optionally, a template nucleic acid, e.g., a template nucleic acid described herein, e.g., in Section IV;

2) a composition comprising:

a) a gRNA molecule (or combination of gRNA molecules, e.g., a gRNA molecule and a second gRNA molecule);

b) a nucleic acid, e.g. a DNA or mRNA encoding an eaCas9 molecule (or combination of eaCas9 molecules, e.g., an eaCas9 molecule and a second eaCas9 molecule); and

c) optionally, a template nucleic acid, e.g., a template nucleic acid described herein, e.g., in Section IV; and

d) a governing gRNA molecule, e.g., a Cas9-targeting gRNA molecule;

3) a composition comprising:

a) a nucleic acid, e.g., a DNA, which encodes a gRNA molecule (or combination of gRNA molecules, e.g., a gRNA molecule and a second gRNA molecule);

b) an eaCas9 molecule (or combination of eaCas9 molecules, e.g., an eaCas9 molecule and a second eaCas9 molecule); and

d) a governing gRNA molecule, e.g., a Cas9-targeting gRNA molecule or a gRNA-targeting gRNA molecule; and/or

4) a composition comprising:

a) nucleic acid, e.g., a DNA, which encodes a gRNA molecule (or combination of gRNA molecules, e.g., a gRNA molecule and a second gRNA molecule);

b) nucleic acid, e.g. a DNA or mRNA encoding eaCas9 molecule (or combination of eaCas9 molecules, e.g., an eaCas9 molecule and a second eaCas9 molecule), (wherein the gRNA molecule encoding nucleic acid and the eaCas9 molecule encoding nucleic acid can be on the same or different molecules); and

c) optionally, a template nucleic acid, e.g., a template nucleic acid described herein, e.g., in Section IV; and d) a governing gRNA molecule, e.g., a Cas9-targeting gRNA molecule or a gRNA-targeting gRNA molecule.

In an embodiment, a gRNA molecule or nucleic acid encoding a gRNA molecule, and an eaCas9 molecule, or nucleic acid encoding an eaCas9 molecule, are delivered in or by, one dosage form, mode of delivery, or formulation.

In an embodiment, a) a gRNA molecule or nucleic acid encoding a gRNA molecule is delivered in or by, a first dosage form, a first mode of delivery, or a first formulation; and b) an eaCas9 molecule, or nucleic acid encoding an eaCas9 molecule, is delivered in or by a second dosage form, second mode of delivery, or second formulation. In an embodiment, a governing gRNA molecule (or a nucleic acide that encodes it), e.g., a Cas9-targeting gRNA molecule or a gRNA-targeting gRNA molecule, is provided in the dosage form that contains the component it inactivates, or in another dosage form, mode of delivery, or formulation.

In an embodiment, the cell is an animal or plant cell. In an embodiment, the cell is a mammalian, primate, or human cell. In an embodiment, the cell is a human cell, e.g., a cell from described herein, e.g., in Section VIIA. In an embodiment, the cell is: a somatic cell, germ cell, prenatal cell, e.g., zygotic, blastocyst or embryonic, blastocyst cell, a stem cell, a mitotically competent cell, a meiotically competent cell. In an embodiment, the cell is a human cell, e.g., a cancer cell or other cell characterized by a disease or disorder.

In an embodiment, the target nucleic acid is a chromosomal nucleic acid. In an embodiment, the target nucleic acid is an organellar nucleic acid. In an embodiment, the target nucleic acid is a mitochondrial nucleic acid. In an embodiment, the target nucleic acid is a chloroplast nucleic acid.

In an embodiment, the cell is a cell of a disease causing organism, e.g., a virus, bacterium, fungus, protozoan, or parasite.

In an embodiment, the target nucleic acid is the nucleic acid of a disease causing organism, e.g., of a disease causing organism, e.g., a virus, bacterium, fungus, protozoan, or parasite.

In an embodiment, said method comprises: modulating the expression of a gene or inactivating a disease organism.

In an embodiment, said cell is a cell characterized by unwanted proliferation, e.g., a cancer cell. In an embodiment, said cell is a cell characterized by an unwanted genomic component, e.g., a viral genomic component. In an embodiment, the cell is a cell described herein, e.g., in Section IIA. In an embodiment, a control or structural sequence of at least, 2 3, 4, 5 or 6 or more genes is altered.

In an embodiment, the target nucleic acid is a rearrangement, a rearrangement that comprises a kinase gene, or a rearrangement that comprises a tumor suppressor gene. In an embodiment, the targent nucleic acid comprises a kinase gene or a tumor suppressor gene.

In an embodiment, the method comprises cleaving a target nucleic acid within 10, 20, 30, 40, 50, 100, 150 or 200 nucleotides of a nucleotide of the target position. In an embodiment, said composition comprises a template nucleic acid.

In an embodiment, the template nucleic acid comprises a nucleotide that corresponds to a nucleotide of the target position.

In an embodiment, said template nucleic acid comprises a nucleotide that corresponds to a nucleotide of the target position from a sequence of: a gene, or a gene from a pathway, described herein, e.g., in Section VIIB, e.g., in Table VII-13, VII-14, VII-15, VII-16, VII-17, VII-18, VII-19, VII-20, VII-21, VII-22, VII-23, VII-24, IX-1, IX-IA, IX-3, or XII-1, or in Section VIII.

In an embodiment, the template nucleic acid is or comprises a fragment of 10 to 500, 10 to 400, 10 to 300, 10 to 200 nucleotides in length from a sequence in: a gene, or a gene from a pathway, described herein, e.g., in Section VIIB, e.g., in Table VII-13, VII-14, VII-15, VII-16, VII-17, VII-18, VII-19, VII-20, VII-21, VII-22, VII-23, VII-24, IX-1, IX-IA, IX-3, or XII-1, or in Section VIII.

In an embodiment, the template nucleic acid is or comprises a fragment of 10 to 500, 10 to 400, 10 to 300, 10 to 200 nucleotides in length, which differs at at least 1 nucleotide, but not more than 5, 10, 20 or 30% of its nucleotides, from a corresponding sequence in: a gene, or a gene from a pathway, described herein, e.g., in Section VIIB, e.g., in Table VII-13, VII-14, VII- 15, VII-16, VII-17, VII-18, VII-19, VII-20, VII-21, VII-22, VII-23, VII-24, IX-1, IX-IA, IX- 3, or XII-1, or in Section VIII.

In an embodiment,

a) a control region, e.g., a cis-acting or tans-acting control region, of a gene is cleaved; b) the sequence of a control region, e.g., a cis-acting or trans-acting control region, of a gene is altered, e.g., by an alteration that modulates, e.g., increases or decreases, expression a gene under control of the control region, e.g., a control sequence is disrupted or a new control sequence is inserted;

c) the coding sequence of a gene is cleaved;

d) the sequence of a transcribed region, e.g., a coding sequence of a gene is altered, e.g., a mutation is corrected or introduced, an alteration that increases expression of or activity of the gene product is effected, e.g., a mutation is corrected; and/or

e) the sequence of a transcribed region, e.g., the coding sequence of a gene is altered, e.g., a mutation is corrected or introduced, an alteration that decreases expression of or activity of the gene product is effected, e.g., a mutation is inserted, e.g., the sequence of one or more

nucleotides is altered so as to insert a stop codon.

In an embodiment, a control region or transcribed region, e.g., a coding sequence, of at least 2, 3, 4, 5, or 6 or more genes are altered.

In another aspect, the disclosure features a method of treating a subject, e.g., by altering the structure, e.g., altering the sequence, of a target nucleic acid, comprising administering to the subject, an effective amount of:

1) a composition comprising:

a) a gRNA molecule (or combination of gRNA molecules, e.g., a gRNA molecule and a second gRNA molecule) ;

b) an eaCas9 molecule (or combination of eaCas9 molecules, e.g., an eaCas9 molecule; and a second eaCas9 molecule); and

2) a composition comprising:

d) a governing gRNA molecule, e.g., a Cas9-targeting gRNA molecule; 3) a composition comprising:

d) a governing gRNA molecule, e.g., a gRNA-targeting gRNA molecule;

and/or

4) a composition comprising:

a) nucleic acid, e.g., a DNA, which encodes a gRNA molecule or ( or combination of gRNA molecules, e.g., a gRNA molecule and a second gRNA molecule); b) nucleic acid, e.g. a DNA or mRNA encoding eaCas9 molecule or (or combination of eaCas9 molecules, e.g., an eaCas9 molecule and a second eaCas9 molecule), (wherein the gRNA molecule encoding nucleic acid and the eaCas9 molecule encoding nucleic acid can be on the same or different molecules); and

d) a governing gRNA molecule, e.g., a Cas9-targeting gRNA molecule or a gRNA-targeting gRNA molecule.

In an embodiment, a gRNA molecule or nucleic acid encoding a gRNA molecule, and an eaCas9 molecule, or nucleic acid encoding an eaCas9 molecule, are delivered in or by one dosage form, mode of delivery, or formulation. In an embodiment, a governing gRNA molecule (or a nucleic acide that encodes it), e.g., a Cas9-targeting gRNA molecule or a gRNA-targeting gRNA molecule, is provided in the dosage form that contains the component it inactivates, or in another dosage form, mode of delivery, or formulation.

In an embodiment, a gRNA molecule or nucleic acid encoding a gRNA molecule is delivered in or by a first dosage form, in a first mode of delivery, or first formulation; and an eaCas9 molecule, or nucleic acid encoding an eaCas9 molecule, is delivered in or by a second dosage form, second mode of delivery, or second formulation. In an embodiment a governing gRNA molecule (or a nucleic acide that encodes it), e.g., a Cas9-targeting gRNA molecule or a gRNA-targeting gRNA molecule, can provided in the dosage form that contains the component it inactivates, or in another dosage form, mode of delivery, or formulation.

In an embodiment, the subject is an animal or plant. In an embodiment, the subject is a mammalian, primate, or human.

In an embodiment, the target nucleic acid is the nucleic acid of a human cell, e.g., a cell described herein, e.g., in Section VIIA. In an embodiment, the target nucleic acid is the nucleic acid of: a somatic cell, germ cell, prenatal cell, e.g., zygotic, blastocyst or embryonic, blasotcyst cell, a stem cell, a mitotically competent cell, a meiotically competent cell.

In an embodiment, the target nucleic acid is a chromosomal nucleic acid. In an embodiment, the target nucleic acid is an organellar nucleic acid. In an embodiment, the nucleic acid is a mitochondrial nucleic acid. In an embodiment, the nucleic acid is a chloroplast nucleic acid.

In an embodiment, the target nucleic acid is the nucleic acid of a disease causing organism, e.g., of a disease causing organism, e.g., a virus, bacterium, fungus, protozoan, or parasite. In an embodiment, said method comprises modulating expression of a gene or inactivating a disease organism.

In an embodiment, the target nucleic acid is the nucleic acid of a cell characterized by unwanted proliferation, e.g., a cancer cell. In an embodiment, said target nucleic acid comprises an unwanted genomic component, e.g., a viral genomic component. In an embodiment, a control or structural sequence of at least, 2 3, 4, 5 or 6 or more genes is altered. In an embodiment, the target nucleic acid is a rearrangement, a rearrangement that comprises a kinase gene, or a rearrangement that comprises a tumor suppressor gene. In an embodiment, the targent nucleic acid comprises a kinase gene or a tumor suppressor gene.

In an embodiment, the method comprises cleaving a target nucleic acid within 10, 20, 30, 40, 50, 100, 150 or 200 nucleotides of a nucleotide of the target position.

In an embodiment, said composition comprises a template nucleic acid. In an

embodiment, the template nucleic acid comprises a nucleotide that corresponds to a nucleotide of the target position.

In an embodiment, said template nucleic acid comprises a nucleotide that corresponds to a nucleotide of the target position from a sequence of: a gene, or a gene from a pathway, described herein, e.g., in Section VIIB, e.g., in Table VII-13, VII-14, VII-15, VII-16, VII-17, VII-18, VII-19, VII-20, VII-21, VII-22, VII-23, VII-24, IX-1, IX-IA, IX-3, or XII-1, or in

Section VIII.

In an embodiment, the template nucleic acid is or comprises a fragment of 10 to 500, 10 to 400, 10 to 300, 10 to 200 nucleotides in length, which differs at at least 1 nucleotide, but not more than 5, 10, 20 or 30% of its nucleotides, from a corresponding sequence in:

In an embodiment,

a) a control region, e.g., a cis-acting or trans-acting control region, of a gene is cleaved; b) the sequence of a control region, e.g., a cis-acting or trans-acting control region, of a gene is altered, e.g., by an alteration that modulates, e.g., increases or decreases, expression a gene under control of the control region, e.g., a control sequence is disrupted or a new control sequence is inserted;

c) the coding sequence of a gene is cleaved;

d) the sequence of a transcribed region, e.g., a coding sequence of a gene is altered, e.g., a mutation is corrected or introduced, an alteration that increases expression of or activity of the gene product is effected, e.g., a mutation is corrected;

e) the non-coding sequence of a gene or an intergenic region between genes is cleaved; and/or

f) the sequence of a transcribed region, e.g., the coding sequence of a gene is altered, e.g., a mutation is corrected or introduced, an alteration that decreases expression of or activity of the gene product is effected, e.g., a mutation is inserted, e.g., the sequence of one or more nucleotides is altered so as to insert a stop codon.

In an embodiment, a control region or transcribed region, e.g., a coding sequence, of at least 2, 3, 4, 5, or 6 or more genes are altered. In one aspect, the disclosure features a composition comprising: a) a gRNA molecule (or combination of gRNA molecules, e.g., a gRNA molecule and a second gRNA molecule); b) a Cas9 molecule, e.g., an eiCas9 molecule (or combination of Cas9 molecules, e.g., an eiCas9 molecule and a second eiCas9 molecule); and c) a payload coupled, covalently or non- covalently, to a complex of the gRNA molecule and the Cas9 molecule, e.g., coupled to the Cas9 molecule or the gRNA molecule.

In another aspect, the disclosure features a composition comprising: a) a gRNA molecule (or combination of gRNA molecules, e.g., a gRNA molecule and a second gRNA molecule); b) a nucleic acid, e.g. a DNA or mRNA encoding a Cas9 molecule, e.g., an eiCas9 molecule (or combination of Cas9 molecules, e.g., an eiCas9 molecule and a second eiCas9 molecule); and c) a payload which is: coupled, covalently or non-covalently, the gRNA molecule; or a fusion partner with the Cas9 molecule.

In yet another aspect, the disclosure features a composition comprising: a) a nucleic acid, e.g., a DNA, which encodes a gRNA molecule (or combination of gRNA molecules, e.g., a gRNA molecule and a second gRNA molecule); b) a Cas9 molecule, e.g., an eiCas9 molecule (or combination of Cas9 molecules, e.g., an eiCas9 molecule and a second eiCas9 molecule); c) a payload which is coupled, covalently or non-covalently, to the Cas9 molecule; and d) a governing gRNA molecule, e.g., a gRNA-targeting gRNA molecule.

In still another aspect, the disclosure features a composition comprising: a) nucleic acid, e.g., a DNA, which encodes a gRNA molecule or (or combination of gRNA molecules, e.g., a gRNA molecule and a second gRNA molecule); b) nucleic acid, e.g. a DNA or mRNA, encoding a Cas9 molecule, e.g., an eiCas9 molecule (or combination of Cas9 molecules, e.g., an eiCas9 molecule and a second eiCas9 molecule), wherein the gRNA molecule encoding nucleic acid and the eaCas9 molecule encoding nucleic acid can be on the same or different molecules; c) a payload which is a fusion partner with the Cas9 molecule; and d) a governing gRNA molecule, e.g., a Cas9-targeting gRNA molecule or a gRNA-targeting gRNA molecule.

In one aspect, the disclosure features a method of delivering a payload to a cell, e.g., by targeting a payload to target nucleic acid, comprising contacting said cell with:

1) a composition comprising: a) a gRNA molecule (or combination of gRNA molecules, e.g., a gRNA molecule and a second gRNA molecule);

b) a Cas9 molecule, e.g., an eiCas9 molecule (or combination of Cas9 molecules, e.g., an eiCas9 molecule and a second eiCas9 molecule); and

c) a payload coupled, covalently or non-covalently, to a complex of the gRNA molecule and the Cas9 molecule, e.g., coupled to the Cas9 molecule or the gRNA molecule;

2) a composition comprising:

b) a nucleic acid, e.g. a DNA or mRNA encoding a Cas9 molecule, e.g., an eiCas9 molecule (or combination of Cas9 molecules, e.g., an eiCas9 molecule and a second eiCas9 molecule);

c) a payload which is: coupled, covalently or non-covalently, the gRNA molecule; or a fusion partner with the Cas9 molecule;

3) a composition comprising:

b) a Cas9 molecule, e.g., an eiCas9 molecule (or combination of Cas9 molecules, e.g., an eiCas9 molecule and a second eiCas9 molecule);

c) a payload which is coupled, covalently or non-covalently, to the Cas9 molecule; and

d) a governing gRNA molecule, e.g., a gRNA-targeting gRNA molecule;

and/or

4) a composition comprising:

a) nucleic acid, e.g., a DNA, which encodes a gRNA molecule or ( or

combination of gRNA molecules, e.g., a gRNA molecule and a second gRNA molecule); b) nucleic acid, e.g. a DNA or mRNA ,encoding a Cas9 molecule, e.g., an eiCas9 molecule (or combination of Cas9 molecules, e.g., an eiCas9 molecule and a second eiCas9 molecule), wherein the gRNA molecule encoding nucleic acid and the eaCas9 molecule encoding nucleic acid can be on the same or different molecules; c) a payload which is a fusion partner with the Cas9 molecule; and d) a governing gRNA molecule, e.g., a Cas9-targeting gRNA molecule or a gRNA-targeting gRNA molecule.

In an embodiment, a gRNA molecule or nucleic acid encoding a gRNA molecule is delivered in or by a first dosage form, first mode of delivery, or first formulation; and a Cas9 molecule, or nucleic acid encoding a Cas9 molecule, is delivered in or by a second dosage form, second mode of delivery, or second formulation. In an embodiment, a governing gRNA molecule (or a nucleic acide that encodes it), e.g., a Cas9-targeting gRNA molecule or a gRNA- targeting gRNA molecule, is provided in the dosage form that contains the component it inactivates, or in another dosage form, mode of delivery, or formulation.

In an embodiment, the cell is an animal or plant cell. In an embodiment, the cell is a mammalian, primate, or human cell. In an embodiment, the cell is a human cell, e.g., a human cell described herein, e.g., in Section VIIA. In an embodiment, the cell is: a somatic cell, germ cell, prenatal cell, e.g., zygotic, blastocyst or embryonic, blasotcyst cell, a stem cell, a mitotically competent cell, a meiotically competent cell. In an embodiment, the cell is a human cell, e.g., a cancer cell, a cell comprising an unwanted genetic element, e.g., all or part of a viral genome.

In an embodiment, the gRNA mediates targeting of a chromosomal nucleic acid. In an embodiment, the gRNA mediates targeting of a selected genomic signature. In an embodiment, the gRNA mediates targeting of an organellar nucleic acid. In an embodiment, the gRNA mediates targeting of a mitochondrial nucleic acid. In an embodiment, the gRNA mediates targeting of a chloroplast nucleic acid.

In an embodiment, the cell is a cell of a disease causing organism, e.g., a virus, bacterium, fungus, protozoan, or parasite. In an embodiment, the gRNA mediates targeting of the nucleic acid of a disease causing organism, e.g., of a disease causing organism, e.g., a virus, bacterium, fungus, protozoan, or parasite.

In an embodiment, the payload comprises a payload described herein, e.g., in Section VI.

In an embodiment, said cell is a cell characterized by unwanted proliferation, e.g., a cancer cell. In an embodiment, said cell is characterized by an unwanted genomic component, e.g., a viral genomic component.

In an embodiment, a control or structural sequence of at least 2 3, 4, 5, or 6 or more genes is altered.

In an embodiment, the gRNA targets a selected genomic signature, e.g., a mutation, e.g., a germline or acquired somatic mutation. In an embodiment, the target nucleic acid is a rearrangement, a rearrangement that comprises a kinase gene, or a rearrangement that comprises a tumor suppressor gene. In an embodiment, the targent nucleic acid comprises a kinase gene or a tumor suppressor gene. In an embodiment, the gRNA targets a cancer cell, e.g., a cancer cell disclosed herein, e.g., in Section VIIA. In an embodiment, the gRNA targets a cell which has been infected with a virus.

In another aspect, the disclosure features a method of treating a subject, e.g., by targeting a payload to target nucleic acid, comprising administering to the subject, an effective amount of:

1) a composition comprising:

c) a payload coupled, covalently or non-covalently, to a complex of the gRNA molecule and the Cas9 molecule, e.g., coupled to the Cas9 molecule;

2) a composition comprising:

a) a gRNA molecule (or combination of gRNA molecules, e.g., a gRNA molecule and a second gRNA molecule); b) a nucleic acid, e.g. a DNA or mRNA encoding a Cas9 molecule, e.g., an eiCas9 molecule (or combination of Cas9 molecules, e.g., an eiCas9 molecule and a second eiCas9 molecule);

c) a payload which is:

coupled, covalently or non-covalently, the gRNA molecule; or

is a fusion partner with the Cas9 molecule; and

d) a governing gRNA molecule, e.g., a Cas9-targeting gRNA molecule;

3) a composition comprising:

d) a governing gRNA molecule, e.g., a gRNA-targeting gRNA molecule; and/or

4) a composition comprising:

a) a nucleic acid, e.g., a DNA, which encodes a gRNA molecule or ( or combination of gRNA molecules, e.g., a gRNA molecule and a second gRNA molecule); b) a nucleic acid, e.g. a DNA or mRNA, encoding a Cas9 molecule, e.g., an eiCas9 molecule (or combination of Cas9 molecules, e.g., an eiCas9 molecule and a second eiCas9 molecule), (wherein the gRNA molecule encoding nucleic acid and the eaCas9 molecule encoding nucleic acid can be on the same or different molecules);

c) a payload which is a fusion partner with the Cas9 molecule; and d) a governing gRNA molecule, e.g., a Cas9-targeting gRNA molecule or a gRNA-targeting gRNA molecule.

In an embodiment, a gRNA molecule or nucleic acid encoding a gRNA molecule, and an eaCas9 molecule, or nucleic acid encoding an eaCas9 molecule, are delivered in or by one dosage form, mode of delivery, or formulation. In an embodiment a governing gRNA molecule (or a nucleic acide that encodes it), e.g., a Cas9-targeting gRNA molecule or a gRNA-targeting gRNA molecule, can provided in the dosage form that contains the component it inactivates, or in another dosage form, mode of delivery, or formulation.

In an embodiment, a gRNA molecule or nucleic acid encoding a gRNA molecule is delivered in or by a first dosage, mode of delivery form or formulation; and a Cas9 molecule, or nucleic acid encoding a Cas9 molecule, is delivered in or by a second dosage form, mode of delivery, or formulation. In an embodiment a governing gRNA molecule (or a nucleic acide that encodes it), e.g., a Cas9-targeting gRNA molecule or a gRNA-targeting gRNA molecule, can provided in the dosage form that contains the component it inactivates, or in another dosage form, mode of delivery, or formulation.

In an embodiment, the subject is an animal or plant cell. In an embodiment, the subject is a mammalian, primate, or human cell.

In an embodiment, the gRNA mediates targeting of a human cell, e.g., a human cell described herein, e.g., in Section VIIA. In an embodiment, the gRNA mediates targeting of: a somatic cell, germ cell, prenatal cell, e.g., zygotic, blastocyst or embryonic, blasotcyst cell, a stem cell, a mitotically competent cell, a meiotically competent cell. In an embodiment, the gRNA mediates targeting of a cancer cell or a cell comprising an unwanted genomic element, e.g., all or part of a viral genome. In an embodiment, the gRNA mediates targeting of a chromosomal nucleic acid. In an embodiment, the gRNA mediates targeting of a selected genomic signature. In an embodiment, the gRNA mediates targeting of an organellar nucleic acid. In an embodiment, the gRNA mediates targeting of a mitochondrial nucleic acid. In an embodiment, the gRNA mediates targeting of a chloroplast nucleic acid. In an embodiment, the gRNA mediates targeting of the nucleic acid of a disease causing organism, e.g., of a disease causing organism, e.g., a virus, bacterium, fungus, protozoan, or parasite. In an embodiment, the gRNA targets a cell characterized by unwanted proliferation, e.g., a cancer cell, e.g., a cancer cell from Section VIIA, e.g., from Table VII-11. In an embodiment, the gRNA targets a cell characterized by an unwanted genomic component, e.g., a viral genomic component.

In an embodiment, a control element, e.g., a promoter or enhancer, is targeted. In an embodiment, the target nucleic acid is a rearrangement, a rearrangement that comprises a kinase gene, or a rearrangement that comprises a tumor suppressor gene. In an embodiment, the targent nucleic acid comprises a kinase gene or a tumor suppressor gene. In an embodiment, the gRNA targets a selected genomic signature, e.g., a mutation, e.g., a germline or acquired somatic mutation.

In an embodiment, the gRNA targets a cancer cell. In an embodiment, the gRNA targets a cell which has been infected with a virus.

In an embodiment, at least one eaCas9 molecule and a payload are administered. In an embodiment, the payload comprises a payload described herein, e.g., in Section VI.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.

Headings, including numeric and alphabetical headings and subheadings, are for organization and presentation and are not intended to be limiting.

Other features and advantages of the invention will be apparent from the detailed description, drawings, and from the claims.

BRIEF DESCRIPTION OF THE DRAWING

The Figures described below, that together make up the Drawing, are for illustration purposes only, not for limitation.

FIG. 1A-G are representations of several exemplary gRNAs.

FIG. 1A depicts a modular gRNA molecule derived in part (or modeled on a sequence in part) from Streptococcus pyogenes (S. pyogenes) as a duplexed structure (SEQ ID NOS 42 and 43, respectively, in order of appearance);

FIG. IB depicts a unimolecular (or chimeric) gRNA molecule derived in part from S. pyogenes as a duplexed structure (SEQ ID NO: 44);

FIG. 1C depicts a unimolecular gRNA molecule derived in part from S. pyogenes as a duplexed structure (SEQ ID NO: 45); FIG. ID depicts a unimolecular gRNA molecule derived in part from S. pyogenes as a duplexed structure (SEQ ID NO: 46);

FIG. IE depicts a unimolecular gRNA molecule derived in part from S. pyogenes as a duplexed structure (SEQ ID NO: 47);

FIG. IF depicts a modular gRNA molecule derived in part from Streptococcus thermophilus (S. thermophilus) as a duplexed structure (SEQ ID NOS 48 and 49, respectively, in order of appearance);

FIG. 1G depicts an alignment of modular gRNA molecules of S. pyogenes and S.

thermophilus (SEQ ID NOS 50-53, respectively, in order of appearance).

FIG. 2 depicts an alignment of Cas9 sequences from Chylinski et al., RNA BIOL. 2013;

10(5): 726-737. The N-terminal RuvC-like domain is boxed and indicated with a "Y". The other two RuvC-like domains are boxed and indicated with a "B". The HNH-like domain is boxed and indicated by a "G". Sm: S. mutans (SEQ ID NO: 1); Sp: S. pyogenes (SEQ ID NO: 2); St: S. thermophilus (SEQ ID NO: 3); Li: L. innocua (SEQ ID NO: 4). Motif: this is a motif based on the four sequences: residues conserved in all four sequences are indicated by single letter amino acid abbreviation; "*" indicates any amino acid found in the corresponding position of any of the four sequences; and "-" indicates any amino acid, e.g., any of the 20 naturally occurring amino acids.

FIG. 3A shows an alignment of the N-terminal RuvC-like domain from the Cas9 molecules disclosed in Chylinski et al. (SEQ ID NOS 54-103, respectively, in order of appearance). The last line of FIG. 3 A identifies 3 highly conserved residues.

FIG. 3B shows an alignment of the N-terminal RuvC-like domain from the Cas9 molecules disclosed in Chylinski et al. with sequence outliers removed (SEQ ID NOS 104-177, respectively, in order of appearance). The last line of FIG. 3B identifies 4 highly conserved residues.

FIG. 4A shows an alignment of the HNH-like domain from the Cas9 molecules disclosed in Chylinski et al. (SEQ ID NOS 178-252, respectively, in order of appearance). The last line of FIG. 4A identifies conserved residues.

FIG. 4B shows an alignment of the HNH-like domain from the Cas9 molecules disclosed in Chylinski et al. with sequence outliers removed (SEQ ID NOS 253-302, respectively, in order of appearance). The last line of FIG. 4B identifies 3 highly conserved residues. FIG. 5 depicts an alignment of Cas9 sequences from S. pyogenes and Neisseria meningitidis (N. meningitidis). The N-terminal RuvC-like domain is boxed and indicated with a "Y". The other two RuvC-like domains are boxed and indicated with a "B". The HNH-like domain is boxed and indicated with a "G". Sp: S. pyogenes; Nm: N. meningitidis. Motif: this is a motif based on the two sequences: residues conserved in both sequences are indicated by a single amino acid designation; "*" indicates any amino acid found in the corresponding position of any of the two sequences; "-" indicates any amino acid, e.g., any of the 20 naturally occurring amino acids, and "-" indicates any amino acid, e.g., any of the 20 naturally occurring amino acids, or absent.

FIG. 6 shows a nucleic acid sequence encoding Cas9 of N. meningitidis (SEQ ID NO:

303). Sequence indicated by an "R" is an SV40 NLS; sequence indicated as "G" is an HA tag; sequence indicated by an "O" is a synthetic NLS sequence. The remaining (unmarked) sequence is the open reading frame (ORF).

FIG. 7 depicts the levels of Cas9 protein expression in cells transfected with each of the Cas9-targeted governing gRNAs at 1, 2, 3, 6 and 9 days following transfection.

DEFINITIONS

"Governing gRNA molecule", as used herein, refers to a gRNA molecule that can complex with a Cas9 molecule to inactivate or silence a component of the Cas9 system. In an embodiment, the governing gRNA molecule inactivates or silences a nucleic acid that comprises the sequence encoding the Cas9 molecule. In an embodiment, it inactivates or silences the nucleic acid that comprises the sequence encoding the gRNA molecule. In an embodiment, the governing gRNA, e.g., a Cas9-targeting gRNA molecule, or a gRNA targeting gRNA molecule, limits the effect of the Cas9 moleclue/gRNA molecule complex-mediated gene targeting. In an embodiment, it places temporal, level of expression, or other limits, on activity of the Cas9 moleclue/gRNA molecule complex. In an embodiment, it reduces off-target or other unwanted activity. Governing gRNA molecules can act as to inhibit, e.g., entirely or substantially inhibit, the production of a component of the Cas9 system, e.g., the Cas9 molecule, and thereby limit, or govern, its activity.

The governing gRNA molecule can target any region of the nucleic acid that comprises the sequence encoding the component to be negatively regulated, within or outside the transcribed or translated region of the component, as long as production of the component is reduced.

In an embodiment, a governing gRNA molecule comprises a targeting sequence that is complementary with a target sequence on the nuciec acid on which the sequence encoding the component to be negatively regulated resides.

In an embodiment, a governing gRNA molecule comprises a targeting sequence that is complementary with a sequence of the component to be negatively regulated.

In an embodiment, a Cas9-targeting gRNA molecule can include a targeting sequence that targets the nucleic acid on which the sequence that encodes the Cas9 molecule resides.

In an embodiment, a Cas9-targeting gRNA molecule can include a targeting sequence that targets the Cas9 molecule sequence.

In an embodiment, a gRNA-targeting gRNA molecule can include a targeting sequence that targets the nucleic acid on which the sequence that encodes the gRNA molecule resides.

In an embodiment, a gRNA-targeting gRNA molecule can include a targeting sequence that targets the gRNA molecule sequence.

"Domain", as used herein, is used to describe segments of a protein or nucleic acid. Unless otherwise indicated, a domain is not required to have any specific functional property.

Calculations of "homology" or "sequence identity" between two sequences (the terms are used interchangeably herein) are performed as follows. The sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment and non-homologous sequences can be disregarded for comparison purposes). The optimal alignment is determined as the best score using the GAP program in the GCG software package with a Blossum 62 scoring matrix with a gap penalty of 12, a gap extend penalty of 4, and a frame shift gap penalty of 5. The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position (as used herein, In an embodiment, amino acid or nucleic acid "identity" is equivalent to amino acid or nucleic acid "homology"). The percent identity between the two sequences is a function of the number of identical positions shared by the sequences. "Modulator", as used herein, refers to an entity, e.g., a drug, that can alter the activity (e.g., enzymatic activity, transcriptional activity, or translational activity), amount, distribution, or structure of a subject molecule or genetic sequence. In an embodiment, modulation comprises cleavage, e.g., breaking of a covalent or non-covalent bond, or the forming of a covalent or non- covalent bond, e.g., the attachment of a moiety, to the subject molecule. In an embodiment, a modulator alters the, three dimensional, secondary, tertiary, or quaternary structure, of a subject molecule. A modulator can increase, decrease, initiate, or eliminate a subject activity.

"Large molecule", as used herein, refers to a molecule having a molecular weight of at least 2, 3, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 kD. Large molecules include proteins, polypeptides, nucleic acids, biologies, and carbohydrates.

"Polypeptide", as used herein, refers to a polymer of amino acids having less than 100 amino acid residues. In an embodiment, it has less than 50, 20, or 10 amino acid residues.

"Reference molecule", e.g., a reference Cas9 molecule or reference gRNA, as used herein, refers to a molecule to which a subject molecule, e.g., a subject Cas9 molecule of subject gRNA molecule, e.g., a modified or candidate Cas9 molecule is compared. For example, a Cas9 molecule can be characterized as having no more than 10% of the nuclease activity of a reference Cas9 molecule. Examples of reference Cas9 molecules include naturally occurring unmodified Cas9 molecules, e.g., a naturally occurring Cas9 molecule such as a Cas9 molecule of S.

pyogenes, or S. thermophilus . In an embodiment, the reference Cas9 molecule is the naturally occurring Cas9 molecule having the closest sequence identity or homology with the Cas9 molecule to which it is being compared. In an embodiment, the reference Cas9 molecule is a sequence, e.g., a naturally occurring or known sequence, which is the parental form on which a change, e.g., a mutation has been made.

"Replacement", or "replaced", as used herein with reference to a modification of a molecule does not require a process limitation but merely indicates that the replacement entity is present.

"Small molecule", as used herein, refers to a compound having a molecular weight less than about 2 kD, e.g., less than about 2 kD, less than about 1.5 kD, less than about 1 kD, or less than about 0.75 kD.

"Subject", as used herein, may mean either a human or non-human animal. The term includes, but is not limited to, mammals (e.g., humans, other primates, pigs, rodents (e.g., mice and rats or hamsters), rabbits, guinea pigs, cows, horses, cats, dogs, sheep, and goats). In an embodiment, the subject is a human. In an embodiment, the subject is poultry.

"Treat", "treating" and "treatment", as used herein, mean the treatment of a disease in a mammal, e.g., in a human, including (a) inhibiting the disease, i.e., arresting or preventing its development; (b) relieving the disease, i.e., causing regression of the disease state; or (c) curing the disease.

"X" as used herein in the context of an amino acid sequence, refers to any amino acid (e.g., any of the twenty natural amino acids) unless otherwise specified. DETAILED DESCRIPTION

I. gRNA Molecules

A gRNA molecule, as that term is used herein, refers to a nucleic acid that promotes the specific targeting or homing of a gRNA molecule/Cas9 molecule complex to a target nucleic acid. gRNA molecules can be unimolecular (having a single RNA molecule), sometimes referred to herein as "chimeric" gRNAs, or modular (comprising more than one, and typically two, separate RNA molecules). A gRNA molecule comprises a number of domains. The gRNA molecule domains are described in more detail below. Typically, gRNA will incorporate the functions or structure of both crRNA and tracrRNA, e.g., the functions of processed or mature crRNA and of processed or mature tracrRNA. Chimieric or unimolecular gRNA molecules can have a single RNA molecule, e.g., which incorporates both crRNA function or structure and the tracrRNA function or structure. A modular gRNA molecule can comprise a RNA molecule that incorporates the crRNA function or structure another that incorporates the tracrRNA function or structure. Several exemplary gRNA structures, with domains indicated thereon, are provided in FIG. 1. While not wishing to be bound by theory with regard to the three dimensional form, or intra- or inter- strand interactions of an active form of a gRNA, regions of high complementarity are sometimes shown as duplexes in FIG. 1 and other depictions provided herein.

In an embodiment, a unimolecular, or chimeric, gRNA comprises, preferably from 5' to

3':

a targeting domain, e.g., comprising 15, 16, 17, 18, 19, or 20 nucleotides (which is complementary to a target nucleic acid); a first complementarity domain;

a linking domain;

a second complementarity domain (which is complementary to the first

complementarity domain);

a proximal domain; and

optionally, a tail domain.

In an embodiment, a modular gRNA comprises:

a first strand comprising, preferably from 5' to 3' ;

a targeting domain (which is complementary with a target sequence from a target nucleic acid disclosed herein, e.g., a sequence from: a gene or pathway described herein, e.g., in Section VIIB, e.g., in Table VII-13, VII-14, VII-15, VII-16, VII-17, VII-18, VII-19, VII-20, VII-21, VII-22, VII-23, VII-24, IX-1, IX-IA, IX-3, or XII-1, or in Section VIII); and a first complementarity domain; and

a second strand, comprising, preferably from 5' to 3': optionally, a 5' extension domain;

a second complementarity domain; and

a proximal domain; and

optionally, a tail domain.

The domains are discussed briefly below:

1) The Targeting Domain:

FIGS. 1A-1G provide examples of the placement of targeting domains.

The targeting domain comprises a nucleotide sequence that is complementary, e.g., at least 80, 85, 90, or 95% complementary, e.g., fully complementary, to the target sequence on the target nucleic acid. The targeting domain is part of an RNA molecule and will therefore comprise the base uracil (U), while any DNA encoding the gRNA molecule will comprise the base thymine (T). While not wishing to be bound by theory, it is believed that the

complementarity of the targeting domain with the target sequence contributes to specificity of the interaction of the gRNA molecule/Cas9 molecule complex with a target nucleic acid. It is understood that in a targeting domain and target sequence pair, the uracil bases in the targeting domain will pair with the adenine bases in the target sequence. In an embodiment, the target domain itself comprises, in the 5' to 3' direction, an optional secondary domain, and a core domain. In an embodiment, the core domain is fully complementary with the target sequence. In an embodiment, the targeting domain is 5 to 50, e.g., 10 to 40, e.g., 10 to 30, e.g., 15 to 30, e.g., 15 to 25 nucleotides in length. In an embodiment, the targeting domain is 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26 nucleotides in length. The strand of the target nucleic acid with which the targeting domain is complementary is referred to herein as the complementary strand. Some or all of the nucleotides of the domain can have a modification, e.g., modification found in Section X herein.

In an embodiment, the targeting domain is 15 nucleotides in length.

In an embodiment, the targeting domain is 16 nucleotides in length.

In an embodiment, the targeting domain is 17 nucleotides in length.

In an embodiment, the targeting domain is 18 nucleotides in length.

In an embodiment, the targeting domain is 19 nucleotides in length.

In an embodiment, the targeting domain is 20 nucleotides in length.

In an embodiment, the targeting domain is 21 nucleotides in length.

In an embodiment, the targeting domain is 22 nucleotides in length.

In an embodiment, the targeting domain is 23 nucleotides in length.

In an embodiment, the targeting domain is 24 nucleotides in length.

In an embodiment, the targeting domain is 25 nucleotides in length.

In an embodiment, the targeting domain is 26 nucleotides in length.

In an embodiment, the targeting domain comprises 15 nucleotides.

In an embodiment, the targeting domain comprises 16 nucleotides.

In an embodiment, the targeting domain comprises 17 nucleotides.

In an embodiment, the targeting domain comprises 18 nucleotides.

In an embodiment, the targeting domain comprises 19 nucleotides.

In an embodiment, the targeting domain comprises 20 nucleotides.

In an embodiment, the targeting domain comprises 21 nucleotides.

In an embodiment, the targeting domain comprises 22 nucleotides.

In an embodiment, the targeting domain comprises 23 nucleotides.

In an embodiment, the targeting domain comprises 24 nucleotides.

In an embodiment, the targeting domain comprises 25 nucleotides.

In an embodiment, the targeting domain comprises 26 nucleotides. Targeting domains are discussed in more detail below.

2) The First Complementarity Domain:

FIGS. 1A-1G provide examples of first complementarity domains.

The first complementarity domain is complementary with the second complementarity domain, and in an embodiment, has sufficient complementarity to the second complementarity domain to form a duplexed region under at least some physiological conditions. In an embodiment, the first complementarity domain is 5 to 30 nucleotides in length. In an

embodiment, the first complementarity domain is 5 to 25 nucleotides in length. In an

embodiment, the first complementary domain is 7 to 25 nucleotides in length. In an

embodiment, the first complementary domain is 7 to 22 nucleotides in length. In an

embodiment, the first complementary domain is 7 to 18 nucleotides in length. In an

embodiment, the first complementary domain is 7 to 15 nucleotides in length. In an

embodiment, the first complementary domain is 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides in length.

In an embodiment, the first complementarity domain comprises 3 subdomains, which, in the 5' to 3' direction are: a 5' subdomain, a central subdomain, and a 3' subdomain. In an embodiment, the 5' subdomain is 4-9, e.g., 4, 5, 6, 7, 8 or 9 nucleotides in length. In an embodiment, the central subdomain is 1, 2, or 3, e.g., 1, nucleotide in length. In an embodiment, the 3' subdomain is 3 to 25, e.g., 4-22, 4-18, or 4 to 10, or 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25, nucleotides in length.

The first complementarity domain can share homology with, or be derived from, a naturally occurring first complementarity domain. In an embodiment, it has at least 50% homology with a first complementarity domain disclosed herein, e.g., an S. pyogenes, or S.

thermophilus, first complementarity domain.

Some or all of the nucleotides of the domain can have a modification, e.g., modification found in Section X herein.

First complementarity domains are discussed in more detail below.

3) The Linking Domain

FIGS. IB-IE provide examples of linking domains. A linking domain serves to link the first complementarity domain with the second complementarity domain of a unimolecular gRNA. The linking domain can link the first and second complementarity domains covalently or non-covalently. In an embodiment, the linkage is covalent. In an embodiment, the linking domain covalently couples the first and second complementarity domains, see, e.g., FIGS. IB-IE. In an embodiment, the linking domain is, or comprises, a covalent bond interposed between the first complementarity domain and the second complementarity domain. Typically, the linking domain comprises one or more, e.g., 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides.

In modular gRNA molecules the two molecules can be associated by virtue of the hybridization of the complementarity domains, see e.g., FIG. 1A.

A wide variety of linking domains are suitable for use in unimolecular gRNA molecules. Linking domains can consist of a covalent bond, or be as short as one or a few nucleotides, e.g., 1, 2, 3, 4, or 5 nucleotides in length.

In an embodiment, a linking domain is 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 or more nucleotides in length. In an embodiment, a linking domain is 2 to 50, 2 to 40, 2 to 30, 2 to 20, 2 to 10, or 2 to 5 nucleotides in length. In an embodiment, a linking domain shares homology with, or is derived from, a naturally occurring sequence, e.g., the sequence of a tracrRNA that is 5' to the second complementarity domain. In an embodiment, the linking domain has at least 50% homology with a linking domain disclosed herein.

Linking domains are discussed in more detail below.

4) The 5' Extension Domain

In an embodiment, a modular gRNA can comprise additional sequence, 5' to the second complementarity domain, referred to herein as the 5' extension domain, see, e.g., FIG. 1A. In an embodiment, the 5' extension domain is, 2-10, 2-9, 2-8, 2-7, 2-6, 2-5, 2-4 nucleotides in length. In an embodiment, the 5' extension domain is 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more nucleotides in length.

5) The Second Complementarity Domain:

FIGS. 1A-1F provide examples of second complementarity domains. The second complementarity domain is complementary with the first complementarity domain, and in an embodiment, has sufficient complementarity to the second complementarity domain to form a duplexed region under at least some physiological conditions. In an embodiment, e.g., as shown in FIG. 1A or FIG. IB, the second complementarity domain can include sequence that lacks complementarity with the first complementarity domain, e.g., sequence that loops out from the duplexed region.

In an embodiment, the second complementarity domain is 5 to 27 nucleotides in length. In an embodiment, it is longer than the first complementarity region.

In an embodiment, the second complementary domain is 7 to 27 nucleotides in length. In an embodiment, the second complementary domain is 7 to 25 nucleotides in length. In an embodiment, the second complementary domain is 7 to 20 nucleotides in length. In an embodiment, the second complementary domain is 7 to 17 nucleotides in length. In an embodiment, the complementary domain is 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or 25 nucleotides in length.

In an embodiment, the second complementarity domain comprises 3 subdomains, which, in the 5' to 3' direction are: a 5' subdomain, a central subdomain, and a 3' subdomain. In an embodiment, the 5' subdomain is 3 to 25, e.g., 4 to 22, 4 tol8, or 4 to 10, or 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides in length. In an embodiment, the central subdomain is 1, 2, 3, 4 or 5, e.g., 3, nucleotides in length. In an embodiment, the 3' subdomain is 4 to 9, e.g., 4, 5, 6, 7, 8 or 9 nucleotides in length.

In an embodiment, the 5' subdomain and the 3' subdomain of the first complementarity domain, are respectively, complementary, e.g., fully complementary, with the 3' subdomain and the 5' subdomain of the second complementarity domain.

The second complementarity domain can share homology with or be derived from a naturally occurring second complementarity domain. In an embodiment, it has at least 50% homology with a second complementarity domain disclosed herein, e.g., an S. pyogenes, or S. thermophilus, first complementarity domain.

Some or all of the nucleotides of the domain can have a modification, e.g., modification found in Section X herein. 6) A Proximal Domain:

FIGS. 1A-1F provide examples of proximal domains.

In an embodiment, the proximal domain is 5 to 20 nucleotides in length. In an embodiment, the proximal domain can share homology with or be derived from a naturally occurring proximal domain. In an embodiment, it has at least 50% homology with a proximal domain disclosed herein, e.g., an S. pyogenes, or S. thermophilus, proximal domain.

7) A Tail Domain:

FIG. 1A and FIGS. 1C-1F provide examples of tail domains.

As can be seen by inspection of the tail domains in FIG. 1A and FIGS. 1C-1F, a broad spectrum of tail domains are suitable for use in gRNA molecules. In an embodiment, the tail domain is 0 (absent), 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides in length. In an embodiment, the tail domain nucleotides are from or share homology with sequence from the 5' end of a naturally occurring tail domain, see e.g., FIG. ID or FIG. IE. In an embodiment, the tail domain includes sequences that are complementary to each other and which, under at least some physiological conditions, form a duplexed region.

In an embodiment, the tail domain is absent or is 1 to 50 nucleotides in length. In an embodiment, the tail domain can share homology with or be derived from a naturally occurring proximal tail domain. In an embodiment, it has at least 50% homology with a tail domain disclosed herein, e.g., an S. pyogenes, or S. thermophilus, tail domain.

In an embodiment, the tail domain includes nucleotides at the 3' end that are related to the method of in vitro or in vivo transcription. When a T7 promoter is used for in vitro transcription of the gRNA, these nucleotides may be any nucleotides present before the 3' end of the DNA template. When a U6 promoter is used for in vivo transcription, these nucleotides may be the sequence UUUUUU. When alternate pol-III promoters are used, these nucleotides may be various numbers or uracil bases or may include alternate bases.

The domains of gRNA molecules are described in more detail below. The Targeting Domain

The "targeting domain" of the gRNA is complementary to the "target domain" on the target nucleic acid. The strand of the target nucleic acid comprising the nucleotide sequence complementary to the core domain of the gRNA is referred to herein as the "complementary strand" of the target nucleic acid. Guidance on the selection of targeting domains can be found, e.g., in Fu Y et al, NAT BIOTECHNOL 2014 (doi: 10.1038/nbt.2808) and Sternberg SH et al., NATURE 2014 (doi: 10.1038/naturel3011).

In an embodiment, the targeting domain is 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or 26 nucleotides in length.

In an embodiment, the targeting domain comprises 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,

25 or 26 nucleotides in length.

In an embodiment, the targeting domain is 15 nucleotides in length.

In an embodiment, the targeting domain is 16 nucleotides in length.

In an embodiment, the targeting domain is 17 nucleotides in length.

In an embodiment, the targeting domain is 18 nucleotides in length.

In an embodiment, the targeting domain is 19 nucleotides in length.

In an embodiment, the targeting domain is 20 nucleotides in length.

In an embodiment, the targeting domain is 21 nucleotides in length.

In an embodiment, the targeting domain is 22 nucleotides in length.

In an embodiment, the targeting domain is 23 nucleotides in length.

In an embodiment, the targeting domain is 24 nucleotides in length.

In an embodiment, the targeting domain is 25 nucleotides in length.

In an embodiment, the targeting domain is 26 nucleotides in length.

In an embodiment, the targeting domain comprises 15 nucleotides.

In an embodiment, the targeting domain comprises 16 nucleotides.

In an embodiment, the targeting domain comprises 17 nucleotides.

In an embodiment, the targeting domain comprises 18 nucleotides.

In an embodiment, the targeting domain comprises 19 nucleotides.

In an embodiment, the targeting domain comprises 20 nucleotides.

In an embodiment, the targeting domain comprises 21 nucleotides.

In an embodiment, the targeting domain comprises 22 nucleotides. In an embodiment, the targeting domain comprises 23 nucleotides.

In an embodiment, the targeting domain comprises 24 nucleotides.

In an embodiment, the targeting domain comprises 25 nucleotides.

In an embodiment, the targeting domain comprises 26 nucleotides.

In an embodiment, the targeting domain is 10 +/-5, 20+/-5, 30+/-5, 40+/-5, 50+/-5, 60+/-

5, 70+/-5, 80+/-5, 90+/-5, or 100+/-5 nucleotides, in length.

In an embodiment, the targeting domain is 20+/-5 nucleotides in length.

In an embodiment, the targeting domain is 20+/- 10, 30+/- 10, 40+/- 10, 50+/- 10, 60+/- 10, 70+/- 10, 80+/- 10, 90+/- 10, or 100+/- 10 nucleotides, in length.

In an embodiment, the targeting domain is 30+/- 10 nucleotides in length.

In an embodiment, the targeting domain is 10 to 100, 10 to 90, 10 to 80, 10 to 70, 10 to 60, 10 to 50, 10 to 40, 10 to 30, 10 to 20 or 10 to 15 nucleotides in length. In an embodiment, the targeting domain is 20 to 100, 20 to 90, 20 to 80, 20 to 70, 20 to 60, 20 to 50, 20 to 40, 20 to 30, or 20 to 25 nucleotides in length.

Typically the targeting domain has full complementarity with the target sequence. In an embodiment the targeting domain has or includes 1, 2, 3, 4, 5, 6, 7 or 8 nucleotides that are not complementary with the corresponding nucleotide of the targeting domain.

In an embodiment, the target domain includes 1, 2, 3, 4 or 5 nucleotides that are complementary with the corresponding nucleotide of the targeting domain within 5 nucleotides of its 5' end. In an embodiment, the target domain includes 1, 2, 3, 4 or 5 nucleotides that are complementary with the corresponding nucleotide of the targeting domain within 5 nucleotides of its 3' end.

In an embodiment, the target domain includes 1, 2, 3, or 4 nucleotides that are not complementary with the corresponding nucleotide of the targeting domain within 5 nucleotides of its 5' end. In an embodiment, the target domain includes 1, 2, 3, or 4 nucleotides that are not complementary with the corresponding nucleotide of the targeting domain within 5 nucleotides of its 3' end.

In an embodiment, the degree of complementarity, together with other properties of the gRNA, is sufficient to allow targeting of a Cas9 molecule to the target nucleic acid.

In an embodiment, the targeting domain comprises two consecutive nucleotides that are not complementary to the target domain ("non-complementary nucleotides"), e.g., two consecutive noncomplementary nucleotides that are within 5 nucleotides of the 5' end of the targeting domain, within 5 nucleotides of the 3' end of the targeting domain, or more than 5 nucleotides away from one or both ends of the targeting domain.

In an embodiment, no two consecutive nucleotides within 5 nucleotides of the 5' end of the targeting domain, within 5 nucleotides of the 3' end of the targeting domain, or within a region that is more than 5 nucleotides away from one or both ends of the targeting domain, are not complementary to the targeting domain.

In an embodiment, there are no noncomplementary nucleotides within 5 nucleotides of the 5' end of the targeting domain, within 5 nucleotides of the 3' end of the targeting domain, or within a region that is more than 5 nucleotides away from one or both ends of the targeting domain.

In an embodiment, the targeting domain nucleotides do not comprise modifications, e.g., modifications of the type provided in Section X. However, in an embodiment, the targeting domain comprises one or more modifications, e.g., modifications that it render it less susceptible to degradation or more bio-compatible, e.g., less immunogenic. By way of example, the backbone of the targeting domain can be modified with a phosphorothioate, or other

modification from Section X. In an embodiment, a nucleotide of the targeting domain can comprise a 2' modification (e.g., a modification at the 2' position on ribose), e.g., a 2' acetylation, e.g., a 2' methylation, or other modification from Section X.

In an embodiment, the targeting domain includes 1, 2, 3, 4, 5, 6, 7 or 8 or more modifications. In an embodiment, the targeting domain includes 1, 2, 3, or 4 modifications within 5 nucleotides of its 5' end. In an embodiment, the targeting domain comprises as many as 1, 2, 3, or 4 modifications within 5 nucleotides of its 3' end.

In an embodiment, the targeting domain comprises modifications at two consecutive nucleotides, e.g., two consecutive nucleotides that are within 5 nucleotides of the 5' end of the targeting domain, within 5 nucleotides of the 3' end of the targeting domain, or more than 5 nucleotides away from one or both ends of the targeting domain.

In an embodiment, no two consecutive nucleotides are modified within 5 nucleotides of the 5' end of the targeting domain, within 5 nucleotides of the 3' end of the targeting domain, or within a region that is more than 5 nucleotides away from one or both ends of the targeting domain. In an embodiment, no nucleotide is modified within 5 nucleotides of the 5' end of the targeting domain, within 5 nucleotides of the 3' end of the targeting domain, or within a region that is more than 5 nucleotides away from one or both ends of the targeting domain.

Modifications in the targeting domain can be selected so as to not interfere with targeting efficacy, which can be evaluated by testing a candidate modification in the system described in Section III. gRNA's having a candidate targeting domain having a selected length, sequence, degree of complementarity, or degree of modification, can be evaluated in a system in Section III. The candidate targeting domain can be placed, either alone, or with one or more other candidate changes in a gRNA molecule/Cas9 molecule system known to be functional with a selected target and evaluated.

In an embodiment, all of the modified nucleotides are complementary to and capable of hybridizing to corresponding nucleotides present in the target domain. In an embodiment, 1, 2, 3, 4, 5, 6, 7 or 8 or more modified nucleotides are not complementary to or capable of hybridizing to corresponding nucleotides present in the target domain.

In an embodiment, the targeting domain comprises, preferably in the 5'→3' direction: a secondary domain and a core domain. These domains are discussed in more detail below.

The Core Domain and Secondary Domain of the Targeting Domain

The "core domain" of the targeting domain is complementary to the "core domain target" on the target nucleic acid. In an embodiment, the core domain comprises about 8 to about 13 nucleotides from the 3' end of the targeting domain (e.g., the most 3' 8 to 13 nucleotides of the targeting domain).

In an embodiment, the core domain is 6 +1-2, 7+/-2, 8+/-2, 9+/-2, 10+/-2, 11+/-2, 12+/-2, 13+/-2, 14+/-2, 15+/-2, or 16+/-2 nucleotides in length.

In an embodiment, the core domain is 10+/-2 nucleotides in length.

In an embodiment, the core domain is 10+/-4 nucleotides in length.

In an embodiment, the core domain is 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or 16 nucleotides in length.

In an embodiment, the core domain is 8 to 13, e.g., 8 to 12, 8 to 11, 8 to 10, 8 to 9, 9 to 13, 9 to 12, 9 to 11, or 9 to 10 nucleotides in length. In an embodiment, the core domain is 6 to 16, e.g., 6 to 15, 6 to 14, 6 to 13, 7 to 14, 7 to 13, 7 to 12, 7 to 11, 7 to 10, 8 to 14, 8 to 13, 8 to 12, 8 to 11, 8 to 10, or 8 to 9 nucleotides in length.

The core domain is complementary with the core domain target. Typically the core domain has exact complementarity with the core domain target. In an embodiment, the core domain can have 1, 2, 3, 4 or 5 nucleotides that are not complementary with the corresponding nucleotide of the core domain. In an embodiment, the degree of complementarity, together with other properties of the gRNA, is sufficient to allow targeting of a Cas9 molecule to the target nucleic acid.

The "secondary domain" of the targeting domain of the gRNA is complementary to the

"secondary domain target" of the target nucleic acid.

In an embodiment, the secondary domain is positioned 5' to the core domain.

In an embodiment, the secondary domain is absent or optional.

In an embodiment, if the targeting domain is, or is at least, 26 nucleotides in length and the core domain (counted from the 3' end of the targeting domain) is 8 to 13 nucleotides in length, the secondary domain is 12 to 17 nucleotides in length.

In an embodiment, if the targeting domain is, or is at least, 25 nucleotides in length and the core domain (counted from the 3' end of the targeting domain) is 8 to 13 nucleotides in length, the secondary domain is 12 to 17 nucleotides in length.

In an embodiment, if the targeting domain is, or is at least, 24 nucleotides in length and the core domain (counted from the 3' end of the targeting domain) is 8 to 13 nucleotides in length, the secondary domain is 11 to 16 nucleotides in length.

In an embodiment, if the targeting domain is, or is at least, 23 nucleotides in length and the core domain (counted from the 3' end of the targeting domain) is 8 to 13 nucleotides in length, the secondary domain is 10 to 15 nucleotides in length.

In an embodiment, if the targeting domain is, or is at least, 22 nucleotides in length and the core domain (counted from the 3' end of the targeting domain) is 8 to 13 nucleotides in length, the secondary domain is 9 to 14 nucleotides in length.

In an embodiment, if the targeting domain is, or is at least, 21 nucleotides in length and the core domain (counted from the 3' end of the targeting domain) is 8 to 13 nucleotides in length, the secondary domain is 8 to 13 nucleotides in length. In an embodiment, if the targeting domain is, or is at least, 20 nucleotides in length and the core domain (counted from the 3' end of the targeting domain) is 8 to 13 nucleotides in length, the secondary domain is 7 to 12 nucleotides in length.

In an embodiment, if the targeting domain is, or is at least, 19 nucleotides in length and the core domain (counted from the 3' end of the targeting domain) is 8 to 13 nucleotides in length, the secondary domain is 6 to 11 nucleotides in length.

In an embodiment, if the targeting domain is, or is at least, 18 nucleotides in length and the core domain (counted from the 3' end of the targeting domain) is 8 to 13 nucleotides in length, the secondary domain is 5 to 10 nucleotides in length.

In an embodiment, if the targeting domain is, or is at least, 17 nucleotides in length and the core domain (counted from the 3' end of the targeting domain) is 8 to 13 nucleotides in length, the secondary domain is 4 to 9 nucleotides in length.

In an embodiment, if the targeting domain is, or is at least, 16 nucleotides in length and the core domain (counted from the 3' end of the targeting domain) is 8 to 13 nucleotides in length, the secondary domain is 3 to 8 nucleotides in length.

In an embodiment, the secondary domain is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 or 15 nucleotides in length.

The secondary domain is complementary with the secondary domain target. Typically the secondary domain has exact complementarity with the secondary domain target. In an embodiment the secondary domain can have 1, 2, 3, 4 or 5 nucleotides that are not

complementary with the corresponding nucleotide of the secondary domain. In an embodiment, the degree of complementarity, together with other properties of the gRNA, is sufficient to allow targeting of a Cas9 molecule to the target nucleic acid.

In an embodiment, the core domain nucleotides do not comprise modifications, e.g., modifications of the type provided in Section X. However, in an embodiment, the core domain comprises one or more modifications, e.g., modifications that it render it less susceptible to degradation or more bio-compatible, e.g., less immunogenic. By way of example, the backbone of the core domain can be modified with a phosphorothioate, or other modification from Section X. In an embodiment, a nucleotide of the core domain can comprise a 2' modification (e.g., a modification at the 2' position on ribose), e.g., a 2' -acetylation, e.g., a 2' methylation, or other modification from Section X. Typically, a core domain will contain no more than 1, 2, or 3 modifications.

Modifications in the core domain can be selected to not interfere with targeting efficacy, which can be evaluated by testing a candidate modification in the system described in Section III. gRNA's having a candidate core domain having a selected length, sequence, degree of complementarity, or degree of modification, can be evaluated in the system described at Section III. The candidate core domain can be placed, either alone, or with one or more other candidate changes in a gRNA molecule /Cas9 molecule system known to be functional with a selected target and evaluated.

In an embodiment, the secondary domain nucleotides do not comprise modifications, e.g., modifications of the type provided in Section X. However, in an embodiment, the secondary domain comprises one or more modifications, e.g., modifications that render it less susceptible to degradation or more bio-compatible, e.g., less immunogenic. By way of example, the backbone of the secondary domain can be modified with a phosphorothioate, or other modification from Section X. In an embodiment, a nucleotide of the secondary domain can comprise a 2' modification (e.g., a modification at the 2' position on ribose), e.g., a 2' -acetylation, e.g., a 2' methylation, or other modification from Section X. Typically, a secondary domain will contain no more than 1, 2, or 3 modifications.

Modifications in the secondary domain can be selected to not interfere with targeting efficacy, which can be evaluated by testing a candidate modification in the system described in Section III. gRNA's having a candidate secondary domain having a selected length, sequence, degree of complementarity, or degree of modification, can be evaluated in the system described at Section III. The candidate secondary domain can be placed, either alone, or with one or more other candidate changes in a gRNA molecule /Cas9 molecule system known to be functional with a selected target and evaluated.

In an embodiment, (1) the degree of complementarity between the core domain and its target, and (2) the degree of complementarity between the secondary domain and its target, may differ. In an embodiment, (1) may be greater than (2). In an embodiment, (1) may be less than (2). In an embodiment, (1) and (2) may be the same, e.g., each may be completely

complementary with its target. In an embodiment, (1) the number of modifications (e.g., modifications from Section X) of the nucleotides of the core domain and (2) the number of modification (e.g., modifications from Section X) of the nucleotides of the secondary domain, may differ. In an embodiment, (1) may be less than (2). In an embodiment, (1) may be greater than (2). In an embodiment, (1) and (2) may be the same, e.g., each may be free of modifications.

The First and Second Complementarity Domains

The first complementarity domain is complementary with the second complementarity domain.

Typically the first domain does not have exact complementarity with the second complementarity domain target. In an embodiment, the first complementarity domain can have 1, 2, 3, 4 or 5 nucleotides that are not complementary with the corresponding nucleotide of the second complementarity domain. In an embodiment, 1, 2, 3, 4, 5 or 6, e.g., 3 nucleotides, will not pair in the duplex, and, e.g., form a non-duplexed or looped-out region. In an embodiment, an unpaired, or loop-out, region, e.g., a loop-out of 3 nucleotides, is present on the second complementarity domain. In an embodiment, the unpaired region begins 1, 2, 3, 4, 5, or 6, e.g., 4, nucleotides from the 5' end of the second complementarity domain.

In an embodiment, the first and second complementarity domains are:

independently, 6 +1-2, 1+1-2, 8+/-2, 9+1-2, 10+/-2, 11+/-2, 12+/-2, 13+/-2, 14+/-2, 15+/-2, 16+/-2, 17+/-2, 18+/-2, 19+/-2, or 20+/-2, 21+/-2, 22+/-2, 23+/-2, or 24+/-2 nucleotides in length;

independently, 6, 7, 8, 9, 10, 11, 12, 13, 14, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26 nucleotides in length; or

independently, 5 to 24, 5 to 23, 5 to 22, 5 to 21, 5 to 20, 7 to 18, 9 to 16, or 10 to 14 nucleotides in length.

In an embodiment, the second complementarity domain is longer than the first complementarity domain, e.g., 2, 3, 4, 5, or 6, e.g., 6, nucleotides longer.

In an embodiment, the first and second complementary domains, independently, do not comprise modifications, e.g., modifications of the type provided in Section X. In an embodiment, the first and second complementary domains, independently, comprise one or more modifications, e.g., modifications that the render the domain less susceptible to degradation or more bio-compatible, e.g., less immunogenic. By way of example, the backbone of the domain can be modified with a phosphorothioate, or other modification from Section X. In an embodiment, a nucleotide of the domain can comprise a 2' modification (e.g., a modification at the 2' position on ribose), e.g., a 2' -acetylation, e.g., a 2' methylation, or other modification from Section X.

In an embodiment, the first and second complementary domains, independently, include 1, 2, 3, 4, 5, 6, 7 or 8 or more modifications. In an embodiment, the first and second

complementary domains, independently, include 1, 2, 3, or 4 modifications within 5 nucleotides of its 5' end. In an embodiment, the first and second complementary domains, independently, include as many as 1, 2, 3, or 4 modifications within 5 nucleotides of its 3' end.

In an embodiment, the first and second complementary domains, independently, include modifications at two consecutive nucleotides, e.g., two consecutive nucleotides that are within 5 nucleotides of the 5' end of the domain, within 5 nucleotides of the 3' end of the domain, or more than 5 nucleotides away from one or both ends of the domain. In an embodiment, the first and second complementary domains, independently, include no two consecutive nucleotides that are modified, within 5 nucleotides of the 5' end of the domain, within 5 nucleotides of the 3' end of the domain, or within a region that is more than 5 nucleotides away from one or both ends of the domain. In an embodiment, the first and second complementary domains, independently, include no nucleotide that is modified within 5 nucleotides of the 5' end of the domain, within 5 nucleotides of the 3' end of the domain, or within a region that is more than 5 nucleotides away from one or both ends of the domain.

Modifications in a complementarity domain can be selected to not interfere with targeting efficacy, which can be evaluated by testing a candidate modification in the system described in Section III. gRNA's having a candidate complementarity domain having a selected length, sequence, degree of complementarity, or degree of modification, can be evaluated in the system described in Section III. The candidate complementarity domain can be placed, either alone, or with one or more other candidate changes in a gRNA molecule /Cas9 molecule system known to be functional with a selected target and evaluated. In an embodiment, the first complementarity domain has at least 60, 70, 80, 85%, 90%, or 95% homology with, or differs by no more than 1, 2, 3, 4, 5, or 6 nucleotides from, a reference first complementarity domain, e.g., a naturally occurring, e.g., an S. pyogenes, or S.

thermophilus, first complementarity domain, or a first complementarity domain described herein, e.g., from FIGS. 1A-1F.

In an embodiment, the second complementarity domain has at least 60, 70, 80, 85%, 90%, or 95 % homology with, or differs by no more than 1, 2, 3, 4, 5, or 6 nucleotides from, a reference second complementarity domain, e.g., a naturally occurring, e.g., an S. pyogenes, or S. thermophilus, second complementarity domain, or a second complementarity domain described herein, e.g., from FIGS. 1A-1F.

The duplexed region formed by first and second complementarity domains is typically 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 or 22 base pairs in length (excluding any looped out or unpaired nucleotides).

In an embodiment, the first and second complementarity domains, when duplexed, comprise 11 paired nucleotides, for example, in the gRNA sequence (one paired strand underlined, one bolded):

NNNNNNNNNNNNNNNNNNNNGUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAA

GGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGC (SEQ ID NO: 5).

In an embodiment, the first and second complementarity domains, when duplexed, comprise 15 paired nucleotides, for example in the gRNA sequence (one paired strand underlined, one bolded):

NNNNNNNNNNNNNNNNNNNNGUUUUAGAGCUAUGCUGAAAAGCAUAGCAAGU UAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGC

(SEQ ID NO: 27).

In an embodiment the first and second complementarity domains, when duplexed, comprise 16 paired nucleotides, for example in the gRNA sequence (one paired strand underlined, one bolded):

NNNNNNNNNNNNNNNNNNNNGUUUUAGAGCUAUGCUGGAAACAGCAUAGCAA GUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGU GC (SEQ ID NO: 28). In an embodiment the first and second complementarity domains, when duplexed, comprise 21 paired nucleotides, for example in the gRNA sequence (one paired strand underlined, one bolded):

NNNNNNNNNNNNNNNNNNNNGUUUUAGAGCUAUGCUGUUUUGGAAACAAAAC AGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCA CCGAGUCGGUGC (SEQ ID NO: 29).

In an embodiment, nucleotides are exchanged to remove poly-U tracts, for example in the gRNA sequences (exchanged nucleotides underlined):

NNNNNNNNNNNNNNNNNNNNGUAUUAGAGCUAGAAAUAGCAAGUUAAUAUAA GGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGC (SEQ ID

NO: 30);

NNNNNNNNNNNNNNNNNNNNGUUUAAGAGCUAGAAAUAGCAAGUUUAAAUAA GGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGC (SEQ ID NO: 31); and

NNNNNNNNNNNNNNNNNNNNGUAUUAGAGCUAUGCUGUAUUGGAAACAAUAC AGCAUAGCAAGUUAAUAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCA CCGAGUCGGUGC (SEQ ID NO: 32).

The 5' Extension Domain

In an embodiment, a modular gRNA can comprise additional sequence, 5' to the second complementarity domain. In an embodiment, the 5' extension domain is 2 to 10, 2 to 9, 2 to 8, 2 to 7, 2 to 6, 2 to 5, or 2 to 4 nucleotides in length. In an embodiment, the 5' extension domain is 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more nucleotides in length.

In an embodiment, the 5' extension domain nucleotides do not comprise modifications, e.g., modifications of the type provided in Section X. However, in an embodiment, the 5' extension domain comprises one or more modifications, e.g., modifications that it render it less susceptible to degradation or more bio-compatible, e.g., less immunogenic. By way of example, the backbone of the 5' extension domain can be modified with a phosphorothioate, or other modification from Section X. In an embodiment, a nucleotide of the 5' extension domain can comprise a 2' modification (e.g., a modification at the 2' position on ribose), e.g., a 2' - acetylation, e.g., a 2' methylation, or other modification from Section X. In an embodiment, the 5' extension domain can comprise as many as 1, 2, 3, 4, 5, 6, 7 or 8 modifications. In an embodiment, the 5' extension domain comprises as many as 1, 2, 3, or 4 modifications within 5 nucleotides of its 5' end, e.g., in a modular gRNA molecule. In an embodiment, the 5' extension domain comprises as many as 1, 2, 3, or 4 modifications within 5 nucleotides of its 3' end, e.g., in a modular gRNA molecule.

In an embodiment, the 5' extension domain comprises modifications at two consecutive nucleotides, e.g., two consecutive nucleotides that are within 5 nucleotides of the 5' end of the 5' extension domain, within 5 nucleotides of the 3' end of the 5' extension domain, or more than 5 nucleotides away from one or both ends of the 5' extension domain. In an embodiment, no two consecutive nucleotides are modified within 5 nucleotides of the 5' end of the 5' extension domain, within 5 nucleotides of the 3' end of the 5' extension domain, or within a region that is more than 5 nucleotides away from one or both ends of the 5' extension domain. In an embodiment, no nucleotide is modified within 5 nucleotides of the 5' end of the 5' extension domain, within 5 nucleotides of the 3' end of the 5' extension domain, or within a region that is more than 5 nucleotides away from one or both ends of the 5' extension domain.

Modifications in the 5' extension domain can be selected to not interfere with gRNA molecule efficacy, which can be evaluated by testing a candidate modification in the system described in Section III. gRNAs having a candidate 5' extension domain having a selected length, sequence, degree of complementarity, or degree of modification, can be evaluated in the system described at Section III. The candidate 5' extension domain can be placed, either alone, or with one or more other candidate changes in a gRNA molecule/Cas9 molecule system known to be functional with a selected target and evaluated.

In an embodiment, the 5' extension domain has at least 60, 70, 80, 85, 90 or 95% homology with, or differs by no more than 1, 2, 3, 4, 5, or 6 nucleotides from, a reference 5' extension domain, e.g., a naturally occurring, e.g., an S. pyogenes, or S. thermophilus, 5' extension domain, or a 5' extension domain described herein, e.g., from FIG. 1A and FIG. IF.

The Linking Domain

In a unimolecular gRNA molecule the linking domain is disposed between the first and second complementarity domains. In a modular gRNA molecule, the two molecules are associated with one another by the complementarity domains. In an embodiment, the linking domain is 10 +/-5, 20+/-5, 30+/-5, 40+/-5, 50+/-5, 60+/-5, 70+/-5, 80+/-5, 90+/-5, or 100+/-5 nucleotides, in length.

In an embodiment, the linking domain is 20+/- 10, 30+/- 10, 40+/- 10, 50+/- 10, 60+/- 10, 70+/- 10, 80+/- 10, 90+/- 10, or 100+/- 10 nucleotides, in length.

In an embodiment, the linking domain is 10 to 100, 10 to 90, 10 to 80, 10 to 70, 10 to 60,

10 to 50, 10 to 40, 10 to 30, 10 to 20 or 10 to 15 nucleotides in length. In an embodiment, the targeting domain is 20 to 100, 20 to 90, 20 to 80, 20 to 70, 20 to 60, 20 to 50, 20 to 40, 20 to 30, or 20 to 25 nucleotides in length.

In an embodiment, the linking domain is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 17, 18, 19, or 20 nucleotides in length.

In an embodiment, the linking domain is a covalent bond.

In an embodiment, the linking domain comprises a duplexed region, typically adjacent to or within 1, 2, or 3 nucleotides of the 3' end of the first complementarity domain and/or the 5- end of the second complementarity domain. In an embodiment, the duplexed region can be 20+/- 10, 30+/- 10, 40, +/-10 or 50+/- 10 base pairs in length. In an embodiment, the duplexed region can be 10+/-5, 15+/-5, 20+/-5, or 30+/-5 base pairs in length. In an embodiment, the duplexed region can be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 base pairs in length.

Typically the sequences forming the duplexed region have exact complementarity with one another, though in an embodiment as many as 1, 2, 3, 4, 5, 6, 7 or 8 nucleotides are not complementary with the corresponding nucleotides.

In an embodiment, the linking domain nucleotides do not comprise modifications, e.g., modifications of the type provided in Section X. However, in an embodiment the linking domain comprises one or more modifications, e.g., modifications that it render it less susceptible to degradation or more bio-compatible, e.g., less immunogenic. By way of example, the backbone of the linking domain can be modified with a phosphorothioate, or other modification from Section X. In an embodiment, a nucleotide of the linking domain can comprise a 2' modification (e.g., a modification at the 2' position on ribose), e.g., a 2' -acetylation, e.g., a 2' methylation, or other modification from Section X.

In an embodiment, the linking domain can comprise as many as 1, 2, 3, 4, 5, 6, 7 or 8 modifications. Modifications in a linking domain can be selected to not interfere with targeting efficacy, which can be evaluated by testing a candidate modification in the system described in Section III. gRNA's having a candidate linking domain having a selected length, sequence, degree of complementarity, or degree of modification, can be evaluated a system described in Section III. A candidate linking domain can be placed, either alone, or with one or more other candidate changes in a gRNA molecule/Cas9 molecule system known to be functional with a selected target and evaluated.

In an embodiment, the linking domain has at least 60, 70, 80, 85, 90 or 95% homology with, or differs by no more than 1, 2, 3, 4, 5 ,or 6 nucleotides from, a reference linking domain, e.g., a linking domain described herein, e.g., from FIG. IB-IE.

The proximal domain

In an embodiment, the proximal domain is 6 +1-2, 7+/-2, 8+/-2, 9+/-2, 10+/-2, 11+/-2, 12+/-2, 13+/-2, 14+/-2, 14+/-2, 16+/-2, 17+/-2, 18+/-2, 19+/-2, or 20+/-2 nucleotides in length.

In an embodiment, the proximal domain is 6, 7, 8, 9, 10, 11, 12, 13, 14, 14, 16, 17, 18, 19, or 20 nucleotides in length.

In an embodiment, the proximal domain is 5 to 20, 7, to 18, 9 to 16, or 10 to 14 nucleotides in length.

In an embodiment, the proximal domain nucleotides do not comprise modifications, e.g., modifications of the type provided in Section X. However, in an embodiment, the proximal domain comprises one or more modifications, e.g., modifications that it render it less susceptible to degradation or more bio-compatible, e.g., less immunogenic. By way of example, the backbone of the proximal domain can be modified with a phosphorothioate, or other

modification from Section X. In an embodiment, a nucleotide of the proximal domain can comprise a 2' modification (e.g., a modification at the 2' position on ribose), e.g., a 2' - acetylation, e.g., a 2' methylation, or other modification from Section X.

In an embodiment, the proximal domain can comprise as many as 1, 2, 3, 4, 5, 6, 7 or 8 modifications. In an embodiment, the proximal domain comprises as many as 1, 2, 3, or 4 modifications within 5 nucleotides of its 5' end, e.g., in a modular gRNA molecule. In an embodiment, the target domain comprises as many as 1, 2, 3, or 4 modifications within 5 nucleotides of its 3' end, e.g., in a modular gRNA molecule. In an embodiment, the proximal domain comprises modifications at two consecutive nucleotides, e.g., two consecutive nucleotides that are within 5 nucleotides of the 5' end of the proximal domain, within 5 nucleotides of the 3' end of the proximal domain, or more than 5 nucleotides away from one or both ends of the proximal domain. In an embodiment, no two consecutive nucleotides are modified within 5 nucleotides of the 5' end of the proximal domain, within 5 nucleotides of the 3' end of the proximal domain, or within a region that is more than 5 nucleotides away from one or both ends of the proximal domain. In an embodiment, no nucleotide is modified within 5 nucleotides of the 5' end of the proximal domain, within 5 nucleotides of the 3' end of the proximal domain, or within a region that is more than 5 nucleotides away from one or both ends of the proximal domain.

Modifications in the proximal domain can be selected to not interfere with gRNA molecule efficacy, which can be evaluated by testing a candidate modification in the system described in Section III. gRNA's having a candidate proximal domain having a selected length, sequence, degree of complementarity, or degree of modification, can be evaluated in the system described at Section III. The candidate proximal domain can be placed, either alone, or with one or more other candidate changes in a gRNA molecule /Cas9 molecule system known to be functional with a selected target and evaluated.

In an embodiment, the proximal domain has at least 60%, 70%, 80%, 85%, 90%, or 95% homology with, or differs by no more than 1, 2, 3, 4, 5 ,or 6 nucleotides from, a reference proximal domain, e.g., a naturally occurring, e.g., an S. pyogenes, or S. thermophilus, proximal domain, or a proximal domain described herein, e.g., from FIG. 1A-1F.

The Tail Domain

In an embodiment, the tail domain is 10 +/-5, 20+/-5, 30+/-5, 40+/-5, 50+/-5, 60+/-5, 70+/-5, 80+/-5, 90+/-5, or 100+/-5 nucleotides, in length.

In an embodiment, the tail domain is 20+/-5 nucleotides in length.

In an embodiment, the tail domain is 20+/- 10, 30+/- 10, 40+/- 10, 50+/- 10, 60+/- 10, 70+/- 10, 80+/- 10, 90+/- 10, or 100+/- 10 nucleotides, in length.

In an embodiment, the tail domain is 25+/- 10 nucleotides in length.

In an embodiment, the tail domain is 10 to 100, 10 to 90, 10 to 80, 10 to 70, 10 to 60, 10 to 50, 10 to 40, 10 to 30, 10 to 20 or 10 to 15 nucleotides in length. In an embodiment, the tail domain is 20 to 100, 20 to 90, 20 to 80, 20 to 70, 20 to 60, 20 to 50, 20 to 40, 20 to 30, or 20 to 25 nucleotides in length.

In an embodiment, the tail domain is 1 to 20, 1 to 1, 1 to 10, or 1 to 5 nucleotides in length.

In an embodiment, the tail domain nucleotides do not comprise modifications, e.g., modifications of the type provided in Section X. However, in an embodiment, the tail domain comprises one or more modifications, e.g., modifications that it render it less susceptible to degradation or more bio-compatible, e.g., less immunogenic. By way of example, the backbone of the tail domain can be modified with a phosphorothioate, or other modification from Section X. In an embodiment, a nucleotide of the tail domain can comprise a 2' modification (e.g., a modification at the 2' position on ribose), e.g., a 2' -acetylation, e.g., a 2' methylation, or other modification from Section X.

In an embodiment, the tail domain can have as many as 1, 2, 3, 4, 5, 6, 7 or 8

modifications. In an embodiment, the target domain comprises as many as 1, 2, 3, or 4 modifications within 5 nucleotides of its 5' end. In an embodiment, the target domain comprises as many as 1, 2, 3, or 4 modifications within 5 nucleotides of its 3' end.

In an embodiment, the tail domain comprises a tail duplex domain, which can form a tail duplexed region. In an embodiment, the tail duplexed region can be 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 base pairs in length. In an embodiment, a further single stranded domain exists 3' to the tail duplexed domain. In an embodiment, this domain is 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides in length. In an embodiment, it is 4 to 6 nucleotides in length.

In an embodiment, the tail domain has at least 60, 70, 80, or 90% homology with, or differs by no more than 1, 2, 3, 4, 5,or 6 nucleotides from, a reference tail domain, e.g., a naturally occurring, e.g., an S. pyogenes, or S. thermophilus, tail domain, or a tail domain described herein, e.g., from FIG. 1A and FIGS. 1C-1F.

In an embodiment, the proximal and tail domain, taken together comprise the following sequences:

AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCU (SEQ ID NO: 33);

AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGGUGC

(SEQ ID NO: 34); AAGGCUAGUCCGUUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCGGAUC

(SEQ ID NO: 35);

AAGGCUAGUCCGUUAUCAACUUGAAAAAGUG (SEQ ID NO: 36);

AAGGCUAGUCCGUUAUCA (SEQ ID NO: 37); or

AAGGCUAGUCCG (SEQ ID NO: 38).

In an embodiment, the tail domain comprises the 3' sequence UUUUUU, e.g., if a U6 promoter is used for transcription.

In an embodiment, the tail domain comprises the 3' sequence UUUU, e.g., if an HI promoter is used for transcription.

In an embodiment, tail domain comprises variable numbers of 3' U's depending, e.g., on the termination signal of the pol-III promoter used.

In an embodiment, the tail domain comprises variable 3' sequence derived from the DNA template if a T7 promoter is used.

In an embodiment, the tail domain comprises variable 3' sequence derived from the DNA template, e.g., if in vitro transcription is used to generate the RNA molecule.

In an embodiment, the tail domain comprises variable 3' sequence derived from the DNA template, e.g, if a pol-II promoter is used to drive transcription.

Modifications in the tail domain can be selected to not interfere with targeting efficacy, which can be evaluated by testing a candidate modification in the system described in Section III. gRNA's having a candidate tail domain having a selected length, sequence, degree of complementarity, or degree of modification, can be evaluated in the system described in Section III. The candidate tail domain can be placed, either alone, or with one or more other candidate changes in a gRNA molecule/Cas9 molecule system known to be functional with a selected target and evaluated.

In an embodiment, the tail domain comprises modifications at two consecutive nucleotides, e.g., two consecutive nucleotides that are within 5 nucleotides of the 5' end of the tail domain, within 5 nucleotides of the 3' end of the tail domain, or more than 5 nucleotides away from one or both ends of the tail domain. In an embodiment, no two consecutive nucleotides are modified within 5 nucleotides of the 5' end of the tail domain, within 5 nucleotides of the 3' end of the tail domain, or within a region that is more than 5 nucleotides away from one or both ends of the tail domain. In an embodiment, no nucleotide is modified within 5 nucleotides of the 5' end of the tail domain, within 5 nucleotides of the 3' end of the tail domain, or within a region that is more than 5 nucleotides away from one or both ends of the tail domain.

In an embodiment a gRNA has the following structure:

5' [targeting domain] -[first complementarity domain] -[linking domain] -[second complementarity domain] -[proximal domain] -[tail domain] -3'

wherein,

the targeting domain comprises a core domain and optionally a secondary domain, and is 10 to 50 nucleotides in length;

the first complementarity domain is 5 to 25 nucleotides in length and, in an embodiment has

at least 50, 60, 70, 80, 85, 90, or 95% homology with a reference first complementarity domain disclosed herein;

the linking domain is 1 to 5 nucleotides in length;

the proximal domain is 5 to 20 nucleotides in length and, in an embodiment has at least 50, 60, 70, 80, 85, 90 or 95% homology with a reference proximal domain disclosed herein;

and

the tail domain is absent or a nucleotide sequence is 1 to 50 nucleotides in length and, in an embodiment has at least 50, 60, 70, 80, 85, 90 or 95% homology with a reference tail domain disclosed herein.

Exemplary Chimeric gRNAs

In an embodiment, a unimolecular, or chimeric, gRNA comprises, preferably from 5' to a targeting domain, e.g., comprsing 15, 16, 17, 18, 19 or 20 nucleotides (which is complementary to a target nucleic acid);

a first complementarity domain;

a linking domain;

a second complementarity domain (which is complementary to the first complementarity domain);

a proximal domain; and a tail domain,

wherein,

(a) the proximal and tail domain, when taken together, comprise

at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides;

(b) there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3' to the last nucleotide of the second complementarity domain; or

(c) there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3' to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the sequence from (a), (b), or (c), has at least 60, 75, 80, 85, 90, 95, or

99% homology with the corresponding sequence of a naturally occurring gRNA, or with a gRNA described herein.

In an embodiment, the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3' to the last nucleotide of the second complementarity domain.

In an embodiment, there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3' to the last nucleotide of the second complementarity domain that is

complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of 16, 17, 18, 19, 20,

21, 22, 23, 24 or 25 nucleotides (e.g., 16, 17, 18, 19, 20, 21, 22, 23, 24 or 25 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 16, 17, 18, 19, 20, 21, 22, 23, 24 or 25 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 16 nucleotides (e.g., 16 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 16 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 17 nucleotides (e.g., 17 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 17 nucleotides in length. In an embodiment, the targeting domain comprises, has, or consists of, 18 nucleotides (e.g., 18 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 18 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 19 nucleotides (e.g., 19 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 19 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 20 nucleotides (e.g., 20 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 20 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 21 nucleotides

(e.g., 21 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 21 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 22 nucleotides (e.g., 22 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 22 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 23 nucleotides (e.g., 23 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 23 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 24 nucleotides (e.g., 24 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 24 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 25 nucleotides (e.g., 25 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 25 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 26 nucleotides

(e.g., 26 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 26 nucleotides in length. In an embodiment, the targeting domain comprises, has, or consists of, 16 nucleotides (e.g., 16 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 16 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides. In an embodiment, the targeting domain comprises, has, or consists of, 16 nucleotides (e.g., 16 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 16 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40,

45, 49, 50, or 53 nucleotides 3' to the last nucleotide of the second complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 16 nucleotides

(e.g., 16 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 16 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41,

46, 50, 51, or 54 nucleotides 3' to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 17 nucleotides

(e.g., 17 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 17 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, the targeting domain comprises, has, or consists of, 17 nucleotides (e.g., 17 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 17 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40,

In an embodiment, the targeting domain comprises, has, or consists of, 17 nucleotides (e.g., 17 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 17 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41,

In an embodiment, the targeting domain comprises, has, or consists of, 18 nucleotides (e.g., 18 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 18 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, the targeting domain comprises, has, or consists of, 18 nucleotides (e.g., 18 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 18 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3' to the last nucleotide of the second complementarity domain. In an embodiment, the targeting domain comprises, has, or consists of, 18 nucleotides (e.g., 18 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 18 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3' to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 19 nucleotides (e.g., 19 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 19 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, the targeting domain comprises, has, or consists of, 19 nucleotides

(e.g., 19 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 19 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40,

In an embodiment, the targeting domain comprises, has, or consists of, 19 nucleotides (e.g., 19 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 19 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41,

In an embodiment, the targeting domaincomprises, has, or consists of, 20 nucleotides (e.g., 20 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 20 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, the targeting domain comprises, has, or consists of, 20 nucleotides (e.g., 20 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 20 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3' to the last nucleotide of the second complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 20 nucleotides (e.g., 20 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 20 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3' to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain. In an embodiment, the targeting domain comprises, has, or consists of, 21 nucleotides (e.g., 21 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 21 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

(e.g., 21 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 21 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40,

In an embodiment, the targeting domain comprises, has, or consists of, 21 nucleotides (e.g., 21 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 21 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41,

In an embodiment, the targeting domain comprises, has, or consists of, 22 nucleotides (e.g., 22 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 22 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, the targeting domaincomprises, has, or consists of, 22 nucleotides (e.g., 22 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 22 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3' to the last nucleotide of the second complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 22 nucleotides (e.g., 22 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 22 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3' to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 23 nucleotides (e.g., 23 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 23 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides. In an embodiment, the targeting domain comprises, has, or consists of, 23 nucleotides (e.g., 23 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 23 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40,

In an embodiment, the targeting domain comprises, has, or consists of, 23 nucleotides

(e.g., 23 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 23 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41,

In an embodiment, the targeting domain comprises, has, or consists of, 24 nucleotides

(e.g., 24 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 24 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, the targeting domain comprises, has, or consists of, 24 nucleotides (e.g., 24 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 24 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40,

In an embodiment, the targeting domain comprises, has, or consists of, 24 nucleotides (e.g., 24 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 24 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41,

In an embodiment, the targeting domain comprises, has, or consists of, 25 nucleotides (e.g., 25 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 25 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, the targeting domain has, or consists of, 25 nucleotides (e.g., 25 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 25 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3' to the last nucleotide of the second complementarity domain. In an embodiment, the targeting domain comprises, has, or consists of, 25 nucleotides (e.g., 25 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 25 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3' to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 26 nucleotides (e.g., 26 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 26 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

(e.g., 26 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 26 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40,

In an embodiment, the targeting domain comprises, has, or consists of, 26 nucleotides (e.g., 26 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 26 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41,

46, 50, 51, or 54 nucleotides 3' to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain. Exemplary Modular gRNAs

In an embodiment, a modular gRNA comprises:

a first strand comprising, preferably from 5' to 3' ;

a targeting domain, e.g., comprising 15, 16, 17, 18, 19, or 20 nucleotides; a first complementarity domain; and

a second strand, comprising, preferably from 5' to 3':

optionally a 5' extension domain;

a second complementarity domain;

a proximal domain; and

a tail domain,

wherein: (a) the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides;

In an embodiment, the sequence from (a), (b), or (c), has at least 60, 75, 80, 85, 90, 95, or 99% homology with the corresponding sequence of a naturally occurring gRNA, or with a gRNA described herein.

In an embodiment, the targeting domain comprises, has, or consists of, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26 nucleotides (e.g., 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or 26 nucleotides in length.

(e.g., 17 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 17 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 18 nucleotides (e.g., 18 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 18 nucleotides in length. In an embodiment, the targeting domain comprises, has, or consists of, 19 nucleotides (e.g., 19 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 19 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 21 nucleotides (e.g., 21 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 21 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 22 nucleotides

(e.g., 22 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 22 nucleotides in length.

In an embodiment, the targeting domain has, or consists of, 24 nucleotides (e.g., 24 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 24 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 25 nucleotides (e.g., 25 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 5 nucleotides in length.

In an embodiment, the targeting domain comprises, has, or consists of, 26 nucleotides (e.g., 26 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 5 nucleotides in length.

(e.g., 16 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 16 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, the targeting domain comprises, has, or consists of, 16 nucleotides (e.g., 16 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 16 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40,

In an embodiment, the targeting domai comprises, n has, or consists of, 16 nucleotides (e.g., 16 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 16 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41,

In an embodiment, the targeting domain comprises, has, or consists of, 17 nucleotides (e.g., 17 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 17 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, the targeting domain comprises, has, or consists of, 17 nucleotides (e.g., 17 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 17 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3' to the last nucleotide of the second complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 17 nucleotides (e.g., 17 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 17 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3' to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 18 nucleotides

(e.g., 18 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 18 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3' to the last nucleotide of the second complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 18 nucleotides (e.g., 18 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 18 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3' to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 19 nucleotides (e.g., 19 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 19 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3' to the last nucleotide of the second complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 19 nucleotides (e.g., 19 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 19 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3' to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 20 nucleotides (e.g., 20 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 20 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, the targeting domain comprises, has, or consists of, 20 nucleotides

(e.g., 20 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 20 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40,

In an embodiment, the targeting domain comprises, has, or consists of, 20 nucleotides (e.g., 20 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 20 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41,

In an embodiment, the targeting domain comprises, has, or consists of, 21 nucleotides (e.g., 21 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 21 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, the targeting domain comprises, has, or consists of, 21 nucleotides (e.g., 21 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 21 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3' to the last nucleotide of the second complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 21 nucleotides (e.g., 21 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 21 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3' to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 22 nucleotides (e.g., 22 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 22 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40,

(e.g., 22 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 22 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41,

(e.g., 23 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 23 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, the targeting domain comprises, has, or consists of, 23 nucleotides (e.g., 23 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 23 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40,

In an embodiment, the targeting domain comprises, has, or consists of, 23 nucleotides (e.g., 23 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 23 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41,

In an embodiment, the targeting domain comprises, has, or consists of, 24 nucleotides (e.g., 24 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 24 nucleotides in length; and the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides.

In an embodiment, the targeting domain comprises, has, or consists of, 24 nucleotides (e.g., 24 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 24 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3' to the last nucleotide of the second complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 24 nucleotides (e.g., 24 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 24 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3' to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 25 nucleotides

(e.g., 25 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 25 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3' to the last nucleotide of the second complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 25 nucleotides (e.g., 25 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 25 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3' to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 26 nucleotides (e.g., 26 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 26 nucleotides in length; and there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3' to the last nucleotide of the second complementarity domain.

In an embodiment, the targeting domain comprises, has, or consists of, 26 nucleotides (e.g., 26 consecutive nucleotides) having complementarity with the target domain, e.g., the targeting domain is 26 nucleotides in length; and there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3' to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain.

Methods for Designing gRNAs

Methods for designing gRNAs are described herein, including methods for selecting, designing and validating target domains. Exemplary targeting domains are also provided herein. Targeting Domains discussed herein can be incorporated into the gRNAs described herein.

Methods for selection and validation of target sequences as well as off-target analyses are described, e.g., in Mali et al, 2013 SCIENCE 339(6121): 823-826; Hsu et al, 2013 NAT

BIOTECHNOL, 31(9): 827-32; Fu et al, 2014 NAT BIOTECHNOL, doi: 10.1038/nbt.2808. PubMed PMID: 24463574; Heigwer et al, 2014 NAT METHODS l l(2): 122-3. doi: 10.1038/nmeth.2812. PubMed PMID: 24481216; Bae et al, 2014 BIOINFORMATICS PubMed PMID: 24463181; Xiao A et al, 2014 BIOINFORMATICS PubMed PMID: 24389662.

For example, a software tool can be used to optimize the choice of gRNA within a user' s target sequence, e.g., to minimize total off-target activity across the genome. Off target activity may be other than cleavage. For each possible gRNA choice e.g., using S. pyogenes Cas9, the tool can identify all off-target sequences (e.g., preceding either NAG or NGG PAMs) across the genome that contain up to certain number (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10) of mismatched base-pairs. The cleavage efficiency at each off-target sequence can be predicted, e.g., using an experimentally-derived weighting scheme. Each possible gRNA is then ranked according to its total predicted off-target cleavage; the top-ranked gRNAs represent those that are likely to have the greatest on-target and the least off-target cleavage. Other functions, e.g., automated reagent design for CRISPR construction, primer design for the on-target Surveyor assay, and primer design for high-throughput detection and quantification of off-target cleavage via next-gen sequencing, can also be included in the tool. Candidate gRNA molecules can be evaluated by art-known methods or as described in Section IV herein. II. Cas9 Molecules

Cas9 molecules of a variety of species can be used in the methods and compositions described herein. While the S. pyogenes and S. thermophilus Cas9 molecules are the subject of much of the disclosure herein, Cas9 molecules of, derived from, or based on the Cas9 proteins of other species listed herein can be used as well. In other words, while the much of the description herein uses S. pyogenes and S. thermophilus Cas9 molecules, Cas9 molecules from the other species can replace them, e.g., Staphylococcus aureus and Neisseria meningitidis Cas9 molecules. Additional Cas9 species include: Acidovorax avenae, Actinobacillus

pleuropneumoniae, Actinobacillus succinogenes, Actinobacillus suis, Actinomyces sp., cycliphilus denitrificans, Aminomonas paucivorans, Bacillus cereus, Bacillus smithii, Bacillus thuringiensis, Bacteroides sp., Blastopirellula marina, Bradyrhizobium sp., Brevibacillus laterosporus, Campylobacter coli, Campylobacter jejuni, Campylobacter lari, Candidatus Puniceispirillum, Clostridium cellulolyticum, Clostridium perfringens, Corynebacterium accolens, Corynebacterium diphtheria, Corynebacterium matruchotii, Dinoroseobacter shibae, Eubacterium dolichum, gamma proteobacterium, Gluconacetobacter diazotrophicus,

Haemophilus parainfluenzae, Haemophilus sputorum, Helicobacter canadensis, Helicobacter cinaedi, Helicobacter mustelae, Ilyobacter polytropus, Kingella kingae, Lactobacillus crispatus, Listeria ivanovii, Listeria monocytogenes, Listeriaceae bacterium, Methylocystis sp.,

Methylosinus trichosporium, Mobiluncus mulieris, Neisseria bacilliformis, Neisseria cinerea, Neisseria flavescens, Neisseria lactamica, Neisseria sp., Neisseria wadsworthii, Nitrosomonas sp., Parvibaculum lavamentivorans, Pasteurella multocida, Phascolarctobacterium

succinatutens, Ralstonia syzygii, Rhodopseudomonas palustris, Rhodovulum sp., Simonsiella muelleri, Sphingomonas sp., Sporolactobacillus vineae, Staphylococcus lugdunensis, Streptococcus sp., Subdoligranulum sp., Tistrella mobilis, Treponema sp., or Verminephrobacter eiseniae.

A Cas9 molecule, as that term is used herein, refers to a molecule that can interact with a gRNA molecule and, in concert with the gRNA molecule, localize (e.g., target or home) to a site which comprises a target domain and PAM sequence.

In an embodiment, the Cas9 molecule is capable of cleaving a target nucleic acid molecule. A Cas9 molecule that is capable of cleaving a target nucleic acid molecule is referred to herein as an eaCas9 (an enzymatically active Cas9) molecule. In an embodiment, an eaCas9 molecule, comprises one or more of the following activities:

a nickase activity, i.e., the ability to cleave a single strand, e.g., the non-complementary strand or the complementary strand, of a nucleic acid molecule;

a double stranded nuclease activity, i.e., the ability to cleave both strands of a double stranded nucleic acid and create a double stranded break, which in an embodiment is the presence of two nickase activities;

an endonuclease activity;

an exonuclease activity; and

a helicase activity, i.e., the ability to unwind the helical structure of a double stranded nucleic acid.

In an embodiment, an enzymatically active Cas9 or an eaCas9 molecule cleaves both

DNA strands and results in a double stranded break. In an embodiment, an eaCas9 molecule cleaves only one strand, e.g., the strand to which the gRNA hybridizes to, or the strand complementary to the strand the gRNA hybridizes with. In an embodiment, an eaCas9 molecule comprises cleavage activity associated with an HNH-like domain. In an embodiment, an eaCas9 molecule comprises cleavage activity associated with an N-terminal RuvC-like domain. In an embodiment, an eaCas9 molecule comprises cleavage activity associated with an HNH-like domain and cleavage activity associated with an N-terminal RuvC-like domain. In an embodiment, an eaCas9 molecule comprises an active, or cleavage competent, HNH-like domain and an inactive, or cleavage incompetent, N-terminal RuvC-like domain. In an embodiment, an eaCas9 molecule comprises an inactive, or cleavage incompetent, HNH-like domain and an active, or cleavage competent, N-terminal RuvC-like domain. In an embodiment, the ability of an eaCas9 molecule to interact with and cleave a target nucleic acid is PAM sequence dependent. A PAM sequence is a sequence in the target nucleic acid. In an embodiment, cleavage of the target nucleic acid occurs upstream from the PAM sequence. EaCas9 molecules from different bacterial species can recognize different sequence motifs (e.g., PAM sequences). In an embodiment, an eaCas9 molecule of S. pyogenes recognizes the sequence motif NGG and directs cleavage of a target nucleic acid sequence 1 to 10, e.g., 3 to 5, base pairs upstream from that sequence. See, e.g., Mali et al, SCIENCE 2013; 339(6121): 823- 826. In an embodiment, an eaCas9 molecule of S. thermophilus recognizes the sequence motif NGGNG and NNAGAAW (W = A or T) and directs cleavage of a core target nucleic acid sequence 1 to 10, e.g., 3 to 5, base pairs upstream from these sequences. See, e.g., Horvath et al, SCIENCE 2010; 327(5962): 167-170, and Deveau et al, J BACTERIOL 2008; 190(4): 1390- 1400. In an embodiment, an eaCas9 molecule of S. mutans recognizes the sequence motif NGG or NAAR (R = A or G) and directs cleavage of a core target nucleic acid sequence 1 to 10, e.g., 3 to 5 base pairs, upstream from this sequence. See, e.g., Deveau et al, J BACTERIOL 2008;

190(4): 1390-1400. In an embodiment, an eaCas9 molecule of S. aureus recognizes the sequence motif NNGRR (R = A or G) and directs cleavage of a target nucleic acid sequence 1 to 10, e.g., 3 to 5, base pairs upstream from that sequence. In an embodiment, an eaCas9 molecule of N. meningitidis recognizes the sequence motif NNNNGATT and directs cleavage of a target nucleic acid sequence 1 to 10, e.g., 3 to 5, base pairs upstream from that sequence. See, e.g., Hou et al, PNAS EARLY EDITION 2013, 1-6. The ability of a Cas9 molecule to recognize a PAM sequence can be determined, e.g., using a transformation assay described in Jinek et al, SCIENCE 2012, 337:816.

Some Cas9 molecules have the ability to interact with a gRNA molecule, and in conjunction with the gRNA molecule home (e.g., targeted or localized) to a core target domain, but are incapable of cleaving the target nucleic acid, or incapable of cleaving at efficient rates. Cas9 molecules having no, or no substantial, cleavage activity are referred to herein as an eiCas9 (an enzymatically inactive Cas9) molecule. For example, an eiCas9 molecule can lack cleavage activity or have substantially less, e.g., less than 20, 10, 5, 1 or 0.1 % of the cleavage activity of a reference Cas9 molecule, as measured by an assay described herein.

Exemplary naturally occurring Cas9 molecules are described in Chylinski et al, RNA

Biology 2013; 10:5, 727-737. Such Cas9 molecules include Cas9 molecules of a cluster 1 bacterial family, cluster 2 bacterial family, cluster 3 bacterial family, cluster 4 bacterial family, cluster 5 bacterial family, cluster 6 bacterial family, a cluster 7 bacterial family, a cluster 8 bacterial family, a cluster 9 bacterial family, a cluster 10 bacterial family, a cluster 11 bacterial family, a cluster 12 bacterial family, a cluster 13 bacterial family, a cluster 14 bacterial family, a cluster 15 bacterial family, a cluster 16 bacterial family, a cluster 17 bacterial family, a cluster 18 bacterial family, a cluster 19 bacterial family, a cluster 20 bacterial family, a cluster 21 bacterial family, a cluster 22 bacterial family, a cluster 23 bacterial family, a cluster 24 bacterial family, a cluster 25 bacterial family, a cluster 26 bacterial family, a cluster 27 bacterial family, a cluster 28 bacterial family, a cluster 29 bacterial family, a cluster 30 bacterial family, a cluster 31 bacterial family, a cluster 32 bacterial family, a cluster 33 bacterial family, a cluster 34 bacterial family, a cluster 35 bacterial family, a cluster 36 bacterial family, a cluster 37 bacterial family, a cluster 38 bacterial family, a cluster 39 bacterial family, a cluster 40 bacterial family, a cluster 41 bacterial family, a cluster 42 bacterial family, a cluster 43 bacterial family, a cluster 44 bacterial family, a cluster 45 bacterial family, a cluster 46 bacterial family, a cluster 47 bacterial family, a cluster 48 bacterial family, a cluster 49 bacterial family, a cluster 50 bacterial family, a cluster 51 bacterial family, a cluster 52 bacterial family, a cluster 53 bacterial family, a cluster 54 bacterial family, a cluster 55 bacterial family, a cluster 56 bacterial family, a cluster 57 bacterial family, a cluster 58 bacterial family, a cluster 59 bacterial family, a cluster 60 bacterial family, a cluster 61 bacterial family, a cluster 62 bacterial family, a cluster 63 bacterial family, a cluster 64 bacterial family, a cluster 65 bacterial family, a cluster 66 bacterial family, a cluster 67 bacterial family, a cluster 68 bacterial family, a cluster 69 bacterial family, a cluster 70 bacterial family, a cluster 71 bacterial family, a cluster 72 bacterial family, a cluster 73 bacterial family, a cluster 74 bacterial family, a cluster 75 bacterial family, a cluster 76 bacterial family, a cluster 77 bacterial family, or a cluster 78 bacterial family.

Exemplary naturally occurring Cas9 molecules include a Cas9 molecule of a cluster 1 bacterial family. Examples include a Cas9 molecule of: S. pyogenes (e.g., strain SF370, MGAS10270, MGAS10750, MGAS2096, MGAS315, MGAS5005, MGAS6180, MGAS9429, NZ131 and SSI-1), S. thermophilus (e.g., strain LMD-9), S. pseudoporcinus (e.g., strain SPIN 20026), S. mutans (e.g., strain UA159, NN2025), S. macacae (e.g., strain NCTC11558), S.

gallolyticus (e.g., strain UCN34, ATCC BAA-2069), S. equines (e.g., strain ATCC 9812, MGCS 124), S. dysdalactiae (e.g., strain GGS 124), S. bovis (e.g., strain ATCC 700338), S. anginosus (e.g., strain F0211), S. agalactiae (e.g., strain NEM316, A909), Listeria monocytogenes (e.g., strain F6854), Listeria innocua (L. innocua, e.g., strain Clipl l262), Enterococcus italicus (e.g., strain DSM 15952), or Enterococcus faecium (e.g., strain 1,231,408). Additional exemplary Cas9 molecules are a Cas9 molecule of Neisseria meningitidis (Hou et al. PNAS Early Edition 2013, 1-6) and a S. aureus Cas9 molecule.

In an embodiment, a Cas9 molecule, e.g., an eaCas9 molecule or eiCas9 molecule, comprises an amino acid sequence:

having 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% homology with;

differs at no more than, 2, 5, 10, 15, 20, 30, or 40% of the amino acid residues when compared with;

differs by at least 1, 2, 5, 10 or 20 amino acids but by no more than 100, 80, 70, 60, 50, 40 or 30 amino acids from; or

is identical to;

any Cas9 molecule sequence described herein or a naturally occurring Cas9 molecule sequence, e.g., a Cas9 molecule from a species listed herein or described in Chylinski et al., RNA Biology 2013, 10:5, 727-737; Hou et al. PNAS Early Edition 2013, 1-6. In an embodiment, the Cas9 molecule comprises one or more of the following activities: a nickase activity; a double stranded cleavage activity (e.g., an endonuclease and/or exonuclease activity); a helicase activity; or the ability, together with a gRNA molecule, to localize to a target nucleic acid.

In an embodiment, a Cas9 molecule comprises the amino acid sequence of the consensus sequence of FIG. 2, wherein "*" indicates any amino acid found in the corresponding position in the amino acid sequence of a Cas9 molecule of S. pyogenes, S. thermophilus, S. mutans and L. innocua, and "-" indicates any amino acid. In an embodiment, a Cas9 molecule differs from the sequence of the consensus sequence disclosed in FIG. 2 by at least 1, but no more than 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid residues. In an embodiment, a Cas9 molecule comprises the amino acid sequence of SEQ ID NO:7 of FIG. 5, wherein "*" indicates any amino acid found in the corresponding position in the amino acid sequence of a Cas9 molecule of S. pyogenes, or N. meningitidis, "-" indicates any amino acid, and "-" indicates any amino acid or absent. In an embodiment, a Cas9 molecule differs from the sequence of SEQ ID NO:6 or 7 by at least 1, but no more than 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid residues. A comparison of the sequence of a number of Cas9 molecules indicate that certain regions are conserved. These are identified below as:

region 1 (residues 1 to 180, or in the case of region residues 120 to 180)

region 2 (residues 360 to 480);

region 3 (residues 660 to 720);

region 4 (residues 817 to 900); and

region 5 (residues 900 to 960).

In an embodiment, a Cas9 molecule comprises regions 1-5, together with sufficient additional Cas9 molecule sequence to provide a biologically active molecule, e.g., a Cas9 molecule having at least one activity described herein. In an embodiment, each of regions 1-6, independently, have, 50%, 60%, 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% homology with the corresponding residues of a Cas9 molecule described herein, e.g., a sequence from FIG. 2 or from FIG. 5.

In an embodiment, a Cas9 molecule, e.g., an eaCas9 molecule or eiCas9 molecule, comprises an amino acid sequence referred to as region 1 :

having 50%, 60%, 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% homology with amino acids 1-180 (the numbering is according to the motif sequence in FIG. 2; 52% of residues in the four Cas9 sequences in FIG. 2 are conserved) of the amino acid sequence of Cas9 of S. pyogenes;

differs by at least 1, 2, 5, 10 or 20 amino acids but by no more than 90, 80, 70, 60, 50, 40 or 30 amino acids from amino acids 1-180 of the amino acid sequence of Cas9 of S. pyogenes, S. thermophilus, S. mutans, L. innocua, N. meningitidis, or S. aureus; or

is identical to 1-180 of the amino acid sequence of Cas9 of S. pyogenes, S. thermophilus, S. mutans, L. innocua, N. meningitidis, or S. aureus.

In an embodiment, a Cas9 molecule, e.g., an eaCas9 molecule or eiCas9 molecule, comprises an amino acid sequence referred to as region 1 ' :

having 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% homology with amino acids 120-180 (55% of residues in the four Cas9 sequences in FIG. 2 are conserved) of the amino acid sequence of Cas9 of S. pyogenes, S. thermophilus, S. mutans or, L. innocua, N. meningitidis, or S. aureus;

differs by at least 1, 2, or 5 amino acids but by no more than 35, 30, 25, 20 or 10 amino acids from amino acids 120-180 of the amino acid sequence of Cas9 of S. pyogenes, S.

thermophilus, S. mutans or, L. innocua, N. meningitidis, or S. aureus ; or

is identical to 120-180 of the amino acid sequence of Cas9 of S. pyogenes, S.

thermophilus, S. mutans or, L. innocua, N. meningitidis, or S. aureus.

In an embodiment, a Cas9 molecule, e.g., an eaCas9 molecule or eiCas9 molecule, comprises an amino acid sequence referred to as region 2:

having 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% homology with amino acids 360-480 (52% of residues in the four Cas9 sequences in FIG. 2 are conserved) of the amino acid sequence of Cas9 of S. pyogenes, S. thermophilus, S. mutans or, L. innocua, N. meningitidis, or S. aureus;

differs by at least 1, 2, or 5 amino acids but by no more than 35, 30, 25, 20 or 10 amino acids from amino acids 360-480 of the amino acid sequence of Cas9 of S. pyogenes, S.

thermophilus, S. mutans or, L. innocua, N. meningitidis, or S. aureus; or

is identical to 360-480 of the amino acid sequence of Cas9 of S. pyogenes, S.

thermophilus, S. mutans or, L. innocua, N. meningitidis, or S. aureus.

In an embodiment, a Cas9 molecule, e.g., an eaCas9 molecule or eiCas9 molecule, comprises an amino acid sequence referred to as region 3:

having 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% homology with amino acids 660-720 (56% of residues in the four Cas9 sequences in FIG. 2 are conserved) of the amino acid sequence of Cas9 of S. pyogenes, S. thermophilus, S. mutans or, L. innocua, N. meningitidis, or S. aureus;

differs by at least 1, 2, or 5 amino acids but by no more than 35, 30, 25, 20 or 10 amino acids from amino acids 660-720 of the amino acid sequence of Cas9 of S. pyogenes, S.

thermophilus, S. mutans or, L. innocua, N. meningitidis, or S. aureus; or

is identical to 660-720 of the amino acid sequence of Cas9 of S. pyogenes, S.

thermophilus, S. mutans or, L. innocua, N. meningitidis, or S. aureus.

In an embodiment, a Cas9 molecule, e.g., an eaCas9 molecule or eiCas9 molecule, comprises an amino acid sequence referred to as region 4:

having 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% homology with amino acids 817-900 (55% of residues in the four Cas9 sequences in FIG. 2 are conserved) of the amino acid sequence of Cas9 of S. pyogenes, S. thermophilus, S. mutans or, L. innocua, N. meningitidis, or S. aureus;

differs by at least 1, 2, or 5 amino acids but by no more than 35, 30, 25, 20 or 10 amino acids from amino acids 817-900 of the amino acid sequence of Cas9 of S. pyogenes, S.

thermophilus, S. mutans or, L. innocua, N. meningitidis, or S. aureus ; or

is identical to 817-900 of the amino acid sequence of Cas9 of S. pyogenes, S.

thermophilus, S. mutans or, L. innocua, N. meningitidis, or S. aureus.

In an embodiment, a Cas9 molecule, e.g., an eaCas9 molecule or eiCas9 molecule, comprises an amino acid sequence referred to as region 5:

having 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% homology with amino acids 900-960 (60% of residues in the four Cas9 sequences in FIG. 2 are conserved) of the amino acid sequence of Cas9 of S. pyogenes, S. thermophilus, S. mutans or, L. innocua, N. meningitidis, or S. aureus;

differs by at least 1, 2, or 5 amino acids but by no more than 35, 30, 25, 20 or 10 amino acids from amino acids 900-960 of the amino acid sequence of Cas9 of S. pyogenes, S.

thermophilus, S. mutans or, L. innocua, N. meningitidis, or S. aureus; or

is identical to 900-960 of the amino acid sequence of Cas9 of S. pyogenes, S.

thermophilus, S. mutans or, L. innocua, N. meningitidis, or S. aureus.

A RuvC-like domain and an HNH-like domain

In an embodiment, a Cas9 molecule comprises an HNH-like domain and an RuvC-like domain. In an embodiment, cleavage activity is dependent on a RuvC-like domain and an HNH- like domain. A Cas9 molecule, e.g., an eaCas9 or eiCas9 molecule, can comprise one or more of the following domains: a RuvC-like domain and an HNH-like domain. In an embodiment, a cas9 molecule is an eaCas9 molecule and the eaCas9 molecule comprises a RuvC-like domain, e.g., a RuvC-like domain described below, and/or an HNH-like domain, e.g., an HNH-like domain described below. In an embodiment, a Cas9 molecule is an eiCas9 molecule comprising one or more difference in an RuvC-like domain and/or in an HNH-like domain as compared to a reference Cas9 molecule, and the eiCas9 molecule does not cleave a nucleic acid, or cleaves with significantly less efficiency than does wildype, e.g., when compared with wild type in a cleavage assay, e.g., as described herein, cuts with less than 50, 25, 10, or 1% of the a reference Cas9 molecule, as measured by an assay described herein. RuvC-like domains

In an embodiment, a RuvC-like domain cleaves, a single strand, e.g., the non- complementary strand of the target nucleic acid molecule. A Cas9 molecule can include more than one RuvC-like domain (e.g., one, two, three or more RuvC-like domains). In an

embodiment, an RuvC-like domain is at least 5, 6, 7, 8 amino acids in length but not more than 20, 19, 18, 17, 16 or 15 amino acids in length. In an embodiment, the cas9 molecule comprises an N-terminal RuvC-like domain of about 10 to 20 amino acids, e.g., about 15 amino acids in length.

N-terminal RuvC-like domains

Some naturally occurring Cas9 molecules comprise more than one RuvC-like domain, with cleavage being dependent on the N-terminal RuvC-like domain. Accordingly, Cas9 molecules can comprise an N-terminal RuvC-like domain. Exemplary N-terminal RuvC-like domains are described below.

In an embodiment, an eaCas9 molecule comprises an N-terminal RuvC-like domain comprising an amino acid sequence of formula I:

D-X 1 -G-X2 -X3 -X 4 -X5 -G-X6 -X 7 -X 8 -X 9 (SEQ ID NO: 8),

wherein,

XI is selected from I, V, M, L and T (e.g., selected from I, V, and L);

X2 is selected from T, I, V, S, N, Y, E and L (e.g., selected from T, V, and I);

X3 is selected from N, S, G, A, D, T, R, M and F (e.g., A or N);

X4 is selected from S, Y, N and F (e.g., S);

X5 is selected from V, I, L, C, T and F (e.g., selected from V, I and L);

X6 is selected from W, F, V, Y, S and L (e.g., W);

X7 is selected from A, S, C, V and G (e.g., selected from A and S);

X8 is selected from V, I, L, A, M and H (e.g., selected from V, I, M and L); and

X9 is selected from any amino acid or is absent (e.g., selected from T, V, I, L, Δ, F, S, A, Y, M and R, or, e.g., selected from T, V, I, L and Δ).

In an embodiment, the N-terminal RuvC-like domain differs from a sequence of SEQ ID NO:8, by as many as 1 but no more than 2, 3, 4, or 5 residues.

In embodiment the N-terminal RuvC-like domain is cleavage competent.

In embodiment the N-terminal RuvC-like domain is cleavage incompetent. In an embodiment, an eaCas9 molecule comprises an N-terminal RuvC-like domain comprising an amino acid sequence of formula II:

D-X 1 -G-X2 -X3 - S -X5 -G-X6 -X 7 -X 8 -X 9 (SEQ ID NO: 9),

wherein

XI is selected from I, V, M, L and T (e.g., selected from I, V, and L);

X3 is selected from N, S, G, A, D, T, R, M and F (e.g., A or N);

X5 is selected from V, I, L, C, T and F (e.g., selected from V, I and L);

X6 is selected from W, F, V, Y, S and L (e.g., W);

X7 is selected from A, S, C, V and G (e.g., selected from A and S);

X9 is selected from any amino acid or is absent (e.g., selected from T, V, I, L, Δ, F, S, A, Y, M and R or selected from e.g., T, V, I, L and Δ).

In an embodiment, the N-terminal RuvC-like domain differs from a sequence of SEQ ID NO:9 by as many as 1, but no more than 2, 3, 4, or 5 residues.

In an embodiment, the N-terminal RuvC-like domain comprises an amino acid sequence of formula III:

D- I -G-X2 -X3 - S -V-G-W-A-X 8 -X 9 (SEQ ID NO: 10),

wherein

X3 is selected from N, S, G, A, D, T, R, M and F (e.g., A or N);

In an embodiment, the N-terminal RuvC-like domain differs from a sequence of SEQ ID NO: 10 by as many as 1, but no more than, 2, 3, 4, or 5 residues.

D- I -G- T -N- S -V-G-W-A-V-X (SEQ ID NO: 11),

wherein

X is a non-polar alkyl amino acid or a hydroxyl amino acid, e.g., X is selected from V, I, L and T (e.g., the eaCas9 molecule can comprise an N-terminal RuvC-like domain shown in FIG. 2 (depicted as "Y")).

In an embodiment, the N-terminal RuvC-like domain differs from a sequence of SEQ ID NO: 11 by as many as 1 but no more than, 2, 3, 4, or 5 residues.

In an embodiment, the N-terminal RuvC-like domain differs from a sequence of an N- terminal RuvC-like domain disclosed herein, e.g., in FIG. 3A or FIG. 5, as many as 1, but no more than 2, 3, 4, or 5 residues. In an embodiment, 1, 2, or all 3 of the highly conserved residues identified in FIG. 3A or FIG. 5 are present.

In an embodiment, the N-terminal RuvC-like domain differs from a sequence of an N- terminal RuvC-like domain disclosed herein, e.g., in FIG. 3B, as many as 1, but no more than 2, 3, 4, or 5 residues. In an embodiment, 1, 2, 3 or all 4 of the highly conserved residues identified in FIG. 3B are present.

Additional RuvC-like domains

In addition to the N-terminal RuvC-like domain, a Cas9 molecule, e.g., an eaCas9 molecule, can comprise one or more additional RuvC-like domains. In an embodiment, a Cas9 molecule can comprise two additional RuvC-like domains. Preferably, the additional RuvC-like domain is at least 5 amino acids in length and, e.g., less than 15 amino acids in length, e.g., 5 to 10 amino acids in length, e.g., 8 amino acids in length.

An additional RuvC-like domain can comprise an amino acid sequence:

I-X1-X2-E-X3-A-R-E (SEQ ID NO: 12), wherein

XI is V or H,

X2 is I, L or V (e.g., I or V); and

X3 is M or T.

In an embodiment, the additional RuvC-like domain comprises the amino acid sequence: I-V-X2-E-M-A-R-E (SEQ ID NO: 13), wherein

X2 is I, L or V (e.g., I or V) (e.g., the eaCas9 molecule can comprise an additional RuvC- like domain shown in FIG. 2 or FIG. 5 (depicted as "B")).

An additional RuvC-like domain can comprise an amino acid sequence:

H-H-A-X1-D-A-X2-X3 (SEQ ID NO: 14), wherein

XI is H or L;

X2 is R or V; and X3 is E or V.

In an embodiment, the additional RuvC-like domain comprises the amino acid sequence: H-H-A-H-D-A-Y-L (SEQ ID NO: 15).

In an embodiment, the additional RuvC-like domain differs from a sequence of SEQ ID NO: 13, 15, 12 or 14 by as many as 1, but no more than 2, 3, 4, or 5 residues.

In an embodiment, the sequence flanking the N-terminal RuvC-like domain is a sequences of formula V:

K-Xl ' -Y-X2 ' -X3 ' -X4 ' -Z-T-D-X9 ' -Y (SEQ ID NO: 16),

wherein

Χ is selected from K and P,

X2' is selected from V, L, I, and F (e.g., V, I and L);

X3' is selected from G, A and S (e.g., G),

X4' is selected from L, I, V and F (e.g., L);

X9' is selected from D, E, N and Q; and

Z is an N-terminal RuvC-like domain, e.g., as described above.

HNH-like domains

In an embodiment, an HNH-like domain cleaves a single stranded complementary domain, e.g., a complementary strand of a double stranded nucleic acid molecule. In an embodiment, an HNH-like domain is at least 15, 20, 25 amino acids in length but not more than 40, 35 or 30 amino acids in length, e.g., 20 to 35 amino acids in length, e.g., 25 to 30 amino acids in length. Exemplary HNH-like domains are described below.

In an embodiment, an eaCas9 molecule comprises an HNH-like domain having an amino acid sequence of formula VI:

X1-X2-X3-H-X4-X5-P-X6-X7-X8-X9-X10-X11-X12-X13-X14-X15-N- X16-X17-X18-X19-X20-X21-X22-X23-N (SEQ ID NO: 17), wherein

XI is selected from D, E, Q and N (e.g., D and E);

X2 is selected from L, I, R, Q, V, M and K;

X3 is selected from D and E;

X4 is selected from I, V, T, A and L (e.g., A, I and V);

X5 is selected from V, Y, I, L, F and W (e.g., V, I and L); X6 is selected from Q, H, R, K, Y, I, L, F and W;

X7 is selected from S, A, D, T and K (e.g., S and A);

X8 is selected from F, L, V, K, Y, M, I, R, A, E, D and Q (e.g., F);

X9 is selected from L, R, T, I, V, S, C, Y, K, F and G;

X10 is selected from K, Q, Y, T, F, L, W, M, A, E, G, and S;

XI 1 is selected from D, S, N, R, L and T (e.g., D);

X12 is selected from D, N and S;

X13 is selected from S, A, T, G and R (e.g., S);

X14 is selected from I, L, F, S, R, Y, Q, W, D, K and H (e.g., I, L and F);

X15 is selected from D, S, I, N, E, A, H, F, L, Q, M, G, Y and V;

X16 is selected from K, L, R, M, T and F (e.g., L, R and K);

X17 is selected from V, L, I, A and T;

X18 is selected from L, I, V and A (e.g., L and I);

X19 is selected from T, V, C, E, S and A (e.g., T and V);

X20 is selected from R, F, T, W, E, L, N, C, K, V, S, Q, I, Y, H and A;

X21 is selected from S, P, R, K, N, A, H, Q, G and L;

X22 is selected from D, G, T, N, S, K, A, I, E, L, Q, R and Y; and

X23 is selected from K, V, A, E, Y, I, C, L, S, T, G, K, M, D and F.

In an embodiment, a HNH-like domain differs from a sequence of SEQ ID NO: 17 by at least 1, but no more than, 2, 3, 4, or 5 residues.

In an embodiment, the HNH-like domain is cleavage competent.

In an embodiment, the HNH-like domain is cleavage incompetent.

In an embodiment, an eaCas9 molecule comprises an HNH-like domain comprising an amino acid sequence of formula VII:

X1-X2-X3-H-X4-X5-P-X6-S-X8-X9-X10-D-D-S-X14-X15-N-K-V-L- X19-X20-X21-X22-X23-N (SEQ ID NO: 18),

wherein

XI is selected from D and E;

X2 is selected from L, I, R, Q, V, M and K;

X3 is selected from D and E;

X4 is selected from I, V, T, A and L (e.g., A, I and V); X5 is selected from V, Y, I, L, F and W (e.g., V, I and L);

X6 is selected from Q, H, R, K, Y, I, L, F and W;

X8 is selected from F, L, V, K, Y, M, I, R, A, E, D and Q (e.g., F);

X9 is selected from L, R, T, I, V, S, C, Y, K, F and G;

X10 is selected from K, Q, Y, T, F, L, W, M, A, E, G, and S;

X14 is selected from I, L, F, S, R, Y, Q, W, D, K and H (e.g., I, L and F);

X15 is selected from D, S, I, N, E, A, H, F, L, Q, M, G, Y and V;

X19 is selected from T, V, C, E, S and A (e.g., T and V);

X20 is selected from R, F, T, W, E, L, N, C, K, V, S, Q, I, Y, H and A;

X21 is selected from S, P, R, K, N, A, H, Q, G and L;

X22 is selected from D, G, T, N, S, K, A, I, E, L, Q, R and Y; and

X23 is selected from K, V, A, E, Y, I, C, L, S, T, G, K, M, D and F.

In an embodiment, the HNH-like domain differs from a sequence of SEQ ID NO: 18 by 1, 2, 3, 4, or 5 residues.

X1-V-X3-H-I-V-P-X6-S-X8-X9-X10-D-D-S-X14-X15-N-K-V-L-T-X20- X21-X22-X23-N (SEQ ID NO: 19),

wherein

XI is selected from D and E;

X3 is selected from D and E;

X6 is selected from Q, H, R, K, Y, I, L and W;

X8 is selected from F, L, V, K, Y, M, I, R, A, E, D and Q (e.g., F);

X9 is selected from L, R, T, I, V, S, C, Y, K, F and G;

X10 is selected from K, Q, Y, T, F, L, W, M, A, E, G, and S;

X14 is selected from I, L, F, S, R, Y, Q, W, D, K and H (e.g., I, L and F);

X15 is selected from D, S, I, N, E, A, H, F, L, Q, M, G, Y and V;

X20 is selected from R, F, T, W, E, L, N, C, K, V, S, Q, I, Y, H and A;

X21 is selected from S, P, R, K, N, A, H, Q, G and L;

X22 is selected from D, G, T, N, S, K, A, I, E, L, Q, R and Y; and

X23 is selected from K, V, A, E, Y, I, C, L, S, T, G, K, M, D and F. In an embodiment, the HNH-like domain differs from a sequence of SEQ ID NO: 19 by 1, 2, 3, 4, or 5 residues.

In an embodiment, an eaCas9 molecule comprises an HNH-like domain having an amino acid sequence of formula VIII:

D-X2-D-H-I-X5-P-Q-X7-F-X9-X10-D-X12-S-I-D-N-X16-V-L-X19- X20-S-X22-X23-N (SEQ ID NO:20),

wherein

X2 is selected from I and V;

X5 is selected from I and V;

X7 is selected from A and S;

X9 is selected from I and L;

X10 is selected from K and T;

X12 is selected from D and N;

X16 is selected from R, K and L; X19 is selected from T and V;

X20 is selected from S and R;

X22 is selected from K, D and A; and

X23 is selected from E, K, G and N (e.g., the eaCas9 molecule can comprise an HNH- like domain as described herein).

In an embodiment, the HNH-like domain differs from a sequence of SEQ ID NO:20 by as many as 1, but no more than 2, 3, 4, or 5 residues.

In an embodiment, an eaCas9 molecule comprises the amino acid sequence of formula

IX:

L-Y-Y-L-Q-N-G-Xl '-D-M-Y-X2 ' -X3 ' -X4 ' -X5 ' -L-D-I-X6 '-X7 '-L-S- X8 '-Y-Z-N-R-X9 '-K-X10 '-D-X11 ' -V-P (SEQ ID NO:21),

wherein

Χ is selected from K and R;

X2' is selected from V and T;

X3' is selected from G and D;

X4' is selected from E, Q and D;

X5' is selected from E and D;

X6' is selected from D, N and H; X7' is selected from Y, R and N;

X8' is selected from Q, D and N; X9' is selected from G and E;

X10' is selected from S and G;

XI 1 ' is selected from D and N; and

Z is an HNH-like domain, e.g., as described above.

In an embodiment, the eaCas9 molecule comprises an amino acid sequence that differs from a sequence of SEQ ID NO:21 by as many as 1, but no more than 2, 3, 4, or 5 residues.

In an embodiment, the HNH-like domain differs from a sequence of an HNH-like domain disclosed herein, e.g., in FIG. 4A or FIG. 5, as many as 1, but no more than 2, 3, 4, or 5 residues.

In an embodiment, the HNH -like domain differs from a sequence of an HNH-like domain disclosed herein, e.g., in FIG. 4B, by as many as 1, but no more than 2, 3, 4, or 5 residues. In an embodiment, 1, 2, all 3 of the highly conserved residues identified in FIG. 4B are present.

Altered Cas9 Molecules

Naturally occurring Cas9 molecules possess a number of properties, including: nickase activity, nuclease activity (e.g., endonuclease and/or exonuclease activity); helicase activity; the ability to associate functionally with a gRNA molecule; and the ability to target (or localize to) a site on a nucleic acid (e.g., PAM recognition and specificity). In an embodiment, a Cas9 molecules can include all or a subset of these properties. In a typical embodiment, Cas9 molecules have the ability to interact with a gRNA molecule and, in concert with the gRNA molecule, localize to a site in a nucleic acid. Other activities, e.g., PAM specificity, cleavage activity, or helicase activity can vary more widely in Cas9 molecules.

Cas9 molecules with desired properties can be made in a number of ways, e.g., by alteration of a parental, e.g., naturally occurring Cas9 molecules to provide an altered Cas9 molecule having a desired property. For example, one or more mutations or differences relative to a parental Cas9 molecule can be introduced. Such mutations and differences comprise:

substitutions (e.g., conservative substitutions or substitutions of non-essential amino acids); insertions; or deletions. In an embodiment, a Cas9 molecule can comprises one or more mutations or differences, e.g., at least 1, 2, 3, 4, 5, 10, 15, 20, 30, 40 or 50 mutations but less than 200, 100, or 80 mutations relative to a reference Cas9 molecule.

In an embodiment, a mutation or mutations do not have a substantial effect on a Cas9 activity, e.g. a Cas9 activity described herein. In an embodiment, a mutation or mutations have a substantial effect on a Cas9 activity, e.g. a Cas9 activity described herein. In an embodiment, exemplary activities comprise one or more of PAM specificity, cleavage activity, and helicase activity. A mutation(s) can be present, e.g., in: one or more RuvC-like domain, e.g., an N- terminal RuvC-like domain; an HNH-like domain; a region outside the RuvC-like domains and the HNH-like domain. In an embodiment, a mutation(s) is present in an N-terminal RuvC-like domain. In an embodiment, a mutation(s) is present in an HNH-like domain. In an embodiment, mutations are present in both an N-terminal RuvC-like domain and an HNH-like domain.

Whether or not a particular sequence, e.g., a substitution, may affect one or more activity, such as targeting activity, cleavage activity, etc, can be evaluated or predicted, e.g., by evaluating whether the mutation is conservative or by the method described in Section III. In an

embodiment, a "non-essential" amino acid residue, as used in the context of a Cas9 molecule, is a residue that can be altered from the wild-type sequence of a Cas9 molecule, e.g., a naturally occurring Cas9 molecule, e.g., an eaCas9 molecule, without abolishing or more preferably, without substantially altering a Cas9 activity (e.g., cleavage activity), whereas changing an "essential" amino acid residue results in a substantial loss of activity (e.g., cleavage activity).

In an embodiment, the altered Cas9 molecule is an eaCas9 molecule comprising the fixed amino acid residues of S. pyogenes shown in the consensus sequence disclosed in FIG. 2, and has one or more amino acids that differ from the amino acid sequence of S. pyogenes (e.g., has a substitution) at one or more residue (e.g., 2, 3, 5, 10, 15, 20, 30, 50, 70, 80, 90, 100, 200 amino acid residues) represented by an "-" in the consensus sequence disclosed in FIG. 2 or SEQ ID NO:7. In an embodiment, the altered Cas9 molecule is an eiCas9 molecule wherein one or more of the fixed amino acid residues of S. pyogenes shown in the consensus sequence disclosed in FIG. 2 (e.g., 2, 3, 5, 10, 15, 20, 30, 50, 70, 80, 90, 100, 200 amino acid residues) is mutated.

In an embodiment, the altered Cas9 molecule comprises a sequence in which:

the sequence corresponding to the fixed sequence of the consensus sequence disclosed in FIG. 2 differs at no more than 1, 2, 3, 4, 5, 10, 15, or 20% of the fixed residues in the consensus sequence disclosed in FIG. 2; the sequence corresponding to the residues identified by "*" in the consensus sequence disclosed in FIG. 2 differ at no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, or 40% of the "*" residues from the corresponding sequence of naturally occurring Cas9 molecule, e.g., an S. pyogenes Cas9 molecule; and,

the sequence corresponding to the residues identified by "-" in the consensus sequence disclosed in FIG. 2 differ at no more than 5, 10, 15, 20, 25, 30, 35, 40, 45, 55, or 60% of the "-" residues from the corresponding sequence of naturally occurring Cas9 molecule, e.g., an S. pyogenes Cas9 molecule.

In an embodiment, the altered Cas9 molecule is an eaCas9 molecule comprising the fixed amino acid residues of S. thermophilus shown in the consensus sequence disclosed in FIG. 2, and has one or more amino acids that differ from the amino acid sequence of S. thermophilus (e.g., has a substitution) at one or more residue (e.g., 2, 3, 5, 10, 15, 20, 30, 50, 70, 80, 90, 100, 200 amino acid residues) represented by an "-" in the consensus sequence disclosed in FIG. 2. In an embodiment, the altered Cas9 molecule is an eiCas9 molecule wherein one or more of the fixed amino acid residues of S. thermophilus shown in the consensus sequence disclosed in FIG. 2 (e.g., 2, 3, 5, 10, 15, 20, 30, 50, 70, 80, 90, 100, 200 amino acid residues) is mutated.

In an embodiment the altered Cas9 molecule comprises a sequence in which:

the sequence corresponding to the fixed sequence of the consensus sequence disclosed in FIG. 2 differs at no more than 1, 2, 3, 4, 5, 10, 15, or 20% of the fixed residues in the consensus sequence disclosed in FIG. 2;

the sequence corresponding to the residues identified by "*" in the consensus sequence disclosed in FIG. 2 differ at no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, or 40% of the "*" residues from the corresponding sequence of naturally occurring Cas9 molecule, e.g., an S. thermophilus Cas9 molecule; and,

the sequence corresponding to the residues identified by "-" in the consensus sequence disclosed in FIG. 2 differ at no more than 5, 10, 15, 20, 25, 30, 35, 40, 45, 55, or 60% of the "-" residues from the corresponding sequence of naturally occurring Cas9 molecule, e.g., an S. thermophilus Cas9 molecule.

In an embodiment, the altered Cas9 molecule is an eaCas9 molecule comprising the fixed amino acid residues of S. mutans shown in the consensus sequence disclosed in FIG. 2, and has one or more amino acids that differ from the amino acid sequence of S. mutans (e.g., has a substitution) at one or more residue (e.g., 2, 3, 5, 10, 15, 20, 30, 50, 70, 80, 90, 100, 200 amino acid residues) represented by an "-" in the consensus sequence disclosed in FIG. 2. In an embodiment, the altered Cas9 molecule is an eiCas9 molecule wherein one or more of the fixed amino acid residues of S. mutans shown in the consensus sequence disclosed in FIG. 2 (e.g., 2, 3, 5, 10, 15, 20, 30, 50, 70, 80, 90, 100, 200 amino acid residues) is mutated.

In an embodiment the altered Cas9 molecule comprises a sequence in which:

the sequence corresponding to the residues identified by "*" in the consensus sequence disclosed in FIG. 2 differ at no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, or 40% of the "*" residues from the corresponding sequence of naturally occurring Cas9 molecule, e.g., an S.

mutans Cas9 molecule; and,

the sequence corresponding to the residues identified by "-" in the consensus sequence disclosed in FIG. 2 differ at no more than 5, 10, 15, 20, 25, 30, 35, 40, 45, 55, or 60% of the "-" residues from the corresponding sequence of naturally occurring Cas9 molecule, e.g., an S. mutans Cas9 molecule.

In an embodiment, the altered Cas9 molecule is an eaCas9 molecule comprising the fixed amino acid residues of L. innocula shown in the consensus sequence disclosed in FIG. 2, and has one or more amino acids that differ from the amino acid sequence of L. innocula (e.g., has a substitution) at one or more residue (e.g., 2, 3, 5, 10, 15, 20, 30, 50, 70, 80, 90, 100, 200 amino acid residues) represented by an "-" in the consensus sequence disclosed in FIG. 2. In an embodiment, the altered Cas9 molecule is an eiCas9 molecule wherein one or more of the fixed amino acid residues of L. innocula shown in the consensus sequence disclosed in FIG. 2 (e.g., 2, 3, 5, 10, 15, 20, 30, 50, 70, 80, 90, 100, 200 amino acid residues) is mutated.

In an embodiment the altered Cas9 molecule comprises a sequence in which:

the sequence corresponding to the residues identified by "*" in the consensus sequence disclosed in FIG. 2 differ at no more than 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, or 40% of the "*" residues from the corresponding sequence of naturally occurring Cas9 molecule, e.g., an L.

innocula Cas9 molecule; and,

the sequence corresponding to the residues identified by "-" in the consensus sequence disclosed in FIG. 2 differ at no more than 5, 10, 15, 20, 25, 30, 35, 40, 45, 55, or 60% of the "-" residues from the corresponding sequence of naturally occurring Cas9 molecule, e.g., an L. innocula Cas9 molecule.

In an embodiment, the altered Cas9 molecule, e.g., an eaCas9 molecule or an eiCas9 molecule, can be a fusion, e.g., of two of more different Cas9 molecules, e.g., of two or more naturally occurring Cas9 molecules of different species. For example, a fragment of a naturally occurring Cas9 molecule of one species can be fused to a fragment of a Cas9 molecule of a second species. As an example, a fragment of Cas9 of S. pyogenes comprising an N-terminal RuvC-like domain can be fused to a fragment of Cas9 of a species other than S. pyogenes (e.g., S. thermophilus) comprising an HNH-like domain. Cas9 Molecules with altered PAM recognition or no PAM recognition

Naturally occurring Cas9 molecules can recognize specific PAM sequences, for example the PAM recognition sequences described above for S. pyogenes, S. thermophilus, S. mutans, S. aureus and N. meningitidis.

In an embodiment, a Cas9 molecule has the same PAM specificities as a naturally occurring Cas9 molecule. In an embodiment, a Cas9 molecule has a PAM specificity not associated with a naturally occurring Cas9 molecule, or a PAM specificity not associated with the naturally occurring Cas9 molecule to which it has the closest sequence homology. For example, a naturally occurring Cas9 molecule can be altered, e.g., to alter PAM recognition, e.g., to alter the PAM sequence that the Cas9 molecule recognizes to decrease off target sites and/or improve specificity; or eliminate a PAM recognition requirement. In an embodiment, a Cas9 molecule can be altered, e.g., to increase length of PAM recognition sequence and/or improve Cas9 specificity to high level of identity to decrease off target sites and increase specificity. In an embodiment, the length of the PAM recognition sequence is at least 4, 5, 6, 7, 8, 9, 10 or 15 amino acids in length. Cas9 molecules that recognize different PAM sequences and/or have reduced off-target activity can be generated using directed evolution. Exemplary methods and systems that can be used for directed evolution of Cas9 molecules are described, e.g., in Esvelt et al, NATURE 2011, 472(7344): 499-503. Candidate Cas9 molecules can be evaluated, e.g., by methods described in Section III.

Non-Cleaving and Modified-Cleavage Cas9 Molecules

In an embodiment, a Cas9 molecule comprises a cleavage property that differs from naturally occurring Cas9 molecules, e.g., that differs from the naturally occurring Cas9 molecule having the closest homology. For example, a Cas9 molecule can differ from naturally occurring Cas9 molecules, e.g., a Cas9 molecule of S. pyogenes, as follows: its ability to modulate, e.g., decreased or increased, cleavage of a double stranded break (endonuclease and/or exonuclease activity), e.g., as compared to a naturally occurring Cas9 molecule (e.g., a Cas9 molecule of S. pyogenes); its ability to modulate, e.g., decreased or increased, cleavage of a single strand of a nucleic acid, e.g., a non-complimentary strand of a nucleic acid molecule or a complementary strand of a nucleic acid molecule (nickase activity), e.g., as compared to a naturally occurring Cas9 molecule (e.g., a Cas9 molecule of S. pyogenes); or the ability to cleave a nucleic acid molecule, e.g., a double stranded or single stranded nucleic acid molecule, can be eliminated.

Modified Cleavage eaCas9 Molecules

In an embodiment, an eaCas9 molecule comprises one or more of the following activities: cleavage activity associated with an N-terminal RuvC-like domain; cleavage activity associated with an HNH-like domain; cleavage activity associated with an HNH domain and cleavage activity associated with an N-terminal RuvC-like domain.

In an embodiment an eaCas9 molecule comprises an active, or cleavage competent, HNH-like domain (e.g., an HNH-like domain described herein, e.g., SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO:20 or SEQ ID NO:21) and an inactive, or cleavage incompetent, N-terminal RuvC-like domain. An exemplary inactive, or cleavage incompetent N- terminal RuvC-like domain can have a mutation of an aspartic acid in an N-terminal RuvC-like domain, e.g., an aspartic acid at position 9 of the consensus sequence disclosed in FIG. 2 or an aspartic acid at position 10 of SEQ ID NO:7, e.g., can be substituted with an alanine. In an embodiment, the eaCas9 differs from wild type in the N-terminal RuvC-like domain and does not cleave the target nucleic acid, or cleaves with significantly less efficiency, e.g., less than 20, 10, 5, 1 or 0.1 % of the cleavage activity of a reference Cas9 molecule, e.g., as measured by an assay described herein. The reference Cas9 molecule can by a naturally occurring unmodified Cas9 molecule, e.g., a naturally occurring Cas9 molecule such as a Cas9 molecule of S.

pyogenes, or S. thermophilus . In an embodiment, the reference Cas9 molecule is the naturally occurring Cas9 molecule having the closest sequence identity or homology.

In an embodiment, an eaCas9 molecule comprises an inactive, or cleavage incompetent,

HNH domain and an active, or cleavage competent, N-terminal RuvC-like domain (e.g., an HNH-like domain described herein, e.g., SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14 or SEQ ID NO: 15). Exemplary inactive, or cleavage incompetent HNH-like domains can have a mutation at one or more of: a histidine in an HNH-like domain, e.g., a histidine at position 856 of the consensus sequence disclosed in FIG. 2, e.g., can be substituted with an alanine; and one or more asparagines in an HNH-like domain, e.g., an asparagine at position 870 of the consensus sequence disclosed in FIG. 2 and/or at position 879 of the consensus sequence disclosed in FIG. 2, e.g., can be substituted with an alanine. In an embodiment, the eaCas9 differs from wild type in the HNH- like domain and does not cleave the target nucleic acid, or cleaves with significantly less efficiency, e.g., less than 20, 10, 5, 1 or 0.1% of the cleavage activity of a reference Cas9 molecule, e.g., as measured by an assay described herein. The reference Cas9 molecule can by a naturally occurring unmodified Cas9 molecule, e.g., a naturally occurring Cas9 molecule such as a Cas9 molecule of S. pyogenes, or S. thermophilus. In an embodiment, the reference Cas9 molecule is the naturally occurring Cas9 molecule having the closest sequence identity or homology.

Non-Cleaving eiCas9 Molecules

In an embodiment, the altered Cas9 molecule is an eiCas9 molecule which does not cleave a nucleic acid molecule (either double stranded or single stranded nucleic acid molecules) or cleaves a nucleic acid molecule with significantly less efficiency, e.g., less than 20, 10, 5, 1 or 0.1% of the cleavage activity of a reference Cas9 molecule, e.g., as measured by an assay described herein. The reference Cas9 molecule can by a naturally occurring unmodified Cas9 molecule, e.g., a naturally occurring Cas9 molecule such as a Cas9 molecule of S. pyogenes, S. thermophilus, S. aureus or N. meningitidis. In an embodiment, the reference Cas9 molecule is the naturally occurring Cas9 molecule having the closest sequence identity or homology. In an embodiment, the eiCas9 molecule lacks substantial cleavage activity associated with an N- terminal RuvC-like domain and cleavage activity associated with an HNH-like domain.

In an embodiment, an eiCas9 molecule comprises an inactive, or cleavage incompetent, N-terminal RuvC-like domain. An exemplary inactive, or cleavage incompetent N-terminal RuvC-like domain can have a mutation of an aspartic acid in an N-terminal RuvC-like domain, e.g., an aspartic acid at position 9 of the consensus sequence disclosed in Figure 2 or an aspartic acid at position 10 of SEQ ID NO:7, e.g., can be substituted with an alanine.

In an embodiment an eiCas9 molecule comprises an inactive, or cleavage incompetent, HNH domain (e.g., an HNH-like domain described herein, e.g., SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14 or SEQ ID NO: 15). Exemplary inactive, or cleavage incompetent HNH-like domains can have a mutation at one or more of: a histidine in an HNH-like domain, e.g., a histidine at position 856 of the consensus sequence disclosed in FIG. 2, e.g., can be substituted with an alanine; and one or more asparagines in an HNH-like domain, e.g., an asparagine at position 870 of the consensus sequence disclosed in FIG. 2 and/or at position 879 of the consensus sequence disclosed in FIG. 2, e.g., can be substituted with an alanine.

A catalytically inactive Cas9 molecule may be fused with a transcription repressor. An eiCas9 fusion protein complexes with a gRNA and localizes to a DNA sequence specified by gRNA's targeting domain, but, unlike an eaCas9, it will not cleave the target DNA. Fusion of an effector domain, such as a transcriptional repression domain, to an eiCas9 enables recruitment of the effector to any DNA site specified by the gRNA. Site specific targeting of an eiCas9 or an eiCas9 fusion protein to a promoter region of a gene can block RNA polymerase binding to the promoter region, a transcription factor (e.g., a transcription activator) and/or a transcriptional enhancer to inhibit transcription activation. Alternatively, site specific targeting of an eiCas9- fusion to a transcription repressor to a promoter region of a gene can be used to decrease transcription activation.

Transcription repressors or transcription repressor domains that may be fused to an eiCas9 molecule can include Kriippel associated box (KRAB or SKD), the Mad mSIN3 interaction domain (SID) or the ERF repressor domain (ERD).

In another embodiment, an eiCas9 molecule may be fused with a protein that modifies chromatin. For example, an eiCas9 molecule may be fused to heterochromatin protein 1 (HP1), a histone lysine methyltransferase (e.g., SUV39H1, SUV39H2, G9A, ESET/SETDB1, Pr-SET7/8, SUV4-20H1, RIZl), a histone lysine demethylates (e.g., LSD1/BHC110, SpLsdl/Sw,l/Safl lO, Su(var)3-3, JMJD2A/JHDM3A, JMJD2B, JMJD2C/GASC1, JMJD2D, Rphl, JARID1A/RBP2, JARIDIB/PLU-I, JAR1D1C/SMCX, JARID1D/SMCY, Lid, Jhn2, Jmj2), a histone lysine deacetylases (e.g., HDAC1, HDAC2, HDAC3, HDAC8, Rpd3, Hosl, Cir6, HDAC4, HDAC5, HDAC7, HDAC9, Hdal, Cir3, SIRT1, SIRT2, Sir2, Hstl, Hst2, Hst3, Hst4, HDAC11) and a DNA methylases (DNMT1, DNMT2a/DMNT3b, MET1). An eiCas9-chomatin modifying molecule fusion protein can be used to alter chromatin status to reduce expression a target gene.

The heterologous sequence (e.g., the transcription repressor domain) may be fused to the N- or C-terminus of the eiCas9 protein. In an alternative embodiment, the heterologous sequence (e.g., the transcription repressor domain) may be fused to an internal portion (i.e., a portion other than the N-terminus or C-terminus) of the eiCas9 protein.

The ability of a Cas9 molecule/gRNA molecule complex to bind to and cleave a target nucleic acid can be evaluated, e.g., by the methods described herein in Section III. The activity of a Cas9 molecule, either an eaCas9 or a eiCas9, alone or in a complex with a gRNA molecule may also be evaluated by methods well-known in the art, including, gene expression assays and chromatin-based assays, e.g., chromatin immunoprecipitation (ChiP) and chromatin in vivo assay (CiA). Nucleic Acids Encoding Cas9 Molecules

Nucleic acids encoding the Cas9 molecules, e.g., an eaCas9 molecule or an eiCas9 molecule are provided herein.

Exemplary nucleic acids encoding Cas9 molecules are described in Cong et ah, SCIENCE 2013, 399(6121):819-823; Wang et al., CELL 2013, 153(4):910-918; Mali et al., SCIENCE 2013, 399(6121):823-826; Jinek et al, SCIENCE 2012, 337(6096):816-821. Another exemplary nucleic acid encoding a Cas9 molecule of N. meningitidis is shown in FIG. 6.

In an embodiment, a nucleic acid encoding a Cas9 molecule can be a synthetic nucleic acid sequence. For example, the synthetic nucleic acid molecule can be chemically modified, e.g., as described in Section X. In an embodiment, the Cas9 mRNA has one or more of, e.g., all of the following properties: it is capped, polyadenylated, substituted with 5-methylcytidine and/or pseudouridine. In addition or alternatively, the synthetic nucleic acid sequence can be codon optimized, e.g., at least one non-common codon or less-common codon has been replaced by a common codon. For example, the synthetic nucleic acid can direct the synthesis of an optimized messenger mRNA, e.g., optimized for expression in a mammalian expression system, e.g., described herein.

In addition, or alternatively, a nucleic acid encoding a Cas9 molecule may comprise a nuclear localization sequence (NLS). Nuclear localization sequences are known in the art.

Provided below is an exemplary codon optimized nucleic acid sequence encoding a Cas9 molecule of S. pyogenes.

ATGGATAAAA AGTACAGCAT CGGGCTGGAC ATCGGTACAA ACTCAGTGGG

GTGGGCCGTG ATTACGGACG AGTACAAGGT ACCCTCCAAA AAATTTAAAG

TGCTGGGTAA CACGGACAGA CACTCTATAA AGAAAAATCT TATTGGAGCC

TTGCTGTTCG ACTCAGGCGA GACAGCCGAA GCCACAAGGT TGAAGCGGAC

CGCCAGGAGG CGGTATACCA GGAGAAAGAA CCGCATATGC TACCTGCAAG

AAATCTTCAG TAACGAGATG GCAAAGGTTG ACGATAGCTT TTTCCATCGC

CTGGAAGAAT CCTTTCTTGT TGAGGAAGAC AAGAAGCACG AACGGCACCC

CATCTTTGGC AATATTGTCG ACGAAGTGGC ATATCACGAA AAGTACCCGA

CTATCTACCA CCTCAGGAAG AAGCTGGTGG ACTCTACCGA TAAGGCGGAC

CTCAGACTTA TTTATTTGGC ACTCGCCCAC ATGATTAAAT TTAGAGGACA

TTTCTTGATC GAGGGCGACC TGAACCCGGA CAACAGTGAC GTCGATAAGC

TGTTCATCCA ACTTGTGCAG ACCTACAATC AACTGTTCGA AGAAAACCCT

ATAAATGCTT CAGGAGTCGA CGCTAAAGCA ATCCTGTCCG CGCGCCTCTC

AAAATCTAGA AGACTTGAGA ATCTGATTGC TCAGTTGCCC GGGGAAAAGA

AAAATGGATT GTTTGGCAAC CTGATCGCCC TCAGTCTCGG ACTGACCCCA

AATTTCAAAA GTAACTTCGA CCTGGCCGAA GACGCTAAGC TCCAGCTGTC

CAAGGACACA TACGATGACG ACCTCGACAA TCTGCTGGCC CAGATTGGGG

ATCAGTACGC CGATCTCTTT TTGGCAGCAA AGAACCTGTC CGACGCCATC

CTGTTGAGCG ATATCTTGAG AGTGAACACC GAAATTACTA AAGCACCCCT

TAGCGCATCT ATGATCAAGC GGTACGACGA GCATCATCAG GATCTGACCC

TGCTGAAGGC TCTTGTGAGG CAACAGCTCC CCGAAAAATA CAAGGAAATC TTCTTTGACC AGAGCAAAAA CGGCTACGCT GGCTATATAG ATGGTGGGGC CAGTCAGGAG GAATTCTATA AATTCATCAA GCCCATTCTC GAGAAAATGG ACGGCACAGA GGAGTTGCTG GTCAAACTTA ACAGGGAGGA CCTGCTGCGG AAGCAGCGGA CCTTTGACAA CGGGTCTATC CCCCACCAGA TTCATCTGGG CGAACTGCAC GCAATCCTGA GGAGGCAGGA GGATTTTTAT CCTTTTCTTA AAGATAACCG CGAGAAAATA GAAAAGATTC TTACATTCAG GATCCCGTAC TACGTGGGAC CTCTCGCCCG GGGCAATTCA CGGTTTGCCT GGATGACAAG GAAGTCAGAG GAGACTATTA CACCTTGGAA CTTCGAAGAA GTGGTGGACA AGGGTGCATC TGCCCAGTCT TTCATCGAGC GGATGACAAA TTTTGACAAG AACCTCCCTA ATGAGAAGGT GCTGCCCAAA CATTCTCTGC TCTACGAGTA CTTTACCGTC TACAATGAAC TGACTAAAGT CAAGTACGTC ACCGAGGGAA TGAGGAAGCC GGCATTCCTT AGTGGAGAAC AGAAGAAGGC GATTGTAGAC CTGTTGTTCA AGACCAACAG GAAGGTGACT GTGAAGCAAC TTAAAGAAGA CTACTTTAAG AAGATCGAAT GTTTTGACAG TGTGGAAATT TCAGGGGTTG AAGACCGCTT CAATGCGTCA TTGGGGACTT ACCATGATCT TCTCAAGATC ATAAAGGACA AAGACTTCCT GGACAACGAA GAAAATGAGG ATATTCTCGA AGACATCGTC CTCACCCTGA CCCTGTTCGA AGACAGGGAA ATGATAGAAG AGCGCTTGAA AACCTATGCC CACCTCTTCG ACGATAAAGT TATGAAGCAG CTGAAGCGCA GGAGATACAC AGGATGGGGA AGATTGTCAA GGAAGCTGAT CAATGGAATT AGGGATAAAC AGAGTGGCAA GACCATACTG GATTTCCTCA AATCTGATGG CTTCGCCAAT AGGAACTTCA TGCAACTGAT TCACGATGAC TCTCTTACCT TCAAGGAGGA CATTCAAAAG GCTCAGGTGA GCGGGCAGGG AGACTCCCTT CATGAACACA TCGCGAATTT GGCAGGTTCC CCCGCTATTA AAAAGGGCAT CCTTCAAACT GTCAAGGTGG TGGATGAATT GGTCAAGGTA ATGGGCAGAC ATAAGCCAGA AAATATTGTG ATCGAGATGG CCCGCGAAAA CCAGACCACA CAGAAGGGCC AGAAAAATAG TAGAGAGCGG ATGAAGAGGA TCGAGGAGGG CATCAAAGAG CTGGGATCTC AGATTCTCAA AGAACACCCC GTAGAAAACA CACAGCTGCA GAACGAAAAA TTGTACTTGT ACTATCTGCA GAACGGCAGA GACATGTACG TCGACCAAGA ACTTGATATT AATAGACTGT CCGACTATGA CGTAGACCAT ATCGTGCCCC AGTCCTTCCT GAAGGACGAC TCCATTGATA ACAAAGTCTT GACAAGAAGC GACAAGAACA GGGGTAAAAG TGATAATGTG CCTAGCGAGG AGGTGGTGAA AAAAATGAAG AACTACTGGC

1 GACAGCTGCT TAATGCAAAG CTCATTACAC AACGGAAGTT CGATAATCTG ACGAAAGCAG AGAGAGGTGG CTTGTCTGAG TTGGACAAGG CAGGGTTTAT TAAGCGGCAG CTGGTGGAAA CTAGGCAGAT CACAAAGCAC GTGGCGCAGA TTTTGGACAG CCGGATGAAC ACAAAATACG ACGAAAATGA TAAACTGATA CGAGAGGTCA AAGTTATCAC GCTGAAAAGC AAGCTGGTGT CCGATTTTCG GAAAGACTTC CAGTTCTACA AAGTTCGCGA GATTAATAAC TACCATCATG CTCACGATGC GTACCTGAAC GCTGTTGTCG GGACCGCCTT GATAAAGAAG TACCCAAAGC TGGAATCCGA GTTCGTATAC GGGGATTACA AAGTGTACGA TGTGAGGAAA ATGATAGCCA AGTCCGAGCA GGAGATTGGA AAGGCCACAG CTAAGTACTT CTTTTATTCT AACATCATGA ATTTTTTTAA GACGGAAATT ACCCTGGCCA ACGGAGAGAT CAGAAAGCGG CCCCTTATAG AGACAAATGG TGAAACAGGT GAAATCGTCT GGGATAAGGG CAGGGATTTC GCTACTGTGA GGAAGGTGCT GAGTATGCCA CAGGTAAATA TCGTGAAAAA AACCGAAGTA CAGACCGGAG GATTTTCCAA GGAAAGCATT TTGCCTAAAA GAAACTCAGA CAAGCTCATC GCCCGCAAGA AAGATTGGGA CCCTAAGAAA TACGGGGGAT TTGACTCACC CACCGTAGCC TATTCTGTGC TGGTGGTAGC TAAGGTGGAA AAAGGAAAGT CTAAGAAGCT GAAGTCCGTG AAGGAACTCT TGGGAATCAC TATCATGGAA AGATCATCCT TTGAAAAGAA CCCTATCGAT TTCCTGGAGG CTAAGGGTTA CAAGGAGGTC AAGAAAGACC TCATCATTAA ACTGCCAAAA TACTCTCTCT TCGAGCTGGA AAATGGCAGG AAGAGAATGT TGGCCAGCGC CGGAGAGCTG CAAAAGGGAA ACGAGCTTGC TCTGCCCTCC AAATATGTTA ATTTTCTCTA TCTCGCTTCC CACTATGAAA AGCTGAAAGG GTCTCCCGAA GATAACGAGC AGAAGCAGCT GTTCGTCGAA CAGCACAAGC ACTATCTGGA TGAAATAATC GAACAAATAA GCGAGTTCAG CAAAAGGGTT ATCCTGGCGG ATGCTAATTT GGACAAAGTA CTGTCTGCTT ATAACAAGCA CCGGGATAAG CCTATTAGGG AACAAGCCGA GAATATAATT CACCTCTTTA CACTCACGAA TCTCGGAGCC CCCGCCGCCT TCAAATACTT TGATACGACT ATCGACCGGA AACGGTATAC CAGTACCAAA GAGGTCCTCG ATGCCACCCT CATCCACCAG TCAATTACTG GCCTGTACGA AACACGGATC GACCTCTCTC AACTGGGCGG CGACTAG

(SEQ ID NO: 22) Provided below is the corresponding amino acid sequence of a S. pyogenes Cas9 molecule.

MDKKYS IGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHS IKKNLIGALLFDSGETAEATRL KRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFGNIVDEVAY HEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTY NQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNF DLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSAS MIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMD GTEELLVKLNREDLLRKQRTFDNGS IPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRI PYYVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLPNEKVLPKHS LLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFD SVEI SGVEDRFNASLGTYHDLLKI IKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYA HLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTF KEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARENQ TTQKGQKNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINR LSDYDVDHIVPQSFLKDDS IDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRK FDNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKS KLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDVRKMIAK SEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDFATVRKVLS MPQV IVKKTEVQTGGFSKES ILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVVAKVEKG KSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLI IKLPKYSLFELENGRKRMLAS AGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHYLDEI IEQI SEFSKRV ILADANLDKVLSAYNKHRDKPIREQAE I IHLFTLTNLGAPAAFKYFDTTIDRKRYTSTKEVLD ATLIHQS ITGLYETRIDLSQLGGD*

(SEQ ID NO: 23)

Provided below is an exemplary codon optimized nucleic acid sequence encoding a Cas9 molecule of N. meningitidis.

ATGGCCGCCTTCAAGCCCAACCCCATCAACTACATCCTGGGCCTGGACATCGGCATCGCCAGCG TGGGCTGGGCCATGGTGGAGATCGACGAGGACGAGAACCCCATCTGCCTGATCGACCTGGGTGT GCGCGTGTTCGAGCGCGCTGAGGTGCCCAAGACTGGTGACAGTCTGGCTATGGCTCGCCGGCTT GCTCGCTCTGTTCGGCGCCTTACTCGCCGGCGCGCTCACCGCCTTCTGCGCGCTCGCCGCCTGC TGAAGCGCGAGGGTGTGCTGCAGGCTGCCGACT TCGACGAGAACGGCCTGATCAAGAGCCTGCC CAACACTCCT TGGCAGCTGCGCGCTGCCGCTCTGGACCGCAAGCTGACTCCTCTGGAGTGGAGC GCCGTGCTGCTGCACCTGATCAAGCACCGCGGCTACCTGAGCCAGCGCAAGAACGAGGGCGAGA CCGCCGACAAGGAGCTGGGTGCTCTGCTGAAGGGCGTGGCCGACAACGCCCACGCCCTGCAGAC TGGTGACT TCCGCACTCCTGCTGAGCTGGCCCTGAACAAGT TCGAGAAGGAGAGCGGCCACATC CGCAACCAGCGCGGCGACTACAGCCACACCT TCAGCCGCAAGGACCTGCAGGCCGAGCTGATCC TGCTGT TCGAGAAGCAGAAGGAGT TCGGCAACCCCCACGTGAGCGGCGGCCTGAAGGAGGGCAT CGAGACCCTGCTGATGACCCAGCGCCCCGCCCTGAGCGGCGACGCCGTGCAGAAGATGCTGGGC CACTGCACCT TCGAGCCAGCCGAGCCCAAGGCCGCCAAGAACACCTACACCGCCGAGCGCT TCA TCTGGCTGACCAAGCTGAACAACCTGCGCATCCTGGAGCAGGGCAGCGAGCGCCCCCTGACCGA CACCGAGCGCGCCACCCTGATGGACGAGCCCTACCGCAAGAGCAAGCTGACCTACGCCCAGGCC CGCAAGCTGCTGGGTCTGGAGGACACCGCCT TCT TCAAGGGCCTGCGCTACGGCAAGGACAACG CCGAGGCCAGCACCCTGATGGAGATGAAGGCCTACCACGCCATCAGCCGCGCCCTGGAGAAGGA GGGCCTGAAGGACAAGAAGAGTCCTCTGAACCTGAGCCCCGAGCTGCAGGACGAGATCGGCACC GCCT TCAGCCTGT TCAAGACCGACGAGGACATCACCGGCCGCCTGAAGGACCGCATCCAGCCCG AGATCCTGGAGGCCCTGCTGAAGCACATCAGCT TCGACAAGT TCGTGCAGATCAGCCTGAAGGC CCTGCGCCGCATCGTGCCCCTGATGGAGCAGGGCAAGCGCTACGACGAGGCCTGCGCCGAGATC TACGGCGACCACTACGGCAAGAAGAACACCGAGGAGAAGATCTACCTGCCTCCTATCCCCGCCG ACGAGATCCGCAACCCCGTGGTGCTGCGCGCCCTGAGCCAGGCCCGCAAGGTGATCAACGGCGT GGTGCGCCGCTACGGCAGCCCCGCCCGCATCCACATCGAGACCGCCCGCGAGGTGGGCAAGAGC T TCAAGGACCGCAAGGAGATCGAGAAGCGCCAGGAGGAGAACCGCAAGGACCGCGAGAAGGCCG CCGCCAAGT TCCGCGAGTACT TCCCCAACT TCGTGGGCGAGCCCAAGAGCAAGGACATCCTGAA GCTGCGCCTGTACGAGCAGCAGCACGGCAAGTGCCTGTACAGCGGCAAGGAGATCAACCTGGGC CGCCTGAACGAGAAGGGCTACGTGGAGATCGACCACGCCCTGCCCT TCAGCCGCACCTGGGACG ACAGCT TCAACAACAAGGTGCTGGTGCTGGGCAGCGAGAACCAGAACAAGGGCAACCAGACCCC CTACGAGTACT TCAACGGCAAGGACAACAGCCGCGAGTGGCAGGAGT TCAAGGCCCGCGTGGAG ACCAGCCGCT TCCCCCGCAGCAAGAAGCAGCGCATCCTGCTGCAGAAGT TCGACGAGGACGGCT TCAAGGAGCGCAACCTGAACGACACCCGCTACGTGAACCGCT TCCTGTGCCAGT TCGTGGCCGA CCGCATGCGCCTGACCGGCAAGGGCAAGAAGCGCGTGT TCGCCAGCAACGGCCAGATCACCAAC CTGCTGCGCGGCT TCTGGGGCCTGCGCAAGGTGCGCGCCGAGAACGACCGCCACCACGCCCTGG ACGCCGTGGTGGTGGCCTGCAGCACCGTGGCCATGCAGCAGAAGATCACCCGCT TCGTGCGCTA CAAGGAGATGAACGCCT TCGACGGTAAAACCATCGACAAGGAGACCGGCGAGGTGCTGCACCAG AAGACCCACTTCCCCCAGCCCTGGGAGTTCTTCGCCCAGGAGGTGATGATCCGCGTGTTCGGCA AGCCCGACGGCAAGCCCGAGTTCGAGGAGGCCGACACCCCCGAGAAGCTGCGCACCCTGCTGGC CGAGAAGCTGAGCAGCCGCCCTGAGGCCGTGCACGAGTACGTGACTCCTCTGTTCGTGAGCCGC GCCCCCAACCGCAAGATGAGCGGTCAGGGTCACATGGAGACCGTGAAGAGCGCCAAGCGCCTGG ACGAGGGCGTGAGCGTGCTGCGCGTGCCCCTGACCCAGCTGAAGCTGAAGGACCTGGAGAAGAT GGTGAACCGCGAGCGCGAGCCCAAGCTGTACGAGGCCCTGAAGGCCCGCCTGGAGGCCCACAAG GACGACCCCGCCAAGGCCTTCGCCGAGCCCTTCTACAAGTACGACAAGGCCGGCAACCGCACCC AGCAGGTGAAGGCCGTGCGCGTGGAGCAGGTGCAGAAGACCGGCGTGTGGGTGCGCAACCACAA CGGCATCGCCGACAACGCCACCATGGTGCGCGTGGACGTGTTCGAGAAGGGCGACAAGTACTAC CTGGTGCCCATCTACAGCTGGCAGGTGGCCAAGGGCATCCTGCCCGACCGCGCCGTGGTGCAGG GCAAGGACGAGGAGGACTGGCAGCTGATCGACGACAGCTTCAACTTCAAGTTCAGCCTGCACCC CAACGACCTGGTGGAGGTGATCACCAAGAAGGCCCGCATGTTCGGCTACTTCGCCAGCTGCCAC CGCGGCACCGGCAACATCAACATCCGCATCCACGACCTGGACCACAAGATCGGCAAGAACGGCA TCCTGGAGGGCATCGGCGTGAAGACCGCCCTGAGCTTCCAGAAGTACCAGATCGACGAGCTGGG CAAGGAGATCCGCCCCTGCCGCCTGAAGAAGCGCCCTCCTGTGCGCTAA

(SEQ ID NO: 24)

Provided below is the corresponding amino acid sequence of a N. meningitidis Cas9 molecule.

MAAFKPNPINYILGLDIGIASVGWAMVEIDEDENPICLIDLGVRVFERAEVPKTGDSLAMARRL ARSVRRLTRRRAHRLLRARRLLKREGVLQAADFDENGLIKSLPNTPWQLRAAALDRKLTPLEWS AVLLHLIKHRGYLSQRKNEGETADKELGALLKGVADNAHALQTGDFRTPAELALNKFEKESGHI RNQRGDYSHTFSRKDLQAELILLFEKQKEFGNPHVSGGLKEGIETLLMTQRPALSGDAVQKMLG HCTFEPAEPKAAKNTYTAERFIWLTKLNNLRILEQGSERPLTDTERATLMDEPYRKSKLTYAQA RKLLGLEDTAFFKGLRYGKDNAEASTLMEMKAYHAI SRALEKEGLKDKKSPLNLSPELQDEIGT AFSLFKTDEDITGRLKDRIQPEILEALLKHI SFDKFVQI SLKALRRIVPLMEQGKRYDEACAEI YGDHYGKKNTEEKIYLPPIPADEIRNPVVLRALSQARKVINGVVRRYGSPARIHIETAREVGKS FKDRKEIEKRQEENRKDREKAAAKFREYFPNFVGEPKSKDILKLRLYEQQHGKCLYSGKEINLG RLNEKGYVEIDHALPFSRTWDDSFNNKVLVLGSENQNKGNQTPYEYFNGKDNSREWQEFKARVE TSRFPRSKKQRILLQKFDEDGFKERNLNDTRYVNRFLCQFVADRMRLTGKGKKRVFASNGQITN LLRGFWGLRKVRAENDRHHALDAVVVACSTVAMQQKITRFVRYKEMNAFDGKTIDKETGEVLHQ KTHFPQPWEFFAQEVMIRVFGKPDGKPEFEEADTPEKLRTLLAEKLSSRPEAVHEYVTPLFVSR APNRKMSGQGHMETVKSAKRLDEGVSVLRVPLTQLKLKDLEKMVNREREPKLYEALKARLEAHK DDPAKAFAEPFYKYDKAGNRTQQVKAVRVEQVQKTGVWVRNHNGIADNATMVRVDVFEKGDKYY LVPIYSWQVAKGILPDRAVVQGKDEEDWQLIDDSFNFKFSLHPNDLVEVITKKARMFGYFASCH RGTGNINIRIHDLDHKIGKNGILEGIGVKTALSFQKYQIDELGKEIRPCRLKKRPPVR* (SEQ ID NO: 25)

Provided below is an amino acid sequence of a S. aureus Cas9 molecule.

MKRNYILGLDIGITSVGYGI IDYETRDVIDAGVRLFKEANVENNEGRRSKRGARRLKRRRRHRI QRVKKLLFDYNLLTDHSELSGINPYEARVKGLSQKLSEEEFSAALLHLAKRRGVHNVNEVEEDT GNELSTKEQI SRNSKALEEKYVAELQLERLKKDGEVRGS INRFKTSDYVKEAKQLLKVQKAYHQ LDQSFIDTYIDLLETRRTYYEGPGEGSPFGWKDIKEWYEMLMGHCTYFPEELRSVKYAYNADLY NALNDLNNLVITRDENEKLEYYEKFQI IENVFKQKKKPTLKQIAKEILVNEEDIKGYRVTSTGK PEFTNLKVYHDIKDITARKEI IENAELLDQIAKILTIYQSSEDIQEELTNLNSELTQEEIEQIS NLKGYTGTHNLSLKAINLILDELWHTNDNQIAIFNRLKLVPKKVDLSQQKEIPTTLVDDFILSP VVKRSFIQS IKVINAI IKKYGLPNDI I IELAREKNSKDAQKMINEMQKRNRQTNERIEEI IRTT GKENAKYLIEKIKLHDMQEGKCLYSLEAIPLEDLLNNPFNYEVDHI IPRSVSFDNSFNNKVLVK QEENSKKGNRTPFQYLSSSDSKI SYETFKKHILNLAKGKGRI SKTKKEYLLEERDINRFSVQKD FINRNLVDTRYATRGLMNLLRSYFRVNNLDVKVKS INGGFTSFLRRKWKFKKERNKGYKHHAED ALI IA ADFIFKEWKKLDKAKKVMENQMFEEKQAESMPEIETEQEYKEIFITPHQIKHIKDFKD YKYSHRVDKKPNRELINDTLYSTRKDDKGNTLIVNNLNGLYDKDNDKLKKLINKSPEKLLMYHH DPQTYQKLKLIMEQYGDEKNPLYKYYEETGNYLTKYSKKDNGPVIKKIKYYGNKLNAHLDITDD YPNSRNKVVKLSLKPYRFDVYLDNGVYKFVTVKNLDVIKKENYYEVNSKCYEEAKKLKKISNQA EFIASFYNNDLIKINGELYRVIGVNNDLLNRIEVNMIDITYREYLENMNDKRPPRI IKTIASKT QS IKKYSTDILGNLYEVKSKKHPQI IKKG*

(SEQ ID NO: 26)

If any of the above Cas9 sequences are fused with a peptide or polypeptide at the C- terminus (e.g., an eiCas9 fused with a transcripon repressor at the C-terminus), it is understood that the stop codon will be removed.

Other Cas Molecules

Various types of Cas molecules can be used to practice the inventions disclosed herein.

In an embodiment, Cas molecules of Type II Cas systems are used. In an embodiment, Cas molecules of other Cas systems are used. For example, Type I or Type III Cas molecules may be used. Exemplary Cas molecules (and Cas systems) are described, e.g., in Haft et ah, PLoS COMPUTATIONAL BIOLOGY 2005, 1(6): e60 and Makarova et al, NATURE REVIEW

MICROBIOLOGY 2011, 9:467-477, the contents of both references are incorporated herein by reference in their entirety. Exemplary Cas molecules (and Cas systems) are also shown in Table II I.

Table II-l: Cas Systems

Gene System type Name from Haft Structure of Families (and Representatives name* or subtype et a/.^§ encoded protein superfamily) of

(PDB encoded

accessions)¹ protein

cas5 • Subtype I- cas5a, cas5d, 3KG4 COG1688 APE1234, BH0337,

A cas5e, cas5h, (RAMP) devS and ygcl

• Subtype I- cas5p, cas5t and

B cmx5

• Subtype I-

C

• Subtype I-

E

cas6 • Subtype I- cas6 and cmx6 3I4H COG1583 and PF1131 and slr7014

A COG5551

• Subtype I- (RAMP)

B

• Subtype I-

D

• Subtype

ΙΙΙ-Α·

Subtype Hi- fi

cas6e • Subtype I- cse3 1WJ9 (RAMP) ygcH

E

cas6f • Subtype I- csy4 2XLJ (RAMP) yl727

F

cas7 • Subtype I- csa2, csd2, cse4, NA COG 1857 and devR and ygcJ

A csh2, cspl and COG3649

• Subtype I- cst2 (RAMP)

B

• Subtype I-

C

• Subtype I- Table II-l: Cas Systems

Gene System type Name from Haft Structure of Families (and Representatives name* or subtype et al encoded protein superfamily) of

(PDB encoded

accessions)¹ protein

E

cas8al • Subtype I- cmxl, cstl, csx8, NA BH0338-like LA3191 and

A** csx 13 and PG2018

cxxc-cxxc

cas8a2 • Subtype I- csa4 and csx9 NA PH0918 AF0070, AF1873,

A** MJ0385, PF0637,

PH0918 and SSO1401 cas8b • Subtype I- cshl and NA BH0338-like MTH1090 and

B** TM1802 TM1802 cas8c • Subtype I- csdl and csp2 NA BH0338-like BH0338

C**

cas9 • Type II** csnl and csxl2 NA COG3513 FTN_0757 and

SPyl046 cas 10 • Type III** cmr2, csml and NA COG1353 MTH326, Rv2823c csx 11 and TM1794 caslOd • Subtype I- csc3 NA COG1353 slr7011

D**

csyl • Subtype I- csyl NA yl724-like yl724

F**

csy2 • Subtype I- csy2 NA (RAMP) yl725

F

csy3 • Subtype I- csy3 NA (RAMP) yl726

F

csel • Subtype I- csel NA YgcL-like ygcL

E**

cse2 • Subtype I- cse2 2ZCA YgcK-like ygcK

E Table II-l: Cas Systems

(PDB encoded

accessions)¹ protein

cscl • Subtype I- cscl NA alrl563-like alrl563

D (RAMP)

cscl • Subtype I- cscl and cscl NA COG1337 slr7012

D (RAMP)

csa5 • Subtype I- csa5 NA AF1870 AF1870, MJ0380,

A PF0643 and SS01398 csnl • Subtype II- csn2 NA SPyl049-like SPyl049

A

csml • Subtype csm2 NA COG1421 MTH1081 and

III-A^M SERP2460 csm.3 • Subtype cscl and csm.3 NA COG1337 MTH1080 and

III-A (RAMP) SERP2459 csm.4 • Subtype csm.4 NA COG 1567 MTH1079 and

III-A (RAMP) SERP2458 csm5 • Subtype csm5 NA COG1332 MTH1078 and

III-A (RAMP) SERP2457 csm.6 • Subtype APE2256 and 2WTE COG1517 APE2256 and

III-A csm6 SS01445 cmrl • Subtype cmrl NA COG 1367 PF1130

III-B (RAMP)

cmr3 • Subtype cmr3 NA COG 1769 PF1128

III-B (RAMP)

cmr4 • Subtype cmr4 NA COG1336 PF1126

III-B (RAMP)

cmr5 • Subtype cmr5 2ZOP and 20EB COG3337 MTH324 and PF1125

III-B^tt

cmr6 • Subtype cmr6 NA COG 1604 PF1124 Table II-l: Cas Systems

(PDB encoded

accessions)¹ protein

III-B (RAMP)

csbl • Subtype I- GSU0053 NA (RAMP) Balac_1306 and

U GSU0053 csbl • Subtype I- NA NA (RAMP) Balac_1305 and

U GSU0054 csb3 • Subtype I- NA NA (RAMP) Balac_1303

U

csx 17 • Subtype I- NA NA NA Btus_2683

U

csx 14 • Subtype I- NA NA NA GSU0052

U

csx 10 • Subtype I- csx 10 NA (RAMP) Caur_2274

U

csx 16 • Subtype VVA1548 NA NA VVA1548

III-U

csaX • Subtype csaX NA NA SS01438

III-U

csx3 • Subtype csx3 NA NA AF1864

III-U

csxl • Subtype csa3, csxl, csxl, lXMX and 2171 COG1517 and MJ1666, NE0113,

III-U DXTHG, COG4006 PF1127 and TM1812

NE0113 and

TIGR02710

csx 15 • Unknown NA NA TTE2665 TTE2665 csfl • Type U csfl NA NA AFE_1038 csfl • Type U csfl NA (RAMP) AFE_1039 Table II-l: Cas Systems

(PDB encoded

accessions)¹ protein

csf3 • Type U csf3 NA (RAMP) AFE_1040 csf4 • Type U csf4 NA NA AFE_1037

III. Functional Analysis of Candidate Molecules

Candidate Cas9 molecules, candidate gRNA molecules, candidate Cas9 molecule/gRNA molecule complexes, can be evaluated by art-known methods or as described herein. For example, exemplary methods for evaluating the endonuclease activity of Cas9 molecule are described, e.g., in Jinek et al, SCIENCE 2012; 337(6096):816-821.

Binding and Cleavage Assay: Testing the endonuclease activity of Cas9 molecule

The ability of a Cas9 molecule/gRNA molecule complex to bind to and cleave a target nucleic acid can be evaluated in a plasmid cleavage assay. In this assay, synthetic or in vitro- transcribed gRNA molecule is pre-annealed prior to the reaction by heating to 95 °C and slowly cooling down to room temperature. Native or restriction digest-linearized plasmid DNA (300 ng (~8 nM)) is incubated for 60 min at 37°C with purified Cas9 protein molecule (50-500 nM) and gRNA (50-500 nM, 1: 1) in a Cas9 plasmid cleavage buffer (20 mM HEPES pH 7.5, 150 mM KC1, 0.5 mM DTT, 0.1 mM EDTA) with or without 10 mM MgCl₂. The reactions are stopped with 5X DNA loading buffer (30% glycerol, 1.2% SDS, 250 mM EDTA), resolved by a 0.8 or 1% agarose gel electrophoresis and visualized by ethidium bromide staining. The resulting cleavage products indicate whether the Cas9 molecule cleaves both DNA strands, or only one of the two strands. For example, linear DNA products indicate the cleavage of both DNA strands. Nicked open circular products indicate that only one of the two strands is cleaved.

Alternatively, the ability of a Cas9 molecule/gRNA molecule complex to bind to and cleave a target nucleic acid can be evaluated in an oligonucleotide DNA cleavage assay. In this assay, DNA oligonucleotides (10 pmol) are radiolabeled by incubating with 5 units T4 polynucleotide kinase and -3-6 pmol (-20-40 mCi) [γ-32Ρ]-ΑΤΡ in IX T4 polynucleotide kinase reaction buffer at 37°C for 30 min, in a 50 μΐ_^ reaction. After heat inactivation (65°C for 20 min), reactions are purified through a column to remove unincorporated label. Duplex substrates (100 nM) are generated by annealing labeled oligonucleotides with equimolar amounts of unlabeled complementary oligonucleotide at 95 °C for 3 min, followed by slow cooling to room temperature. For cleavage assays, gRNA molecules are annealed by heating to 95°C for 30 s, followed by slow cooling to room temperature. Cas9 (500 nM final concentration) is pre- incubated with the annealed gRNA molecules (500 nM) in cleavage assay buffer (20 mM

HEPES pH 7.5, 100 mM KC1, 5 mM MgC12, 1 mM DTT, 5% glycerol) in a total volume of 9 μΐ. Reactions are initiated by the addition of 1 μΐ target DNA (10 nM) and incubated for 1 h at 37°C. Reactions are quenched by the addition of 20 μΐ of loading dye (5 mM EDTA, 0.025% SDS, 5% glycerol in formamide) and heated to 95°C for 5 min. Cleavage products are resolved on 12% denaturing polyacrylamide gels containing 7 M urea and visualized by phosphorimaging. The resulting cleavage products indicate that whether the complementary strand, the non- complementary strand, or both, are cleaved.

One or both of these assays can be used to evaluate the suitability of a candidate gRNA molecule or candidate Cas9 molecule.

Binding Assay: Testing the binding of Cas9 molecule to target DNA

Exemplary methods for evaluating the binding of Cas9 molecule to target DNA are described, e.g., in Jinek et al, SCIENCE 2012; 337(6096):816-821.

For example, in an electrophoretic mobility shift assay, target DNA duplexes are formed by mixing of each strand (10 nmol) in deionized water, heating to 95 °C for 3 min and slow cooling to room temperature. All DNAs are purified on 8% native gels containing IX TBE. DNA bands are visualized by UV shadowing, excised, and eluted by soaking gel pieces in DEPC-treated H₂0. Eluted DNA is ethanol precipitated and dissolved in DEPC-treated H₂0.

DNA samples are 5' end labeled with [γ-32Ρ]-ΑΤΡ using T4 polynucleotide kinase for 30 min at 37°C. Polynucleotide kinase is heat denatured at 65°C for 20 min, and unincorporated radiolabel is removed using a column. Binding assays are performed in buffer containing 20 mM HEPES pH 7.5, 100 mM KC1, 5 mM MgCl₂, 1 mM DTT and 10% glycerol in a total volume of 10 μΐ. Cas9 protein molecule is programmed with equimolar amounts of pre-annealed gRNA molecule and titrated from 100 pM to 1 μΜ. Radiolabeled DNA is added to a final concentration of 20 pM. Samples are incubated for 1 h at 37°C and resolved at 4°C on an 8% native polyacrylamide gel containing IX TBE and 5 mM MgCl₂. Gels are dried and DNA visualized by

pho sphorimaging . IV. Template Nucleic Acids (Genome Editing Approaches)

The terms "template nucleic acid" and "swap nucleic acid" are used interchangeably and have identical meaning in this document and its priority documents.

Mutations in a gene or pathway described herein, e.g., in Section VIIB, e.g., in Table VII-13, VII-14, VII-15, VII-16, VII-17, VII-18, VII-19, VII-20, VII-21, VII-22, VII-23, VII- 24, IX- 1, IX- 1A, IX-3, or XII-1, or in Section VIII, may be corrected using one of the approaches discussed herein. In an embodiment, a mutation in a gene or pathway described herein, e.g., in Section VIIB, e.g., in Table VII-13, VII-14, VII-15, VII-16, VII-17, VII-18, VII-19, VII-20, VII-21, VII-22, VII-23, VII-24, IX-1, IX- 1A, IX-3, or XII-1, or in Section VIII, is corrected by homology directed repair (HDR) using a template nucleic acid (see Section IV.1). In an embodiment, a mutation in a gene or pathway described herein, e.g., in Section VIIB, e.g., in Table VII-13, VII-14, VII-15, VII-16, VII-17, VII-18, VII-19, VII-20, VII-21, VII-22, VII-23, VII-24, IX-1, IX- 1A, IX-3, or XII-1, or in Section VIII, is corrected by Non- Homologous End Joining (NHEJ) repair using a template nucleic acid (see Section IV.2). IV.l HDR Repair and Template Nucleic Acids

As described herein, nuclease-induced homology directed repair (HDR) can be used to alter a target sequence and correct (e.g., repair or edit) a mutation in the genome. While not wishing to be bound by theory, it is believed that alteration of the target sequence occurs by homology-directed repair (HDR) with a donor template or template nucleic acid. For example, the donor template or the template nucleic acid provides for alteration of the target sequence. It is contemplated that a plasmid donor can be used as a template for homologous recombination. It is further contemplated that a single stranded donor template can be used as a template for alteration of the target sequence by alternate methods of homology directed repair (e.g., single strand annealing) between the target sequence and the donor template. Donor template-effected alteration of a target sequence depends on cleavage by a Cas9 molecule. Cleavage by Cas9 can comprise a double strand break or two single strand breaks. In an embodiment, a mutation can be corrected by either a single double-strand break or two single strand breaks. In an embodiment, a mutation can be corrected by (1) a single double- strand break, (2) two single strand breaks, (3) two double stranded breaks with a break occurring on each side of the target sequence, (4) one double stranded breaks and two single strand breaks with the double strand break and two single strand breaks occurring on each side of the target sequence or (5) four single stranded breaks with a pair of single stranded breaks occurring on each side of the target sequence.

Double strand break mediated correction

In an embodiment, double strand cleavage is effected by a Cas9 molecule having cleavage activity associated with an HNH-like domain and cleavage activity associated with a RuvC-like domain, e.g., an N-terminal RuvC-like domain, e.g., a wild type Cas9. Such an embodiment requires only a single gRNA. Single strand break mediated correction

In an embodiment, two single strand breaks, or nicks, are effected by a Cas9 molecule having nickase activity, e.g., cleavage activity associated with an HNH-like domain or cleavage activity associated with an N-terminal RuvC-like domain. Such an embodiment requires two gRNAs, one for placement of each single strand break. In an embodiment, the Cas9 molecule having nickase activity cleaves the strand to which the gRNA hybridizes, but not the strand that is complementary to the strand to which the gRNA hybridizes. In an embodiment, the Cas9 molecule having nickase activity does not cleave the strand to which the gRNA hybridizes, but rather cleaves the strand that is complementary to the strand to which the gRNA hybridizes.

In an embodiment, the nickase has HNH activity, e.g., a Cas9 molecule having the RuvC activity inactivated, e.g., a Cas9 molecule having a mutation at D10, e.g., the DIOA mutation. DIOA inactivates RuvC; therefore, the Cas9 nickase has (only) HNH activity and will cut on the strand to which the gRNA hybridizes (e.g., the complementary strand, which does not have the NGG PAM on it). In an embodiment, a Cas9 molecule having an H840, e.g., an H840A, mutation can be used as a nickase. H840A inactivates HNH; therefore, the Cas9 nickase has (only) RuvC activity and cuts on the non-complementary strand (e.g., the strand that has the NGG PAM and whose sequence is identical to the gRNA). In an embodiment, in which a nickase and two gRNAs are used to position two single strand nicks, one nick is on the + strand and one nick is on the - strand of the target nucleic acid. The PAMs are outwardly facing. The gRNAs can be selected such that the gRNAs are separated by, from about 0-50, 0-100, or 0-200 nucleotides. In an embodiment, there is no overlap between the target sequence that is complementary to the targeting domains of the two gRNAs. In an embodiment, the gRNAs do not overlap and are separated by as much as 50, 100, or 200 nucleotides. In an embodiment, the use of two gRNAs can increase specificity, e.g., by decreasing off-target binding (Ran et al., CELL 2013).

In an embodiment, a single nick can be used to induce HDR. It is contemplated herein that a single nick can be used to increase the ratio of HR to NHEJ at a given cleavage site.

Placement of the double strand break or a single strand break relative to target position The double strand break or single strand break in one of the strands should be sufficiently close to target position such that correction occurs. In an embodiment, the distance is not more than 50, 100, 200, 300, 350 or 400 nucleotides. While not wishing to be bound by theory, it is believed that the break should be sufficiently close to target position such that the break is within the region that is subject to exonuclease-mediated removal during end resection. If the distance between the target position and a break is too great, the mutation may not be included in the end resection and, therefore, may not be corrected, as donor sequence may only be used to correct sequence within the end resection region.

In an embodiment, in which a gRNA (unimolecular (or chimeric) or modular gRNA) and Cas9 nuclease induce a double strand break for the purpose of inducing HDR-mediated correction, the cleavage site is between 0-200 bp (e.g., 0 to 175, 0 to 150, 0 to 125, 0 to 100, 0 to 75, 0 to 50, 0 to 25, 25 to 200, 25 to 175, 25 to 150, 25 to 125, 25 to 100, 25 to 75, 25 to 50, 50 to 200, 50 to 175, 50 to 150, 50 to 125, 50 to 100, 50 to 75, 75 to 200, 75 to 175, 75 to 150, 75 to 125, 75 to 100 bp) away from the target position. In an embodiment, the cleavage site is between 0-100 bp (e.g., 0 to 75, 0 to 50, 0 to 25, 25 to 100, 25 to 75, 25 to 50, 50 to 100, 50 to 75 or 75 to 100 bp) away from the target position.

In an embodiment, in which two gRNAs (independently, unimolecular (or chimeric) or modular gRNA) complexing with Cas9 nickases induce two single strand breaks for the purpose of inducing HDR-mediated correction, the closer nick is between 0-200 bp (e.g., 0 to 175, 0 to 150, 0 to 125, 0 to 100, 0 to 75, 0 to 50, 0 to 25, 25 to 200, 25 to 175, 25 to 150, 25 to 125, 25 to 100, 25 to 75, 25 to 50, 50 to 200, 50 to 175, 50 to 150, 50 to 125, 50 to 100, 50 to 75, 75 to 200, 75 to 175, 75 to 150, 75 to 125, 75 to 100 bp) away from the target position and the two nicks will ideally be within 25-55 bp of each other (e.g., 25 to 50, 25 to 45, 25 to 40, 25 to 35, 25 to 30, 30 to 55, 30 to 50, 30 to 45, 30 to 40, 30 to 35, 35 to 55, 35 to 50, 35 to 45, 35 to 40, 40 to 55, 40 to 50, 40 to 45 bp) and no more than 100 bp away from each other (e.g., no more than 90, 80, 70, 60, 50, 40, 30, 20, 10 or 5 bp away from each other). In an embodiment, the cleavage site is between 0-100 bp (e.g., 0 to 75, 0 to 50, 0 to 25, 25 to 100, 25 to 75, 25 to 50, 50 to 100, 50 to 75 or 75 to 100 bp) away from the target position.

In one embodiment, two gRNAs, e.g., independently, unimolecular (or chimeric) or modular gRNA, are configured to position a double-strand break on both sides of a target position. In an alternate embodiment, three gRNAs, e.g., independently, unimolecular (or chimeric) or modular gRNA, are configured to position a double strand break (i.e., one gRNA complexes with a cas9 nuclease) and two single strand breaks or paired single stranded breaks (i.e., two gRNAs complex with Cas9 nickases) on either side of the target position (e.g., the first gRNA is used to target upstream (i.e., 5') of the target positionand the second gRNA is used to target downstream (i.e., 3') of the target position). In another embodiment, four gRNAs, e.g., independently, unimolecular (or chimeric) or modular gRNA, are configured to generate two pairs of single stranded breaks (i.e., two pairs of two gRNAs complex with Cas9 nickases) on either side of the target position (e.g., the first gRNA is used to target upstream (i.e., 5') of the target position and the second gRNA is used to target downstream (i.e., 3') of the target position). The double strand break(s) or the closer of the two single strand nicks in a pair will ideally be within 0-500 bp of the target position (e.g., no more than 450, 400, 350, 300, 250, 200, 150, 100, 50 or 25 bp from the target position). When nickases are used, the two nicks in a pair are within 25-55 bp of each other (e.g., between 25 to 50, 25 to 45, 25 to 40, 25 to 35, 25 to 30, 50 to 55, 45 to 55, 40 to 55, 35 to 55, 30 to 55, 30 to 50, 35 to 50, 40 to 50 , 45 to 50, 35 to 45, or 40 to 45 bp) and no more than 100 bp away from each other (e.g., no more than 90, 80, 70, 60, 50, 40, 30, 20 or 10 bp).

In one embodiment, two gRNAs, e.g., independently, unimolecular (or chimeric) or modular gRNA, are configured to position a double-strand break on both sides of a target position. In an alternate embodiment, three gRNAs, e.g., independently, unimolecular (or chimeric) or modular gRNA, are configured to position a double strand break (i.e., one gRNA complexes with a cas9 nuclease) and two single strand breaks or paired single stranded breaks (i.e., two gRNAs complex with Cas9 nickases) on either side of the target position (e.g., the first gRNA is used to target upstream (i.e., 5') of the mutation in a gene or pathway described herein, e.g., in Section VIIB, e.g., in Table VII-13, VII-14, VII-15, VII-16, VII-17, VII-18, VII-19, VII-20, VII-21, VII-22, VII-23, VII-24, IX-1, IX-IA, IX-3, or XII-1, or in Section VIII and the second gRNA is used to target downstream (i.e., 3') of the mutation in a gene or pathway described herein, e.g., in Section VIIB, e.g., in Table VII-13, VII-14, VII-15, VII-16, VII-17, VII-18, VII-19, VII-20, VII-21, VII-22, VII-23, VII-24, IX-1, IX-IA, IX-3, or XII-1, or in Section VIII). In another embodiment, four gRNAs, e.g., independently, unimolecular (or chimeric) or modular gRNA, are configured to generate two pairs of single stranded breaks (i.e., two pairs of two gRNAs complex with Cas9 nickases) on either side of the target position (e.g., the first gRNA is used to target upstream (i.e., 5') of the mutation in a gene or pathway described herein, and the second gRNA is used to target downstream (i.e., 3') of the mutation in a gene or pathway described herein). The double strand break(s) or the closer of the two single strand nicks in a pair will ideally be within 0-500 bp of the target position (e.g., no more than 450, 400, 350, 300, 250, 200, 150, 100, 50 or 25 bp from the target position). When nickases are used, the two nicks in a pair are within 25-55 bp of each other (e.g., between 25 to 50, 25 to 45, 25 to 40, 25 to 35, 25 to 30, 50 to 55, 45 to 55, 40 to 55, 35 to 55, 30 to 55, 30 to 50, 35 to 50, 40 to 50 , 45 to 50, 35 to 45, or 40 to 45 bp) and no more than 100 bp away from each other (e.g., no more than 90, 80, 70, 60, 50, 40, 30, 20 or 10 bp).

Length of the homology arms

The homology arm should extend at least as far as the region in which end resection may occur, e.g., in order to allow the resected single stranded overhang to find a complementary region within the donor template. The overall length could be limited by parameters such as plasmid size or viral packaging limits. In an embodiment, a homology arm does not extend into repeated elements, e.g., ALU repeats, LINE repeats.

Exemplary homology arm lengths include a least 50, 100, 250, 500, 750 or 1000 nucleotides. Target position, as used herein, refers to a site on a target nucleic acid (e.g., the chromosome) that is modified by a Cas9 molecule-dependent process. For example, the target position can be a modified Cas9 molecule cleavage of the target nucleic acid and template nucleic acid directed modification, e.g., correction, of the target position. In an embodiment, a target position can be a site between two nucleotides, e.g., adjacent nucleotides, on the target nucleic acid into which one or more nucleotides is added. The target position may comprise one or more nucleotides that are altered, e.g., corrected, by a template nucleic acid. In an

embodiment, the target position is within a target sequence (e.g., the sequence to which the gRNA binds). In an embodiment, a target position is upstream or downstream of a target sequence (e.g., the sequence to which the gRNA binds).

A template nucleic acid, as that term is used herein, refers to a nucleic acid sequence which can be used in conjunction with a Cas9 molecule and a gRNA molecule to alter the structure of a target position. The term "template nucleic acid" is synonymous with the term "swap nucleic acid" used in the priority document and herein. The terms "template nucleic acid" and "swap nucleic acid" have exactly the same meaning and can be used interchangeably. In an embodiment, the target nucleic acid is modified to have some or all of the sequence of the template nucleic acid, typically at or near cleavage site(s). In an embodiment, the template nucleic acid is single stranded. In an alternate embodiment, the tempolate nuceic acid is double stranded. In an embodiment, the template nucleic acid is DNA, e.g., double stranded DNA. In an alternate embodiment, the template nucleic acid is single stranded DNA.

In an embodiment, the template nucleic acid alters the structure of the target position by participating in a homology directed repair event. In an embodiment, the template nucleic acid alters the sequence of the target position. In an embodiment, the template nucleic acid results in the incorporation of a modified, or non-naturally occurring, nucleotide into the target nucleic acid.

Typically, the template sequence undergoes a breakage mediated or catalyzed

recombination with the target sequence. In an embodiment, the template nucleic acid includes sequence that corresponds to a site on the target sequence that is cleaved by an eaCas9 mediated cleavage event. In an embodiment, the template nucleic acid includes sequence that corresponds to both, a first site on the target sequence that is cleaved in a first Cas9 mediated event, and a second site on the target sequence that is cleaved in a second Cas9 mediated event. In an embodiment, the template nucleic acid can include sequence which results in an alteration in the coding sequence of a translated sequence, e.g., one which results in the substitution of one amino acid for another in a protein product, e.g., transforming a mutant allele into a wild type allele, transforming a wild type allele into a mutant allele, and/or introducing a stop codon, insertion of an amino acid residue, deletion of an amino acid residue, or a nonsense mutation.

In an embodiment, the template nucleic acid can include sequence which results in an alteration in a non-coding sequence, e.g., an alteration in an exon or in a 5' or 3' non-translated or non-transcribed region. Such alterations include an alteration in a control element, e.g., a promoter, enhancer, and an alteration in a cis-acting or trans-acting control element.

A template nucleic acid having homology with a target position in a gene or pathway described herein, e.g., in Section VIIB, e.g., in Table VII-13, VII-14, VII-15, VII-16, VII-17, VII-18, VII-19, VII-20, VII-21, VII-22, VII-23, VII-24, IX-1, IX-1A, IX-3, or XII-1, or in Section VIII, can be used to alter the structure of a target sequence. The template sequence can be used to alter an unwanted structure, e.g., an unwanted or mutant nucleotide.

The template nucleic acid can include sequence which, when integrated, results in: decreasing the activity of a positive control element;

increasing the activity of a positive control element;

decreasing the activity of a negative control element;

increasing the activity of a negative control element;

decreasing the expression of a gene;

increasing the expression of a gene;

increasing resistance to a disorder or disease;

increasing resistance to viral entry;

correcting a mutation or altering an unwanted amino acid residue conferring, increasing, abolishing or decreasing a biological property of a gene product, e.g., increasing the enzymatic activity of an enzyme, or increasing the ability of a gene product to interact with another molecule.

The template nucleic acid can include sequence which results in: a change in sequence of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or more nucleotides of the target sequence.

In an embodiment, the template nucleic acid is 20+/- 10, 30+/- 10, 40+/- 10, 50+/- 10, 60+/- 10, 70+/-10, 80+/-10, 90+/-10, 100+/-10, 110+/-10, 120+/- 10, 130+/- 10, 140+/- 10, 150+/-10, 160+/-10, 170+/-10, 180+/- 10, 190+/-10, 200+/-10, 210+/-10, of 220+/-10 nucleotides in length.

In an embodiment, the template nucleic acid is 30+/-20, 40+/-20, 50+/-20, 60+/-20, 70+/- 20, 80+/-20, 90+/-20, 100+/-20, 110+/-20, 120+/-20, 130+/-20, 140+/-20, 150+/-20, 160+/-20, 170+/-20, 180+/-20, 190+/-20, 200+/-20, 210+/-20, of 220+/-20 nucleotides in length.

In an embodiment, the template nucleic acid is 10 to 1,000, 20 to 900, 30 to 800, 40 to 700, 50 to 600, 50 to 500, 50 to 400, 50 to300, 50 to 200, or 50 to 100 nucleotides in length.

A template nucleic acid comprises the following components:

[5' homology arm] -[replacement sequence] -[3' homology arm].

The homology arms provide for recombination into the chromosome, thus replacing the undesired element, e.g., a mutation or signature, with the replacement sequence. In an embodiment, the homology arms flank the most distal cleavage sites.

In an embodiment, the 3' end of the 5' homology arm is the position next to the 5' end of the replacement sequence. In an embodiment, the 5' homology arm can extend at least 10, 20, 30, 40, 50, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1500, or 2000 nucleotides 5' from the 5' end of the replacement sequence.

In an embodiment, the 5' end of the 3' homology arm is the position next to the 3' end of the replacement sequence. In an embodiment, the 3' homology arm can extend at least 10, 20, 30, 40, 50, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1500, or 2000 nucleotides 3' from the 3' end of the replacement sequence.

It is contemplated herein that one or both homology arms may be shortened to avoid including certain sequence repeat elements, e.g., Alu repeats, LINE elements. For example, a 5' homology arm may be shortened to avoid a sequence repeat element. In an embodiment, a 3' homology arm may be shortened to avoid a sequence repeat element. In an embodiment, both the 5' and the 3' homology arms may be shortened to avoid including certain sequence repeat elements.

It is contemplated herein that template nucleic acids for correcting a mutation may designed for use as a single- stranded oligonucleotide (ssODN). When using a ssODN, 5' and 3' homology arms may range up to about 200 base pairs (bp) in length, e.g., at least 25, 50, 75, 100, 125, 150, 175, or 200 bp in length. Longer homology arms are also contemplated for ssODNs as improvements in oligonucleotide synthesis continue to be made.

In an embodiment, an ssODN may be used to correct a mutation in a gene or pathway described herein, e.g., in Section VIIB, e.g., in Table VII-13, VII-14, VII-15, VII-16, VII-17, VII-18, VII-19, VII-20, VII-21, VII-22, VII-23, VII-24, IX-1, IX-1A, IX-3, or XII-1, or in Section VIII.

IV.2 NHE.T Approaches for Gene Targeting

As described herein, nuclease-induced non-homologous end-joining (NHEJ) can be used to target gene-specific knockouts. Nuclease-induced NHEJ can also be used to remove (e.g., delete) sequence in a gene of interest.

While not wishing to be bound by theory, it is believed that, in an embodiment, the genomic alterations associated with the methods described herein rely on nuclease-induced NHEJ and the error-prone nature of the NHEJ repair pathway. NHEJ repairs a double-strand break in the DNA by joining together the two ends; however, generally, the original sequence is restored only if two compatible ends, exactly as they were formed by the double-strand break, are perfectly ligated. The DNA ends of the double-strand break are frequently the subject of enzymatic processing, resulting in the addition or removal of nucleotides, at one or both strands, prior to rejoining of the ends. This results in the presence of insertion and/or deletion (indel) mutations in the DNA sequence at the site of the NHEJ repair. Two-thirds of these mutations typically alter the reading frame and, therefore, produce a non-functional protein. Additionally, mutations that maintain the reading frame, but which insert or delete a significant amount of sequence, can destroy functionality of the protein. This is locus dependent as mutations in critical functional domains are likely less tolerable than mutations in non-critical regions of the protein.

The indel mutations generated by NHEJ are unpredictable in nature; however, at a given break site certain indel sequences are favored and are over represented in the population, likely due to small regions of microhomology. The lengths of deletions can vary widely; most commonly in the 1-50 bp range, but they can easily reach greater than 100-200 bp. Insertions tend to be shorter and often include short duplications of the sequence immediately surrounding the break site. However, it is possible to obtain large insertions, and in these cases, the inserted sequence has often been traced to other regions of the genome or to plasmid DNA present in the cells.

Because NHEJ is a mutagenic process, it can also be used to delete small sequence motifs as long as the generation of a specific final sequence is not required. If a double- strand break is targeted near to a short target sequence, the deletion mutations caused by the NHEJ repair often span, and therefore remove, the unwanted nucleotides. For the deletion of larger DNA segments, introducing two double-strand breaks, one on each side of the sequence, can result in NHEJ between the ends with removal of the entire intervening sequence. Both of these approaches can be used to delete specific DNA sequences; however, the error-prone nature of NHEJ may still produce indel mutations at the site of repair.

Both double strand cleaving eaCas9 molecules and single strand, or nickase, eaCas9 molecules can be used in the methods and compositions described herein to generate NHEJ- mediated indels. NHEJ-mediated indels targeted to the gene, e.g., a coding region, e.g., an early coding region of a gene of interest can be used to knockout (i.e., eliminate expression of) a gene of interest. For example, early coding region of a gene of interest includes sequence

immediately following a transcription start site, within a first exon of the coding sequence, or within 500 bp of the transcription start site (e.g., less than 500, 450, 400, 350, 300, 250, 200, 150, 100 or 50 bp).

Placement of double strand or single strand breaks relative to the target position

In an embodiment, in which a gRNA and Cas9 nuclease generate a double strand break for the purpose of inducing NHEJ-mediated indels, a gRNA, e.g., a unimolecular (or chimeric) or modular gRNA molecule, is configured to position one double-strand break in close proximity to a nucleotide of the target position. In an embodiment, the cleavage site is between 0-500 bp away from the target position (e.g., less than 500, 400, 300, 200, 100, 50, 40, 30, 25, 20, 15, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 bp from the target position).

In an embodiment, in which two gRNAs complexing with Cas9 nickases induce two single strand breaks for the purpose of inducing NHEJ-mediated indels, two gRNAs, e.g., independently, unimolecular (or chimeric) or modular gRNA, are configured to position two single-strand breaks to provide for NHEJ repair a nucleotide of the target position. In an embodiment, the gRNAs are configured to position cuts at the same position, or within a few nucleotides of one another, on different strands, essentially mimicking a double strand break. In an embodiment, the closer nick is between 0-30 bp away from the target position (e.g., less than 30, 25, 20, 15, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 bp from the target position), and the two nicks are within 25-55 bp of each other (e.g., between 25 to 50, 25 to 45, 25 to 40, 25 to 35, 25 to 30, 50 to 55, 45 to 55, 40 to 55, 35 to 55, 30 to 55, 30 to 50, 35 to 50, 40 to 50 , 45 to 50, 35 to 45, or 40 to 45 bp) and no more than 100 bp away from each other (e.g., no more than 90, 80, 70, 60, 50, 40, 30, 20 or 10 bp). In an embodiment, the gRNAs are configured to place a single strand break on either side of a nucleotide of the target position.

Both double strand cleaving eaCas9 molecules and single strand, or nickase, eaCas9 molecules can be used in the methods and compositions described herein to generate breaks both sides of a target position. Double strand or paired single strand breaks may be generated on both sides of a target position (e.g., of a gene or pathway described herein, e.g., in Section VIIB, e.g., in Table VII-13, VII-14, VII-15, VII-16, VII-17, VII-18, VII-19, VII-20, VII-21, VII-22, VII- 23, VII-24, IX-1, IX-1A, IX-3, or XII- 1, or in Section VIII, to remove the nucleic acid sequence between the two cuts (e.g., the region between the two breaks is deleted). In one embodiment, two gRNAs, e.g., independently, unimolecular (or chimeric) or modular gRNA, are configured to position a double-strand break on both sides of a target position (e.g., the first gRNA is used to target upstream (i.e., 5') of the mutation in a gene or pathway described herein, and the second gRNA is used to target downstream (i.e., 3') of the mutation in a gene or pathway described herein). In an alternate embodiment, three gRNAs, e.g., independently, unimolecular (or chimeric) or modular gRNA, are configured to position a double strand break (i.e., one gRNA complexes with a cas9 nuclease) and two single strand breaks or paired single stranded breaks (i.e., two gRNAs complex with Cas9 nickases) on either side of a target position (e.g., the first gRNA is used to target upstream (i.e., 5') of the mutation in a gene or pathway described herein, and the second gRNA is used to target downstream (i.e., 3') of the mutation in a gene or pathway described herein). In another embodiment, four gRNAs, e.g., independently, unimolecular (or chimeric) or modular gRNA, are configured to generate two pairs of single stranded breaks (i.e., two pairs of two gRNAs complex with Cas9 nickases) on either side of the target position (e.g., the first gRNA is used to target upstream (i.e., 5') of the mutation in a gene or pathway described herein, and the second gRNA is used to target downstream (i.e., 3') of the mutation in a gene or pathway described herein). The double strand break(s) or the closer of the two single strand nicks in a pair will ideally be within 0-500 bp of the target position (e.g., no more than 450, 400, 350, 300, 250, 200, 150, 100, 50 or 25 bp from the target position). When nickases are used, the two nicks in a pair are within 25-55 bp of each other (e.g., between 25 to 50, 25 to 45, 25 to 40, 25 to 35, 25 to 30, 50 to 55, 45 to 55, 40 to 55, 35 to 55, 30 to 55, 30 to 50, 35 to 50, 40 to 50 , 45 to 50, 35 to 45, or 40 to 45 bp) and no more than 100 bp away from each other (e.g., no more than 90, 80, 70, 60, 50, 40, 30, 20 or 10 bp).

IV.3 Targeted Knockdown

Unlike CRISPR/Cas-mediated gene knockout, which permanently eliminates expression by mutating the gene at the DNA level, CRISPR/Cas knockdown allows for temporary reduction of gene expression through the use of artificial transcription factors. Mutating key residues in both DNA cleavage domains of the Cas9 protein (e.g. the DIOA and H840A mutations) results in the generation of a catalytically inactive Cas9 (eiCas9 which is also known as dead Cas9 or dCas9). A catalytically inactive Cas9 complexes with a gRNA and localizes to the DNA sequence specified by that gRNA's targeting domain, however, it does not cleave the target DNA. Fusion of the dCas9 to an effector domain, e.g., a transcription repression domain, enables recruitment of the effector to any DNA site specified by the gRNA. While it has been show that the eiCas9 itself can block transcription when recruited to early regions in the coding sequence, more robust repression can be achieved by fusing a transcriptional repression domain (for example KRAB, SID or ERD) to the Cas9 and recruiting it to the promoter region of a gene. It is likely that targeting DNAsel hypersensitive regions of the promoter may yield more efficient gene repression or activation because these regions are more likely to be accessible to the Cas9 protein and are also more likely to harbor sites for endogenous transcription factors. Especially for gene repression, it is contemplated herein that blocking the binding site of an endogenous transcription factor would aid in downregulating gene expression. In another embodiment, an eiCas9 can be fused to a chromatin modifying protein. Altering chromatin status can result in decreased expression of the target gene.

In an embodiment, a gRNA molecule can be targeted to a known transcription response elements (e.g., promoters, enhancers, etc.), a known upstream activating sequences (UAS), and/or sequences of unknown or known function that are suspected of being able to control expression of the target DNA.

CRISPR/Cas-mediated gene knockdown can be used to reduce expression of an unwanted allele or transcript. Contemplated herein are scenarios wherein permanent destruction of the gene is not ideal. In these scenarios, site-specific repression may be used to temporarily reduce or eliminate expression. It is also contemplated herein that the off-target effects of a Cas- repressor may be less severe than those of a Cas-nuclease as a nuclease can cleave any DNA sequence and cause mutations whereas a Cas-repressor may only have an effect if it targets the promoter region of an actively transcribed gene. However, while nuclease-mediated knockout is permanent, repression may only persist as long as the Cas-repressor is present in the cells. Once the repressor is no longer present, it is likely that endogenous transcription factors and gene regulatory elements would restore expression to its natural state.

IV.4 Examples of gRNAs in Genome Editing Methods

gRNA molecules as described herein can be used with Cas9 molecules that generate a double strand break or a single strand break to alter the sequence of a target nucleic acid, e.g., a target position or target genetic signature. gRNA molecules useful in these methods are described below.

In an embodiment, the gRNA, e.g., a chimeric gRNA, is configured such that it comprises one or more of the following properties;

a) it can position, e.g., when targeting a Cas9 molecule that makes double strand breaks, a double strand break (i) within 50, 100, 150 or 200 nucleotides of a target position, or (ii) sufficiently close that the target position is within the region of end resection;

b) it has a targeting domain of at least 15, 16, 17, 18, 19 or 20, nucleotides, e.g., a targeting domain of (i) 17, (ii) 18, or (iii) 20 nucleotides; and

c)

(i) the proximal and tail domain, when taken together, comprise at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides, e.g., at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides from a naturally occurring S.

pyogenes, S. thermophilus, S. aureus, or N. meningitidis tail and proximal domain, or a sequence that differs by no more than 1, 2, 3, 4, 5; 6, 7, 8, 9 or 10 nucleotides therefrom;

(ii) there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3' to the last nucleotide of the second complementarity domain, e.g., at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides from the corresponding sequence of a naturally occurring S. pyogenes, S. thermophilus, S. aureus, or N. meningitidis gRNA, or a sequence that differs by no more than 1, 2, 3, 4, 5; 6, 7, 8, 9 or 10 nucleotides therefrom;

(iii) there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3' to the last nucleotide of the second complementarity domain that is

complementary to its corresponding nucleotide of the first complementarity domain, e.g., at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides from the corresponding sequence of a naturally occurring S. pyogenes, S.

thermophilus, S. aureus, or N. meningitidis gRNA, or a sequence that differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 nucleotides therefrom;

iv) the tail domain is at least 10, 15, 20, 25, 30, 35 or 40 nucleotides in length, e.g., it comprises at least 10, 15, 20, 25, 30, 35 or 40 nucleotides from a naturally occurring S. pyogenes, S. thermophilus, S. aureus, or N. meningitidis tail domain; or, or a sequence that differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 nucleotides therefrom; or

(v) the tail domain comprises 15, 20, 25, 30, 35, 40 nucleotides or all of the corresponding portions of a naturally occurring tail domain, e.g., a naturally occurring S. pyogenes, S. thermophilus, S. aureus, or N. meningitidis tail domain.

In an embodiment, the gRNA is configured such that it comprises properties: a and b(i).

In an embodiment, the gRNA is configured such that it comprises properties: a and b(ii).

In an embodiment, the gRNA is configured such that it comprises properties: a and b(iii).

In an embodiment, the gRNA is configured such that it comprises properties: a and c.

In an embodiment, the gRNA is configured such that in comprises properties: a, b, and c.

In an embodiment, the gRNA is configured such that in comprises properties: a(i), b(i), In an embodiment, the gRNA is configured such that in comprises properties: a(i), b(i), and c(ii).

In an embodiment, the gRNA is configured such that in comprises properties: a(i), b(iii), and c(i).

In an embodiment, the gRNA is configured such that in comprises properties: a(i), b(iii), and c(ii).

a) it can position, e.g., when targeting a Cas9 molecule that makes single strand breaks, a single strand break (i) within 50, 100, 150 or 200 nucleotides of a target position, or (ii) sufficiently close that the target position is within the region of end resection;

b) it has a targeting domain of at least 15, 16, 17, 18, 19, or 20, nucleotides, e.g., a targeting domain of (i) 17, (ii) 18, or (iii) 20 nucleotides; and

c)

pyogenes, S. thermophilus, S. aureus, or N. meningitidis tail and proximal domain, or a sequence that differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 nucleotides therefrom;

(ii) there are at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides 3' to the last nucleotide of the second complementarity domain, e.g., at least 15, 18, 20, 25, 30, 31, 35, 40, 45, 49, 50, or 53 nucleotides from the corresponding sequence of a naturally occurring S. pyogenes, S. thermophilus, S. aureus, or N. meningitidis gRNA, or a sequence that differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 nucleotides therefrom;

(iii) there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3' to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain, e.g., at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides from the corresponding sequence of a naturally occurring S. pyogenes, S. thermophilus, S. aureus, or N. meningitidis gRNA, or a sequence that differs by no more than 1, 2, 3, 4, 5; 6, 7, 8, 9 or 10 nucleotides therefrom;

iv) the tail domain is at least 10, 15, 20, 25, 30, 35 or 40 nucleotides in length, e.g., it comprises at least 10, 15, 20, 25, 30, 35 or 40 nucleotides from a naturally occurring S. pyogenes, S. thermophilus, S. aureus, or N. meningitidis tail domain; or, a sequence that differs by no more than 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 nucleotides therefrom; or

In an embodiment, the gRNA is configured such that in comprises properties: a(i), b(i), and c(i).

In an embodiment, the gRNA is configured such that in comprises properties: a(i), b(i), and c(ii).

In an embodiment, the gRNA is used with a Cas9 nickase molecule having HNH activity, e.g., a Cas9 molecule having the RuvC activity inactivated, e.g., a Cas9 molecule having a mutation at D10, e.g., the D10A mutation.

In an embodiment, the gRNA is used with a Cas9 nickase molecule having RuvC activity, e.g., a Cas9 molecule having the HNH activity inactivated, e.g., a Cas9 molecule having a mutation at H840, e.g., a H840A. In an embodiment, a pair of gRNAs, e.g., a pair of chimeric gRNAs, comprising a first and a second gRNA, is configured such that they comprises one or more of the following properties;

a) one or both of the gRNAs can position, e.g., when targeting a Cas9 molecule that makes single strand breaks, a single strand break within (i) 50, 100, 150 or 200 nucleotides of a target position, or (ii) sufficiently close that the target position is within the region of end resection;

b) one or both have a targeting domain of at least 17 nucleotides, e.g., a targeting domain of (i) 17 or (ii) 18 nucleotides;

c) one or both:

(iii) there are at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides 3' to the last nucleotide of the second complementarity domain that is complementary to its corresponding nucleotide of the first complementarity domain, e.g., at least 16, 19, 21, 26, 31, 32, 36, 41, 46, 50, 51, or 54 nucleotides from the corresponding sequence of a naturally occurring S. pyogenes, S.

thermophilus, S. aureus, or N. meningitidis gRNA, or a sequence that differs by no more than 1, 2, 3, 4, 5; 6, 7, 8, 9 or 10 nucleotides therefrom;

(v) the tail domain comprises 15, 20, 25, 30, 35, 40 nucleotides or all of the corresponding portions of a naturally occurring tail domain, e.g., a naturally occurring S. pyogenes, S. thermophilus, S. aureus, or N. meningitidis tail domain; d) the gRNAs are configured such that, when hybridized to target nucleic acid, they are separated by 0-50, 0-100, 0-200, at least 10, at least 20, at least 30 or at least 50 nucleotides; e) the breaks made by the first gRNA and second gRNA are on different strands; and f) the PAMs are facing outwards.

In an embodiment, one or both of the gRNAs is configured such that it comprises properties: a and b(i).

In an embodiment, one or both of the gRNAs is configured such that it comprises properties: a and b(ii).

In an embodiment, one or both of the gRNAs is configured such that it comprises properties: a and b(iii).

In an embodiment, one or both of the gRNAs configured such that it comprises properties: a and c.

In an embodiment, one or both of the gRNAs is configured such that in comprises properties: a, b, and c.

In an embodiment, one or both of the gRNAs is configured such that in comprises properties: a(i), b(i), and c(i).

In an embodiment, one or both of the gRNAs is configured such that in comprises properties: a(i), b(i), and c(ii).

In an embodiment, one or both of the gRNAs is configured such that in comprises properties: a(i), b(i), c, and d.

In an embodiment, one or both of the gRNAs is configured such that in comprises properties: a(i), b(i), c, and e.

In an embodiment, one or both of the gRNAs is configured such that in comprises properties: a(i), b(i), c, d, and e. In an embodiment, one or both of the gRNAs is configured such that in comprises properties: a(i), b(iii), and c(i).

In an embodiment, one or both of the gRNAs is configured such that in comprises properties: a(i), b(iii), and c(ii).

In an embodiment, one or both of the gRNAs is configured such that in comprises properties: a(i), b(iii), c, and d.

In an embodiment, one or both of the gRNAs is configured such that in comprises properties: a(i), b(iii), c, and e.

In an embodiment, one or both of the gRNAs is configured such that in comprises properties: a(i), b(iii), c, d, and e.

In an embodiment, the gRNAs are used with a Cas9 nickase molecule having HNH activity, e.g., a Cas9 molecule having the RuvC activity inactivated, e.g., a Cas9 molecule having a mutation at D 10, e.g., the D10A mutation.

In an embodiment, the gRNAs are used with a Cas9 nickase molecule having RuvC activity, e.g., a Cas9 molecule having the HNH activity inactivated, e.g., a Cas9 molecule having a mutation at H840, e.g., a H840A.

V. Constructs/Components

The components, e.g., a Cas9 molecule or gRNA molecule, or both, can be delivered, formulated, or administered in a variety of forms, see, e.g., Table V-la and Table V-lb. When a component is delivered encoded in DNA the DNA will typically include a control region, e.g., comprising a promoter, to effect expression. Useful promoters for Cas9 molecule sequences include CMV, EF-la, MSCV, PGK, CAG control promoters. Useful promoters for gRNAs include HI, EF-la and U6 promoters. Promoters with similar or dissimilar strengths can be selected to tune the expression of components. Sequences encoding a Cas9 molecule can comprise a nuclear localization signal (NLS), e.g., an SV40 NLS. In an embodiment, a promoter for a Cas9 molecule or a gRNA molecule can be, independently, inducible, tissue specific, or cell specific.

Table V-la and Table V-lb provide examples of how the components can be

formulated, delivered, or administered. Table V-la

eaCas9 molecule, and a gRNA are transcribed from DNA. In this embodiment, they are encoded on separate molecules. In this embodiment, the donor template is provided on the same DNA molecule that encodes the gRNA. A governing gRNA molecule can also be present. It can be encoded on the molecule that encodes the Cas9 molecule and the gRNA molecule or can be on a second nucleic acid molecule. The governing gRNA molecule can be a Cas9-targeting gRNA molecule or a gRNA- targeting gRNA molecule. In an embodiment, both are present. In an embodiment, the governing gRNA molecule is a Cas9-targeting gRNA molecule which targets, by binding and/or cleavage, the sequence that encodes the Cas9 molecule and results in substantial reduction of the production of Cas9 molecule. In an embodiment, the governing gRNA molecule is a gRNA-targeting gRNA molecule which targets, by binding and/or cleavage, the sequence that encodes the gRNA molecule and results in substantial reduction of the production of gRNA molecule.

DNA DNA In an embodiment, a Cas9 molecule, typically an eaCas9 molecule, and a gRNA are transcribed from DNA, here from a single molecule. In this embodiment, the donor template is provided as a separate DNA molecule. A governing gRNA molecule can also be present. It can be encoded on the molecule that encodes the Cas9 molecule and the gRNA molecule or can be on a second nucleic acid molecule. The governing gRNA molecule can be a Cas9-targeting gRNA molecule or a gRNA-targeting gRNA molecule. In an embodiment, both are present. In an embodiment, the governing gRNA molecule is a Cas9-targeting gRNA molecule which targets, by binding and/or cleavage, the sequence that encodes the Cas9 molecule and results in substantial reduction of the production of Cas9 molecule. In an embodiment, the governing gRNA molecule is a gRNA-targeting gRNA molecule which targets, by binding and/or cleavage, the sequence that encodes the gRNA molecule and results in substantial reduction of the production of gRNA molecule.

DNA DNA DNA In an embodiment, a Cas9 molecule, typically an eaCas9 molecule, and a gRNA are transcribed from DNA. In this embodiment, they are encoded on separate molecules. In this embodiment, the donor template is provided on the same DNA molecule that encodes the Cas9. A governing gRNA molecule can also be present. It can be encoded on the molecule that encodes the Cas9 molecule or the gRNA molecule or can be on a third nucleic acid molecule. The governing gRNA molecule can be a Cas9-targeting gRNA molecule or a gRNA- targeting gRNA molecule. In an embodiment, both are present. In an embodiment, the governing gRNA molecule is a Cas9-targeting gRNA molecule which targets, by binding and/or cleavage, the sequence that encodes the Cas9 molecule and results in substantial reduction of the production of Cas9 molecule. In an embodiment, the governing gRNA molecule is a gRNA-targeting gRNA molecule which targets, by binding and/or cleavage, the sequence that encodes the gRNA molecule and results in substantial reduction of the production of gRNA molecule.

DNA RNA DNA In an embodiment, a Cas9 molecule, typically an eaCas9 molecule, is transcribed from DNA, and a gRNA is provided as in vitro transcribed or synthesized RNA. In this embodiment, the donor template is provided as a separate DNA molecule. In an embodiment, the gRNA comprises one or more modifications, e.g., as described in Section X. A governing gRNA molecule can also be present. It can be encoded on the molecule that encodes the Cas9 molecule or can be on a second nucleic acid molecule. In an embodiment, the governing gRNA molecule is a Cas9-targeting gRNA molecule which targets, by binding and/or cleavage, the sequence that encodes the Cas9 molecule and results in substantial reduction of the production of Cas9 molecule.

DNA RNA DNA In an embodiment, a Cas9 molecule, typically an eaCas9 molecule, is transcribed from DNA, and a gRNA is provided as in vitro transcribed or synthesized RNA. In this embodiment, the donor template is provided on the same DNA molecule that encodes the Cas9. In an embodiment, the gRNA comprises one or more modifications, e.g., as described in Section X. A governing gRNA molecule can also be present. It can be encoded on the molecule that encodes the Cas9 molecule or can be on a second nucleic acid molecule. In an embodiment, the governing gRNA molecule is a Cas9-targeting gRNA molecule which targets, by binding and/or cleavage, the sequence that encodes the Cas9 molecule and results in substantial reduction of the production of Cas9 molecule.

mRNA RNA DNA In an embodiment, a Cas9 molecule, typically an eaCas9 molecule, is translated from in vitro transcribed mRNA, and a gRNA is provided as in vitro transcribed or synthesized RNA. In this embodiment, the donor template is provided as a DNA molecule. In an embodiment, the gRNA comprises one or more modifications, e.g., as described in Section X. In an embodiment, the mRNA comprises one or more modifications, e.g., as described in Section X.

mRNA DNA DNA In an embodiment, a Cas9 molecule, typically an eaCas9 molecule, is translated from in vitro transcribed mRNA, and a gRNA is transcribed from DNA. In this embodiment, the donor template is provided as a separate DNA molecule. In an embodiment, the mRNA comprises one or more modifications, e.g., as described in Section X. A governing gRNA molecule can also be present. It can be encoded on the molecule that encodes the gRNA molecule or can be on a second nucleic acid molecule. In an embodiment, the governing gRNA molecule is a gRNA-targeting gRNA molecule which targets, by binding and/or cleavage, the sequence that encodes the gRNA molecule and results in substantial reduction of the production of gRNA molecule.

mRNA DNA In an embodiment, a Cas9 molecule, typically an eaCas9 molecule, is translated from in vitro transcribed mRNA, and a gRNA is transcribed from DNA. In this embodiment, the donor template is provided on the same DNA molecule that encodes the gRNA. In an embodiment, the mRNA comprises one or more modifications, e.g., as described in Section X. A governing gRNA molecule can also be present. It can be encoded on the molecule that encodes the gRNA molecule or can be on a second nucleic acid molecule. In an embodiment, the governing gRNA molecule is a gRNA-targeting gRNA molecule which targets, by binding and/or cleavage, the sequence that encodes the gRNA molecule and results in substantial reduction of the production of gRNA molecule.

Protein DNA DNA In an embodiment, a Cas9 molecule, typically an eaCas9 molecule, is provided as a protein, and a gRNA is transcribed from DNA. In this embodiment, the donor template is provided as a separate DNA molecule. A governing gRNA molecule can also be present. It can be encoded on the molecule that encodes the gRNA molecule or can be on a second nucleic acid molecule. In an embodiment the governing gRNA molecule is a gRNA-targeting gRNA molecule which targets, by binding and/or cleavage, the sequence that encodes the gRNA molecule and results in substantial reduction of the production of gRNA molecule.

Protein DNA In an embodiment, a Cas9 molecule, typically an eaCas9 molecule, is provided as a protein, and a gRNA is transcribed from DNA. In this embodiment, the donor template is provided on the same DNA molecule that encodes the gRNA. A governing gRNA molecule can also be present. It can be encoded on the molecule that encodes the gRNA molecule or can be on a second nucleic acid molecule. In an embodiment the governing gRNA molecule is a gRNA- targeting gRNA molecule which targets, by binding and/or cleavage, the sequence that encodes the gRNA molecule and results in substantial reduction of the production of gRNA molecule.

Protein RNA DNA In an embodiment, an eaCas9 molecule is

provided as a protein, and a gRNA is provided as transcribed or synthesized RNA. In this embodiment, the donor template is provided as a DNA molecule. In an embodiment, the gRNA comprises one or more modifications, e.g., as described in Section X. Table V-lb

governing gRNA molecule can also be present.

It can be encoded on the molecule that encodes the Cas9 molecule or the gRNA molecule or can be on a second nucleic acid molecule. The governing gRNA molecule can be a Cas9- targeting gRNA molecule or a gRNA-targeting gRNA molecule. In an embodiment, both are present. In an embodiment, the governing gRNA molecule is a Cas9-targeting gRNA molecule which targets, by binding and/or cleavage, the sequence that encodes the Cas9 molecule and results in substantial reduction of the production of Cas9 molecule. In an embodiment, the governing gRNA molecule is a gRNA-targeting gRNA molecule which targets, by binding and/or cleavage, the sequence that encodes the gRNA molecule and results in substantial reduction of the production of gRNA molecule.

DNA RNA Yes In this embodiment, a Cas9 molecule, typically an eiCas9 molecule, is transcribed from DNA. A gRNA is provided as RNA. In an

embodiment, the gRNA comprises one or more modifications, e.g., as described in Section X. A governing gRNA molecule can also be present. It can be encoded on the molecule that encodes the Cas9 molecule or can be on a second nucleic acid molecule. In an

embodiment the governing gRNA molecule is a Cas9-targeting gRNA molecule which targets, by binding and/or cleavage, the sequence that encodes the Cas9 molecule and results in

substantial reduction of the production of Cas9 molecule.

mRNA RNA Yes In this embodiment, a Cas9 molecule, typically an eiCas9 molecule, is provided as encoded in mRNA. A gRNA is provided as RNA. In an embodiment, the gRNA comprises one or more modifications, e.g., as described in Section X. In an embodiment, the mRNA comprises one or more modifications, e.g., as described in section X.

Protein DNA Yes In this embodiment a Cas9 molecule, typically an eiCas9 molecule, is provided as a protein. A gRNA is provided encoded in DNA. A governing gRNA molecule can also be present. It can be encoded on the molecule that encodes the gRNA molecule or can be on a second nucleic acid molecule. In an embodiment the governing gRNA molecule is a gRNA-targeting gRNA molecule which targets, by binding and/or cleavage, the sequence that encodes the gRNA molecule and results in substantial reduction of the production of the gRNA molecule.

Protein RNA Yes In this embodiment, a Cas9 molecule, typically an eiCas9 molecule, is provided as a protein. A gRNA is provided as RNA. In an embodiment, the gRNA comprises one or more modifications, e.g., as described in Section X. In an embodiment, the components of a Cas system are delivered in vivo, e.g., using a method describe herein. In another embodiment, the components a Cas system are delievered ex vivo, e.g., using a method described herein. Table V-2 summerizes various delivery methods the components of a Cas system, e.g., the Cas9 molecule component and the gRNA molecule component are described herein, e.g., in Table V-2.

Table V-2

Mammalian YES Transient NO Nucleic Acids

Virus-like

Particles

Biological YES Transient NO Nucleic Acids liposomes:

Erythrocyte

Ghosts and

Exosomes

DNA-based Delivery of a Cas9 molecule and or a gRNA molecule

DNA encoding Cas9 molecules (e.g., eaCas9 molecules or eiCas9 molecules), gRNA molecules, and/or template nucleic acids, can be administered to subjects or delivered into cells by art-known methods or as described herein. For example, Cas9-encoding and/or gRNA- encoding DNA can be delivered, e.g., by vectors (e.g., viral or non- viral vectors), non- vector based methods (e.g., using naked DNA or DNA complexes), or a combination thereof.

In an embodiment, the DNA includes a nucleic acid that encodes a governing gRNA molecule. The governing gRNA molecule can complex with the Cas9 molecule to inactivate or silence a component of the system, e.g., the nucleic acid that encodes the Cas9 molecule or the nucleic acid that encodes the gRNA molecule. In either case, the governing gRNA, e.g., a Cas9- targeting gRNA molecule, or a gRNA targeting gRNA molecule, limits the effect of the

Cas9/gRNA complex mediated gene targeting, and can place temporal limits on activity or reduce off-target activity.

In an embodiment, the Cas9- and/or gRNA-encoding DNA is delivered by a vector (e.g., viral vector/virus or plasmid).

A vector can comprise a sequence that encodes a Cas9 molecule and/or a gRNA molecule. A vector can also comprise a sequence encoding a signal peptide (e.g., for nuclear localization, nucleolar localization, mitochondrial localization), fused, e.g., to a Cas9 molecule sequence. For example, a vector can comprise a nuclear localization sequence (e.g., from SV40) fused to the sequence encoding the Cas9 molecule.

One or more regulatory/control elements, e.g., a promoter, an enhancer, an intron, a polyadenylation signal, a Kozak consensus sequence, internal ribosome entry sites (IRES), a 2A sequence, and a splice acceptor or donor can be included in the vectors. In an embodiment, the promoter is recognized by RNA polymerase II (e.g., a CMV promoter). In an embodiment, the promoter is recognized by RNA polymerase III (e.g., a U6 promoter). In an embodiment, the promoter is a regulated promoter (e.g., inducible promoter). In an embodiment, the promoter is a constitutive promoter. In an embodiment, the promoter is a tissue specific promoter. In an embodiment, the promoter is a viral promoter. In an embodiment, the promoter is a non- viral promoter.

In an embodiment, the vector or delivery vehicle is a viral vector (e.g., for generation of recombinant viruses). In an embodiment, the virus is a DNA virus (e.g., dsDNA or ssDNA virus). In an embodiment, the virus is an RNA virus (e.g., an ssRNA virus). Exemplary viral vectors/viruses include, e.g., retroviruses, lentiviruses, adenovirus, adeno-associated virus (AAV), vaccinia viruses, poxviruses, and herpes simplex viruses. In an embodiment, the viral vector, e.g., an AAV, comprises a sequence that encodes a governing gRNA molecule, e.g., a Cas9-targeting gRNA molecule or a gRNA-targeting gRNA molecule.

In an embodiment, the viral vector has the ability of cell type and/or tissue type recognition. For example, the viral vectors can be pseudotyped with different/alternative viral envelope glycoproteins; engineered with cell type-specific receptors (e.g., genetically

modification of viral envelope glycoproteins to incorporate targeting ligands such as peptide ligands, single chain antibodies, growth factors); and/or engineered to have a molecular bridge with dual specificities with one end recognizing viral glycoproteins and the other end

recognizing a moiety of the target cell surface (e.g., ligand-receptor, monoclonal antibodies, avidin-biotin and chemical conjugation).

In an embodiment, the viral vector achieves cell type specific expression. For example, tissue-specific promoter can be constructed to restrict expression of the transgene (Cas 9 and gRNA) in only the target cells. The specificity of the vectors can also be mediated by

microRNA-dependent control of transgene expression. In an embodiment, the viral vector has increased efficiency of fusion of viral vector and target cell membrane. For example, fusion proteins such as fusion-competent hemagglutin (HA) can be incorporated to increase viral uptake into cells. In an embodiment, the viral vector has the ability of nuclear localization. For example, certain viruses that require the breakdown of the cell wall (during cell division) will not infect non-diving cell. Incorporated nuclear localization peptides into the matrix proteins of the virus allow transduction into non-proliferating cells.

In an embodiment, the virus infects dividing cells. In an embodiment, the virus infects non-dividing cells. In an embodiment, the virus infects both dividing and non-dividing cells. In an embodiment, the virus can integrate into the host genome. In an embodiment, the virus is engineered to have reduced immunity, e.g., in human. In an embodiment, the virus is replication-competent. In an embodiment, the virus is replication-defective, e.g., having one or more coding regions for the genes necessary for additional rounds of virion replication and/or packaging replaced with other genes or deleted. In an embodiment, the virus causes transient expression of the Cas9 molecule and/or the gRNA molecule. In an embodiment, the virus causes long-lasting, e.g., at least 1 week, 2 weeks, 1 month, 2 months, 3 months, 6 months, 9 months, 1 year, 2 years, or permanent expression, of the Cas9 molecule and/or the gRNA molecule. The packaging capacity of the viruses may vary, e.g., from at least about 4 kb to at least about 30 kb, e.g., at least about 5 kb, 10 kb, 15 kb, 20 kb, 25 kb, 30 kb, 35 kb, 40 kb, 45 kb, or 50 kb.

In an embodiment, the Cas9- and/or gRNA-encoding DNA is delivered by a recombinant retrovirus. In an embodiment, the retrovirus (e.g., Moloney murine leukemia virus) comprises a reverse transcriptase, e.g., that allows integration into the host genome. In an embodiment, the retrovirus is replication-competent. In an embodiment, the retrovirus is replication-defective, e.g., having one of more coding regions for the genes necessary for additional rounds of virion replication and packaging replaced with other genes, or deleted.

In an embodiment, the Cas9- and/or gRNA-encoding DNA is delivered by a recombinant lentivirus. For example, the lentivirus is replication-defective, e.g., does not comprise one or more genes required for viral replication.

In an embodiment, the Cas9- and/or gRNA-encoding DNA is delivered by a recombinant adenovirus. In an embodiment, the adenovirus is engineered to have reduced immunity in human.

In an embodiment, the Cas9- and/or gRNA-encoding DNA is delivered by a recombinant AAV. In an embodiment, the AAV can incorporate its genome into that of a host cell, e.g., a target cell as described herein. In an embodiment, the AAV is a self-complementary adeno- associated virus (scAAV), e.g., a scAAV that packages both strands which anneal together to form double stranded DNA. AAV serotypes that may be used in the disclosed methods include, e.g., AAV1, AAV2, modified AAV2 (e.g., modifications at Y444F, Y500F, Y730F and/or S662V), AAV3, modified AAV3 (e.g., modifications at Y705F, Y731F and/or T492V), AAV4, AAV5, AAV6, modified AAV6 (e.g., modifications at S663V and/or T492V), AAV8, AAV 8.2, AAV9, AAV rh 10, and pseudotyped AAV, such as AAV2/8, AAV2/5 and AAV2/6 can also be used in the disclosed methods.

In an embodiment, the Cas9- and/or gRNA-encoding DNA is delivered by a hybrid virus, e.g., a hybrid of one or more of the viruses described herein.

A packaging cell is used to form a virus particle that is capable of infecting a host or target cell. Such a cell includes a 293 cell, which can package adenovirus, and a ψ2 cell or a PA317 cell, which can package retrovirus. A viral vector used in gene therapy is usually generated by a producer cell line that packages a nucleic acid vector into a viral particle. The vector typically contains the minimal viral sequences required for packaging and subsequent integration into a host or target cell (if applicable), with other viral sequences being replaced by an expression cassette encoding the protein to be expressed. For example, an AAV vector used in gene therapy typically only possesses inverted terminal repeat (ITR) sequences from the AAV genome which are required for packaging and gene expression in the host or target cell. The missing viral functions are supplied in trans by the packaging cell line. Henceforth, the viral DNA is packaged in a cell line, which contains a helper plasmid encoding the other AAV genes, namely rep and cap, but lacking ITR sequences. The cell line is also infected with adenovirus as a helper. The helper virus promotes replication of the AAV vector and expression of AAV genes from the helper plasmid. The helper plasmid is not packaged in significant amounts due to a lack of ITR sequences. Contamination with adenovirus can be reduced by, e.g., heat treatment to which adenovirus is more sensitive than AAV.

In an embodiment, the viral vector has the ability of cell type and/or tissue type recognition. For example, the viral vector can be pseudotyped with a different/alternative viral envelope glycoprotein; engineered with a cell type-specific receptor (e.g., geneticmodification of the viral envelope glycoproteins to incorporate targeting ligands such as a peptide ligand, a single chain antibodie, a growth factor); and/or engineered to have a molecular bridge with dual specificities with one end recognizing a viral glycoprotein and the other end recognizing a moiety of the target cell surface (e.g., ligand-receptor, monoclonal antibody, avidin-biotin and chemical conjugation).

In an embodiment, the viral vector achieves cell type specific expression. For example, a tissue-specific promoter can be constructed to restrict expression of the transgene (Cas 9 and gRNA) in only the target cell. The specificity of the vector can also be mediated by microRNA- dependent control of transgene expression. In an embodiment, the viral vector has increased efficiency of fusion of the viral vector and a target cell membrane. For example, a fusion protein such as fusion-competent hemagglutin (HA) can be incorporated to increase viral uptake into cells. In an embodiment, the viral vector has the ability of nuclear localization. For example, aviruse that requires the breakdown of the cell wall (during cell division) and therefore will not infect a non-diving cell can be altered to incorporate a nuclear localization peptide in the matrix protein of the virus thereby enabling the transduction of non-proliferating cells. In an embodiment, the Cas9- and/or gRNA-encoding DNA is delivered by a non- viral vector or non- vector based method (e.g., using naked DNA or DNA complexes). For example, the DNA can be delivered, e.g., by organically modified silica or silicate (Ormosil), electroporation, gene gun, sonoporation, magnetofection, lipid-mediated transfection, dendrimers, inorganic nanoparticles, calcium phosphates, or a combination thereof. In an embodiment, the DNA is delivered by an inorganic nanoparticle (e.g., attached to the payload to the surface of the nanoparticle).

Exemplary inorganic nanoparticles include, e.g., magnetic nanoparticles (e.g., Fe3Mn02), silica (e.g., can integrate multi-functionality, e.g., conjugate the outer surface of the nanoparticle with a positively charged polymer (e.g., polyethylenimine, polylysine, polyserine) which allows for attachment (e.g., conjugation or entrapment) of payload and internal magnetic component, mesaporous silica nanoparticles with a positive charged polymer loaded with chloroquine to enhance transfection of the non- viral vector in vitro, high density lipoproteins and gold nanoparticles, gold nanoparticles coated with payload which gets released when nanoparticles are exposed to increased temperature by exposure to near infrared light, gold, iron or silver nanoparticles with surface modified with polylysine or another charge polymer to capture the nucleic acid cargo. In an embodiment, the DNA is delivered by an organic nanoparticle (e.g., entrapment of the payload inside the nanoparticle). Exemplary organic nanoparticles include, e.g., SNALP liposomes that contain cationic lipids together with neutral helper lipids which are coated with polyethylene glycol (PEG) and protamine and nucleic acid complex coated with lipid coating.

In an embodiment, the delivery vehicle is a physical vehicle. In an embodiment, the vehicle is low density ultrasound. For example, microbubbles containing payload (e.g., made of biocompatible material such protein, surfactant, or biocompatible polymer or lipid shell) can be used and the microbubbles can be destructed by a focused ultrasound bean during microvascular transit. In an embodiment, the vehicle is electroporation. For example, naked nucleic acids or proteins can be delivered by electroporation, e.g., into cell suspensions or tissue environment, such as retina and embryonic tissue. In an embodiment, the vehicle is needle or jet injection. For example, naked nucleic acids or protein can be injected into, e.g., muscular, liver, skin, brain or heart tissue.

In an embodiment, the Cas9- and/or gRNA-encoding DNA is delivered by a combination of a vector and a non- vector based method. For example, a virosome comprises a liposome combined with an inactivated virus (e.g., HIV or influenza virus), which can result in more efficient gene transfer, e.g., in a respiratory epithelial cell than either a viral or a liposomal method alone.

In an embodiment, the delivery vehicle is a non- viral vector. In an embodiment, the non- viral vector is an inorganic nanoparticle (e.g., attached to the payload to the surface of the nanoparticle). Exemplary inorganic nanoparticles include, e.g., magnetic nanoparticles (e.g., Fe₃Mn0₂), or silica. The outer surface of the nanoparticle can be conjugated with a positively charged polymer (e.g., polyethylenimine, polylysine, polyserine) which allows for attachment (e.g., conjugation or entrapment) of payload. In an embodiment, the non-viral vector is an organic nanoparticle (e.g., entrapment of the payload inside the nanoparticle). Exemplary organic nanoparticles include, e.g., SNALP liposomes that contain cationic lipids together with neutral helper lipids which are coated with polyethylene glycol (PEG) and protamine and nucleic acid complex coated with lipid coating.

Exemplary lipids for gene transfer are shown in Table V-3.

Table V-3: Lipids Used for Gene Transfer

N-(3-Aminopropyl)-N,N-dimethyl-2,3-bis(dodecyloxy)- 1 - GAP-DLRIE Cationic propanaminium bromide

Cetyltrimethylammonium bromide CTAB Cationic

6-Lauroxyhexyl ornithinate LHON Cationic l-(2,3-Dioleoyloxypropyl)-2,4,6-trimethylpyridinium 20c Cationic

2,3-Dioleyloxy-N-[2(sperminecarboxamido-ethyl]-N,N-dimethyl- DOSPA Cationic 1 -propanaminium trifluoroacetate

l,2-Dioleyl-3-trimethylammonium-propane DOPA Cationic

N-(2-Hydroxyethyl)-N,N-dimethyl-2,3-bis(tetradecyloxy)-l- MDRIE Cationic propanaminium bromide

Dimyristooxypropyl dimethyl hydroxyethyl ammonium bromide DMRI Cationic

3P-[N-(N',N'-Dimethylaminoethane)-carbamoyl]cholesterol DC-Choi Cationic

Bis-guanidium-tren-cholesterol BGTC Cationic l,3-Diodeoxy-2-(6-carboxy-spermyl)-propylamide DOSPER Cationic

Dimethyloctadecylammonium bromide DDAB Cationic

Dioctadecylamidoglicylspermidin DSL Cationic rac- [ (2, 3 -Dioctadecyloxypropyl) (2-hydroxyethyl) ] - CLIP-1 Cationic dimethylammonium chloride

rac-[2(2,3-Dihexadecyloxypropyl- CLIP-6 Cationic oxymethyloxy)ethyl] trimethylammonium bromide

Ethyldimyristoylphosphatidylcholine EDMPC Cationic l,2-Distearyloxy-N,N-dimethyl-3-aminopropane DSDMA Cationic

1 ,2-Dimyristoyl-trimethylammonium propane DMTAP Cationic

0,0' -Dimyristyl-N-lysyl aspartate DMKE Cationic l,2-Distearoyl-sn-glycero-3-ethylphosphocholine DSEPC Cationic

N-Palmitoyl D-erythro-sphingosyl carbamoyl- spermine CCS Cationic

N-t-Butyl-N0-tetradecyl-3-tetradecylaminopropionamidine diC14-amidine Cationic

Octadecenolyoxy[ethyl-2-heptadecenyl-3 hydroxyethyl] DOTIM Cationic imidazolinium chloride

Nl-Cholesteryloxycarbonyl-3,7-diazanonane-l,9-diamine CD AN Cationic 2-(3-[Bis(3-amino-propyl)-amino]propylamino)-N- RPR209120 Cationic ditetradecylcarbamoylme-ethyl-acetamide

1 ,2-dilinoleyloxy-3- dimethylaminopropane DLinDMA Cationic

2,2-dilinoleyl-4-dimethylaminoethyl- [1,3]- dioxolane DLin-KC2- Cationic

DMA

dilinoleyl- methyl-4-dimethylaminobutyrate DLin-MC3- Cationic

DMA

Exemplary polymers for gene transfer are shown below in Table V-4.

Table V-4: Polymers Used for Gene Transfer

Polymer Abbreviation

Poly(ethylene)glycol PEG

Polyethylenimine PEI

Dithiobis(succinimidylpropionate) DSP

Dimethyl-3,3'-dithiobispropionimidate DTBP

Poly(ethylene imine)biscarbamate PEIC

Poly(L-lysine) PLL

Histidine modified PLL

Poly(N-vinylpyrrolidone) PVP

Poly(propylenimine) PPI

Poly(amidoamine) PAMAM

Poly(amidoethylenimine) SS-PAEI

Triethylenetetramine TETA

Poly ( β- aminoester)

Poly(4-hydroxy-L-proline ester) PHP

Poly(allylamine)

Poly(a-[4-aminobutyl]-L-glycolic acid) PAGA

Poly(D,L-lactic-co-glycolic acid) PLGA

Poly(N-ethyl-4-vinylpyridinium bromide) Poly (pho sphazene) s PPZ

Poly (pho sphoester) s PPE

Poly (pho sphoramidate) s PPA

Poly(N-2-hydroxypropylmethacrylamide) pHPMA

Poly (2-(dimethylamino)ethyl methacrylate) pDMAEMA

Poly(2-aminoethyl propylene phosphate) PPE-EA

Chitosan

Galactosylated chitosan

N-Dodacylated chitosan

Histone

Collagen

Dextran- spermine D-SPM

In an embodiment, the vehicle has targeting modifications to increase target cell uptake of nanoparticles and liposomes, e.g., cell specific antigens, monoclonal antibodies, single chain antibodies, aptamers, polymers, sugars, and cell penetrating peptides. In an embodiment, the vehicle uses fusogenic and endosome-destabilizing peptides/polymers. In an embodiment, the vehicle undergoes acid-triggered conformational changes (e.g., to accelerate endosomal escape of the cargo). In an embodiment, a stimuli-cleavable polymer is used, e.g., for release in a cellular compartment. For example, disulfide-based cationic polymers that are cleaved in the reducing cellular environment can be used.

In an embodiment, liposomes are used for delivery, e.g., to blood or bone marrow, e.g., as a way of targeting hematopoietic stem cells (HSCs) and progenitors. For example, long-term treatment can be enabled by direct delivery using liposomes for conditions where obtaining HSCs is difficult (e.g., HSCs are not stable or HSCs are rare). These conditions can include, e.g., sickle cell anemia, Fanconi anemia, and aplastic anemia. In an embodiment, liposomes are used for delivery to localized specific tissues, e.g., to liver or lung, via intravenous delivery or via localized injection to target organ or its blood flow. For example, long-term treatment can be enable to concentrate effect in that specific organ or tissue type. These conditions can include urea cycle disorders, alpha- 1-anti-trypsin or cystic fibrosis. In an embodiment, the delivery vehicle is a biological non-viral delivery vehicle. In an embodiment, the vehicle is an attenuated bacterium (e.g., naturally or artificially engineered to be invasive but attenuated to prevent pathogenesis and expressing the transgene (e.g., Listeria monocytogenes, certain Salmonella strains, Bifidobacterium longum, and modified Escherichia coli), bacteria having nutritional and tissue-specific tropism to target specific tissues, bacteria having modified surface proteins to alter target tissue specificity). In an embodiment, the vehicle is a genetically modified bacteriophage (e.g., engineered phages having large packaging capacity, less immunogenic, containing mammalian plasmid maintenance sequences and having incorporated targeting ligands). In an embodiment, the vehicle is a mammalian virus-like particle. For example, modified viral particles can be generated (e.g., by purification of the

"empty" particles followed by ex vivo assembly of the virus with the desired cargo). The vehicle can also be engineered to incorporate targeting ligands to alter target tissue specificity. In an embodiment, the vehicle is a biological liposome. For example, the biological liposome is a phospholipid-based particle derived from human cells (e.g., erythrocyte ghosts, which are red blood cells broken down into spherical structures derived from the subject (e.g., tissue targeting can be achieved by attachment of various tissue or cell-specific ligands), or secretory exosomes - subject (i.e., patient) derived membrane-bound nanovescicle (30 -100 nm) of endocytic origin (e.g., can be produced from various cell types and can therefore be taken up by cells without the need of for targeting ligands).

In an embodiment, delivery of Cas components by nanoparticles in the bone marrow is an in vivo approach to curing blood and immune diseases.

In an embodiment, the components of a Cas system, e.g., the Cas9 molecule component and the gRNA molecule component described herein is delivered by nucleofection. For example, Nucleofector™ (Lonza Cologne AG) is a transfection technology that can be used for delivery to primary cells and difficult- to-transfect cell lines. It is a non-viral method based on a combination of electrical parameters and cell-type specific solutions. It allows transfected nucleic acids to directly enter the nucleus (e.g., without relying on cell division for the transfer of nucleic acids into the nucleus), providing the ability to transfect non-dividing cells, such as neurons and resting blood cells. In an embodiment, nucleofection is used as an ex vivo delivery method. In an embodiment, the components of a Cas system, e.g., the Cas9 molecule component and the gRNA molecule component described herein is delivered by methods utilizing endogenous receptor-mediate transporters, e.g., antibody-based molecular Trojan Horses (ArmaGen). Such methods can allow for non-invasive delivery of therapeutics to locations that are otherwise difficult to reach, e.g., brain (e.g., to cross blood brain barrier (BBB), e.g., via endogenous receptor-mediated transport processes).

In an embodiment, one or more nucleic acid molecules (e.g., DNA molecules) other than the components of a Cas system, e.g., the Cas9 molecule component and/or the gRNA molecule component described herein, are delivered. In an embodiment, the nucleic acid molecule is delivered at the same time as one or more of the components of the Cas system are delivered. In an embodiment, the nucleic acid molecule is delivered before or after (e.g., less than about 30 minutes, 1 hour, 2 hours, 3 hours, 6 hours, 9 hours, 12 hours, 1 day, 2 days, 3 days, 1 week, 2 weeks, or 4 weeks) one or more of the components of the Cas system are delivered. In an embodiment, the nucleic acid molecule is delivered by a different means than one or more of the components of the Cas system, e.g., the Cas9 molecule component and/or the gRNA molecule component, are delivered. The nucleic acid molecule can be delivered by any of the delivery methods described herein. For example, the nucleic acid molecule can be delivered by a viral vector, e.g., an integration-deficient lentivirus, and the Cas9 molecule component and/or the gRNA molecule component can be delivered by electroporation, e.g., such that the toxicity caused by nucleic acids (e.g., DNAs) can be reduced. In an embodiment, the nucleic acid molecule encodes a therapeutic protein, e.g., a protein described herein. In an embodiment, the nucleic acid molecule encodes an RNA molecule, e.g., an RNA molecule described herein.

Delivery of RNA encoding a Cas9 molecule

RNA encoding Cas9 molecules (e.g., eaCas9 molecules, eiCas9 molecules or eiCas9 fusion proteins) and/or gRNA molecules, can be delivered into cells, e.g., target cells described herein, by art-known methods or as described herein. For example, Cas9-encoding and/or gRNA-encoding RNA can be delivered, e.g., by microinjection, electroporation, lipid-mediated transfection, peptide-mediated delivery, or a combination thereof. Delivery Cas9 molecule protein

Cas9 molecules (e.g., eaCas9 molecules, eiCas9 molecules or eiCas9 fusion proteins) can be delivered into cells by art-known methods or as described herein. For example, Cas9 protein molecules can be delivered, e.g., by microinjection, electroporation, lipid-mediated transfection, peptide-mediated delivery, or a combination thereof. Delivery can be accompanied by DNA encoding a gRNA or by a gRNA.

Route of Administration

Systemic modes of administration include oral and parenteral routes. Parenteral routes include, by way of example, intravenous, intrarterial, intraosseous, intramuscular, intradermal, subcutaneous, intranasal and intraperitoneal routes. Components administered systemically may be modified or formulated to target the components to a specific organ or cell type.

Local modes of administration include, by way of example, intrathecal,

intracerebro ventricular, intraparenchymal (e.g., localized intraparenchymal delivery to the striatum (e.g., into the caudate or into the putamen)), cerebral cortex, precentral gyrus, hippocampus (e.g., into the dentate gyrus or CA3 region), temporal cortex, amygdala, frontal cortex, thalamus, cerebellum, medulla, hypothalamus, tectum, tegmentum or substantia nigra intraocular, intraorbital, subconjuctival, intravitreal, subretinal or transscleral routes. In an embodiment, significantly smaller amounts of the components (compared with systemic approaches) may exert an effect when administered locally (for example, intraparenchymal or intravitreal) compared to when administered systemically (for example, intravenously). Local modes of administration can reduce or eliminate the incidence of potentially toxic side effects that may occur when therapeutically effective amounts of a component are administered systemically.

In an embodiment, components described herein are delivered by intraparenchymal injection into discrete regions of the brain, including, e.g., regions comprising medium spiny neurons, or regions comprising cortical neurons. Injections may be made directly into more than one region of the brain.

In an embodiment, components described herein are delivered by subretinally, e.g., by subretinal injection. Subretinal injections may be made directly into the macular, e.g., submacular injection. In an embodiment, components described herein are delivered by intravitreal injection. Intravitreal injection has a relatively low risk of retinal detachment risk. In an embodiment, a nanoparticle or viral vector, e.g., AAV vector, e.g., an AAV2 vector, e.g., a modified AAV2 vector, is delivered intravitreally.

In an embodiment, a nanoparticle or viral vector, e.g., AAV vector, delivery is via intraparenchymal injection.

Methods for administration of agents to the eye are known in the medical arts and can be used to administer components described herein. Exemplary methods include intraocular injection (e.g., retrobulbar, subretinal, submacular, intravitreal and intrachoridal), iontophoresis, eye drops, and intraocular implantation (e.g., intravitreal, sub-Tenons and sub-conjunctival).

Administration may be provided as a periodic bolus (for example, subretinally, intravenously or intravitreally) or as continuous infusion from an internal reservoir (for example, from an implant disposed at an intra- or extra-ocular location (see, U.S. Pat. Nos. 5,443,505 and 5,766,242)) or from an external reservoir (for example, from an intravenous bag). Components may be administered locally, for example, by continuous release from a sustained release drug delivery device immobilized to an inner wall of the eye or via targeted transscleral controlled release into the choroid (see, for example, PCT/USOO/00207, PCT/US02/14279, Ambati et al, (2000) INVEST. OPHTHALMOL. VIS. SCI. 41: 1181-1185, and Ambati et al, (2000) INVEST. OPHTHALMOL. VIS. SCI. 41: 1186-1191). A variety of devices suitable for administering components locally to the inside of the eye are known in the art. See, for example, U.S. Pat. Nos. 6,251,090, 6,299,895, 6,416,777, 6,413,540, and PCT/USOO/28187.

In addition, components may be formulated to permit release over a prolonged period of time. A release system can include a matrix of a biodegradable material or a material which releases the incorporated components by diffusion. The components can be homogeneously or heterogeneously distributed within the release system. A variety of release systems may be useful, however, the choice of the appropriate system will depend upon rate of release required by a particular application. Both non-degradable and degradable release systems can be used. Suitable release systems include polymers and polymeric matrices, non-polymeric matrices, or inorganic and organic excipients and diluents such as, but not limited to, calcium carbonate and sugar (for example, trehalose). Release systems may be natural or synthetic. However, synthetic release systems are preferred because generally they are more reliable, more reproducible and produce more defined release profiles. The release system material can be selected so that components having different molecular weights are released by diffusion through or degradation of the material.

Representative synthetic, biodegradable polymers include, for example: polyamides such as poly(amino acids) and poly(peptides); polyesters such as poly(lactic acid), poly(glycolic acid), poly(lactic-co-glycolic acid), and poly(caprolactone); poly(anhydrides); polyorthoesters;

polycarbonates; and chemical derivatives thereof (substitutions, additions of chemical groups, for example, alkyl, alkylene, hydroxylations, oxidations, and other modifications routinely made by those skilled in the art), copolymers and mixtures thereof. Representative synthetic, non- degradable polymers include, for example: polyethers such as poly(ethylene oxide),

poly(ethylene glycol), and poly(tetramethylene oxide); vinyl polymers-polyacrylates and polymethacrylates such as methyl, ethyl, other alkyl, hydroxyethyl methacrylate, acrylic and methacrylic acids, and others such as poly(vinyl alcohol), poly(vinyl pyrolidone), and poly(vinyl acetate); poly(urethanes); cellulose and its derivatives such as alkyl, hydroxyalkyl, ethers, esters, nitrocellulose, and various cellulose acetates; polysiloxanes; and any chemical derivatives thereof (substitutions, additions of chemical groups, for example, alkyl, alkylene, hydroxylations, oxidations, and other modifications routinely made by those skilled in the art), copolymers and mixtures thereof.

Poly(lactide-co-glycolide) microsphere can also be used for intraocular injection.

Typically the microspheres are composed of a polymer of lactic acid and glycolic acid, which are structured to form hollow spheres. The spheres can be approximately 15-30 microns in diameter and can be loaded with components described herein.

Bi-Modal or Differential Delivery of Components

Separate delivery of the components of a Cas system, e.g., the Cas9 molecule component and the gRNA molecule component, and more particularly, delivery of the components by differing modes, can enhance performance, e.g., by improving tissue specificity and safety.

In an embodiment, the Cas9 molecule and the gRNA molecule are delivered by different modes, or as sometimes referred to herein as differential modes. Different or differential modes, as used herein, refer modes of delivery that confer different pharmacodynamic or

pharmacokinetic properties on the subject component molecule, e.g., a Cas9 molecule, gRNA molecule, or template nucleic acid. For example, the modes of delivery can result in different tissue distribution, different half-life, or different temporal distribution, e.g., in a selected compartment, tissue, or organ.

Some modes of delivery, e.g., delivery by a nucleic acid vector that persists in a cell, or in progeny of a cell, e.g., by autonomous replication or insertion into cellular nucleic acid, result in more persistent expression of and presence of a component. Examples include viral, e.g., adeno associated virus or lentivirus, delivery.

By way of example, the components, e.g., a Cas9 molecule and a gRNA molecule, can be delivered by modes that differ in terms of resulting half life or persistent of the delivered component the body, or in a particular compartment, tissue or organ. In an embodiment, a gRNA molecule can be delivered by such modes. The Cas9 molecule component can be delivered by a mode which results in less persistence or less exposure of its to the body or a particular compartment or tissue or organ.

More generally, in an embodiment, a first mode of delivery is used to deliver a first component and a second mode of delivery is used to deliver a second component. The first mode of delivery confers a first pharmacodynamic or pharmacokinetic property. The first pharmacodynamic property can be, e.g., distribution, persistence, or exposure, of the component, or of a nucleic acid that encodes the component, in the body, a compartment, tissue or organ.

The second mode of delivery confers a second pharmacodynamic or pharmacokinetic property. The second pharmacodynamic property can be, e.g., distribution, persistence, or exposure, of the component, or of a nucleic acid that encodes the component, in the body, a compartment, tissue or organ.

In an embodiment, the first pharmacodynamic or pharmacokinetic property, e.g., distribution, persistence or exposure, is more limited than the second pharmacodynamic or pharmacokinetic property.

In an embodiment, the first mode of delivery is selected to optimize, e.g., minimize, a pharmacodynamic or pharmacokinetic property, e.g., distribution, persistence or exposure.

In an embodiment, the second mode of delivery is selected to optimize, e.g., maximize, a pharmacodynamic or pharmcokinetic property, e.g., distribution, persistence or exposure. In an embodiment, the first mode of delivery comprises the use of a relatively persistent element, e.g., a nucleic acid, e.g., a plasmid or viral vector, e.g., an AAV or lentivirus. As such vectors are relatively persistent product transcribed from them would be relatively persistent.

In an embodiment, the second mode of delivery comprises a relatively transient element, e.g., an RNA or protein.

In an embodiment, the first component comprises gRNA, and the delivery mode is relatively persistent, e.g., the gRNA is transcribed from a plasmid or viral vector, e.g., an AAV or lentivirus. Transcription of these genes would be of little physiological consequence because the genes do not encode for a protein product, and the gRNAs are incapable of acting in isolation. The second component, a Cas9 molecule, is delivered in a transient manner, for example as mRNA or as protein, ensuring that the full Cas9 molecule/gRNA molecule complex is only present and active for a short period of time.

Furthermore, the components can be delivered in different molecular form or with different delivery vectors that complement one another to enhance safety and tissue specificity.

Use of differential delivery modes can enhance performance, safety and efficacy. For example, the likelihood of an eventual off-target modification can be reduced. Delivery of immunogenic components, e.g., Cas9 molecules, by less persistent modes can reduce

immunogenicity, as peptides from the bacterially-derived Cas enzyme are displayed on the surface of the cell by MHC molecules. A two-part delivery system can alleviate these drawbacks.

Differential delivery modes can be used to deliver components to different, but overlapping target regions. The formation active complex is minimized outside the overlap of the target regions. Thus, in an embodiment, a first component, e.g., a gRNA molecule is delivered by a first delivery mode that results in a first spatial, e.g., tissue, distribution. A second component, e.g., a Cas9 molecule is delivered by a second delivery mode that results in a second spatial, e.g., tissue, distribution. In an embodiment, the first mode comprises a first element selected from a liposome, nanoparticle, e.g., polymeric nanoparticle, and a nucleic acid, e.g., viral vector. The second mode comprises a second element selected from the group. In an embodiment, the first mode of delivery comprises a first targeting element, e.g., a cell specific receptor or an antibody, and the second mode of delivery does not include that element. In an embodiment, the second mode of delivery comprises a second targeting element, e.g., a second cell specific receptor or second antibody. When the Cas9 molecule is delivered in a virus delivery vector, a liposome, or polymeric nanoparticle, there is the potential for delivery to and therapeutic activity in multiple tissues, when it may be desirable to only target a single tissue. A two-part delivery system can resolve this challenge and enhance tissue specificity. If the gRNA molecule and the Cas9 molecule are packaged in separated delivery vehicles with distinct but overlapping tissue tropism, the fully functional complex is only be formed in the tissue that is targeted by both vectors.

VI. PAYLOADS

Cas9 molecules, typically eiCas9 molecules and gRNA molecules, e.g., an eiCas9 molecule/gRNA molecule complex, can be used to deliver a wide variety of payloads. In an embodiment, the payload is delivered to target nucleic acids or to chromatin, or other components, near or associated with a target nucleic acid.

While not wishing to be bound by theory, it is believed that the sequence specificity of the gRNA molecule of an eiCas9 molecule/gRNA molecule complex contributes to a specific interaction with the target sequence, thereby effecting the delivery of a payload associated with, e.g., covalently or noncovalently coupled to, the Cas9 molecule/gRNA molecule complex.

In an embodiment, the payload is covalently or non-covalently coupled to a Cas9, e.g., an eiCas9 molecule. In an embodiment, the payload is covalently or non-covalently coupled to a gRNA molecule. In an embodiment, the payload is linked to a Cas9 molecule, or gRNA molecule, by a linker, e.g., a linker which comprises a bond cleavable under physiological conditions. In an embodiment the bond is not cleavable or is only poorly cleavable, under physiological conditions. In an embodiment, "covalently coupled" means as part of a fusion protein containing a Cas9 molecule.

Delivery of Multiple Payloads

In an embodiment, a first payload molecule is delivered by a first Cas9 molecule and a second payload molecule is delivered by a second Cas9 molecule. In an embodiment, the first and second payloads are the same. In an embodiment, first and second Cas9 molecules are the same, e.g. are from the same species, have the same PAM, and/or have the same sequence. In an embodiment, first and second Cas9 molecules are different, e.g. are from different species, have the different PAMs, and/or have different sequences. Examples of configurations are provided in Table VI-1. Typically the Cas9 molecules of Table VI-1 are eiCas9 molecules. In an embodiment, a Cas9 molecule is selected such that payload delivery and cleavage are both effected. In an embodiment, multiple payloads, e.g., two payloads, is delivered with a single Cas9 molecule. Table VI- 1: Configurations for delivery of payloads by more than one Cas9

molecule/gRNA molecule complex

In an embodiment, two different drugs are delivered. In an embodiment, a first payload, e.g., a drug, coupled by a first linker to a first Cas9 molecule and a second payload, e.g., a drug, coupled by a second linker to a second Cas9 molecule are delivered. In an embodiment, the first and second payloads are the same, and, in an embodiment, are coupled to the respective Cas9 molecule by different linkers, e.g., having different release kinetics. In an embodiment, the first and second payloads are different, and, in an embodiment, are coupled to the respective Cas9 molecule by the same linker. In an embodiment, the first and second payload interact. E.g., the first and second payloads form a complex, e.g., a dimeric or multimeric complex, e.g., a dimeric protein. In an embodiment, the first payload can activate the second payload, e.g., the first payload can modify, e.g., cleave or phosphorylate, the second payload. In an embodiment the first payload interacts with the second payload to modify, e.g., increase or decrease, an activity of the second payload.

A payload can be delivered in vitro, ex vivo, or in vivo.

Classes of Payloads

A payload can comprise a large molecule or biologies (e.g., antibody molecules), a fusion protein, an amino acid sequence fused, as a fusion partner, to a Cas9 molecule, e.g., an eiCas9 molecule, an enzyme, a small molecules (e.g., HDAC and other chromatin modifiers/inhibitors, exon skipping molecules, transcription inhibitors), a microsatellite extension inhibitor, a carbohydrate, and DNA degraders (e.g., in an infectious disease or "foreign" DNA setting), a nucleic acid, e.g., a DNA, RNA, mRNA, siRNA, RNAi, or an antisense oligonucleotide. Table VI-2 provides exemplary classes of payloads.

Table VI-2

Exemplary Classes of Payloads

Large Molecules

Small Molecules

Polymers

Biologies

Proteins and polypeptides, e.g., antibodies,

enzymes, structural peptides, ligands, receptors,

fusion proteins, fusion partners (as a fusion protein

with a Cas9, e.g., and eiCas9) Carbohydrates

HDAC and other chromatin modifiers/inhibitors

Exon skipping molecules,

Transcription inhibitors

Microsatellite extension inhibitors

Entities that degrade DNA

Large Molecules

In an embodiment a payload comprises a polymer, e.g., a biological polymer, e.g., a protein, nucleic acid, or carbohydrate.

In an embodiment the payload comprises a protein, biologic, or other large molecule (i.e., a molecule having a molecular weight of at least, 3, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 kD). In an embodiment a payload comprises a polymer, e.g., a biological polymer, e.g., a protein, nucleic acid, or carbohydrate. The polymer can be a naturally occurring or non-naturally occurring polymer. In an embodiment, the payload is a natural product. For example, the natural product can be a large molecule or a small molecule.

Polypeptides, Proteins

In an embodiment the payload comprises a protein or polypeptide, e.g., a protein or polypeptide covalently or non-covalently coupled to a Cas9 molecule.

In an embodiment, the protein or polypeptide is dimeric or multimeric, and each subunit is delivered by a Cas9 molecule. In an embodiment, a first protein and second protein are delivered by one or more Cas9 molecules, e.g., each by a separate Cas9 molecule or both by the same Cas9 molecule.

In an embodiment, the protein or polypeptide is linked to a Cas9 molecule by a linker, e.g., a linker which comprises a bond cleavable under physiological conditions. In an

embodiment, a linker is a linker from Section XI herein. In an embodiment, the bond is not cleavable under physiological conditions. Specific Binding Ligands, Antibodies

In an embodiment the payload comprises a ligand, e.g., a protein, having specific affinity for a counter ligand. In an embodiment, the ligand can be a receptor (or the ligand for a receptor), or an antibody.

In an embodiment a payload comprises an antibody molecule. Exemplary antibody molecules include, e.g., proteins or polypeptides that include at least one immunoglobulin variable domain. For example, an antibody can include a heavy (H) chain variable region (abbreviated herein as VH), and a light (L) chain variable region (abbreviated herein as VL). In another example, an antibody includes two heavy (H) chain variable regions and two light (L) chain variable regions. The term "antibody" encompasses antigen-binding fragments of antibodies (e.g., single chain antibodies, Fab and sFab fragments, F(ab')2, Fd fragments, Fv fragments, scFv, and domain antibodies (dAb) fragments (de Wildt et al., EUR J IMMUNOL. 1996; 26(3):629-639)). For example, antigen-binding fragments of antibodies can include, e.g., (i) a Fab fragment, a monovalent fragment consisting of the VL, VH, CL and CHI domains; (ii) a F(ab')₂ fragment, a bivalent fragment including two Fab fragments linked by a disulfide bridge at the hinge region; (iii) a Fd fragment consisting of the VH and CHI domains; (iv) a Fv fragment consisting of the VL and VH domains of a single arm of an antibody, (v) a dAb fragment (Ward et al, (1989) NATURE 341 :544-546), which consists of a VH domain; and (vi) an isolated complementarity determining region (CDR) that retains functionality. Furthermore, although the two domains of the Fv fragment, VL and VH, are coded for by separate genes, they can be joined, using recombinant methods, by a synthetic linker that enables them to be made as a single protein chain in which the VL and VH regions pair to form monovalent molecules known as single chain Fv (scFv). See, e.g., US patents 5,260,203, 4,946,778, and 4,881 , 175; Bird et al, ( 1988) SCIENCE 242:423-426; and Huston et al, ( 1988) PROC. NATL. ACAD. SCI. USA 85:5879- 5883. An antibody can have the structural features of IgA, IgG, IgE, IgD, IgM (as well as subtypes thereof). Antibodies may be from any source, but primate (human and non-human primate) and primatized are preferred. In an embodiment, the antibody is a human antibody or humanized antibody.

In an embodiment, the antibody molecule is a single-domain antibody (e.g., an sdAb, e.g., a nanobody), e.g., an antibody fragment consisting of a single monomeric variable antibody domain. In an embodiment, the molecular weight of the single-domain antibody is about 12-15 kDa. For example, the single-domain antibody can be engineered from heavy-chain antibodies found in camelids (e.g., VHH fragments). Cartilaginous fishes also have heavy-chain antibodies (IgNAR, 'immunoglobulin new antigen receptor'), from which single-domain antibodies called VNAR fragments can be obtained. An alternative approach is to split the dimeric variable domains from common immunoglobulin G (IgG), e.g., from humans or mice, into monomers. Single-domain antibodies derived from either heavy or light chain can be obtained to bind specifically to target epitopes. For example, a single-domain antibody can be a peptide chain of about 110 amino acids long, comprising one variable domain (VH) of a heavy-chain antibody, or of a common IgG.

Single-domain antibodies can have similar affinity to antigens as whole antibodies. They can also be more heat-resistant and/or stable towards detergents and high concentrations of urea. Those, e.g., derived from camelid and fish antibodies can be less lipophilic and more soluble in water, owing to their complementarity determining region 3 (CDR3), which forms an extended loop covering the lipophilic site that normally binds to a light chain. In an embodiment, the single-domain antibody does not show complement system triggered cytotoxicity, e.g., because they lack an Fc region. Single-domain antibodies, e.g., camelid and fish derived sdAbs, can bind to hidden antigens that may not be accessible to whole antibodies, for example to the active sites of enzymes. This property can result from their extended CDR3 loop, which is able to penetrate such sites.

A single-domain antibody can be obtained by immunization of, e.g., dromedaries, camels, llamas, alpacas or sharks with the desired antigen and subsequent isolation of the mRNA coding for heavy-chain antibodies. By reverse transcription and polymerase chain reaction, a gene library of single-domain antibodies containing several million clones is produced.

Screening techniques like phage display and ribosome display help to identify the clones binding the antigen.

A different method uses gene libraries from animals that have not been immunized beforehand. Such naive libraries usually contain only antibodies with low affinity to the desired antigen, making it necessary to apply affinity maturation by random mutagenesis as an additional step.

When the most potent clones have been identified, their DNA sequence can be optimized, for example to improve their stability towards enzymes. Another goal is humanization to prevent immunological reactions of the human organism against the antibody. The final step is the translation of the optimized single-domain antibody in E. coli, Saccharomyces cerevisiae or other suitable organisms.

Alternatively, single-domain antibodies can be made from common murine or human IgG with four chains. The process is similar, comprising gene libraries from immunized or naive donors and display techniques for identification of the most specific antigens. Monomerization is usually accomplished by replacing lipophilic by hydrophilic amino acids. If affinity can be retained, the single-domain antibodies can likewise be produced in E. coli, S. cerevisiae or other organisms.

In an embodiment, a payload comprises a transcription activator protein or domain, e.g., a

VP 16 protein or domain, or a transcription repressor protein or domain.

Fusion Proteins and Fusion Partners

In an embodiment the payload comprises a fusion protein. Exemplary fusion proteins include a first and second fusion partner, which can possess different functional properties or which can be derived from different proteins. In an embodiment, the fusion protein can comprise a first fusion partner that binds a nucleic acid and a second fusion partner that that comprises an enzymatic activity or that promotes or inhibits gene expression. In an embodiment, the payload itself is a fusion protein. In an embodiment, the payload is fused to a Cas9 molecule.

For example, the fusion protein can contain a segment that adds stability and/or deliverability to the fused protein. In an embodiment, the fusion protein can be a protein described herein (e.g., a receptor) fused to an immunoglobulin fragment (e.g., Fc fragment), transferring, or a plasma protein, e.g., albumin. The fusion protein can also contain a segment that adds toxicity to the fused protein (e.g. conveyed by toxins, enzymes or cytokines). Fusion proteins can also be used to enable delivery and/or targeting routes (e.g., by HIV-1 TAT protein). Other examples include, e.g., fusions that allow for mutivalency, such as streptavidin fusions, or fusions of two active components (e.g., with or without a cleavable linker in between).

In an embodiment, the protein or polypeptide is a fusion partner with a Cas9 molecule, e.g., an eiCas9 molecule. In an embodiment, a payload comprises fusion partner with a Cas9 molecule comprising a transcription activator protein or domain, e.g., a VP16 protein or domain, or a transcription repressor protein or domain. Enzymes

In an embodiment a payload comprises an enzyme. Exemplary enzymes include, e.g., oxidoreductases (e.g., catalyze oxidation/reduction reactions), transferases (e.g., transfer a functional group (e.g. a methyl or phosphate group)), hydrolases (e.g., catalyze the hydrolysis of various bonds), lyases (e.g., cleave various bonds by means other than hydrolysis and oxidation), isomerases (catalyze isomerization changes within a single molecule), and ligases (e.g., join two molecules with covalent bonds). In an embodiment an enzymes mediates or is associated with one or more functions in the cell nucleus, e.g., DNA synthesis, transcription, epigenetic modification of DNA and histones, RNA post-transcriptional modification, cell cycle control, DNA damage repair, or genomic instability.

Small Molecules

In an embodiment a payload comprises a small molecule compounds.

In an embodiment a small molecule is a regulator of a biological process. For example, a small molecule can bind to a second molecule, e.g., biopolymer, e.g., a carbohydrate, protein, polypeptide, or a nucleic acid, and in an embodiment, alter one or more of the structure, distribution, activity, or function of the second molecule. In an embodiment, the size of the small molecule is on the order of 10^~9 m. In an embodiment, the molecular weight of the small molecule is, e.g., between 200 amu and 500 amu, between 300 amu and 700 amu, between 500 amu and 700 amu, between 700 amu and 900 amu, or between 500 amu and 900 amu.

Exemplary small molecules include histone deacetylase (HDAC) inhibitors (e.g., suberoylanilide hydroxamic acid (SAHA), or romidepsin), histone methyltransferase inhibitors (, DNA methyltransferase inhibitors (e.g., azacitidine (or 5-azacitidine), decitabine (or 5-aza-2'- deoxycytidine), or DNA replication inhibitors. Small molecules can also include, e.g., small nucleic acid molecules (1-4 bases depending upon the base, e.g., that would be under 2 kD) and peptides. Microsatellite extension inhibitors

In an embodiment a payload comprises a microsatellite extension inhibitor. In an embodiment, the microsatellite extension inhibitor is a DNA mismatch repair protein.

Exemplary DNA mismatch repair proteins that can be delivered by the molecules and methods described herein include, e.g., MSH2, MSH3, MSH6, MLH1, MLH3, PMS1, PMS2.

Signal generators, radionuclides, reporter molecules, diagnostic probes

In an embodiment a payload comprises a molecule that generates a signal. Such payloads are useful, e.g., in research, therapeutic (e.g., cancer therapy) and diagnostic applications. In an embodiment, the signal comprises: an electromagnetic emission, e.g., in the infrared, visible, or ultraviolet range; a particle, e.g., a product of radioactive decay, e.g., an alpha, beta, or gamma particle; a detectable substrate, e.g., a colored substrate; a reaction product, e.g., the product of an enzymatic reaction; or a ligand detectable by a specific binding agent, e.g., an antibody; or a dye. In an embodiment the signal comprises a fluorescent emission, e.g., by a fluorescent protein. Exemplary fluorescent proteins include, Blue/UV Proteins (e.g., TagBFP, mTagBFP, Azurite, EBFP2, mKalamal, Sirius, Sapphire, T-Sapphire), Cyan Proteins (e.g., ECFP, Cerulean, SCFP3A, mTurquoise, mTurquoise2, monomeric Midoriishi-Cyan, TagCFP, mTFPl), Green Proteins (e.g., EGFP, Emerald, Superfolder GFP, Monomeric Azami Green, TagGFP2, mUKG, mWasabi, Clover, mNeonGreen), Yellow Proteins (e.g., EYFP, Citrine, Venus, SYFP2, TagYFP), Orange Proteins (e.g., Monomeric Kusabira-Orange, ιηΚΟκ, mK02, mOrange, mOrange2), Red Proteins (mRaspberry, mCherry, mStrawberry, mTangerine, tdTomato, TagRFP, TagRFP-T, mApple, mRuby, mRuby2), Far- Red Proteins (e.g., mPlum, HcRed- Tandem, mKate2, mNeptune, NirFP, TagRFP657, IFP1.4, iRFP), Long Stokes Shift Proteins (e.g., mKeima Red, LSS-mKatel, LSS-mKate2, mBeRFP), Photoactivatible Proteins (e.g., PA- GFP, PAmCherryl, PATagRFP), Photoconvertible Proteins (e.g., Kaede (green), Kaede (red), KikGRl (green), KikGRl (red), PS-CFP2, mEos2 (green), mEos2 (red), mEos3.2 (green), mEos3.2 (red), PSmOrange), Photo switchable Proteins (e.g., Dronpa).

In an embodiment, a signal producing moiety is provided as the fusion partner of a Cas9 molecule, e.g., an eiCas9 molecule.

Signal generators or reporters, useful, e.g., for labelingr polypeptides include, but are not limited to, the following: radioisotopes or radionuclides (e.g., indium (^mIn), iodine (¹³¹I or ¹²⁵I), yttrium (^yuY), lutetium Γ u), actinium (^//3Ac), bismuth (^Z1/Bi or ^/1JBi), sulfur (^J3S), carbon

( 14 C), tritium ( 3 H), rhodium ( 188 Rh), technetium ( 99 mTc), praseodymium, or phosphorous ( 32 P) or a positron-emitting radionuclide, e.g., carbon-11 (^UC), potassium-40 (⁴⁰K), nitrogen-13 (¹³N), oxygen-15 (¹⁵0), fluorine-18 (¹⁸F), and iodine-121 (¹²¹I)), fluorescent labels (e.g., FITC, rhodamine, lanthanide phosphors), enzymatic labels (e.g., horseradish peroxidase, beta- galactosidase, luciferase, alkaline phosphatase), chemiluminescent, biotinyl groups (which can be detected by a marked avidin, e.g., a molecule containing a streptavidin moiety and a fluorescent marker or an enzymatic activity that can be detected by optical or calorimetric methods), and predetermined polypeptide epitopes recognized by a secondary reporter (e.g., leucine zipper pair sequences, binding sites for secondary antibodies, metal binding domains, epitope tags). In an embodiment, labels are attached by spacer arms of various lengths to reduce potential steric hindrance.

In an embodiment, a payload comprises a radionuclide. The radionuclide can be incorporated into the gRNA molecule, the Cas9 molecule, or into a payload molecule.

Exemplary radionuclides include, e.g., beta emitters, alpha emitters or gamma emitters. In an embodiment the radionuclide is iodine, e.g., 131 l or 125 I, yttrium, e.g., 90 Y, lutetium, e.g., 177 Lu,

Actinium, e.g., 225 Ac, bismuth, e.g., 212 Bi or 213 Bi), sulfur, e.g., 35 S), carbon, e.g., 14 C, tritium,

3 H), rhodium, e.g., 188 Rh, technetium, e.g., 99 Tc, praseodymium, or phosphorous, e.g., 32 P. Modulators of DNA and Chromatin Structure

In an embodiment, a payload comprises an endogenous or exogenous modulator of DNA structure. A modulator, as is typical of payloads, can be delivered in vitro, ex vivo, or in vivo.

In an embodiment, the payload comprises a modulator of an epigenetic state or characteristic of DNA. In an embodiment an epigenetic state or characteristic can be altered to treat a disorder, or to influence the developmental or other state of a cell.

In an embodiment, the epigenetic state or characteristic comprises DNA methylation. For example, the payloads described herein can modulate the addition of methyl groups to DNA, e.g., to convert cytosine to 5-methylcytosine, e.g., at CpG sites.

Aberrant DNA methylation patterns (e.g., hypermethylation and hypomethylation compared to normal tissue) are associated with various diseases and conditions, e.g., cancer. The modulators described herein can be used to reactivate transcriptionally silenced genes or to inhibit transcriptionally hyperactive genes, e.g., to treat diseases, e.g., cancer.

DNA methylation can affect gene transcription. Genes with high levels of 5- methylcytosine, e.g., in their promoter region, can be transcriptionally less active or silent. Thus, methods described herein can be used to target and suppress transcriptional activity, e.g., of genes described herein.

In an embodiment, the modulator promotes maintenance of DNA methylation. For example, the modulators can have DNA methyltransferase (DNMT) activity or modulate DNMT activity, e.g., to maintain DNA methylation or reduce passive DNA demethylation, e.g., after DNA replication.

In an embodiment, the modulator promotes de novo DNA methylation. For example, the modulators described herein can have de novo DNA methyltransferase (DNMT) (e.g., DNMT3a, DNMT3b, DNMT3L) activity or modulate de novo DNMT (e.g., DNMT3a, DNMT3b,

DNMT3L) activity, e.g., to produce DNA methylation patterns, e.g., early in development.

Epigenetic changes in DNA (e.g., methylation), can be evaluated by art-known methods or as described herein. Exemplary methods for detecting DNA methylation include, e.g., Methylation-Specific PCR (MSP), whole genome bisulfite sequencing (BS-Seq), HELP (Hpall tiny fragment Enrichment by Ligation-mediated PCR) assay, ChlP-on-chip assays, restriction landmark genomic scanning, Methylated DNA immunoprecipitation (MeDIP), pyrosequencing of bisulfite treated DNA, molecular break light assay for DNA adenine methyltransferase activity, methyl sensitive Southern Blotting, separation of native DNA into methylated and unmethylated fractions using MethylCpG Binding Proteins (MBPs) and fusion proteins containing just the Methyl Binding Domain (MBD).

In an embodiment, the modulator cleaves DNA. For example, a modulator can catalyze the hydrolytic cleavage of phosphodiester linkages in the DNA backbone. In an embodiment, the modulator (e.g., DNase I) cleaves DNA preferentially at phosphodiester linkages adjacent to a pyrimidine nucleotide, yielding 5'-phosphate-terminated polynucleotides with a free hydroxyl group on position 3'. In an embodiment, the modulator (e.g., DNase II) hydrolyzes

deoxyribonucleotide linkages in DNA, yielding products with 3'-phosphates. In an embodiment, the modulator comprises endodeoxyribonuclease activity. In an embodiment, the modulator comprises exodeoxyribonuclease activity (e.g., having 3' to 5' or 5' to 3' exodeoxyribonuclease activity). In an embodiment, the modulator recognizes a specific DNA sequence (e.g., a restriction enzyme). In an embodiment, the modulator does not cleave DNA in a sequence- specific manner. A modulator can cleave single- stranded DNA (e.g., having nickase activity), double- stranded DNA, or both.

In an embodiment, modulator affects, e.g., alters or preserves, tertiary or quaternary DNA structure. For example, the modulators described herein can modulate tertiary structure, e.g., handedness (right or left), length of the helix turn, number of base pairs per turn, and/or difference in size between the major and minor grooves. In an embodiment, the modulator mediates the formation of B-DNA, A-DNA, and/or Z-DNA. The modulators described herein can also modulate quaternary structure, e.g., the interaction of DNA with other molecules (DNA or non-DNA molecules, e.g., histones), e.g., in the form of chromatin. In an embodiment, the modulator that mediate or modify tertiary or quaternary DNA structure comprises DNA helicases activity or modulates DNA helicase activity.

In an embodiment, the modulator promotes or inhibits DNA damage response and/or repair. For example, a modulator can promote one or more DNA damage response and repair mechanisms, e.g., direct reversal, base excision repair (BER), nucleotide excision repair (NER) (e.g., global genomic repair (GG-NER), transcription-coupled repair (TC-NER)), mismatch repair (MMR), non-homologous end joining (NHEJ), microhomology-mediated end joining (MMEJ), homologous recombination, and/or translesion synthesis (TLS). In an embodiment, a modulator promotes the step of damage recognition. In an embodiment, a modulator promotes the step of DNA repair.

Aberrant DNA damage repair is associated with various diseases and conditions, e.g., aging, hereditary DNA repair disorders, and cancer. For example, DNA repair gene mutations that can increase cancer risk include, e.g., BRCA1 and BRCA2 (e.g., involved in homologous recombination repair (HRR) of double-strand breaks and daughter strand gaps, e.g., in breast and ovarian cancer); ATM (e.g., different mutations reduce HRR, single strand annealing (SSA), NHEJ or homology-directed DSBR (HDR), e.g., in leukemia, lymphoma, and breast cancer), NBS (e.g., involved in NHEJ, e.g., in lymphoid malignancies); MRE11 (e.g., involved in HRR, e.g., in breast cancer); BLM (e.g., involved in HRR, e.g., in leukemia, lymphoma, colon, breast, skin, auditory canal, tongue, esophagus, stomach, tonsil, larynx, lung, and uterus cancer); WRN (e.g., involved in HRR, NHEJ, long-patch BER, e.g., in soft tissue sarcomas, colorectal, skin, thyroid, and pancreatic cancer); RECQ4 (RECQL4) (e.g., involved in HRR, e.g., causing Rothmund- Thomson syndrome (RTS), RAPADILINO syndrome or Bailer Gerold syndrome, cutaneous carcinomas, including basal cell carcinoma, squamous cell carcinoma, and Bowen's disease); FANCA, FANCB, FANCC, FANCDl, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCJ, FANCL, FANCM, and FANCN (e.g., involved in HRR and TLS, e.g., in leukemia, liver tumors, solid tumors in many locations), XPC and XPE(DDB2) (e.g., involved in

NER(GGR type), e.g., in skin cancer (melanoma and non-melanoma)); XPA, XPB, XPD, XPF, and XPG (e.g., involved in NER (both GGR type and TCR type), e.g., in skin cancer (melanoma and non-melanoma) and central nervous system); XPV(POLH) (e.g., involved in TLS, e.g., in skin cancer (melanoma and non-melanoma)); hMSH2, hMSH6, hMLHl, and hPMS2 (involved in MMR, e.g., in colorectal, endometrial and ovarian cancer); MUTYH (e.g., involved in BER of A mispaired with 80H-dG, as well as mispairs with G, FapydG and C, e.g., in colon cancer) Modulators can be used to treat a disease or condition associated with aberrant DNA damage repair, e.g., by modulating one or more DNA damage repair mechanisms described herein.

In an embodiment, the modulator is selected from, or modulates, one or more proteins involved in direct reversal, e.g., methyl guanine methyl transferase (MGMT).

In an embodiment, the modulator is selected from, or modulates, one or more proteins involved in BER, e.g., DNA glycosylase, AP endonuclease, DNA polymerase, DNA ligase.

In an embodiment, the modulator is selected from, or modulates, one or more proteins involved in GG-NER, e.g., XPC, HR23b, CAK, TFIIH, XPA, RPA, XPG, XPF, ERCCl, TFIIH, PCNA, RFC, ADN Pol, and Ligase I.

In an embodiment, the modulator is selected from ,or modulates, one or more proteins involved in TC-NER, e.g., CSB, XPA, RPA, XPG, XPF, ERCCl, CSA-CNS, TFIIH, CAK, PCNA, RFC, Ligase I, and RNA Polymerase II.

In an embodiment, the modulator is selected from, or modulates, one or more DNA mismatch repair proteins.

In an embodiment, the modulator is selected from, or modulates, one or more proteins involved in NHEJ, e.g., Ku70/80, DNA-PKcs, DNA Ligase IV, XRCC4, XLF, Artemis, DNA polymerase mu, DNA polymerase lambda, PNKP, Aprataxin, and APLF. In an embodiment, the modulator is selected from, or modulates, one or more proteins involved in homologous recombination, e.g., as described herein.

In an embodiment, the modulator is selected from, or modulates, one or more proteins involved in TLS, e.g., DNA polymerase eta, iota, kappa, zeta, and PCNA.

In an embodiment, a modulator can modulate global response to DNA damage, e.g.,

DNA damage checkpoints and/or transcriptional responses to DNA damage. For example, DNA damage checkpoints can occur at the Gl/S and G2/M boundaries. An intra-S checkpoint can also exist. Checkpoint activation can be modulated by two master kinases, ATM and ATR. ATM can respond to DNA double- strand breaks and disruptions in chromatin structure and ATR can respond to stalled replication forks. These kinases can phosphorylate downstream targets in a signal transduction cascade, e.g., leading to cell cycle arrest. A class of checkpoint mediator proteins (e.g., BRCA1, MDC1, and 53BP1), which transmit the checkpoint activation signal to downstream proteins, can be modulated. Exemplary downstream proteins that can be modulated include, e.g., p53, p21, and cyclin/cyclin-dependent kinase complexes.

In an embodiment, the modulator modulates nuclear DNA damage response and repair.

In an embodiment, the modulator modulates mitochondrial DNA damage response and repair.

In an embodiment, the modulator promotes or inhibits DNA replication. For example, a modulator can promote or inhibit one or more stages of DNA replication, e.g., initiation (e.g., assembly of pre-replicative complex and/or initiation complex), elongation (e.g., formation of replication fork), and termination (e.g., formation of replication fork barrier). In an embodiment, the modulator is selected from, or modulates, one or more proteins involved in initiation, e.g., the origin recognition complex (ORC), CDC6, CDT1, minichromosome maintenance proteins (e.g., MCM2, MCM3, MCM4, MCM5, MCM6, MCM7, and MCM10), CDC45, CDK, DDK,

CDC 101, CDC 102, CDC 103, and CDC 105. In an embodiment, the modulator is selected from, or modulates ,one or more proteins involved in elongation, e.g., DNA helicases, DNA

polymerase, PCNA, CDC45-MCM-GINS helicase complex, and Replication Factor C complex.

In an embodiment, the modulator is selected, from or modulates, one or more proteins involved in termination, e.g., type II topoisomerase and telomerase. In an embodiment, the modulator is selected from, or modulates, one or more replication checkpoint proteins, e.g., ATM, ATR, ATRIP, TOPBP1, RAD9, HUS1, Radl, and CHK1. In an embodiment, the payload comprises a modulator of nuclear DNA replication. In an embodiment, the modulator promotes or inhibits mitochondrial DNA replication.

Defects in DNA replication can be associated with various diseases and conditions, e.g., cancer and neurological diseases (e.g., Alzheimer's disease). Defects in mitochondrial DNA replication can also be associated with diseases and conditions, e.g., mtDNA depletion syndromes (e.g., Alpers or early infantile hepatocerebral syndromes) and mtDNA deletion disorders (e.g., progressive external ophthalmoplegia (PEO), ataxia-neuropathy, or mitochondrial neurogastrointestinal encephalomyopathy (MNGIE)). A modulator can be used to treat a disease or condition associated with aberrant DNA replication, e.g., by modulating DNA replication as described herein.

Exemplary endogenous or exogenous modulators of DNA structure are described herein, e.g., in Table VI-3.

Table VI-3

DNAH14 dynein, axonemal, heavy chain 14

DNAH17 dynein, axonemal, heavy chain 17

DNAH17-AS1 DNAH17 antisense RNA 1

DNAI1 dynein, axonemal, intermediate chain 1

DNAI2 dynein, axonemal, intermediate chain 2

DNAJB8-AS1 DNAJB8 antisense RNA 1

DNAJC3-AS1 DNAJC3 antisense RNA 1 (head to head)

DNAJC9- AS 1 DNAJC9 antisense RNA 1

DNAJC25- DNAJC25-GNG10 readthrough

GNG10

DNAJC27-AS1 DNAJC27 antisense RNA 1

DNAL1 dynein, axonemal, light chain 1

DNAL4 dynein, axonemal, light chain 4

DNALI1 dynein, axonemal, light intermediate chain 1

DNASE1 deoxyribonuclease I

DNASE1L1 deoxyribonuclease I-like 1

DNASE1L2 deoxyribonuclease I-like 2

DNASE1L3 deoxyribonuclease I-like 3

DNASE2 deoxyribonuclease II, lysosomal

DNASE2B deoxyribonuclease II beta

CD226 CD226 molecule

FAM120A family with sequence similarity 120 A

GAK cyclin G associated kinase

GCFC2 GC-rich sequence DNA-binding factor 2

MCM10 minichromosome maintenance complex component 10

PRKDC protein kinase, DN A- activated, catalytic polypeptide

SACS spastic ataxia of Charlevoix-Saguenay (sacsin)

SCNN1D sodium channel, non- voltage-gated 1, delta subunit

SPATS2L spermatogenesis associated, serine-rich 2-like

MT7SDNA mitochondrially encoded 7S DNA DCLRE1A DNA cross-link repair 1A

DCLRE1B DNA cross-link repair IB

DCLRE1C DNA cross-link repair 1C

DDIT3 DNA-damage-inducible transcript 3

DDIT4 DNA-damage-inducible transcript 4

DDIT4L DNA-damage-inducible transcript 4-like

DFFA DNA fragmentation factor, 45kDa, alpha polypeptide

DFFB DNA fragmentation factor, 40kDa, beta polypeptide (caspase-activated

DNase)

DMAP1 DNA methyltransferase 1 associated protein 1

DMC1 DNA meiotic recombinase 1

DNMT1 DNA (cytosine-5-)-methyltransferase 1

DNMT3A DNA (cytosine-5-)-methyltransferase 3 alpha

DNMT3B DNA (cytosine-5-)-methyltransferase 3 beta

DNMT3L DNA (cytosine-5-)-methyltransferase 3-like

DNTT DNA nucleotidylexotransferase

DRAM1 DNA-damage regulated autophagy modulator 1

DRAM2 DNA-damage regulated autophagy modulator 2

DSCC1 DNA replication and sister chromatid cohesion 1

ZBP1 Z-DNA binding protein 1

SON SON DNA binding protein

TARDBP TAR DNA binding protein

BMF Bcl2 modifying factor

CENPBD1 CENPB DNA-binding domains containing 1

UNG uracil-DNA glycosylase

PDRG1 p53 and DNA-damage regulated 1

TDG thymine-DNA glycosylase

TDP1 tyrosyl-DNA phosphodiesterase 1

TDP2 tyrosyl-DNA phosphodiesterase 2

AHDC1 AT hook, DNA binding motif, containing 1 GMNN geminin, DNA replication inhibitor

PRIM1 primase, DNA, polypeptide 1 (49kDa)

PRIM2 primase, DNA, polypeptide 2 (58kDa)

HELB helicase (DNA) B

LIG1 ligase I, DNA, ATP-dependent

SUMF1 sulfatase modifying factor 1

SUMF2 sulfatase modifying factor 2

LIG4 ligase IV, DNA, ATP-dependent

LIG3 ligase III, DNA, ATP-dependent

MDC1 mediator of DNA-damage checkpoint 1

MMS22L MMS22-like, DNA repair protein

POLA1 polymerase (DNA directed), alpha 1, catalytic subunit

POLA2 polymerase (DNA directed), alpha 2, accessory subunit

POLB polymerase (DNA directed), beta

POLD1 polymerase (DNA directed), delta 1, catalytic subunit

POLD2 polymerase (DNA directed), delta 2, accessory subunit

POLD3 polymerase (DNA-directed), delta 3, accessory subunit

POLD4 polymerase (DNA-directed), delta 4, accessory subunit

POLDIP2 polymerase (DNA-directed), delta interacting protein 2

POLDIP3 polymerase (DNA-directed), delta interacting protein 3

POLE polymerase (DNA directed), epsilon, catalytic subunit

POLE2 polymerase (DNA directed), epsilon 2, accessory subunit

POLE3 polymerase (DNA directed), epsilon 3, accessory subunit

POLE4 polymerase (DNA-directed), epsilon 4, accessory subunit

POLG polymerase (DNA directed), gamma

POLG2 polymerase (DNA directed), gamma 2, accessory subunit

POLH polymerase (DNA directed), eta

POLI polymerase (DNA directed) iota

POLK polymerase (DNA directed) kappa

POLL polymerase (DNA directed), lambda POLM polymerase (DNA directed), mu

POLN polymerase (DNA directed) nu

POLQ polymerase (DNA directed), theta

ID1 inhibitor of DNA binding 1, dominant negative helix-loop-helix protein

ID2 inhibitor of DNA binding 2, dominant negative helix-loop-helix protein

ID3 inhibitor of DNA binding 3, dominant negative helix-loop-helix protein

ID4 inhibitor of DNA binding 4, dominant negative helix-loop-helix protein

OGG1 8-oxoguanine DNA glycosylase

MSANTD1 Myb/SANT-like DNA-binding domain containing 1

MSANTD2 Myb/SANT-like DNA-binding domain containing 2

MSANTD3 Myb/SANT-like DNA-binding domain containing 3

MSANTD4 Myb/SANT-like DNA-binding domain containing 4 with coiled-coils

PIF1 PIF1 5'-to-3' DNA helicase

TONSL tonsoku-like, DNA repair protein

MPG N-methylpurine-DNA glycosylase

TOPI topoisomerase (DNA) I

TOP1MT topoisomerase (DNA) I, mitochondrial

TOP2A topoisomerase (DNA) II alpha 170kDa

TOP2B topoisomerase (DNA) II beta 180kDa

TOP3A topoisomerase (DNA) III alpha

TOP3B topoisomerase (DNA) III beta

TOPBP1 topoisomerase (DNA) II binding protein 1

DDB1 damage- specific DNA binding protein 1, 127kDa

DDB2 damage- specific DNA binding protein 2, 48kDa

SSBP1 single- stranded DNA binding protein 1, mitochondrial

SSBP2 single- stranded DNA binding protein 2

SSBP3 single stranded DNA binding protein 3

SSBP4 single stranded DNA binding protein 4

GADD45A growth arrest and DNA-damage-inducible, alpha

GADD45B growth arrest and DNA-damage-inducible, beta GADD45G growth arrest and DNA-damage-inducible, gamma

GADD45GIP1 growth arrest and DNA-damage-inducible, gamma interacting protein 1

MGMT O-6-methylguanine-DNA methyltransferase

REV1 REV1, polymerase (DNA directed)

RECQL RecQ protein-like (DNA helicase Ql-like)

CCDC6 coiled-coil domain containing 6

KLRK1 killer cell lectin-like receptor subfamily K, member 1

N6AMT1 N-6 adenine-specific DNA methyltransferase 1 (putative)

N6AMT2 N-6 adenine-specific DNA methyltransferase 2 (putative)

POLR2A polymerase (RNA) II (DNA directed) polypeptide A, 220kDa

POLR2B polymerase (RNA) II (DNA directed) polypeptide B, 140kDa

POLR2C polymerase (RNA) II (DNA directed) polypeptide C, 33kDa

POLR2D polymerase (RNA) II (DNA directed) polypeptide D

POLR2E polymerase (RNA) II (DNA directed) polypeptide E, 25kDa

POLR2F polymerase (RNA) II (DNA directed) polypeptide F

POLR2G polymerase (RNA) II (DNA directed) polypeptide G

POLR2H polymerase (RNA) II (DNA directed) polypeptide H

POLR2I polymerase (RNA) II (DNA directed) polypeptide I, 14.5kDa

POLR2J polymerase (RNA) II (DNA directed) polypeptide J, 13.3kDa

POLR2J2 polymerase (RNA) II (DNA directed) polypeptide J2

POLR2J3 polymerase (RNA) II (DNA directed) polypeptide J3

POLR2K polymerase (RNA) II (DNA directed) polypeptide K, 7.0kDa

POLR2L polymerase (RNA) II (DNA directed) polypeptide L, 7.6kDa

POLR2M polymerase (RNA) II (DNA directed) polypeptide M

TRDMT1 tRNA aspartic acid methyltransferase 1

CHD1 chromodomain helicase DNA binding protein 1

CHD1L chromodomain helicase DNA binding protein 1-like

CHD2 chromodomain helicase DNA binding protein 2

CHD3 chromodomain helicase DNA binding protein 3

CHD4 chromodomain helicase DNA binding protein 4 CHD5 chromodomain helicase DNA binding protein 5

CHD6 chromodomain helicase DNA binding protein 6

CHD7 chromodomain helicase DNA binding protein 7

CHD8 chromodomain helicase DNA binding protein 8

CHD9 chromodomain helicase DNA binding protein 9

KLLN killin, p53-regulated DNA replication inhibitor

POLR3A polymerase (RNA) III (DNA directed) polypeptide A, 155kDa

POLR3B polymerase (RNA) III (DNA directed) polypeptide B

POLR3C polymerase (RNA) III (DNA directed) polypeptide C (62kD)

POLR3D polymerase (RNA) III (DNA directed) polypeptide D, 44kDa

POLR3E polymerase (RNA) III (DNA directed) polypeptide E (80kD)

POLR3F polymerase (RNA) III (DNA directed) polypeptide F, 39 kDa

POLR3G polymerase (RNA) III (DNA directed) polypeptide G (32kD)

POLR3GL polymerase (RNA) III (DNA directed) polypeptide G (32kD)-like

POLR3H polymerase (RNA) III (DNA directed) polypeptide H (22.9kD)

POLR3K polymerase (RNA) III (DNA directed) polypeptide K, 12.3 kDa

WDHD1 WD repeat and HMG-box DNA binding protein 1

PGAP1 post-GPI attachment to proteins 1

PGAP2 post-GPI attachment to proteins 2

PGAP3 post-GPI attachment to proteins 3

REV3L REV3-like, polymerase (DNA directed), zeta, catalytic subunit

CDT1 chromatin licensing and DNA replication factor 1

PANDAR promoter of CDKN1A antisense DNA damage activated RNA

APEX1 APEX nuclease (multifunctional DNA repair enzyme) 1

CHMP1A charged multivesicular body protein 1A

CHMP1B charged multivesicular body protein IB

CHMP2A charged multivesicular body protein 2A

CHMP2B charged multivesicular body protein 2B

CHMP4A charged multivesicular body protein 4A

CHMP4B charged multivesicular body protein 4B CHMP4C charged multivesicular body protein 4C

CHMP5 charged multivesicular body protein 5

CHMP6 charged multivesicular body protein 6

POLRMT polymerase (RNA) mitochondrial (DNA directed)

SPIDR scaffolding protein involved in DNA repair

MCIDAS multiciliate differentiation and DNA synthesis associated cell cycle protein

PAPD7 PAP associated domain containing 7

RFX8 RFX family member 8, lacking RFX DNA binding domain

DEK DEK oncogene

NUB1 negative regulator of ubiquitin-like proteins 1

PAXBP1 PAX3 and PAX7 binding protein 1

RAMP1 receptor (G protein-coupled) activity modifying protein 1

RAMP2 receptor (G protein-coupled) activity modifying protein 2

RAMP3 receptor (G protein-coupled) activity modifying protein 3

RC3H2 ring finger and CCCH-type domains 2

ARHGAP35 Rho GTPase activating protein 35

SMUG1 single- strand- selective monofunctional uracil-DNA glycosylase 1

CXXC1 CXXC finger protein 1

FAM50A family with sequence similarity 50, member A

FANCG Fanconi anemia, complementation group G

GLI3 GLI family zinc finger 3

GTF2H5 general transcription factor IIH, polypeptide 5

LAGE3 L antigen family, member 3

MYCNOS MYCN opposite strand/antisense RNA

NFRKB nuclear factor related to kappaB binding protein

RAD51D RAD51 paralog D

RFX2 regulatory factor X, 2 (influences HLA class II expression)

RFXANK regulatory factor X-associated ankyrin-containing protein

RRP1 ribosomal RNA processing 1

SPRTN SprT-like N-terminal domain XRCC4 X-ray repair complementing defective repair in Chinese hamster cells 4

CDK11A cyclin-dependent kinase 11 A

CDK11B cyclin-dependent kinase 1 IB

LURAP1L leucine rich adaptor protein 1-like

MAD2L2 MAD2 mitotic arrest deficient-like 2 (yeast)

PRDM2 PR domain containing 2, with ZNF domain

NABP2 nucleic acid binding protein 2

NABP1 nucleic acid binding protein 1

PPP1R15A protein phosphatase 1, regulatory subunit 15A

TATDN1 TatD DNase domain containing 1

TATDN2 TatD DNase domain containing 2

TATDN3 TatD DNase domain containing 3

CEBPB CCAAT/enhancer binding protein (C/EBP), beta

INIP INTS3 and NABP interacting protein

INTS3 integrator complex subunit 3

SDIM1 stress responsive DNAJB4 interacting membrane protein 1

DHX9 DEAH (Asp-Glu-Ala-His) (SEQ ID NO: 39) box helicase 9

SATB 1 SATB homeobox 1

FEN1 flap structure- specific endonuclease 1

HCST hematopoietic cell signal transducer

TYROBP TYRO protein tyrosine kinase binding protein

AFA ankyloblepharon filiforme adnatum

C9orfl69 chromosome 9 open reading frame 169

TSP02 translocator protein 2

TCIRG1 T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal VO subunit A3

Clorf61 chromosome 1 open reading frame 61

HLA-DOA major histocompatibility complex, class II, DO alpha

SPINK 13 serine peptidase inhibitor, Kazal type 13 (putative) In an embodiment, the payload comprises a modulator of an epigenetic state or characteristic of a component of chromatin, e.g., a chromatin associated protein, e.g., a histone. For example, the epigenetic state or characteristic can comprise histone acetylation,

deacetylation, methylation (e.g., mono, di, or tri-methylation), demethylation, phosphorylation, dephosphorylation, ubiquitination (e.g., mono or polyubiquitination), deubiquitination, sumoylation, ADP-ribosylation, deimination, or a combination thereof.

In an embodiment, the modulator is selected from, or modulates, one or more histone modifying enzymes. In an embodiment, the histone modifying enzyme is a histone

methyltransf erase (HMT). In an embodiment, the histone modifying enzyme is a histone demethyltransferase (HDMT). In an embodiment, the histone modification enzyme is a histone acetyltransferase (HAT). In an embodiment, the histone modifying enzyme is a histone deacetylase (HDAC). In an embodiment, the histone modification enzyme is a kinase. In an embodiment, the histone modifying enzyme is a phosphatase. In an embodiment, the histone modifying enzyme is ubiquitin- activating enzymes (Els), ubiquitin-conjugating enzymes (E2s), or ubiquitin ligases (E3s). In an embodiment, the histone modifying enzyme is a

deubiquitinating (DUB) enzyme.

In an embodiment, histone modifications involved in regulation of gene transcription are modulated. For example, mono-methylation of H3K4, H3K9, H3K27, H3K79, H4K20, H2BK5, di-methylation of H3K79, tri-methylation of H3K4, H3K79, H3K36, and acetylation of H3K9, H3K14, H3K27, can be associated with transcription activation. As another example, di- methylation of H3K9, H3K27, and tri-methylation of H3K9, H3K27, H3K79, H2BK5 can be associated with transcription repression. In an embodiment, the modulator modulates trimethylation of H3 lysine 4 (H3K4Me3) and/or trimethylation of H3 lysine 36 (H3K36Me3), e.g., in active genes. In an embodiment, the modulator modulates trimethylation of H3 lysine 27 (H3K27Me3), di- and tri-methylation of H3 lysine 9 (H3K9Me2/3), and/or trimethylation of H4 lysine 20 (H4K20Me3), e.g., in repressed genes. In an embodiment, the modulator modulates both activating (e.g., H3K4Me3) and repressing (e.g., H3K27Me3) marks, e.g., in stem cells.

In an embodiment, histone modifications involved in DNA damage response and repair are modulated. For example, the modulators described herein can modulate phosphorylation of H2AX at Serine 139 and/or acetylation of H3 lysine 56 (H3K56Ac). Aberrant histone modifications are associated with various diseases and conditions, e.g., cancer, cardiovascular disease, and neurodegenerative disorder. The modulators described herein can be used to treat a disease or condition described herein, e.g., by modulating one or more histone modifications, as described herein.

Epigenetic changes in histones can be evaluated by art-known methods or as described herein. Exemplary methods for detecting histone modifications include, e.g., chromatin immunoprecipitation (ChIP) using antibodies against modified histones, e.g., followed by quantitative PCR.

Exemplary endogenous or exogenous modulators of chromatin structure are described herein, e.g., in Table VI-4.

Table VI-4

KMT2B lysine (K)-specific methyltransferase KIAA0304, MLL2, NM_014727 2B TRX2, HRX2, WBP7,

MLL1B, MLL4

KMT2C lysine (K)-specific methyltransferase KIAA1506, HALR

2C

KMT2D lysine (K)-specific methyltransferase ALR, MLL4,

2D CAGL114

KMT2E lysine (K)-specific methyltransferase HDCMC04P

2E

SETD1A SET domain containing 1A KIAA0339, Setl, NM_014712

KMT2F

SETD1B SET domain containing IB KIAA1076, SetlB, XM_037523

KMT2G

ASH1L ashl (absent, small, or homeotic)-like huASHl, ASH1, NM_018489

(Drosophila) ASH 1 LI, KMT2H

SETD2 SET domain containing 2 HYPB, HIF-1, NM_014159

KIAA1732, FLJ23184,

KMT3A

NSD1 nuclear receptor binding SET domain ARA267, FLJ22263, NM_172349 protein 1 KMT3B

SMYD2 SET and MYND domain containing HSKM-B, ZMYND14, NM_020197

2 KMT3C

SMYD1 SET and MYND domain containing BOP, ZMYND22, XM_097915

1 KMT3D

SMYD3 SET and MYND domain containing KMT3E NM_022743

3

DOT1L DOTl-like histone H3K79 KIAA1814, DOT1, NM_032482 methyltransferase KMT4

SETD8 SET domain containing (lysine SET8, SET07, PR- NM_020382 methyltransferase) 8 Set7, KMT5A SUV420H suppressor of variegation 4-20 CGI-85, KMT5B NM_017635 1 homolog 1 (Drosophila)

SUV420H suppressor of variegation 4-20 MGC2705, KMT5C NM_032701 2 homolog 2 (Drosophila)

EZH2 enhancer of zeste homolog 2 EZH1, ENX-1, KMT6,

(Drosophila) KMT6A

EZH1 enhancer of zeste homolog 1 KIAA0388, KMT6B NM_001991

(Drosophila)

SETD7 SET domain containing (lysine KIAA1717, SET7, NM_030648 methyltransferase) 7 SET7/9, Set9, KMT7

PRDM2 PR domain containing 2, with ZNF RIZ, RIZ1, RIZ2, NM_012231 domain KMT8, MTB-ZF,

HUMHOXY1

HAT1 histone acetyltransferase 1 KAT1 NM_003642

KAT2A K(lysine) acetyltransferase 2A GCN5, PCAF-b NM_021078

KAT2B K(lysine) acetyltransferase 2B P/CAF, GCN5, NM_003884

GCN5L

CREBBP CREB binding protein RTS, CBP, KAT3A NM_004380

EP300 E1A binding protein p300 p300, KAT3B NM_001429

TAFl TAFl RNA polymerase II, TATA NSCL2, TAFII250, NM_004606 box binding protein (TBP)-associated KAT4, DYT3/TAF1

factor, 250kDa

KAT5 K(lysine) acetyltransferase 5 TIP60, PLIP, cPLA2, NM_006388

HTATIP1, ESA1,

ZC2HC5

KAT6A K(lysine) acetyltransferase 6A MOZ, ZC2HC6A NM_006766

KAT6B K(lysine) acetyltransferase 6B querkopf, qkf, Morf, NM_012330

MOZ2, ZC2HC6B

KAT7 K(lysine) acetyltransferase 7 HBOA, HBOl, NM_007067

ZC2HC7 KAT8 K(lysine) acetyltransferase 8 MOF, FLJ 14040, NM_032188 hMOF, ZC2HC8

ELP3 elongator acetyltransferase complex FLJ 10422, KAT9 NM_018091 subunit 3

GTF3C4 general transcription factor IIIC, TFIIIC90, KAT12

polypeptide 4, 90kDa

NCOA1 nuclear receptor co activator 1 SRCl. F-SRC-l, NM_147223

NCoA-1, KAT13A,

RIP 160, bHLHe74

NCOA3 nuclear receptor co activator 3 RAC3, AIB1, ACTR, NM_006534 p/CIP, TRAM-1,

CAGH16, TNRC16,

KAT13B, bHLHe42,

SRC-3, SRC3

NCOA2 nuclear receptor co activator 2 TIF2, GRIP1, NCoA-2,

KAT13C, bHLHe75

CLOCK clock circadian regulator KIAA0334, KAT13D, NM_004898 bHLHe8

KDM1A lysine (K)-specific demethylase 1A KIAA0601, BHC110, NM_015013

LSD1

KDM1B lysine (K)-specific demethylase IB FLJ34109, FLJ33898, NM_153042 dJ298J15.2,

bA204B7.3, FLJ43328,

LSD2

KDM2A lysine (K)-specific demethylase 2A KIAA1004, FBL11, NM_012308

LILINA,

DKFZP434M1735,

FBL7, FLJ00115,

CXXC8, JHDM1A

KDM2B lysine (K)-specific demethylase 2B PCCX2, CXXC2, NM_032590

FbllO, JHDM1B KDM3A lysine (K)-specific demethylase 3A TSGA, KIAA0742, NM_018433

JHMD2A

KDM3B lysine (K)-specific demethylase 3B KIAA1082, NET22 NM_016604

KDM4A lysine (K)-specific demethylase 4A KIAA0677, JHDM3A, NM_014663

TDRD14A

KDM4B lysine (K)-specific demethylase 4B KIAA0876, TDRD14B NM_015015

KDM4C lysine (K)-specific demethylase 4C GASC1, KIAA0780, NM_015061

TDRD14C

KDM4D lysine (K)-specific demethylase 4D FLJ 10251 NM_018039

KDM4E lysine (K)-specific demethylase 4E JMJD2E NM_001161630

KDM5A lysine (K)-specific demethylase 5A NM_005056

KDM5B lysine (K)-specific demethylase 5B RBBP2H1A, PLU-1, NM_006618

CT31

KDM5C lysine (K)-specific demethylase 5C DXS1272E, XE169 NM_004187

KDM5D lysine (K)-specific demethylase 5D KIAA0234 NM_004653

KDM6A lysine (K)-specific demethylase 6A NM_021140

KDM6B lysine (K)-specific demethylase 6B KIAA0346 XM_043272

JHDM1D jumonji C domain containing histone KIAA1718 NM_030647 demethylase 1 homolog D (S.

cerevisiae)

PHF8 PHD finger protein 8 ZNF422, KIAA1111, NM_015107

JHDM1F

PHF2 PHD finger protein 2 KIAA0662, JHDM1E, NM_005392

CENP-35

KDM8 lysine (K)-specific demethylase 8 FLJ 13798 NM_024773

Modulators of Gene Expression

In an embodiment a payload comprises a modulator of gene expression. A modulator of gene expression can be delivered in vitro, ex vivo, or in vivo.

In an embodiment, the payload comprises a transcription factor. Transcription factors can bind to specific DNA sequences (e.g., an enhancer or promoter region) adjacent to the genes that they regulate. For example, transcription factors can stabilize or inhibit the binding of RNA polymerase to DNA, catalyze the acetylation or deacetylation of histone proteins (e.g., directly or by recruiting other proteins with such catalytic activity), or recruit coactivator or corepressor proteins to the transcription factor/DNA complex. Modulators of gene expression also include, e.g., any proteins that interact with transcription factors directly or indirectly.

In an embodiment, the transcription factor is a general transcription factor, e.g., is ubiquitous and interacts with the core promoter region surrounding the transcription start site(s) of many, most or all class II genes. Exemplary general transcription factors include, e.g., TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH. In an embodiment, the transcription factor is an upstream transcription factor, e.g., binds upstream of the initiation site to stimulate or repress transcription. In an embodiment, the transcription factor is a specific transcription factor, e.g., a transcription factor dependent on a recognition sequence present in the proximity of the gene. Exemplary specific transcription factors include, e.g., SP1, AP-1, C/EBP, heat shock factor, ATF/CREB, -Myc, OCT-1, and NF-1.

In an embodiment, the transcription factor is constitutively active, e.g., a general transcription factor, SP1, NF-1, or CCAAT. In an embodiment, the transcription factor is conditionally active, e.g. it requires activation, e.g., developmental (e.g., GATA, HNF, PIT-1, MyoD, Myf5, Hox, Winged Helix), signal-dependent (e.g., extracellular ligand (endocrine or paracrine)-dependent, intracellular ligand (autocrine)-dependent (e.g., SREBP, p53, orphan nuclear receptors), cell membrane receptor-dependent (e.g., resident nuclear factors (e.g., CREB, AP-1, Mef2) or latent cytoplasmic factors (e.g., STAT, R-SMAD, NF-κΒ, Notch, TUBBY, NFAT).

Other exemplary transcription factors are described herein, e.g., in Table VI-5. Table VI-5. Selected Transcription Factors with Anotations

CSL(2) Exemplary functions include universal transcriptional effector of Notch signaling. For example, Notch signaling is dysregulated in many cancers and faulty notch signaling is implicated in many diseases. Exemplary disease include T-ALL (T-cell acute

lymphoblastic leukemia), CADASIL (Cerebral Autosomal-Dominant Arteriopathy with Sub-cortical Infarcts and Leukoencephalopathy), MS (Multiple Sclerosis), Tetralogy of Fallot, Alagille syndrome.

ETS(29) Exemplary functions include regulation of cellular differentiation, cell cycle control, cell migration, cell proliferation, apoptosis

(programmed cell death) and angiogenesis. Exemplary diseases include dieases associated with cancer, such as through gene fusion, e.g., prostate cancer.

HMGI/HMGY(2) Overexpression in certain cancers

MH1(8) Exemplary diseases include cancer, fibrosis and autoimmune

diseases.

Nuclear orphan Exemplary functions include superfamily of transcription regulators receptor(3) that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and

homeostasis. Exemplary diseases include inflammation, cancer, and metabolic disorders.

PC4(1) Exemplary functions include replication, DNA repair and

transcription.

RFX(8) Exemplary functions include regulation of development and function of cilia. Exemplary diseases include Bardet-Biedl syndrome.

STAT(7) Exemplary functions include regulation of many aspects of growth, survival and differentiation in cells. Exemplary diseases include angiogenesis, enhanced survival of tumors and immunosuppression.

Thyroid hormone Involved in widely diverse physiological functions, including control receptor(25) of embryonic development, cell differentiation and homeostasis zf-C2HC(6) Highly transcribed in the developing nervous system. Exemplary diseases include Duane Radial Ray Syndrome.

Androgen Exemplary functions include diverse physiological functions, receptor(l) including control of embryonic development, cell differentiation and homeostasis. Exemplary diseases include X-linked spinal, bulbar muscular atrophy and prostate cancer.

CG-1(2) Exemplary functions include calcium signaling by direct binding of calmodulin. CTF/NFI(4) Exemplary functions include both viral DNA replication and

regulation of gene expression. Exemplary diseases include leukemia, juvenile myelomonocytic.

Fork head(49) Involvement in early developmental decisions of cell fates during embryogenesis. Exemplary diseases include lymphedema-distichiasis, developmental verbal dyspraxia, autoimmune diseases.

Homeobox(205) Exemplary functions include involvement in a wide range of critical activities during development. Exemplary diseases include limb malformations, eye disorders, and abnormal head, face, and tooth development. Additionally, increased or decreased activity of certain homeobox genes has been associated with several forms of cancer.

MYB(25) Exemplary functions include regulator of proliferation, differentiation and cell fate. Exemplary diseases include cancer (e.g., oncogenic disease).

Oestrogen Control of embryonic development, cell differentiation and receptor(l) homeostasis. Exemplary diseases include estrogen resistance, familial breast cancer, migrane, myocardial infaction.

POU(21) Wide variety of functions, related to the function of the

neuroendocrine system and the development of an organism.

Exemplary diseases include non-syndromic deafness.

RHD(IO) Exemplary diseases include autoimmune arthritis, asthma, septic shock, lung fibrosis, glomerulonephritis, atherosclerosis, and AIDS.

T-box(17)

TSC22(4)

zf-GATA(14)

AP-2(5)

COE(4)

CUT(7)

GCM(2)

HSF(8)

NDT80/PhoG(l)

Other nuclear

receptor(2)

PPAR

receptor(3)

ROR receptor(4)

TEA(4)

Tub(5) zf-LITAF-like(2)

ARID(15)

COUP(3)

DM(7)

GCR(l)

HTF 2)

NF-YA(l)

Others(3)

Progesterone receptor(l)

Runt(3)

TF_bZIP(46)

ZBTB(48) zf-MIZ(7) bHLH(106)

CP2(7)

E2F(11)

GTF2I(5)

IRF(9)

NF-YB/C(2)

P53(3)

Proxl(2)

SAND(8)

TF_Otx(3) zf-BED(5) zf-NF-Xl(2)

C/EBP(10)

CSD(8)

Ecdystd receptor(2)

HMG(50)

MBD(9)

Nrfl(l)

PAX(9)

Retinoic acid receptor(7)

SRF(6)

THAP(12) zf-C2H2(634) CRX Exemplary diseases include dominant cone-rod dystrophy. Repair

mutation.

FOCX2 Exemplary diseases include lymphedema-distichiasis. Repair

mutation.

FOXP2 Exemplary diseases include developmental verbal dyspraxia. Repair

mutation.

FOXP3 Exemplary diseases include autoimmune diseases. Repair mutation.

GAT4 Exemplary diseases include congenital heart defects. Repair mutation.

HNF1 through Exemplary diseases include mature onset diabetes of the young

HNF6 (MODY), hepatic adenomas and renal cysts. Repair mutation.

LHX3 Exemplary diseases include Pituitary disease. Repair mutation.

MECP2 Exemplary diseases include Rett syndrome. Repair mutation.

MEF2A Exemplary diseases include Coronary artery disease. Repair mutation.

NARA2 Exemplary diseases include Parkinson disease. Repair mutation.

NF-KB Exemplary diseases include autoimmune arthritis, asthma, septic

Activation shock, lung fibrosis, glomerulonephritis, atherosclerosis, and AIDS.

Repair mutation.

NF-KB Inhibition Exemplary diseases include apoptosis, inappropriate immune cell

development, and delayed cell growth. Repair mutation.

NIKX2-5 Exemplary diseases include cardiac malformations and

atrioventricular conduction abnormalities.

NOTCH 1 Exemplary diseases include aortic valve abnormalities.

Modulators of alternative splicing

In an embodiment, the modulator of gene expression modulates splicing. For example, modulator can modulate exon skipping or cassette exon, mutually exclusive exons, alternative donor site, alternative acceptor site, intron retention, or a combination thereof. In an embodiment, the modulator is selected from or modulates one or more general or alternative splicing factors, e.g., ASFl. In an embodiment, the modulator modulates alternative splicing (e.g., influences splice site selection) in a concentration-dependent manner. Modulators of post-transcriptional modification

In an embodiment, the modulator of gene expression modulates post-transcriptional modification. For example, the modulators described herein can promote or inhibit 5' capping, 3' polyadenylation, and RNA splicing. In an embodiment, the modulator is selected from, or modulates, one or more factors involved in 5' capping, e.g., phosphatase and guanosyl transferase. In an embodiment, the modulator is selected from, or modulates, one or more factors involved in 3' polyadenylation, e.g., polyadenylate polymerase, cleavage and

polyadenylation specificity factor (CPSF), and poly(A) binding proteins. In an embodiment, the modulator is selected from, or modulates, one or more factors involved in RNA splicing, e.g., general or alternative splicing factors.

Exemplary endogenous or exogenous modulators of post-transcriptional modification are described herein, e.g., in Table VI-6.

Table VI-6

SAM synthase

ubiquitin-conjugating enzyme E2R1

Splicing

SR proteins SFRS1 - SFR11 which, when bound to exons, tend to promote

hnRNP proteins: coded by the following genes:HNRNPA0, HNRNPA1, HNRNPA1L1, HNRNPA1L2, HNRNP A3, HNRNPA2B1, HNRNP AB, HNRNPB1, HNRNPC, HNRNPCL1, HNRNPD, HNRPDL, HNRNPF, HNRNPH1, HNRNPH2, HNRNPH3, HNRNPK, HNRNPL, HNRPLL, HNRNPM, HNRNPR, HNRNPU, HNRNPUL1, HNRNPUL2, HNRNPUL3

Editing protein

ADAR

Nuclear export proteins

Mex67

Mtr2

Nab2

DEAD-box helicase ("DEAD" disclosed as SEQ ID NO: 40)

TRANSLATION

Initiation

eIF4A, eIF4B, eIF4E, and eIF4G: Eukaryotic initiation factors GEF: Guanine exchange factor

GCN2, PKR, HRI and PERK: Kinases involved in phosphorylating some of the initiation factors

Elongation

eEFl and eEF2: elongation factors

GCN: kinase Termination

eRF3: translation termination factor

POSl r-TRANSl LATIONAL CONTROL

mRNA Degradation

ARE- specific binding proteins

EXRN1: exonuclease

DCP1, DCP2: Decapping enzymes

RCK/p54, CPEB, eIF4E: Translation repression

microRNAs and siRNAs: Probably regulate 30% of all genes

DICER

Ago proteins

Nonsense-mediated mRNA decay proteins

UPF3A

UPF3B

eIF4A3

MLN51

Y14/MAGOH

MG-1

SMG-5

SMG-6

SMG-7

mRNA Modification

Enzymes carry the following functions

Phosphorylation

N-linked glycosylation

Acetylation

Amidation

Hydroxylation

Methylation

O-linked glycosylation

Ubiquitylation Inhibitors

In an embodiment a payload comprises an inhibitor of a payload described above, e.g., an inhibitor of an enzyme transcription factor. In an embodiment a payload comprises an inhibitor of any of the aforementioned payload molecules, processes, activities or mechanisms. In an embodiment, the inhibitor is an antibody molecule (e.g., a full antibody or antigen binding fragment thereof) specific for one of the payload molecules described herein. In an embodiment the inhibitor is a small molecule compound. In an embodiment, the inhibitor is a nucleic acid (e.g., siRNA, shRNA, ribozyme, antisense-oligonucleotide, and aptamer). For example, the payload is an inhibitor of a target, e.g., a trasnscription factor, a post-translational modification enzyme, a post-transcriptional modification enzyme, etc., or a nucleic acid sequence encoding any of the foregoing.

Orthologs

If a non-human gene or protein is recited herein it is understood that the invention also comprises the human counterpart or ortholog and uses thereof.

VIIA. Targets: Cells

Cas9 molecules and gRNA molecules, e.g., a Cas9 molecule/gRNA molecule complex, can be used to manipulate a cell (e.g., an animal cell or a plant cell), e.g., to deliver a payload, or edit a target nucleic acid, in a wide variety of cells. Typically an eiCas9 molecule/gRNA molecule complex is used to deliver a payload and an eaCas9 molecule/gRNA complex is used to edit or alter the structure of a target nucleic acid. Delivery or editing can be performed in vitro, ex vivo, or in vivo.

In an embodiment, a cell is manipulated by editing (e.g., introducing a mutation or correcting) one or more target genes, e.g., as described herein. In an embodiment, a cell is manipulated by delivering a payload comprising one or more modulators (e.g., as described herein) to the cell, e.g., to a target sequence in the genome of the cell. In an embodiment, the expression of one or more target genes (e.g., one or more target genes described herein) is modulated, e.g., in vivo. In an embodiment, the expression of one or more target genes (e.g., one or more target genes described herein) is modulated, e.g., ex vivo. In an embodiment, the cells are manipulated (e.g., converted or differentiated) from one cell type to another. In an embodiment, a pancreatic cell is manipulated into a beta islet cell. In an embodiment, a fibroblast is manipulated into an iPS cell. In an embodiment, a preadipocyte is manipulated into a brown fat cell. Other exemplary cells include, e.g., muscle cells, neural cells, leukocytes, and lymphocytes.

In an embodiment, the cell is a diseased or mutant-bearing cell. Such cells can be manipulated to treat the disease, e.g., to correct a mutation, or to alter the phenotyope of the cell, e.g., to inhibit the growth of a cancer cell. For examples, a cell is associated with one or more diseases or conditions describe herein. In an embodiment, the cell is a cancer stem cell. For example, cancer stem cells can be manipulated by modulating the expression of one or more genes selected from: TWIST (TF), HIF-lcc, HER2/neu, Snail (TF), or Wnt.

In an embodiment, the manipulated cell is a normal cell.

In an embodiment, the manipulated cell is a stem cell or progenitor cell (e.g., iPS, embryonic, hematopoietic, adipose, germline, lung, or neural stem or progenitor cells).

In an embodiment, the manipulated cells are suitable for producing a recombinant biological product. For example, the cells can be CHO cells or fibroblasts. In an embodiment, a manipulated cell is a cell that has been engineered to express a protein.

In an embodiment, the cell being manipulated is selected from fibroblasts, monocytic precursors, B cells, exocrine cells, pancreatic progenitors, endocrine progenitors, hepatoblasts, myoblasts, or preadipocytes. In an embodiment, the cell is manipulated (e.g., converted or differentiated) into muscle cells, erythroid-megakaryocytic cells, eosinophils, iPS cells, macrophages, T cells, islet beta-cells, neurons, cardiomyocytes, blood cells, endocrine progenitors, exocrine progenitors, ductal cells, acinar cells, alpha cells, beta cells, delta cells, PP cells, hepatocytes, cholangiocytes, or brown adipocytes.

In an embodiment, the cell is a muscle cell, erythroid-megakaryocytic cell, eosinophil, iPS cell, macrophage, T cell, islet beta-cell, neuron, cardiomyocyte, blood cell, endocrine progenitor, exocrine progenitor, ductal cell, acinar cell, alpha cell, beta cell, delta cell, PP cell, hepatocyte, cholangiocyte, or white or brown adipocyte.

The Cas9 and gRNA molecules described herein can be delivered to a target cell. In an embodiment, the target cell is a normal cell. In an embodiment, the target cell is a stem cell or progenitor cell (e.g., iPS, embryonic, hematopoietic, adipose, germline, lung, or neural stem or progenitor cells).

In an embodiment, the target cell is a CHO cell.

In an embodiment, the target cell is a fibroblast, monocytic precursor, B cells exocrine cell, pancreatic progenitor, endocrine progenitor, hepatoblast, myoblast, or preadipocyte.

In an embodiment, the target cell is a muscle cell, erythroid-megakaryocytic cell, eosinophil, iPS cell, macrophage, T cell, islet beta-cell, neurons (e.g., a neuron in the brain, e.g., a neuron in the striatum (e.g., a medium spiny neuron), cerebral cortex, precentral gyrus, hippocampus (e.g., a neuron in the dentate gyrus or the CA3 region of the hippocampus), temporal cortex, amygdala, frontal cortex, thalamus, cerebellum, medulla, putamen,

hypothalamus, tectum, tegmentum or substantia nigra), cardiomyocyte, blood cell, endocrine progenitor, exocrine progenitor, ductal cell, acinar cell, alpha cell, beta cell, delta cell, PP cell, hepatocyte, cholangiocyte, or brown adipocyte.

In an embodiment, the target cell is manipulated ex vivo by editing (e.g., introducing a mutation or correcting) one or more target genes and/or modulating the expression of one or more target genes, and administered to the subject.

Exemplary cells that can be manipulated and exemplary genes that can be modulated are described in Table VII-8.

TableVII-8

required for differentiation in vivo. Klf4

Multiplex. Myc

B cells Macrophages Deliver Cas9-activators to target C/EBPcc activation of transcription factors

required for differentiation in vivo.

B cells T cells, Delivery Cas9-repressors OR Pax5 macrophages deliver Cas9 endonuclease to

ablate Pax5

Exocrine Islet β-cells Deliver Cas9-activators to target Pdxl cells activation of transcription factors Ngn3 required for differentiation in vivo. MafA Multiplex.

Fibroblasts Neurons Deliver Cas9-activators to target Ascll activation of transcription factors Brn2 required for differentiation in vivo. Mytll Multiplex.

fibroblasts cardiomyocytes Deliver Cas9-activators to target Gata4 activation of transcription factors Mef2c required for differentiation in vivo. Tbx5 Multiplex.

Fibroblasts Blood cells Deliver Cas9-activators to target Oct4 activation of transcription factors

required for differentiation in vivo.

Fibroblasts cardiomyocytes Deliver Cas9-activators to target Oct4 activation of transcription factors Sox2 required for differentiation in vivo. Klf4 Multiplex.

Pancreatic Endocrine Deliver Cas9-activators to target Ngn3 progenitor progenitor activation of transcription factors

required for differentiation in vivo. Pancreatic Exocrine Deliver Cas9-activators to target P48 progenitor progenitor activation of transcription factors

required for differentiation in vivo.

Pancreatic Duct Deliver Cas9-activators to target Hnf6/OC-l progenitor activation of transcription factors

required for differentiation in vivo.

Pancreatic acinar Deliver Cas9-activators to target Ptfla progenitor activation of transcription factors Rpbjl required for differentiation in vivo.

Multiplex.

Endocrine a cell Deliver Cas9-activators to target Foxa2 progenitor activation of transcription factors Nkx2.2

(to make required for differentiation in vivo. Pax6 glucagon) Multiplex. Arx

Endocrine cell Deliver Cas9-activators to target Mafa progenitor activation of transcription factors Pdxl

(to make required for differentiation in vivo. Hlxb9 insulin) Multiplex. Pax4

Pax6 l

Nkx2.2

Nkx6.1

Endocrine 5 cell Deliver Cas9-activators to target Pax4 progenitor activation of transcription factors Pax6

(to make required for differentiation in vivo.

somatostatin) Multiplex.

Endocrine PP cell Deliver Cas9-activators to target Nkx2.2 progenitor activation of transcription factors

(to make required for differentiation in vivo.

pancreatic polypeptide)

Hepatoblast hepatocyte Deliver Cas9-activators to target Hnf4

activation of transcription factors

required for differentiation in vivo.

Hepatoblast Cholangiocyte Deliver Cas9-activators to target Hnf6/OC-l activation of transcription factors

required for differentiation in vivo.

Myoblasts Brown Deliver Cas9-activators to target PRDM16 adipocyte activation of transcription factors C/EBP required for differentiation in vivo. PGClcc Multiplex. PPARy preadipocytes Brown Deliver Cas9-activators to target PRDM16 adipocyte activation of transcription factors C/EBP required for differentiation in vivo.

Multiplex.

Table VII-9: Exemplary cells for manipulation

Pancreatic cells, e.g., beta cells

Muscle cells

Adipocytes

Pre-adipocytes

Neural cells

Blood cells

Leukocytes

Lymphocyes

B cells

T cells

Table VII-10: Exemplary stem cells for manipulation

embryonic stem cells I non-embryonic stem cells

hematopoietic stem cells

adipose stem cells

germline stem cells

lung stem cells

neural stem cells

Table VII-11: Exemplary cancer cells for manipulation

lung cancer cells

breast cancer cells

skin cancer cells

brain cancer cells,

pancreatic cancer cells

hematopoietic cancer cells

liver cancer cells

kidney cancer cells

ovarian cancer cells

Table VII-12: Exemplary non-human cells for manipulation

Plant cells, e.g., crop cells, e.g., corn, wheat,

soybean, citrus or vegetable cells

Animal cells, e.g., a cow, pig, horse, goat, dog or cat

cell

Exemplary endogenous or exogenous modulators of cancer stem cells (CSCs) are described herein, e.g., in Table VII-13.

Table VII-13

• TWIST 1 (TF)

• HIF-lcc (TF) • HER2/neu

• Snail (TF)

• Wnt

• TGFP

• FGF

• EGF

• HGF

• STAT3 (TF)

• Notch

• P63 (TF)

• PI3K)/AKT

• Hedgehog

• NF-κΒ (TF)

• ATF2 (TF)

• miR-200 and miR-34

• P53 (TF)

• E-cadherin

• Transcription factors that inhibit E-cadherin directly

• ZEB1

• ZEB2

• E47

• KLF8

• Transcription factors that inhibit E-cadherin directly

• TCF4

• SIX 1

• FOXC2

• G-CSF and CD34 in AML

• PML and FOXO in CML

• CD133 in glioblastoma multiforme, osteosarcoma, Ewing' s sarcoma, endometrial, hepatocellular, colon and lung carcinomas and ovarian and pancreatic adenocarcinoma

• CD44 in head and neck cancer, prostate, gastric and colorectal

carcinoma stem cells

• CD34 in leukemia

• CD38 in leukemia

• IL3Ra in leukemia

• EpCAM in colon carcinoma and pancreatic adenocarcinoma stem

cells

• ALDH in melanoma, colorectal, breast, prostate and squamous cell

carcinomas, pancreatic adenocarcinoma, and osteosarcoma

• MAP2 in melanoma

• a6-integrin in glioblastoma

• SSEA-1 in gliobalstoma

• CD24 in breast cancer and other tumors

Cas9 molecules and gRNA molecules, e.g., a Cas9 molecule/gRNA molecule complex, can be used to manipulate a cell (e.g., a cell described herein), e.g., to deliver a payload, or edit a target nucleic acid, e.g., to increase cell engraftment, e.g., to achieve stable engraftment of cells into a native microenvironment. The engrafting cells, the cells in the native microenvironment, or both, can be manipulated. Typically an eiCas9 molecule/gRNA molecule complex is used to deliver a payload and an eaCas9 molecule/gRNA complex is used to edit or alter the structure of a target nucleic acid.

For example, increased efficiency of engraftment of cells can be achieved by: increasing the expression of one or more of the genes described herein, e.g., homing genes, adhesion genes, survival genes, proliferative genes, immune evasion genes, and/or cell protection genes, and/or decreasing the expression of one or more of the genes described herein, e.g., quiescence genes, death/apoptosis genes, and/or immune recognition genes.

In an embodiment, the gene encodes a homing receptor or an adhesion molecule, e.g., that is involved in directing cell migration towards a tissue in association with a tissue-expressed ligand or region rich in soluble cytokine. In an embodiment, the homing receptor or adhesion molecule is expressed on leukocytes, e.g., lymphocytes or hematopoietic stem cells. In an embodiment, the tissue is bone marrow, e.g., extracellular matrix or stromal cells. In an embodiment, the homing receptor or adhesion molecule is C-X-C chemokine receptor type 4 (CXCR4, also known as fusin or CD 184). For example, the expression of CXCR4 on hematopoietic stem cells is upregulated. In an embodiment, the ligand is stromal-derived-factor- 1 (SDF-1, also known as CXCL12). In an embodiment, the homing receptor or adhesion molecule is CD34. In an embodiment, the ligand is addressin (also known as mucosal vascular addressin cell adhesion molecule 1 (MAdCAM-1)).

In an embodiment, the gene encodes a receptor, e.g., expressed on a stem cell or progenitor cell, that binds to a ligand, e.g., a chemokine or cytokine. For example, the receptor can be associated with sternness of the cell and/or attracting the cell to a desired

microenvironment. In an embodiment, the receptor is expressed on a hematopoietic stem cell. In an embodiment, the receptor is expressed on a neural stem cell. In an embodiment, the receptor is mast/stem cell growth factor receptor (SCFR, also known as proto-oncogene c-Kit or tyro sine-protein kinase Kit or CD117). In an embodiment, the ligand is stem cell factor (SCF, also known as steel factor or c-kit ligand). In an embodiment, the receptor is myeloproliferative leukemia virus oncogene (MPL, also known as CD110). In an embodiment, the ligand is thrombopoietin (TPO).

In an embodiment, the gene encodes a marker, e.g., that promotes survival or

proliferation of the cells expressing that marker, or allows the cells expressing that marker to evade an immune response or to be protected from an adverse environment, e.g., that leads to cell death. For example, cells expressing CD47 (also known as integrin associated protein (IAP) can avoid phagocytosis, e.g., during cell migration. As another example, cells that express BCL2 can be protected from apoptosis. In an embodiment, the cell is a blood cell, e.g., an erythrocyte or leukocyte. In an embodiment, the cell is a hematopoietic stem cell or progenitor cell.

In an embodiment, the expression of one or more of CXCR4, SDF1, CD117, MPL,

CD47, or BCL2, in a stem cell or progenitor cell, e.g., a hematopoietic stem cell or progenitor cell, is upregulated.

Cas9 molecules and gRNA molecules, e.g., a Cas9 molecule/gRNA molecule complex, can be used to manipulate a cell (e.g., a cell described herein), e.g., to deliver a payload, or edit a target nucleic acid, e.g., to manipulate (e.g., dictate) the fate of a targeted cell, e.g., to better target specific cell type of interest and/or as a suicide mechanism. Typically an eiCas9 molecule/gRNA molecule complex is used to deliver a payload and/or an eaCas9

molecule/gRNA complex is used to edit or alter the structure of a target nucleic acid. Exemplary genes that can be modulated include, e.g., one or more of chemotherapy resistance genes, chemotherapy sensitivity genes, antibiotic resistance genes, antibiotic sensitivity genes, and cell surface receptor genes, e.g., as described herein.

In an embodiment, a chemotherapy resistance gene, a chemotherapy sensitivity gene, an antibiotic resistance gene, and/or an antibiotic sensitivity gene is modulated, e.g., such that modified or undesirable cells (e.g., modified or undesirable hematopoietic stem cells (HSCs), e.g., in bone marrow) can be reduced or removed, e.g., by chemotherapeutic or antibiotic treatment.

For example, genes or gene products that modulate (e.g., increase) chemotherapy resistance or antibiotic resistance can be delivered into the cells. Cells modified by the chemotherapy or antibiotic resistance gene or gene product can have a higher (e.g., at least about 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 50, 75, or 100 fold higher) survival rate than cells without such modification after chemotherapeutic or antibiotic treatment. In an embodiment, the

chemotherapeutic or antibiotic treatment is performed in vivo. In an embodiment, the chemotherapeutic or antibiotic treatment is performed in vitro or ex vivo. In an embodiment, the chemotherapy resistance gene is a gene encoding 0⁶-alkylguanine DNA alkyltransferase (MGMT). In an embodiment, the chemotherapy comprises temozolomide.

As another example, genes or gene products that modulate (e.g., increase) chemotherapy sensitivity or antibiotic sensitivity can be delivered into the cells. The genes or gene products that confer chemotherapy sensitivity or antibiotic sensitivity can be used as suicide signals, e.g., causing apoptosis of the cells. Cells modified by the chemotherapy or antibiotic sensitivity gene or gene product can have a lower (e.g., at least about 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 50, 75, or 100 fold lower) survival rate than cells without such modification after chemotherapeutic or antibiotic treatment. In an embodiment, the chemotherapeutic or antibiotic treatment is performed in vivo. In an embodiment, the chemotherapeutic or antibiotic treatment is performed in vitro or ex vivo.

The method described herein can be used to select or enrich cells that have a modified or desired phenotype, e.g., chemotherapy resistance and/or antibiotic resistance. The method described herein can also be used to remove or reduce the number of cells that have a modified or undesired phenotype, e.g., chemotherapy sensitivity and/or antibiotic sensitivity. For example, cells that exhibit an undesired effect, e.g., an off-target effect or a cancer phenotype, e.g., caused by editing of a nucleic acid in an undesired genomic location or cell type, can be removed.

In an embodiment, a cell surface receptor gene is modulated (e.g., the expression of the cell surface receptor is increased or decreased), such that a therapeutic agent (e.g., a therapeutic antibody) can be used to target a cell (e.g., to kill the cell) that has increased or decreased expression of the cell surface receptor. In an embodiment, the cell surface receptor is CD20. In an embodiment, the therapeutic antibody is Rituximab.

In an embodiment, the cell surface receptor is selected from, e.g., CD52, VEGFR, CD30,

EGFR, CD33, or ErbB2. In an embodiment, the therapeutic antibody is selected from, e.g., Alemtuzumab, Rituximab, Cetuximab, Panitumumab, Gentuzaumab, and Trastuzumab. In an embodiment, the cell surface receptor is CD52 and the therapeutic antibody is Alemtuzumab. In an embodiment, the gene encodes VEGF and the therapeutic antibody is Rituximab. In an embodiment, the cell surface receptor is EGFR and the therapeutic antibody is Cetuximab or

Panitumumab. In an embodiment, the cell surface receptor is CD33 and the therapeutic antibody is Gentuzaumab. In an embodiment, the cell surface receptor is ErbB2 and the therapeutic antibody is Trastuzumab.

In an embodiment, the expression or activity of the Cas9 molecule and/or the gRNA molecule is induced or repressed, e.g., when the cell is treated with a drug, e.g., an antibiotic, e.g., in vivo. For example, the induction or repression of the expression or activity of the Cas9 molecule and/or the gRNA molecule can be used to reduce toxicity and/or off-target effects, e.g., in certain tissues. In an embodiment, the expression of the Cas9 molecule, the gRNA molecule, or both, is driven by an inducible promoter. In an embodiment, binding of a drug (e.g., an antibiotic) to the Cas9 molecule and/or the gRNA molecule activates or inhibits the activity of the Cas9 molecule and/or the gRNA molecule. In an embodiment, the drug (e.g., antibiotic) is administered locally. In an embodiment, the cell treated with the drug (e.g., antibiotic) is located in the eye, ear, nose, mouth, or skin.

Cas9 molecules and gRNA molecules, e.g., a Cas9 molecule/gRNA molecule complex, can be used to manipulate a cell (e.g., a cell described herein), e.g., to deliver a payload, or edit a target nucleic acid, e.g., in directed enzyme prodrug therapy (DEPT). Typically an eiCas9 molecule/gRNA molecule complex is used to deliver a payload and an eaCas9 molecule/gRNA complex is used to edit or alter the structure of a target nucleic acid.

Directed enzyme prodrug therapy (DEPT) uses enzymes artificially introduced into the body to convert prodrugs, which have no or poor biological activity, to the active form in the desired location within the body. For example, directed enzyme prodrug therapy can be used to reduce the systemic toxicity of a drug, by achieving high levels of the active drug only at the desired site.

In an embodiment, an enzyme required for prodrug conversion or a gene encoding such an enzyme is delivered to a target cell, e.g., a cancer cell. For example, the enzymes or genes can be delivered by a method described herein. In an embodiment, the gene encoding the enzyme required for prodrug conversion is delivered by a viral vector.

Cas9 molecules and gRNA molecules, e.g., a Cas9 molecule/gRNA molecule complex, can be used to manipulate a cell (e.g., a cell described herein), e.g., to deliver a payload, or edit a target nucleic acid, e.g., to improve immunotherapy, e.g. cancer immunotherapy. Typically an eiCas9 molecule/gRNA molecule complex is used to deliver a payload and an eaCas9 molecule/gRNA complex is used to edit or alter the structure of a target nucleic acid. Exemplary genes that can be modulated include, e.g., one or more genes described herein, e.g., PD-L1 and/or PD-L2 genes. VIIB. Targets: Pathways and Genes

Cas9 molecules and gRNA molecules, e.g., a Cas9 molecule/gRNA molecule complex, can be used to manipulate one, two, three or more, elements or a pathway, e.g., by targeting sequences that encode an RNA or protein of a pathway, or sequences that control the expression of an RNA or protein of a pathway. In an embodiment, an element of a first pathway and an element of a second pathway are manipulated. In an embodiment, manipulation comprises delivery of a payload to, or editing, a target nucleic acid. Typically an eiCas9 molecule/gRNA molecule complex is used to deliver a payload and an eaCas9 molecule/gRNA complex is used to edit or alter the structure of a target nucleic acid. Delivery or editing can be performed in vitro, ex vivo, or in vivo.

An element of a pathway can be up or down regulated, e.g., the expression of a gene encoding a protein of a pathway can be increased or decreased. The increase or decrease can be effected by delivery of a payload (e.g., a transcription factor or inhibitor of a transcription factor) or by editing a target nucleic acid (e.g., the use of a template nucleic acid to alter a sequence, e.g., correct or introduce a mutation, in e.g., a control or coding region).

Exemplary pathways comprise pathways associated with: cell proliferation; cell cycle; carbon metabolism; energy metabolism; glycolysis, anerobic respiration, anerobic respiration; transmembrane signal transduction, angiogenesis, DNA replication or repair, or pain.

Exemplary pathways and genes are discussed herein. It will be understood that a pathway or gene can be associated with one or more aspect of cell or organismal function, e.g., a pathway or gene can be involved in both cancer and energy metabolism. Manipulation of a pathway or gene is not limited to the exemplary cell or organismal function listed below. In an embodiment a pathway is associated with one or more diseases or conditions.

In an embodiment, the pathway is associated with cancer, e.g., associated with

proliferation (e.g., RAF pathway), evading growth repressors, resisting cell death, enabling replicative immortality/aging, inducing angiogenesis, activating invasion and metastasis, energy metabolism and evading, cancer stem cells, cytokine-receptor interactions, or tumor suppressors. In an embodiment, the pathway is associated with cell cycle control. In an embodiment, the pathway is associated with angiogenesis.

Pathways and genes associated with cancer are described herein, e.g., include the following:

Table VII-14. Target Genes from Selected Pathways

Protein/Gene Pathway l)i sease CRISPR iilion Cancer

PI3K Proliferation Down

B-Raf Proliferation 66 % of all melanoma cancers have a Down sin gle substitution in codon 599

AKT Proliferation Down

PTEN Proliferation Germline mutations leading to a Down predisposition to breast and thyroid cancer

Mutations found in sporadic

brain, breast and prostate

mTOR Proliferation Down

JUN Proliferation Down

FOS Proliferation Down

ERK Proliferation Down

MEK Proliferation Down

TGF-b Proliferation Down

Myc Proliferation Down

K-Ras Proliferation Mutated in lung cancer (10% of all Down

Asians and 30% of all Caucasians)

Src Proliferation Down

PYK2 Proliferation Down

PAK Proliferation Down

FAK Proliferation Down

PKA Proliferation Down

RAC Proliferation Down

ALK Proliferation Mutated in a subset (2-7%) of lung

cancers

Rb Evading growth Up suppressors/ pro- apoptotic

P53 Evading growth Mutation in colon, lung, esophagus, Up suppressors/ pro- breast, liver, brain reticuloendothelial apoptotic tissues, and hemopoietic tissues

APC Evading growth Mutations found in colon and intestine

suppressors/ pro- apoptotic

CDK4/6 Evading growth Up suppressors/ pro- apoptotic

INK4B Evading growth Up suppressors/ pro- apoptotic

CDK2 Evading growth Up suppressors/ pro- apoptotic

WNT Evading growth Up suppressors/ pro- apoptotic

WAF1 Evading growth Up suppressors/ pro- apoptotic

Frizzled Evading growth Up suppressors/ pro- apoptotic

VHL Evading growth Mutated in all clear cell renal Up suppressors/ pro- carcinomas

apoptotic

Fas ligand Resisting cell death/ Down anti-apoptotic

Fas receptor Resisting cell death/ Down anti-apoptotic

Caspase 8 Resisting cell death/ Down anti-apoptotic

Caspase 9 Resisting cell death/ Down anti-apoptotic

Bcl-2 Resisting cell death/ Correct mutation large deletion in Down anti-apoptotic follicular lymphoma, breast prostate CLL, melanoma

Bcl-xL Resisting cell death/ Down anti-apoptotic

Bcl-w Resisting cell death/ Down anti-apoptotic

Mcl-1 Resisting cell death/ Down anti-apoptotic

Bax Resisting cell death/ Down anti-apoptotic

Bak Resisting cell death/ Down anti-apoptotic

IGF-1 Resisting cell death/ Down anti-apoptotic

Puma Resisting cell death/ Down anti-apoptotic

Bim Resisting cell death/ Down anti-apoptotic

Beclin-1 Resisting cell death/ Down anti-apoptotic

TGF-b Enabling replicative

immortality/aging

Telomerase/TERT Enabling replicative Down immortality/aging

ATAD2 Enabling replicative

immortality/aging

DAF-2 Enabling replicative

immortality/aging

SRT Enabling replicative

immortality/aging

Eph-A/B Inducing angiogenesis Down Robo Inducing angiogenesis Down

Neuropilin Inducing angiogenesis Down

Notch Inducing angiogenesis Down

Endo statin Inducing angiogenesis Down

Angio statin Inducing angiogenesis Down

FGF family Inducing angiogenesis Down

Extracellular Inducing angiogenesis Down matrix-degrading

proteases (e.g.,

MMP-2 & MMP-

9)

VEGF-A Inducing angiogenesis Down

TSP-1 Inducing angiogenesis Down

VEGFPv-1 Inducing angiogenesis Down

VEGFR-2 Inducing angiogenesis Down

VEGFR-3 Inducing angiogenesis Down

NF2 Activating invasion and Down metastasis

LKB1 Activating invasion and Up- regulated in multiple cancer, Down metastasis including intestine

Snail Activating invasion and Down metastasis

Slug Activating invasion and Down metastasis

Twist Activating invasion and Down metastasis

Zebl/2 Activating invasion and Down metastasis

CCLR5 Activating invasion and Down metastasis cysteine cathepsin Activating invasion and Down protease family metastasis

Extracellular Activating invasion and Down matrix-degrading metastasis

proteases (e.g.,

MMP-2 & MMP-

9)

EGF Activating invasion and Down metastasis

CSF-1 Activating invasion and

metastasis

PP2 Energy metabolism Down eIF4E Energy metabolism Down

RSK Energy metabolism Down

PIK3CA Energy metabolism Mutated in many breast, bladder Down cancers and hepatocellular carcinoma

BAP1 Energy metabolism Mutated in renal cell carcinoma Down

TWIST (TF) Cancer Stem Cells Down

HIF-lcc Cancer Stem Cells Over expressed in renal cell carcinoma Down

HER2/neu Cancer Stem Cells Down

Snail (TF) Cancer Stem Cells Down

Wnt Cancer Stem Cells Down

EPCAM Cancer Stem Cells Overexpressed in breast, colon, uterus Down and other cancers

EGF Cytokine-receptor Down interactions

TGFa Cytokine-receptor Down interactions

PDGF Cytokine-receptor Down IGF-1 interactions

H3K27Me Histone methylation Lsh Helicase activity

BLM Helicase activity Bloom's syndrome >Cancer Correct

WRN Helicase activity Werner's syndrome > Cancer Correct

RTS Helicase activity Rothmund- Thompson > Cancer Correct

XPA through XPG Nucleotide excision Xeroderma pigmentosa

repair

XPB Nucleotide excision Cockayne's syndrome

repair

XAB2 Nucleotide excision

repair

XPD Nucleotide excision Cockayne's syndrome

repair

TFIIH Nucleotide excision

repair

RFC Nucleotide excision

repair

PCNA Nucleotide excision

repair

LIG 1 Nucleotide excision

repair

Flap Nucleotide excision

endonueclease 1 repair

MNAT Nucleotide excision

repair

MMS19 Nucleotide excision

repair

RAD23A Nucleotide excision

repair

RAD23B Nucleotide excision

repair RPA1 Nucleotide excision

repair

RPA2 Nucleotide excision

repair

CCNH Nucleotide excision

repair

CDK7 Nucleotide excision

repair

CETN2 Nucleotide excision

repair

DDB1 Nucleotide excision

repair

DDB2 Nucleotide excision

repair

ERCC1 Nucleotide excision

repair

ATM Recombinational repair

NBN Recombinational repair

BRCA1 Recombinational repair Breast, ovarian and pancreatic cancer Correct susceptibility or Up

BRCA2 Recombinational repair Breast cancer and ovarian Correct susceptibility or UP

RAD51 Recombinational repair

RAD52 Recombinational repair

WRN Recombinational repair

BLM Recombinational repair

FANCB Recombinational repair

MLH1 Mismatch repair Multiple (including colon and uterus)

MLH2 Mismatch repair Multiple (including colon and uterus)

MSH2 Mismatch repair MSH3 Mismatch repair

MSH4 Mismatch repair

MSH5 Mismatch repair

MSH6 Mismatch repair Multiple (including colon and uterus)

PMS1 Mismatch repair

PMS2 Mismatch repair Multiple (including colon and uterus)

PMS2L3 Mismatch repair

Aiiinii

DAF-2

IGF-1

SRT1

Table VII-15

BRAF, CDKA, CDKN2A, CDKN2B, CDKND, MC1R, TERT,

Melanoma

ATF1, CREB1, EWSR1

Non-Hodgkin Lymphoma CASP10, EGFR, IRF1, PIK3CA

Osteosarcoma CKEK2, LOJ18CR1, RBI

Ovarian PRKN, AKT1

KRAS, BRCA2, CDKN2A, MANF, PALB2, SMAD4, TP53,

Pancreatic

IPF1

MLHl, MSH2, MSH6, and PMS2, BRCA 1, HOXB13, CHEK2,

Prostate

ELAC2, EPHB2, SDR5A2, PRKAR1A, PMC1

Papillary and Follicular BRAF, NARAS, ERCl, FOXEl, GOLGA5, NCOA4, NKX2-1, Thyroid PMC1, RET, TFG, TPR, TRIM24, TRIM27, TRIM33

Erwing Sarcoma ERG, ETV1, ETV4, EWSR1, FLU

BRC, AMCR2, GMPS, JAK2, AF10, ARFGEF12, CEBPA, FLT3, KIT, LPP, MLF1, NPM1, NSD1, NUP214, PICALM,

Leukemia

RUNX1, SH3GL1, WHSC1L1, ETV6, RARA, BCR,

ARHGAP26, NF1, PTPN11, GATA1

Any of the following cancer associated genes provided in Table VII-16 can be targeted.

Table VII-16

Exemplary Target Genes Associated With Cancer

ABL1, ABL2, ACSL3, AF15Q14, AF1Q, AF3p21, AF5q31, AKAP9, AKT1, AKT2, ALDH2, ALK, AL017, APC, ARHGEF12, ARHH, ARID 1 A, ARID2, ARNT, ASPSCR1, ASXL1, ATF1, ATIC, ATM, ATRX, AXIN1, BAP1, BCL10, BCL11A, BCL11B, BCL2, BCL3, BCL5, BCL6, BCL7A, BCL9, BCOR, BCR, BHD, BIRC3, BLM, BMPR1A, BRAF, BRCA1, BRCA2, BRD3, BRD4, BRIP1, BTG1, BUB IB, C12orf9, C15orf21, C15orf55, C16orf75, C2orf44, CAMTA1, CANT1, CARD11, CARS, CBFA2T1, CBFA2T3, CBFB, CBL, CBLB, CBLC, CCDC6, CCNB1IP1, CCND1, CCND2, CCND3, CCNE1, CD273, CD274, CD74, CD79A, CD79B, CDH1, CDH11, CDK12, CDK4, CDK6, CDKN2A, CDKN2a(pl4), CDKN2C, CDX2, CEBPA, CEPl, CHCHD7, CHEK2, CHIC2, CHNl, CIC, CIITA, CLTC, CLTCL1, CMKOR1, CNOT3, COL1A1, COPEB, COX6C, CREB1, CREB3L1, CREB3L2, CREBBP, CRLF2, CRTC3, CTNNB 1, CYLD, D10S170, DAXX, DDB2, DDIT3, DDX10, DDX5, DDX6, DEK, DICERl, DNM2, DNMT3A, DUX4, EBF1, ECT2L, EGFR, EIF4A2, ELF4, ELK4, ELKS, ELL, ELN, EML4, EP300, EPS 15, ERBB2, ERCC2, ERCC3, ERCC4, ERCC5, ERG, ETVl, ETV4, ETV5, ETV6, EVIl, EWSRl, EXTl, EXT2, EZH2, EZR, FACL6, FAM22A, FAM22B, FAM46C, FANCA, FANCC, FANCD2, FANCE, FANCF, FANCG, FBXOl l, FBXW7, FCGR2B, FEV, FGFR1, FGFRIOP, FGFR2, FGFR3, FH, FHIT, FIP1L1, FLU, FLJ27352, FLT3, FNBP1, FOXL2, FOXOIA, FOX03A, FOXP1, FSTL3, FUBP1, FUS, FVT1, GAS7, GATA1, GATA2, GAT A3, GMPS, GNA11, GNAQ, GNAS, GOLGA5, GOPC, GPC3, GPHN, GRAF, H3F3A,

HCMOGT-1, HEAB, HERPUD1, HEY1, HIP1, HIST1H3B, HIST1H4I, HLF, HLXB9, HMGA1, HMGA2, HNRNPA2B1, HOOK3, HOXA11, HOXA13, HOXA9, HOXC11, HOXC13, HOXD11, HOXD13, HRAS, HRPT2, HSPCA, HSPCB, IDHl, IDH2, IGH@, IGK@, IGL@, IKZFl, IL2, IL21R, IL6ST, IL7R, IRF4, IRTA1, ITK, JAK1, JAK2, JAK3, JAZF1, JUN, KCNJ5, KDM5A, KDM5C, KDM6A, KDR, KIAA1549, KIF5B, KIT, KLF4, KLK2, KRAS, KTN1, LAF4, LASP1, LCK, LCP1, LCX, LHFP, LIFR, LMOl , LM02, LPP, LRIG3, LYL1, MADH4, MAF, MAFB, MALT1, MAML2, MAP2K1, MAP2K2, MAP2K4, MAX, MDM2, MDM4, MDS1, MDS2, MECT1, MED 12, MEN1, MET, MITF, MKL1, MLF1, MLH1, MLL, MLL2, MLL3, MLLT1, MLLT10, MLLT2, MLLT3, MLLT4, MLLT6, MLLT7, MNl, MPL, MSF, MSH2, MSH6, MSI2, MSN, MTCPl, MUCl, MUTYH, MYB, MYC, MYCL1, MYCN, MYD88, MYH11, MYH9, MYST4, NACA, NBS1, NCOA1, NCOA2, NCOA4, NDRG1, NF1, NF2, NFE2L2, NFIB, NFKB2, NIN, NKX2-1, NONO, NOTCH1, NOTCH2, NPM1, NR4A3, NRAS, NSD1, NT5C2, NTRK1, NTRK3, NUMA1, NUP214, NUP98, OLIG2, OMD, Exemplary Target Genes Associated With Cancer

P2RY8, PAFAH1B2, PALB2, PAX3, PAX5, PAX7, PAX 8, PBRM1, PBX1, PCM1, PCSK7,

PDE4DIP, PDGFB, PDGFRA, PDGFRB, PERI, PHF6, PHOX2B, PICALM, PIK3CA, PIK3R1, PIMl, PLAG1, PML, PMS1, PMS2, PMX1, PNUTL1, POT1, POU2AF1, POU5F1, PPARG, PPP2R1A, PRCC, PRDM1, PRDM16, PRF1, PRKAR1A, PRO1073, PSIP2, PTCH, PTEN, PTPN11, RAB5EP, RACl, RAD51L1, RAFl, RALGDS, RANBP17, RAPIGDSI, RARA, RBI, RBM15, RECQL4, REL, RET, RNF43, ROS1, RPL10, RPL22, RPL5, RPN1, RUNDC2A, RUNX1, RUNXBP2, SBDS, SDC4, SDH5, SDHB, SDHC, SDHD, SEPT6, SET, SETBP1, SETD2, SF3B1, SFPQ, SFRS3, SH2B3, SH3GL1, SIL, SLC34A2, SLC45A3, SMARCA4, SMARCB1, SMARCE1, SMO, SOCS1, SOX2, SRGAP3, SRSF2, SS18, SS18L1, SSH3BP1, SSX1, SSX2, SSX4, STAT3, STK11, STL, SUFU, SUZ12, SYK, TAF15, TALI, TAL2, TCEA1, TCF1, TCF12, TCF3, TCF7L2, TCL1A, TCL6, TERT, TET2, TFE3, TFEB, TFG, TFPT, TFRC, THRAP3, TIF1, TLX1, TLX3, TMPRSS2, TNFAIP3, TNFRSF14, TNFRSF17, TNFRSF6, TOPI, TP53, TPM3, TPM4, TPR, TRA@, TRAF7, TRB @, TRD@, TRIM27, TRIM33, TRIP11, TSC1, TSC2, TSHR, TTL, U2AF1, USP6, VHL, VTI1A, WAS, WHSC1, WHSC1L1, WIF1, WRN, WT1, WTX, WWTR1, XPA, XPC, XPOl, YWHAE, ZNF145, ZNF198, ZNF278, ZNF331, ZNF384, ZNF521, ZNF9, or ZRSR2

Exemplary pathways and genes associated with energy metabolism are provided in Table VII-17. Exemplary metabolic targets disclosed herein may be modulated using CRISPR/Cas9 as described herein. Modulation may be used to knockdown a gene of interest, correct a defect or mutation in the gene, or to activate a gene of interest.

Table VII-17

PL, pancreatic lipase Knock down sPLA2, secretory phospholipase A2 Knock down

ACC, acetyl-CoA carboxylase Knock down

CPT, carnitine palmitoyl transferase Knock down

FAS, fatty- acid synthase Knock down

MTP, microsomal triglyceride-transfer protein Knock down

Insulin receptor Correct defects or activate

SU receptor/K+ ATP channel Activate with mutation a-glucosidase Knock down

PPARy Activate with mutation

Glycogen phosphorylase Knock down

Fructose- 1, 6-bisphosphatase Knock down

gluco se- 6-pho sphatase Knock down

PTP-1B Knock down

SHIP-2 Knock down

GSK-3 Knock down

lkB kinase Knock down

PKCq Knock down

GLP1R Correct mutation

GIPR Correct mutation

GPR40 Correct mutation

GPR119 Correct mutation

GPR41 Correct mutation

GPR43 Correct mutation

GPR120 Correct mutation

GCGR Correct mutation

PAC1 Correct mutation

VPAC2 Correct mutation

Yl Knock down

GHSR Knock down CCKAR Correct mutation b2 Correct mutation a2 Knock down

MT1 Knock down

M3 Correct mutation

CBI Knock down

P2Y Correct mutation

H3 Inhibit

MCH-R1 Correct mutation

MCH-R2 Correct mutation

Ghrelin R Inhibit

FASN Inhibit

Bombesin-R3 Inhibit

CCK-A Receptor Correct mutation

Seratonin System Correct mutation

CBI Cannabinoid Receptors Inhibit

Dopaminergic System Correct mutation

Enter o statin Mutate to super agonist

CNTF Mutate to super agonist

CNTF-R Correct mutation

SOCS-3 Knock down

46a Knock down

PrPP Receptors Correct mutation

Amylin Mutate to super agonist

CRH System Mutate to super agonist

Galanin Receptors Knock down

Orexin Receptors Knock down

Noradrenalin System Mutate to super agonist

CART Mutate to super agonist

FATP4 Knock down Pancreatic Lipase Knock down

ACRP30 Super agonist mutations

Thyroid Hormone Correct mutation

B-3 Adrenergic Receptor Correct mutation

UCPs Upregulate

PTP-1B Knock down

MC3 Correct mutation

ACC2 Knock down

Perilipin Knock down

HMGIC Knock down

l lBHSD-1 Knock down

Glucagon R Knock down

Glucocoricoid R Knock down

l lbeta-HSD I Knock down

PGC-1 Correct mutation

DPPP-rV Knock down

GLP Mutate to super agonist

GIP Mutate to super agonist

GLP-IR Correct mutation

AMP Kinase Correct mutation

IKK-b Knock down

PPARa/g Knock down

INS-R Knock down

SGLT Knock down

a-glucosidase Knock down

HMGCR Knock down

PCSK9 Knock down

ApoB-100 Knock down

Leptin Mutate to super agonist

Leptin Receptor Mutate to constitutively active receptor

MC4R Mutate to constitutively active

receptor

VOMC Mutate MSH region to super

agonist

AGRP Knock down

IVPY Receptors Introduce constitutively active

mutations

5HT2C Introduce constitutively active

mutations

GLP-1 Mutate to super agonist

GLP-1 Receptor Mutate to constitutively active

receptor

In an embodiment, the pathways and genes described herein, e.g., in Table VII-17, are also associated with diabetes, obesity, and/or cholesterol and lipids.

Exemplary pathways and genes associated with the cell cycle are provided in Table VII- 18.

Table VII-18

CELL CYCLE PATHWAYS and REPRESENTATI VE CEN ES

FANCD2 Exonuclease RIPI

SMC1 DNA Polymerase delta MyD88

BLM1 (POLDl, POLD2,POLD3, IRAK

BRCA1 and POLD4 -genes NIL

H2AX encoding subunits) IKK

ATR Topoisomerase 1 NF-Κβ

RPA Topoisomerase 2 IKBCC

ATRIP RNAseHl IAP

RAD9 Ligase 1 Caspase 3

RAD1 DNA polymerase 1 Caspase 6

HUS DNA polymerase 3 Caspase 7

RAD 17 Primase Caspase 8

RFC Helicase Caspase 10

CHK1 Single- strand binding HDAC1

TLK1 proteins HDAC2

CDC25 Cytochrome C

Bxl-xL

STAT3

STAT5

DFF45

Vcl-2

ENDO-G

PI3K

Akt

Calpain

Bad

Bax

Ubiquitin-mediated proteolysis Hypoxia Cell Proliferation

HIF-lcc MAPK

El HERC1 TRAF6 MAPKK E2 UBE2Q MEKK1 HIF-Ιβ MAPKKK

E3 UBE2R COP1 Refl c-Met

UBLE1A UBE2S PIFH2 HSP90 HGF

UBLE1B UBE2U cIAP VEGF ERKS1/2

UBLE1C UBE2W PIAS PAS ATK

UBE2A UBE2Z SYVN ARNT PKCs

UBE2B AFCLLCN NHLRC1 VHL Paxilin

UBE2C UBE1 AIRE HLF FAK

UBE2A E6AP MGRN1 EPF Adducin

UBE2E UBE3B BRCA1 VDU2 PYK1

UBE2F Smurf FANCL SUMORESUME RB

UBE2G1 Itch MIDI SENP1 RBI

UBE2G2 HERC2 Cdc20 Calcineurin A Raf-1

UBE2I HERC3 Cdhl RACK1 A-Raf

UBE2J1 HERC4 Apcl PTB B-raf

UBE2J2 UBE4A Apc2 Hur MEK1/2

UBE2L3 UBE4B Apc3 PHD2 ERK1/2

UBE2L6 CHIP Apc4 SSAT2 Ets

UBE2M CYC4 Apc5 SSAT1 Elkl

UBE2N PPR19 Apc6 GSK3 SAP1

UBE20 UIP5 Apc7 CBP cPLA2

WWPI Mdm2 Apc8 FOX04

WWP2 Parkin Apc9 FIH-1

TRIP12 Trim32 Ape 10

NEED4 Trim37 Apcl l

ARF-BP1 SIAH-1 Ape 12

EDD1 PML

Cell survival Cell cycle arrest

SMAD1 P21

SMAD5 BAX

SAMD8 MDR LEF1 DRAIL IGFBP3

TCF3 GADD45

TCF4

P300

HAT1

PI3K

Akt

GF1

Exemplary cell cycle genes characterized by their function are provided in Table VII-19.

Table VII-19

CIP/KIP family CHk2

P21 ATM

P27 ATR

P57 CDC2

HDAC1

HDAC2

Exemplary pathways and genes associated with the angiogenesis are described provided in Table VII-20.

Table VII-20

ERK1

ERK2

cPLA2

MEK1

MEK2

Exemplary pathways and genes associated with the mitochondrial function are provided in Table VII-24. Table VII-24

FATP1-6 aminotransferase 2, aminotransferase 2,

CPT-1 mitochondrial mitochondrial

CACT Isobutytyl-CoA 2-methylbutytyl-CoA

CPT-II dehydrogenase Dehydrogenase

SCAD (Branched Chain (Branched Chain

MCAD Keto Acid Keto Acid

VLCAD Dehydrogase Dehydrogenase

ETF-DH Complex) Complex)

Alpha-ETF Hydratase Hydratase

Beta-ETF HMG-CoA lyase 2- methyl-3-OH-

SCHAD butyryl-CoA

LCHAD dehydrogenase

MTP 3- Oxothiolase

LKAT

DECR1

HMGCS2

HMGCL

Additional mitochond rial acnes and related disea ses caused b mutation s

Mt-NDl Leber's hereditary optic neuropathy

Mt-ND4 Leber's hereditary optic neuropathy

Mt-ND6 Leber's hereditary optic neuropathy

OPA1 Autosomal dominant optic atrophy

CMT2A Charcot-Marie-Toothhereditary neuropathy type 2A

mt-TK Myoclonic epilepsy with ragged red fibres

Mitochondrial Related diseases

Respiraton chain

genes

NADH CoQ Alpers, Alzheimer's, Parkinsonism, Cardiomyopathy, Deficiency (Barth Reductase and/or Lethal Infantile), Encephalopathy, Infantile CNS, Leber's, Leigh,

Longevity, MELAS, MERRF, Myopathy + CNS, PEO, Spinal cord disorders Succinate-CoQ Kearns-Sayre, Leigh's, Myopathy (e.g., Infantile + CNS), Paraganglioma,

Reductase Pheochromocytoma

CoQ-Cytochrome C Cardiomyopathy, Fatal infantile, GRACILE, Leber's, Myopathy (e.g., +

Reductase CNS, PEO)

Cytochrome C Alper's, Ataxia, Deafness, Leber's, Leigh's, Myopathy (e.g., Infantile (e.g.,

Oxidase Fatal, Benign), Adult), Rhabdomyolysis, PEO, KSS, MNGIE, MERRF,

MELAS

ATP Synthase Cardiomyopathy, Encephalopathy, Leber's, Leigh, Multisystem, NARP Complex 1 (Wl)l l-l 1 milrinone Oxidoreduclase)

Nuclear encoded Mitochondral DNA Supernumerary Subunits involved proteins encoded proteins subunits in regulation of

NDUFS1: Childhood ND1 NDUFAB1 (SDAP): Complext I activity encephalopathy; Most ND2 Carrier of fatty acid NDUFS4 (AQDQ) common Complex I ND3 chain Functions:

mutations (3%) ND4 NDUFA1 (MWFE) Increased Complex

NDUFS2: ND4L Primarily expressed I activity with

Cardiomyopathy + ND5 in heart & skeletal phosphorylation

Encephalomyopathy ND6 muscle Disorders:

NDUFS3: Leigh Disorders: Multisystem

NDUFS7: Leigh Encephalopathies childhood

NDUFS8: Leigh NDUFA2: encephalopathy

NDUFV1: Childhood Encephalopathy & with Complex I encephalopathy Cardiomyopathy deficiency; Leigh

NDUFV2: NDUFA9: Leigh syndrome

Encephalopathy + syndrome

Cardiomyopathy NDUFA10: Leigh

ELAC2: syndrome

Cardiomyopathy, NDUFA11

Hypertrophic Disorder:

Encephalopathy &

Cardiomyopathy NDUFA12: Leigh syndrome

NDUFB9:

Hypotonia

NDUFS6: Lethal

Infantile

Mitochondrial

Disease

Proteins involved in Other

Complex I assembly NDUFA13: Thyroid

• NDUFAF1: carcinoma (Hurthle

Cardiomyopathy + cell)

Encephalomyopathy NDUFB3: Severe

• NDUFAF2 lethal mitochondrial

(NDUFA12L): complex I deficiency

Childhood MTHFR deficiency

encephalopathy; MGME1: PEO +

Usually null Myopathy

mutations

• NDUFAF3: Lethal

neonatal

encephalopathy

• NDUFAF4:

Encephalopathy

• C60RF66:

Encephalopathy

• C8orf38: Leigh

syndrome

• C20orf7: Lethal

UQCRH (Subunit 6) May mediate formation of complex between cytochromes c and cl

Ubiquinone-binding protein (UOBC; Redox-linked proton pumping

UQPC; UQCRB; UQBP; Subunit 7)

UOCRO (Subunit 8) Binds to ubiquinone

Ubiquinol-cytochrome C reductase Interacts with cytochrome cl

complex, 7.2-KD Subunit (UCRC;

UQCR10; Subunit 9)

UQCR (UQCR11; Subunit 10) function as iron-sulfur protein binding factor

Cleavage product of UQCRFS1

(Cytochrome b-cl complex subunit 11)

In ner mom hrane rotei ns and related d i sorde rs

ABCB7: Ataxia + Anemia

ACADVL: Myopathy

ADCK3: SACR9

AGK: Sengers

ATP5A1: Encephalopathy, neonatal

ATP5E: Retardation + Neuropathy

BRP44L: Encephalopathy

cl2orf62: Encephalocardiomyopathy

Cardiolipin: Barth

COX4I2: Pancreas + Anemia

COX6B 1 : Encephalomyopathy

CPT2: Myopathy

CRAT: Encephalomyopathy

CYC1: Hyperglycemia & Encephalopathy

CYCS

CYP11A1

CYP11B1

CYP11B2

CYP24A1 CYP27A1: Cerebrotendinous Xanthomatosis

CYP27B1

DHODH

DNAJC19: Cardiac + Ataxia

FASTKD2: Encephalomyopathy

GPD2

HADHA: Multisystem; Myopathy

HADHB: Encephalomyopathy

HCCS: MIDAS

L2HGDH: Encephalopathy

MMAA

MPV17: Hepatocerebral

NDUFA1: Encephalopathy

NDUFA2: Leigh + Cardiac

NDUFA4: Leigh

NDUFA9: Leigh

NDUFA10: Leigh

NDUFAl l: Encephalocardiomyopathy

NDUFA12: Leigh

NDUFA13

NDUFB3: Lethal infantile

NDUFB9: Encephalopathy

NDUFV1: Encephalopathy

NDUFV2: Encephalopathy + Cardiac NDUFS1: Leukodystrophy

NDUFS2: Encephalopathy + Cardiac NDUFS3: Dystonia

NDUFS4: Encephalopathy

NDUFS6: Lethal infantile

NDUFS7: Encephalopathy

NDUFS8: CNS + Cardiac OPA1: Optic atrophy

OPA3: Optic atrophy

PDSS1: Coenzyme Q10 deficiency

SDHA: Leigh; Cardiac; Paraganglioma

SDHB: Paraganglioma

SDHC: Paraganglioma

SDHD: Paraganglioma

SLC25A carriers

SLC25A1: Epileptic encephalopathy

SLC25A3: Cardiac; Exercise intolerance

SLC25A4: PEOA2

SLC25A12: Hypomyelination

SLC25A13: Citrullinemia

SLC25A15: HHH

SLC25A19: Microcephaly

SLC25A20: Encephalocardiomyopathy

SLC25A22: Myoclonic epilepsy

SLC25A38: Anemia

Paraplegin: SPG7

TEV1M8A: Deaf-Dystonia-Dementia

UCP1

UCP2

UCP3

UQCRB: Hypoglycemia, Hepatic

UQCRC2: Episodic metabolic encephalopathy

UQCRQ: Encephalopathy

Pathways and genes associated with DNA damage and genomic instability include the following methyl transferases, histone methylation, helicase activity, nucleotide excision repair, recombinational repair, or mismatch repair provided in Table VII-21. See also Table VI-22. Table VII-21

Dssl

Histone Methylation

ASH1L SETD4

DOT1L SETD5

EHMT1 SETD6

EHMT2 SETD7

EZH1 SETD8

EZH2 SETD9

MLL SETDB 1

MLL2 SETDB2

MLL3 SETMAR

MLL4 SMYD1

MLL5 SMYD2

NSD1 SMYD3

PRDM2 SMYD4

SET SMYD5

SETBP1 SUV39H1

SETD1A SUV39H2

SETD1B SUV420H1

SETD2 SUV420H2

SETD3

Table VII-22

MEF2A Coronary artery disease

CRX Dominant cone-rod dystrophy

FOCX2 Lymphedema-distichiasis

NF-κΒ Autoimmune arthritis, asthma, septic Activation shock, lung fibrosis,

glomerulonephritis , athero sclero sis , and AIDS

NF-KB Inhibition Apoptosis, inappropriate immune cell development, and delayed cell growth

NARA2 Parkinson disease

LHX3 Pituitary disease

GAT4 Congenital heart defects

P53, APC Cancer

CTCF Epigenetics and cell growth regulation

EGR2 Congenital hypomyelinating

neuropathy (CHN) and Charcot-Marie- Tooth type 1 (CMT1)

STAT family Cancer and immunosuppression

NF-AT family Cancer and inflammation

AP-1 family Cancer and inflammation

A gene including receptors and ionophores relevant to pain in this table can be targeted, by editing or payload delivery. Pathways and genes associated with pain are described herein, e.g., include the following those in Table VII-23.

Table VII-23

nociceptive central 5HT1A central inhibition agonists (activation) serve as analgesic,

antidepressants, anxiolytics, psychosis

nociceptive central 5HT1A central inhibition antagonists can work as antidepressants, nootropics nociceptive central 5HT1B central inhibition migraines

nociceptive central 5HT1D central inhibition migraines

nociceptive central 5HT1E central inhibition

nociceptive central 5HT1F central inhibition agonists - psychedelics nociceptive central 5HT1F central inhibition antagonists - atypical

antipsychotics, NaSSAsm treatig sertonin syndrome, sleeping aid

nociceptive central 5HT2A central inhibition agonists - psychadelics nociceptive central 5HT2A central inhibition antagonists - atypical

antipsychotics, NaSSAs, treating seratonin syndrome, sleeping aid

nociceptive central 5HT2B central inhibition migraines

nociceptive central 5HT2C central inhibition antidepressant, orexigenic, anorectic, antipsychotic nociceptive central 5HT3 central inhibition antiemetic

nociceptive central 5HT4 central inhibition gastroproknetics

nociceptive central 5HT5A central inhibition

nociceptive central 5HT5B central inhibition

nociceptive central 5HT6 central inhibition antidepressant (antagonists and agonists), anxiolytic (antagonists and agonists), nootropic (antagonists), anorectic (antagonists) nociceptive central 5HT7 central inhibition antidepressant (antagonists), anxiolytics (antagonists), nootropic (antagonists) nociceptive central CB1 central inhibition

nociceptive central GABA central inhibition

nociceptive central GABAA-$ central inhibition

nociceptive central GABAB-R central inhibition

nociceptive central Glucine-R central inhibition

nociceptive central NE central inhibition

nociceptive central Opiod central inhibition

receptors

nociceptive central c-fos gene expression

nociceptive central c-jun gene expression

nociceptive central CREB gene expression

nociceptive central DREAM gene expression

nociceptive peripheral K+ channel membrane

excitability of

primary afferents

nociceptive peripheral Navl.8 membrane

excitability of

primary afferents

nociceptive peripheral Navl.9 membrane

excitability of

primary afferents

nociceptive peripheral CaMKIV peripheral

sensitization

nociceptive peripheral COX2 peripheral

sensitization

nociceptive peripheral cPLA2 peripheral sensitization nociceptive peripheral EP1 peripheral sensitization nociceptive peripheral EP3 peripheral sensitization nociceptive peripheral EP4 peripheral sensitization nociceptive peripheral ERK1/2 peripheral sensitization nociceptive peripheral IL-lbeta peripheral sensitization nociceptive peripheral JNK peripheral sensitization nociceptive peripheral Navl.8 peripheral sensitization nociceptive peripheral NGF peripheral sensitization nociceptive peripheral p38 peripheral sensitization nociceptive peripheral PKA peripheral sensitization nociceptive peripheral PKC peripheral isoforms sensitization nociceptive peripheral TNFalpha peripheral sensitization nociceptive peripheral TrkA peripheral sensitization nociceptive peripheral TRPV1 peripheral sensitization nociceptive central AMPA/kain postsynaptic ate-R transmission nociceptive central K+ channels postsynaptic transmission nociceptive central mGlu-$ postsynaptic transmission nociceptive central Navl.3 postsynaptic transmission nociceptive central NK1 postsynaptic transmission nociceptive central NMDA-R postsynaptic transmission nociceptive peripheral Adenosine- presynaptic

R transmission nociceptive peripheral mGluR presynaptic transmission nociceptive peripheral VGCC presynaptic transmission nociceptive central ERK signal

transduction nociceptive central JNK signal

transduction nociceptive central p38 signal

transduction nociceptive central PKA signal

transduction nociceptive central PKC signal

isoforms transduction nociceptive peripheral ASIC transduction nociceptive peripheral BK1 transduction nociceptive peripheral BK2 transduction nociceptive peripheral DRASIC transduction nociceptive peripheral MDEG transduction nociceptive peripheral P2X3 transduction nociceptive peripheral TREK-1 transduction nociceptive peripheral TRPM8 transduction nociceptive peripheral TRPV1 transduction nociceptive peripheral TRPV2 transduction nociceptive peripheral TRPV3 transduction neuropathic

pain

Inflammatory histamine

pain

Inflammatory ATP

pain

Inflammatory bradykinin

pain

Inflammatory CB2

pain

Inflammatory Endothelins

pain

Inflammatory H+

pain

Inflammatory Interleukins

pain

Inflammatory NGF

pain

Inflammatory prostaglandi

pain ns

Inflammatory serotonin

pain Inflammatory TNFalpha

pain

VIII. Targets: Disorders Associated with Disease Causing Organisms

Cas9 molecules, typically eiCas9 molecules or eaCas9 molecules, and gRNA molecules, e.g., an eiCas9 molecule/gRNA molecule complex, e.g., an eaCas9 molecule/gRNA molecule complex, can be used to treat or control diseases associated with disease causing organisms, e.g., to treat infectious diseases. In an embodiment, the infectious disease is treated by editing (e.g., correcting) one or more target genes, e.g., of the organism or of the subject. In an embodiment, the infectious disease is treated by delivering one or more payloads (e.g., as described herein) to the cell of a disease causing organism or to an infected cell of the subject, e.g., to a target gene. In an embodiment, the target gene is in the infectious pathogen. Exemplary infectious pathogens include, e.g., viruses, bacteria, fungi, protozoa, or mutlicellular parasites.

In an embodiment, the target gene is in the host cell. For example, modulation of a target gene in the host cell can result in resistance to the infectious pathogen. Host genes involved in any stage of the life cycle of the infectious pathogen (e.g., entry, replication, latency) can be modulated. In an embodiment, the target gene encodes a cellular receptor or co-receptor for the infectious pathogen. In an embodiment, the infectious pathogen is a virus, e.g., a virus described herein, e.g., HIV. In an embodiment, the target gene encodes a co-receptor for HIV, e.g., CCR5 or CXCR4.

Exemplary infectious diseases that can be treated by the molecules and methods described herein, include, e.g., AIDS, Hepatitis A, Hepatitis B, Hepatitis C, Herpes simplex, HPV infection, or Influenza.

Exemplary targets are provided in Table VIII- 1. The disease and causative organism are provided. Table VIII-1

African sleeping sickness

(African trypanosomiasis) Trypanosoma brucei

AIDS (Acquired

immunodeficiency syndrome) HIV (Human immunodeficiency virus)

Amebiasis Entamoeba histolytica

Anaplasmosis Anaplasma genus

Anthrax Bacillus anthracis

Arcanobacterium haemolyticum

infection Arcanobacterium haemolyticum

Argentine hemorrhagic fever Junin virus

Ascariasis Ascaris lumbricoides

Aspergillosis Aspergillus genus

Astrovirus infection Astroviridae family

Babesiosis Babesia genus

Bacillus cereus infection Bacillus cereus

Bacterial pneumonia multiple bacteria

Bacterial vaginosis (BV) multiple bacteria

Bacteroides infection Bacteroides genus

Balantidiasis Balantidium coli

Baylisascaris infection Baylisascaris genus

BK virus infection BK virus

Black piedra Piedraia hortae

Blastocystis hominis infection Blastocystis hominis

Blastomycosis Blastomyces dermatitidis

Bolivian hemorrhagic fever Machupo virus

Borrelia infection Borrelia genus

Clostridium botulinum; Note: Botulism is not an infection by Clostridium botulinum

Botulism (and Infant botulism) but caused by the intake of botulinum toxin.

Brazilian hemorrhagic fever Sabia

Brucellosis Brucella genus

Bubonic plague the bacterial family Enterobacteriaceae usually Burkholderia cepacia and other

Burkholderia infection Burkholderia species

Buruli ulcer Mycobacterium ulcerans

Calicivirus infection (Norovirus

and Sapovirus) Caliciviridae family

Campylobacteriosis Campylobacter genus

usually Candida albicans and other Candida

Candidiasis (Moniliasis; Thrush) species

Cat-scratch disease Bartonella henselae usually Group A Streptococcus and

Cellulitis Staphylococcus

Chagas Disease (American

trypanosomiasis) Trypanosoma cruzi

Chancroid Haemophilus ducreyi

Chickenpox Varicella zoster virus (VZV)

Chlamydia Chlamydia trachomatis

Chlamydophila pneumoniae

infection (Taiwan acute

respiratory agent or TWAR) Chlamydophila pneumoniae

Cholera Vibrio cholerae

Chromoblastomycosis usually Fonsecaea pedrosoi

Clonorchiasis Clonorchis sinensis

Clostridium difficile infection Clostridium difficile

Coccidioides immitis and Coccidioides

Coccidioidomycosis posadasii

Colorado tick fever (CTF) Colorado tick fever virus (CTFV)

Common cold (Acute viral

rhinopharyngitis; Acute coryza) usually rhinoviruses and coronaviruses.

Creutzfeldt-Jakob disease (CJD) PRNP

Crimean-Congo hemorrhagic

fever (CCHF) Crimean-Congo hemorrhagic fever virus

Cryptococcosis Cryptococcus neoformans

Cryptosporidiosis Cryptosporidium genus

usually Ancylostoma braziliense; multiple

Cutaneous larva migrans (CLM) other parasites

Cyclosporiasis Cyclospora cayetanensis

Cysticercosis Taenia solium

Cytomegalovirus infection Cytomegalovirus

Dengue viruses (DEN-1, DEN-2, DEN-3 and

Dengue fever DEN-4) - Flaviviruses

Dientamoebiasis Dientamoeba fragilis

Diphtheria Corynebacterium diphtheriae

Diphyllobothriasis Diphyllobothrium

Dracunculiasis Dracunculus medinensis

Ebola hemorrhagic fever Ebolavirus (EBOV)

Echinococcosis Echinococcus genus

Ehrlichiosis Ehrlichia genus

Enterobiasis (Pinworm infection) Enterobius vermicularis

Enterococcus infection Enterococcus genus

Enterovirus infection Enterovirus genus

Epidemic typhus Rickettsia prowazekii Erythema infectiosum (Fifth

disease) Parvovirus B19

Exanthem subitum (Sixth Human herpesvirus 6 (HHV-6) and Human disease) herpesvirus 7 (HHV-7)

Fasciolopsiasis Fasciolopsis buski

Fasciolosis Fasciola hepatica and Fasciola gigantica

Fatal familial insomnia (FFI) PRNP

Filariasis Filarioidea superfamily

Food poisoning by Clostridium

perfringens Clostridium perfringens

Free-living amebic infection multiple

Fusobacterium infection Fusobacterium genus

Gas gangrene (Clostridial usually Clostridium perfringens; other myonecrosis) Clostridium species

Geotrichosis Geotrichum candidum

Gerstmann-Straussler-Scheinker

syndrome (GSS) PRNP

Giardiasis Giardia intestinalis

Glanders Burkholderia mallei

Gnathostoma spinigerum and Gnathostoma

Gnathostomiasis hispidum

Gonorrhea Neisseria gonorrhoeae

Granuloma inguinale

(Donovanosis) Klebsiella granulomatis

Group A streptococcal infection Streptococcus pyogenes

Group B streptococcal infection Streptococcus agalactiae

Haemophilus influenzae

infection Haemophilus influenzae

Hand, foot and mouth disease Enteroviruses, mainly Coxsackie A virus and

(HFMD) Enterovirus 71 (EV71)

Hantavirus Pulmonary Syndrome

(HPS) Sin Nombre virus

Helicobacter pylori infection Helicobacter pylori

Hemolytic-uremic syndrome Escherichia coli 0157:H7, 0111 and (HUS) O104:H4

Hemorrhagic fever with renal

syndrome (HFRS) Bunyaviridae family

Hepatitis A Hepatitis A Virus

Hepatitis B Hepatitis B Virus

Hepatitis C Hepatitis C Virus

Hepatitis D Hepatitis D Virus

Hepatitis E Hepatitis E Virus Herpes simplex virus 1 and 2 (HS V- 1 and

Herpes simplex HSV-2)

Histoplasmosis Histoplasma capsulatum

Ancylostoma duodenale and Necator

Hookworm infection americanus

Human bocavirus infection Human bocavirus (HBoV)

Human ewingii ehrlichiosis Ehrlichia ewingii

Human granulocytic

anaplasmosis (HGA) Anaplasma phagocytophilum

Human metapneumo virus

infection Human metapneumovirus (hMPV)

Human monocytic ehrlichiosis Ehrlichia chaffeensis

Human papillomavirus (HPV)

infection Human papillomavirus (HPV)

Human parainfluenza virus

infection Human parainfluenza viruses (HPIV)

Hymenolepis nana and Hymenolepis

Hymenolepiasis diminuta

Epstein-Barr Virus Infectious

Mononucleosis (Mono) Epstein-Barr Virus (EBV)

Influenza (flu) Orthomyxoviridae family

Isosporiasis Isospora belli

unknown; evidence supports that it is

Kawasaki disease infectious

Keratitis multiple

Kingella kingae infection Kingella kingae

Kuru PRNP

Lassa fever Lassa virus

Legionellosis (Legionnaires'

disease) Legionella pneumophila

Legionellosis (Pontiac fever) Legionella pneumophila

Leishmaniasis Leishmania genus

Mycobacterium leprae and Mycobacterium

Leprosy lepromatosis

Leptospirosis Leptospira genus

Listeriosis Listeria monocytogenes

usually Borrelia burgdorferi and other

Lyme disease (Lyme borreliosis) Borrelia species

Lymphatic filariasis

(Elephantiasis) Wuchereria bancrofti and Brugia malayi

Lymphocytic choriomeningitis virus

Lymphocytic choriomeningitis (LCMV) Malaria Plasmodium genus

Marburg hemorrhagic fever

(MHF) Marburg virus

Measles Measles virus

Melioidosis (Whitmore's disease) Burkholderia pseudomallei

Meningitis multiple

Meningococcal disease Neisseria meningitidis

Metagonimiasis usually Metagonimus yokagawai

Microsporidiosis Microsporidia phylum

Molluscum contagiosum (MC) Molluscum contagiosum virus (MCV)

Monkeypox Monkeypox virus

Mumps Mumps virus

Murine typhus (Endemic typhus) Rickettsia typhi

Mycoplasma pneumonia Mycoplasma pneumoniae

numerous species of bacteria

Mycetoma (Actinomycetoma) and fungi (Eumycetoma)

Myiasis parasitic dipterous fly larvae

Neonatal conjunctivitis most commonly Chlamydia trachomatis and (Ophthalmia neonatorum) Neisseria gonorrhoeae

(New) Variant Creutzfeldt-Jakob

disease (vCJD, nvCJD) PRNP

usually Nocardia asteroides and other

Nocardiosis Nocardia species

Onchocerciasis (River blindness) Onchocerca volvulus

Paracoccidioidomycosis (South

American blastomycosis) Paracoccidioides brasiliensis

usually Paragonimus westermani and other

Paragonimiasis Paragonimus species

Pasteurellosis Pasteurella genus

Pediculosis capitis (Head lice) Pediculus humanus capitis

Pediculosis corporis (Body lice) Pediculus humanus corporis

Pediculosis pubis (Pubic lice,

Crab lice) Phthirus pubis

Pelvic inflammatory disease

(PID) multiple

Pertussis (Whooping cough) Bordetella pertussis

Plague Yersinia pestis

Pneumococcal infection Streptococcus pneumoniae

Pneumocystis pneumonia (PCP) Pneumocystis jirovecii

Pneumonia multiple

Poliomyelitis Poliovirus

Prevotella infection Prevotella genus Primary amoebic

meningoencephalitis (PAM) usually Naegleria fowled

Progressive multifocal

leukoencephalopathy JC virus

Psittacosis Chlamydophila psittaci

Q fever Coxiella burnetii

Rabies Rabies virus

Streptobacillus moniliformis and Spirillum

Rat-bite fever minus

Respiratory syncytial virus

infection Respiratory syncytial virus (RSV)

Rhinosporidiosis Rhinosporidium seeberi

Rhinovirus infection Rhinovirus

Rickettsial infection Rickettsia genus

Rickettsialpox Rickettsia akari

Rift Valley fever (RVF) Rift Valley fever virus

Rocky Mountain spotted fever

(RMSF) Rickettsia rickettsii

Rotavirus infection Rotavirus

Rubella Rubella virus

Salmonellosis Salmonella genus

SARS (Severe Acute Respiratory

Syndrome) SARS coronavirus

Scabies Sarcoptes scabiei

Schistosomiasis Schistosoma genus

Sepsis multiple

Shigellosis (Bacillary dysentery) Shigella genus

Shingles (Herpes zoster) Varicella zoster virus (VZV)

Smallpox (Variola) Variola major or Variola minor

Sporotrichosis Sporothrix schenckii

Staphylococcal food poisoning Staphylococcus genus

Staphylococcal infection Staphylococcus genus

Strongyloidiasis Strongyloides stercoralis

Subacute sclerosing

panencephalitis Measles virus

Syphilis Treponema pallidum

Taeniasis Taenia genus

Tetanus (Lockjaw) Clostridium tetani

Tinea barbae (Barber's itch) usually Trichophyton genus

Tinea capitis (Ringworm of the

Scalp) usually Trichophyton tonsurans Tinea corporis (Ringworm of the

Body) usually Trichophyton genus

usually Epidermophyton floccosum, Trichophyton rubrum, and Trichophyton

Tinea cruris (Jock itch) mentagrophytes

Tinea manuum (Ringworm of the

Hand) Trichophyton rubrum

Tinea nigra usually Hortaea werneckii

Tinea pedis (Athlete's foot) usually Trichophyton genus

Tinea unguium (Onychomycosis) usually Trichophyton genus

Tinea versicolor (Pityriasis

versicolor) Malassezia genus

Toxocariasis (Ocular Larva

Migrans (OLM)) Toxocara canis or Toxocara cati

Toxocariasis (Visceral Larva

Migrans (VLM)) Toxocara canis or Toxocara cati

Toxoplasmosis Toxoplasma gondii

Trichinellosis Trichinella spiralis

Trichomoniasis Trichomonas vaginalis

Trichuriasis (Whipworm

infection) Trichuris trichiura

Tuberculosis usually Mycobacterium tuberculosis

Tularemia Francisella tularensis

Ureaplasma urealyticum

infection Ureaplasma urealyticum

Coccidioides immitis or Coccidioides

Valley fever posadasii.

Venezuelan equine encephalitis Venezuelan equine encephalitis virus

Venezuelan hemorrhagic fever Guanarito virus

Viral pneumonia multiple viruses

West Nile Fever West Nile virus

White piedra (Tinea blanca) Trichosporon beigelii

Yersinia pseudotuberculosis

infection Yersinia pseudotuberculosis

Yersiniosis Yersinia enterocolitica

Yellow fever Yellow fever virus

Mucorales order (Mucormycosis) and Entomophthorales order

Zygomycosis (Entomophthoramycosis) AIDS/HIV

HIV genomic structural elements

Long terminal repeat (LTR) refers to the DNA sequence flanking the genome of integrated proviruses. It contains important regulatory regions, especially those for transcription initiation and polyadenylation.

Target sequence (TAR) for viral transactivation, the binding site for Tat protein and for cellular proteins; consists of approximately the first 45 nucleotides of the viral mRNAs in HIV-1 (or the first 100 nucleotides in HIV-2 and SIV.) TAR RNA forms a hairpin stem-loop structure with a side bulge; the bulge is necessary for Tat binding and function.

Rev responsive element (RPE) refers to an RNA element encoded within the env region of HIV-1. It consists of approximately 200 nucleotides (positions 7327 to 7530 from the start of transcription in HIV-1, spanning the border of gpl20 and gp41). The RRE is necessary for Rev function; it contains a high affinity site for Rev; in all, approximately seven binding sites for Rev exist within the RRE RNA. Other lentiviruses (HIV-2, SIV, visna, CAEV) have similar RRE elements in similar locations within env, while HTLVs have an analogous RNA element (RXRE) serving the same purpose within their LTR; RRE is the binding site for Rev protein, while RXRE is the binding site for Rex protein. RRE (and RXRE) form complex secondary structures, necessary for specific protein binding.

Psi elements (PE) are a set of 4 stem-loop structures preceding and overlapping the Gag start codon which are the sites recognized by the cysteine histidine box, a conserved motif with the canonical sequence CysX2CysX4HisX4Cys (SEQ ID NO: 41), present in the Gag p7 MC protein. The Psi Elements are present in unspliced genomic transcripts but absent from spliced viral mRNAs.

SLIP, an slippery site, followed by a stem-loop structure, is responsible for regulating the -1 ribosomal frameshift out of the Gag reading frame into the Pol reading frame.

Cis-acting repressive sequences (CRS) are postulated to inhibit structural protein expression in the absence of Rev. One such site was mapped within the pol region of HIV-1. The exact function has not been defined; splice sites have been postulated to act as CRS sequences.

Inhibitory/Instability RNA sequences (INS) are found within the structural genes of HIV- 1 and of other complex retroviruses. Multiple INS elements exist within the genome and can act independently; one of the best characterized elements spans nucleotides 414 to 631 in the gag region of HIV-1. The INS elements have been defined by functional assays as elements that inhibit expression posttranscriptionally. Mutation of the RNA elements was shown to lead to INS inactivation and up regulation of gene expression. Genes and gene products

Essential for Replication

The genomic region (GAG) encoding the capsid proteins (group specific antigens). The precursor is the p55 myristylated protein, which is processed to pl7 (MAtrix), p24 (CApsid), p7 (NucleoCapsid), and p6 proteins, by the viral protease. Gag associates with the plasma membrane where the virus assembly takes place. The 55 kDa Gag precursor is called assemblin to indicate its role in viral assembly.

The genomic region, POL, encoding the viral enzymes protease, reverse transcriptase, RNAse, and integrase. These enzymes are produced as a Gag-Pol precursor polyprotein, which is processed by the viral protease; the Gag-Pol precursor is produced by ribosome frameshifting near the end of gag.

Viral glycoproteins (e.g., ENV) produced as a precursor (gpl60) which is processed to give a noncovalent complex of the external glycoprotein gpl20 and the transmembrane glycoprotein gp41. The mature gpl20-gp41 proteins are bound by non-covalent interactions and are associated as a trimer on the cell surface. A substantial amount of gpl20 can be found released in the medium. gpl20 contains the binding site for the CD4 receptor, and the seven transmembrane do- main chemokine receptors that serve as co-receptors for HIV-1.

The transactivator (TAT) of HIV gene expression is one of two essential viral regulatory factors (Tat and Rev) for HIV gene expression. Two forms are known, Tat-1 exon (minor form) of 72 amino acids and Tat-2 exon (major form) of 86 amino acids. Low levels of both proteins are found in persistently infected cells. Tat has been localized primarily in the nucleolus/nucleus by immunofluorescence. It acts by binding to the TAR RNA element and activating transcription initiation and elongation from the LTR promoter, preventing the LTR AATAAA

polyadenylation signal from causing premature termination of transcription and polyadenylation. It is the first eukaryotic transcription factor known to interact with RNA rather than DNA and may have similarities with prokaryotic anti-termination factors. Extracellular Tat can be found and can be taken up by cells in culture. The second necessary regulatory factor for HIV expression is REV. A 19 kDa phosphoprotein, localized primarily in the nucleolus/nucleus, Rev acts by binding to RRE and promoting the nuclear export, stabilization and utilization of the un- spliced viral mRNAs containing RRE. Rev is considered the most functionally conserved regulatory protein of lentiviruses. Rev cycles rapidly between the nucleus and the cytoplasm.

Others

Viral infectivity factor (VIF) is a basic protein of typically 23 kDa. Promotes the infectivity but not the production of viral particles. In the absence of Vif the produced viral particles are defective, while the cell-to-cell transmission of virus is not affected significantly. Found in almost all lentiviruses, Vif is a cytoplasmic protein, existing in both a soluble cytosolic form and a membrane-associated form. The latter form of Vif is a peripheral membrane protein that is tightly associated with the cytoplasmic side of cellular membranes. In 2003, it was discovered that Vif prevents the action of the cellular APOBEC-3G protein which deaminates DNA:RNA heteroduplexes in the cytoplasm.

Viral Protein R (VPR) is a 96-amino acid (14 kDa) protein, which is incorporated into the virion. It interacts with the p6 Gag part of the Pr55 Gag precursor. Vpr detected in the cell is localized to the nucleus. Proposed functions for Vpr include the targeting the nuclear import of preintegration complexes, cell growth arrest, transactivation of cellular genes, and induction of cellular differentiation. In HIV-2, SIV-SMM, SIV- RCM, SIV-MND-2 and SPZ-DRL the Vpx gene is apparently the result of a Vpr gene duplication event, possibly by recombination.

Viral Protein U (VPU)) is unique to HIV-1, SIVcpz (the closest SW relative of HIV-1), SIV-GSN, SIV-MUS, SIV- MON and SIV-DEN. There is no similar gene in HIV-2, SIV-SMM or other SIVs. Vpu is a 16 kDa (81-amino acid) type I integral membrane protein with at least two different biological functions: (a) degradation of CD4 in the endoplasmic reticulum, and (b) enhancement of virion release from the plasma membrane of HIV-1 -infected cells. Env and Vpu are expressed from a bicistronic mRNA. Vpu probably possesses an N-terminal hydrophobic membrane anchor and a hydrophilic moiety. It is phosphorylated by casein kinase II at positions Ser52 and Ser56. Vpu is involved in Env maturation and is not found in the virion. Vpu has been found to increase susceptibility of HIV-1 infected cells to Fas killing. NEF is amultifunctional 27-kDa myristylated protein produced by an ORF located at the 3 0 end of the primate lentiviruses. Other forms of Nef are known, including nonmyristylated variants. Nef is predominantly cytoplasmic and associated with the plasma membrane via the myristyl residue linked to the conserved second amino acid (Gly). Nef has also been identified in the nucleus and found associated with the cytoskeleton in some experiments. One of the first HIV proteins to be produced in infected cells, it is the most immunogenic of the accessory proteins. The nef genes of HIV and SIV are dispensable in vitro, but are essential for efficient viral spread and disease progression in vivo. Nef is necessary for the maintenance of high virus loads and for the development of AIDS in macaques, and viruses with defective Nef have been detected in some HIV-1 infected long term survivors. Nef downregulates CD4, the primary viral receptor, and MHC class I molecules, and these functions map to different parts of the protein. Nef interacts with components of host cell signal transduction and clathrin-dependent protein sorting pathways. It increases viral infectivity. Nef contains PxxP motifs that bind to SH3 domains of a subset of Src kinases and are required for the enhanced growth of HIV but not for the downregulation of CD4.

VPX is a virion protein of 12 kDa found in HIV-2, SIV-SMM, SIV-RCM, SIV-MND-2 and SIV-DRL and not in HIV-1 or other SIVs. This accessory gene is a homolog of HIV-1 vpr, and viruses with Vpx carry both vpr and vpx. Vpx function in relation to Vpr is not fully elucidated; both are incorporated into virions at levels comparable to Gag proteins through interactions with Gag p6. Vpx is necessary for efficient replication of SIV-SMM in PBMCs. Progression to AIDS and death in SIV-infected animals can occur in the absence of Vpr or Vpx. Double mutant virus lacking both vpr and vpx was attenuated, whereas the single mutants were not, suggesting a redundancy in the function of Vpr and Vpx related to virus pathogenicity.

Hepatitis A Viral Target Sequences

5' untranslated region contains IRES - internal ribosome entry site PI Region of genome - capsid proteins

VP1

VP2

VP3

VP4

P2 Region of genome 2A

2B

2C

P3 Region of genome

3A

3B

3C - viral protease

3D - RNA polymerase Hepatitis B Viral Target Sequences

Precursor Polypeptide encoding all HCV protein is produced and then spliced into functional proteins. The following are the proteins (coding regions) encoded:

C - core protein - coding region consists of a Pre-C and Core coding region X - function unclear but suspected to play a role in activation of viral transcription process

P - RNA polymerase

S - surface antigen - coding region consists of a Pre-Sl, Pre-S2 and Surface antigen coding regions Hepatitis C Viral Target Sequences

RES - non-coding internal ribosome entry site (5' to polyprotein encoding sequence)

3' non-coding sequences -

C region - encodes p22 a nucleocapsid protein

El region - encodes gp35 envelope glycoprotein - important in cell entry E2 region - encodes gp70 envelope glycoprotein - important in cell entry NS 1 - encodes p7 - not necessary for replication but critical in viral morphogenesis

NS2 - encodes p23 a transmembrane protein with protease activity NS3 - encodes p70 having both serine protease and RNA helicase activities NS4A - encodes p8 co-factor

NS4B - encodes p27 cofactor - important in recruitment of other viral proteins NS5A - encodes p56/58 an interferon resistance protein - important in viral replication

NS5B - encodes RNA polymerase

Herpes Simplex Virus Target Sequence

kinase replication G

repressor.

transcript

HPV Target Sequences

E2. For example, a full length Ε2/Ε8^ΛΕ2 dimer may bind DNA but

fail to recruit El to initiate virus replication. Similarly, such a

dimer may be unable to interact with cellular transcription factors to alter virus genome transcription.

E4 Remodels cytokeratin network; cell cycle arrest; virion assembly

E5 Control of cell growth and differentiation; immune modulation

Inhibits apoptosis and differentiation; regulates cell shape,

polarity, mobility and signaling. Four mRNA isoforms (FLE6,

E6*I, E6*II, E6*X) have been observed in HPV16 infected

cervical epithelial cells and two in HPV18 infection. A role for the

E6 E6*I isoform in antagonizing FLE6 function has been suggested,

as has opposing roles for FLE6 and E6*I in regulation of

procaspase 8 in the extrinsic apoptotic pathway. More recently, a stand-alone function of the E6*I isoform has been determined in cellular protein degradation.

E7 Cell cycle control; controls centrosome duplication

LI Major capsid protein

L2 Minor capsid protein; recruits LI; virus assembly

LCR Viral long control region (location of early promoters)

Keratinocyte/auxiliary

enhancer

P97 Promoter Early (E) gene promoter for subtype HPV16

P₁₀5 Promoter Early (E) gene promoter for subtype HPV18

P₆7o Promoter Late (L) gene promoter for HPV16

P742 Promoter Late (L) gene promoter for HPV31

Influenza A Target Sequences

Influenza A is the most common flu virus that infects humans. The influenza A virion is made up of 8 different single stranded RNA segments which encodes 11-14 proteins. These segments can vary in sequence, with most variation occurring in the hemagglutinin (H or HA) surface protein and neuraminidase (NA or N). The eight RNA segments (and the proteins they encode) are:

HA - encodes hemagglutinin (about 500 molecules of hemagglutinin are needed to make one virion).

NA - encodes neuraminidase (about 100 molecules of neuraminidase are needed to make one virion).

NP encodes nucleoprotein.

M encodes two matrix proteins (the Ml and the M2) by using different reading frames from the same RNA segment (about 3000 matrix protein molecules are needed to make one virion). M42 is produced by alternative splicing, and can partially replace an M2.

NS encodes two distinct non- structural proteins (NS1 and NEP) by using different reading frames from the same RNA segment.

PA encodes an RNA polymerase; an alternate form is sometimes made through a ribosomal skip, with +1 frameshift, reading through to the next stop codon.

PB 1 encodes an RNA polymerase, plus two other transcripts read from alternate start sites, named PB1-N40 and PB1-F2 protein (induces apoptosis) by using different reading frames from the same RNA segment.

PB2 encodes an RNA polymerase.

M. tuberculosis Target Sequences

The methods and composition described herein can be used to target M. tuberculosis and treat a subject suffering from an infection with M. tuberculosis. Other

In an embodiment, the target gene is associated with multiple drug resistance (MDR), e.g., in bacterial infection. Infectious pathogens can use a number of mechanisms in attaining multi-drug resistance, e.g., no longer relying on a glycoprotein cell wall, enzymatic deactivation of antibiotics, decreased cell wall permeability to antibiotics, altered target sites of antibiotic, efflux pumps to remove antibiotics, increased mutation rate as a stress response, or a

combination thereof. IX. Targets: Gene Editing/Correction

Candidate Cas9 molecules, candidate gRNA molecules, and/or candidate Cas9 molecule/gRNA molecule complexes, can be used to modulate genes (e.g., mutated genes) responsible for diseases. In an embodiment, the gene is modulated by editing or correcting a target gene, e.g., as described herein. In an embodiment, the human gene is modulated by delivery of one or more regulators/effectors (e.g., as described herein) inside cells to the target gene. For example, the genes described herein can be modulated, in vitro, ex vivo, or in vivo.

Table IX- 1. Selected Diseases in which a gene can be therapeutically targeted.

o Kinases (cancer)

o Energy metabolism (cancer)

o CFTR (cystic fibrosis)

o Color blindness

o Hemochromatosis

o Hemophilia

o Phenylketonuria

o Polycystic kidney disease

o Sickle-cell disease

o Tay-Sachs disease

o Siderius X-linked mental retardation syndrome

o Lysosomal storage disorders, e.g., Alpha-galactosidase A deficiency

o Anderson-Fabry disease

o Angiokeratoma Corporis Diffusum

o CADASIL syndrome

o Carboxylase Deficiency, Multiple, Late-Onset

o Cerebelloretinal Angiomatosis, familial

o Cerebral arteriopathy with subcortical infarcts and leukoencephalopathy

o Cerebral autosomal dominant arteriopathy with subcortical infarcts and

leukoencephalopathy

o Cerebroside Lipidosis syndrome o Choreoathetosis self-mutilation hyperuricemia syndrome

o Classic Galactosemia

o Crohn's disease, fibrostenosing

o Phenylalanine Hydroxylase Deficiency disease,

o Fabry disease

o Hereditary coproporphyria

o Incontinentia pigmenti

o Microcephaly

o Polycystic kidney disease

o Rett's

o Alpha- 1 antitrypsin deficiency

o Wilson's Disease

o Tyrosinemia

o Frameshift related diseases

o Cystic fibrosis

o Triplet repeat diseases (also referred herein as trinucleotide repeat diseases)

Trinucleotide repeat diseases (also known as triplet repeat disease, trinucleotide repeat expansion disorders, triplet repeat expansion disorders, or codon reiteration disorders) are a set of genetic disorders caused by trinucleotide repeat expansion, e.g., a type of mutation where trinucleotide repeats in certain genes exceed the normal and/or stable threshold. The mutation can be a subset of unstable microsatellite repeats that occur in multiple or all genomic sequences. The mutation can increase the repeat count (e.g., result in extra or expanded repeats) and result in a defective gene, e.g., producing an abnormal protein. Trinucleotide repeats can be classified as insertion mutations or as a separate class of mutations. Candidate Cas9 molecules, candidate gRNA molecules, and/or candidate Cas9 molecule/gRNA molecule complexes, can be used to modulate one or more genes (e.g., mutated genes) associated with a trinucleotide repeat disease, e.g., by reducing the number of (e.g., removing) the extra or expanded repeats, such that the normal or wild- type gene product (e.g., protein) can be produced.

Exemplary trinucleotide repeat diseases and target genes involved in trinucleotide repeat diseases are shown in Table IX-1A. Table IX- 1 A. Exemplary trinucleotide repeat diseases and target genes involved in trinucleotide repeat diseases

Exemplary target genes include those genes involved in various diseases or conditions, e.g., cancer (e.g., kinases), energy metabolism, cystic fibrosis (e.g., CFTR), color blindness, hemochromatosis, hemophilia, phenylketonuria, polycystic kidney disease, Sickle-cell disease, Tay-Sachs disease, Siderius X-linked mental retardation syndrome, Lysosomal storage disorders (e.g., Alpha-galactosidase A deficiency), Anderson-Fabry disease, Angiokeratoma Corporis Diffusum, CADASIL syndrome, Carboxylase Deficiency, Multiple, Late-Onset, Cerebelloretinal Angiomatosis, familial, Cerebral arteriopathy with subcortical infarcts and leukoencephalopathy, Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy, Cerebroside Lipidosis syndrome, Choreoathetosis self-mutilation hyperuricemia syndrome, Classic Galactosemia, Crohn's disease, fibrostenosing, Phenylalanine Hydroxylase Deficiency disease, Fabry disease, Hereditary coproporphyria, Incontinentia pigmenti , Microcephaly, Polycystic kidney disease, Rett's, Alpha- 1 antitrypsin deficiency, Wilson's Disease,

Tyrosinemia, Frameshift related diseases, and Triplet repeat diseases.

Additional exemplary target genes include genes associated with diseases including, e.g., Crigler-Najjer syndrome, Glycogen storage disease type IV (GSD type IV), Familial

hemophagocytic lymphohistiocytosis (FHL-Perforin deficiency), Ornithine transcarbamylase deficiency (OTC deficiency) or other Urea Cycle Disorders, Primary Hyperoxaluria, Leber congenital amaurosis (LCA), Batten disease, Chronic Granulomatous Disease, Wiskott-Aldrich syndrome, Usher Syndrome, and hemoglobinoapthies.

Crigler-Najjer syndrome. Crigler-Najjer syndrome is a severe condition characterized by high levels of bilirubin in the blood (hyperbilirubinemia). Bilirubin is produced when red blood cells are broken down. This substance is removed from the body only after it undergoes a chemical reaction in the liver, which converts the toxic form of bilirubin (unconjugated bilirubin) to a nontoxic form (conjugated bilirubin). People with Crigler-Najjar syndrome have a buildup of unconjugated bilirubin in their blood (unconjugated hyperbilirubinemia). Crigler-Najjar syndrome is divided into two types. Type 1 (CN1) is very severe and Type 2 (CN2) is less severe.

Mutations in the UGT1A1 gene can cause Crigler-Najjar syndrome. This gene provides instructions for making the bilirubin uridine diphosphate glucuronosyl transferase (bilirubin- UGT) enzyme, which is found primarily in liver cells and is necessary for the removal of bilirubin from the body. The bilirubin-UGT enzyme is involved in glucuronidation, in which the enzyme transfers glucuronic acid to unconjugated bilirubin, converting it to conjugated bilirubin. Glucuronidation makes bilirubin dissolvable in water so that it can be removed from the body. Mutations in the UGT1A1 gene that cause Crigler-Najjar syndrome result in reduced or absent function of the bilirubin-UGT enzyme. People with CN1 have no enzyme function, while people with CN2 can have less than 20 percent of normal function. The loss of bilirubin-UGT function decreases glucuronidation of unconjugated bilirubin. This toxic substance then builds up in the body, causing unconjugated hyperbilirubinemia and jaundice.

Glycogen storage disease type IV. Glycogen storage disease type IV (also known as GSD type IV, Glycogenosis type IV, Glycogen Branching Enzyme Deficiency (GBED), polyglucosan body disease, or Amylopectinosis) is an inherited disorder caused by the buildup of a complex sugar called glycogen in the body's cells. The accumulated glycogen is structurally abnormal and impairs the function of certain organs and tissues, especially the liver and muscles.

Mutations in the GBE1 gene cause GSD IV. The GBE1 gene provides instructions for making the glycogen branching enzyme. This enzyme is involved in the production of glycogen, which is a major source of stored energy in the body. GBE1 gene mutations that cause GSD IV lead to a shortage (deficiency) of the glycogen branching enzyme. As a result, glycogen is not formed properly. Abnormal glycogen molecules called polyglucosan bodies accumulate in cells, leading to damage and cell death. Polyglucosan bodies accumulate in cells throughout the body, but liver cells and muscle cells are most severely affected in GSD IV. Glycogen accumulation in the liver leads to hepatomegaly and interferes with liver functioning. The inability of muscle cells to break down glycogen for energy leads to muscle weakness and wasting.

Generally, the severity of the disorder is linked to the amount of functional glycogen branching enzyme that is produced. Individuals with the fatal perinatal neuromuscular type tend to produce less than 5 percent of usable enzyme, while those with the childhood neuromuscular type may have around 20 percent of enzyme function. The other types of GSD Γ are usually associated with between 5 and 20 percent of working enzyme. These estimates, however, vary among the different types.

Familial hemophagocytic lymphohistiocytosis. Familial hemophagocytic

lymphohistiocytosis (FHL) is a disorder in which the immune system produces too many activated immune cells (lymphocytes), e.g., T cells, natural killer cells, B cells, and macrophages (histiocytes). Excessive amounts of cytokines are also produced. This overactivation of the immune system causes fever and damages the liver and spleen, resulting in enlargement of these organs. Familial hemophagocytic lymphohistiocytosis also destroys blood-producing cells in the bone marrow, a process called hemophagocytosis. The brain may also be affected in familial hemophagocytic lymphohistiocytosis. In addition to neurological problems, familial

hemophagocytic lymphohistiocytosis can cause abnormalities of the heart, kidneys, and other organs and tissues. Affected individuals also have an increased risk of developing cancers of blood-forming cells (leukemia and lymphoma).

Familial hemophagocytic lymphohistiocytosis may be caused by mutations in any of several genes. These genes provide instructions for making proteins that help destroy or deactivate lymphocytes that are no longer needed. By controlling the number of activated lymphocytes, these genes help regulate immune system function.

Approximately 40 to 60 percent of cases of familial hemophagocytic lymphohistiocytosis are caused by mutations in the PRF1 or UNCI 3D genes. Smaller numbers of cases are caused by mutations in other known genes such as STXl 1 or STXBP2. The gene mutations that cause familial hemophagocytic lymphohistiocytosis can impair the body's ability to regulate the immune system. These changes result in the exaggerated immune response characteristic of this condition.

Ornithine transcarbamylase deficiency. Ornithine transcarbamylase deficiency (OTC) is an inherited disorder that causes ammonia to accumulate in the blood.

Mutations in the OTC gene cause ornithine transcarbamylase deficiency.

Ornithine transcarbamylase deficiency belongs to a class of genetic diseases called urea cycle disorders. The urea cycle is a sequence of reactions that occurs in liver cells. It processes excess nitrogen, generated when protein is used by the body, to make a compound called urea that is excreted by the kidneys.

In ornithine transcarbamylase deficiency, the enzyme that starts a specific reaction within the urea cycle is damaged or missing. The urea cycle cannot proceed normally, and nitrogen accumulates in the bloodstream in the form of ammonia.

Ammonia is especially damaging to the nervous system, so ornithine transcarbamylase deficiency causes neurological problems as well as eventual damage to the liver.

Other urea cycle disorders and associate genes include, e.g., N-Acetylglutamate synthase deficiency (NAGS), Carbamoyl phosphate synthetase I deficiency (CPS1), "AS deficiency" or citrullinemia (ASS), "AL deficiency" or arginino succinic aciduria (ASL), and "Arginase deficiency" or argininemia (ARG).

Primary hyperoxaluria. Primary hyperoxaluria, e.g., primary hyperoxaluria type 1 (PHI), is a rare, autosomal recessive inherited genetic condition in which an error in the glyoxylate metabolism pathway in the liver leads to an overproduction of oxalate, which crystalizes in soft tissues including the kidney, bone marrow, and eyes. The disease manifests as progressive deterioration of the kidneys, and treatment is a complicated double transplant of kidney (the damaged organ) and liver (the diseased organ).

Primary hyperoxaluria is caused by the deficiency of an enzyme that normally prevents the buildup of oxalate. There are two types of primary hyperoxaluria, distinguished by the enzyme that is deficient. People with type 1 primary hyperoxaluria have a shortage of a liver enzyme called alanine-glyoxylate aminotransferase (AGXT). Type 2 primary hyperoxaluria is characterized by a shortage of an enzyme called glyoxylate reductase/hydroxypyruvate reductase (GRHPR).

Mutations in the AGXT and GRHPR genes cause primary hyperoxaluria. The breakdown and processing of certain sugars and amino acids produces a glyoxylate. Normally, glyoxylate is converted to the amino acid glycine or to glycolate through the action of two enzymes, alanine-glyoxylate aminotransferase and glyoxylate reductase/hydroxypyruvate reductase, respectively. Mutations in the AGXT or GRHPR gene cause a shortage of these enzymes, which prevents the conversion of glyoxylate to glycine or glycolate. As levels of glyoxylate build up, it is converted to oxalate. Oxalate combines with calcium to form calcium oxalate deposits, which can damage the kidneys and other organs.

In an embodiment, the genetic defect in AGXT is corrected, e.g., by homologous recombination, using the Cas9 molecule and gRNA molecule described herein. For example, the functional enzyme encoded by the corrected AGXT gene can be redirected to its proper subcellular organelle. Though >50 mutations have been identified in the gene, the most common (40% in Caucasians) is a missense G170R mutation. This mutation causes the AGT enzyme to be localized to the mitochondria rather than to the peroxisome, where it must reside to perform its function. Other common mutations include, e.g., I244T (Canary Islands), F152I, G41R, G630A (Italy), and G588A (Italy). In an embodiment, one or more genes encoding enzymes upstream in the glyoxylate metabolism pathway are targeted, using the Cas9 molecule and gRNA molecule described herein. Exemplary targets include, e.g., glycolate oxidase (gene HAOl, OMIM ID 605023). Glycolate oxidase converts glycolate into glyoxylate, the substrate for AGT. Glycolate oxidase is only expressed in the liver and, because of its peroxisomal localization, makes it a suitable target in this metabolic pathway. In an embodiment, a double- strand break in the HAOl gene is introduced and upon repair by NHEJ a frame-shift results in a truncated protein. In an embodiment, a transcriptional repressor (e.g., a transcriptional repressor described herein) is delivered as a payload to the HAOl gene to reduce the expression of HAOl.

Leber congenital amaurosis. Leber congenital amaurosis (LCA) is an eye disorder that primarily affects the retina. People with this disorder typically have severe visual impairment beginning in infancy. The visual impairment tends to be stable, although it may worsen very slowly over time. At least 13 types of Leber congenital amaurosis have been described. The types are distinguished by their genetic cause, patterns of vision loss, and related eye abnormalities.

Leber congenital amaurosis can result from mutations in at least 14 genes, all of which are necessary for normal vision. These genes play a variety of roles in the development and function of the retina. For example, some of the genes associated with this disorder are necessary for the normal development of photoreceptors. Other genes are involved in phototransduction. Still other genes play a role in the function of cilia, which are necessary for the perception of several types of sensory input, including vision.

Mutations in any of the genes associated with Leber congenital amaurosis (e.g., AIPL1, CEP290, CRB1, CRX, GUCY2D, IMPDH1, LCA5, LRAT, RD3, RDH12, RPE65, RPGRIP1, SPATA7, TULP1) can disrupt the development and function of the retina, resulting in early vision loss. Mutations in the CEP290, CRB1, GUCY2D, and RPE65 genes are the most common causes of the disorder, while mutations in the other genes generally account for a smaller percentage of cases.

Batten disease. Batten disease or juvenile Batten disease is an inherited disorder that primarily affects the nervous system. After a few years of normal development, children with this condition develop progressive vision loss, intellectual and motor disability, and seizures. Juvenile Batten disease is one of a group of disorders known as neuronal ceroid lipofuscinoses (NCLs). These disorders all affect the nervous system and typically cause progressive problems with vision, movement, and thinking ability. Some people refer to the entire group of NCLs as Batten disease, while others limit that designation to the juvenile form of the disorder. The different types of NCLs are distinguished by the age at which signs and symptoms first appear.

Most cases of juvenile Batten disease are caused by mutations in the CLN3 gene. These mutations can disrupt the function of cellular structures called lysosomes. Lysosome

malfunction leads to a buildup of lipopigments within these cell structures. These accumulations occur in cells throughout the body, but neurons in the brain seem to be particularly vulnerable to the damage caused by lipopigments. The progressive death of cells, especially in the brain, leads to vision loss, seizures, and intellectual decline in people with juvenile Batten disease.

A small percentage of cases of juvenile Batten disease are caused by mutations in other genes (e.g., ATP13A2, CLN5, PPT1, TPP1). Many of these genes are involved in lysosomal function, and when mutated, can cause this or other forms of NCL.

Chronic granulomatous disease. Chronic granulomatous disease is a disorder that causes the immune system to malfunction, resulting in a form of immunodeficiency. Individuals with chronic granulomatous disease have recurrent bacterial and fungal infections. People with this condition often have areas of inflammation (granulomas) in various tissues that can be damaging to those tissues. The features of chronic granulomatous disease usually first appear in childhood, although some individuals do not show symptoms until later in life.

Mutations in the CYBA, CYBB, NCF1, NCF2, or NCF4 gene can cause chronic granulomatous disease. There are five types of this condition that are distinguished by the gene that is involved. The proteins produced from the affected genes are subunits of NADPH oxidase, which plays an important role in the immune system. Specifically, NADPH oxidase is primarily active in phagocytes. Within phagocytes, NADPH oxidase is involved in the production of superoxide, which plays a role in killing foreign invaders and preventing them from reproducing in the body and causing illness. NADPH oxidase also regulates the activity of neutrophils, which play a role in adjusting the inflammatory response to optimize healing and reduce injury to the body. Mutations in the CYBA, CYBB, NCF1, NCF2, and NCF4 genes result in the production of proteins with little or no function or the production of no protein at all. Without any one of its subunit proteins, NADPH oxidase cannot assemble or function properly. As a result, phagocytes are unable to kill foreign invaders and neutrophil activity is not regulated. A lack of NADPH oxidase leaves affected individuals vulnerable to many types of infection and excessive inflammation.

Wiskott-Aldrich syndrome. Wiskott-Aldrich syndrome is characterized by abnormal immune system function (immune deficiency) and a reduced ability to form blood clots. This condition primarily affects males. Individuals with Wiskott-Aldrich syndrome have

micro thrombocytopenia, which is a decrease in the number and size of blood cells involved in clotting (platelets), which can lead to easy bruising or episodes of prolonged bleeding following minor trauma. Wiskott-Aldrich syndrome causes many types of white blood cells to be abnormal or nonfunctional, leading to an increased risk of several immune and inflammatory disorders. Many people with this condition develop eczema, an inflammatory skin disorder characterized by abnormal patches of red, irritated skin. Affected individuals also have an increased susceptibility to infection. People with Wiskott-Aldrich syndrome are at greater risk of developing autoimmune disorders. The chance of developing some types of cancer, such as cancer of the immune system cells (lymphoma), is also greater in people with Wiskott-Aldrich syndrome.

Mutations in the WAS gene cause Wiskott-Aldrich syndrome. The WAS gene provides instructions for making WASP protein, which is found in all blood cells. WASP is involved in relaying signals from the surface of blood cells to the actin cytoskeleton. WASP signaling activates the cell when it is needed and triggers its movement and attachment to other cells and tissues (adhesion). In white blood cells, this signaling allows the actin cytoskeleton to establish the interaction between cells and the foreign invaders that they target (immune synapse).

WAS gene mutations that cause Wiskott-Aldrich syndrome lead to a lack of any functional WASP. Loss of WASP signaling disrupts the function of the actin cytoskeleton in developing blood cells. White blood cells that lack WASP have a decreased ability to respond to their environment and form immune synapses. As a result, white blood cells are less able to respond to foreign invaders, causing many of the immune problems related to Wiskott-Aldrich syndrome. Similarly, a lack of functional WASP in platelets impairs their development, leading to reduced size and early cell death.

Usher syndrome. Usher syndrome is a condition characterized by hearing loss or deafness and progressive vision loss. The loss of vision is caused by retinitis pigmentosa (RP), which affects the layer of light-sensitive tissue at the back of the eye (the retina). Vision loss occurs as the light-sensing cells of the retina gradually deteriorate.

Three major types of Usher syndrome, designated as types I (subtypes IA through IG), II

(subtypes IIA, IIB, and IIC), and III, have been identified. These types are distinguished by their severity and the age when signs and symptoms appear.

Mutations in the CDH23, CLRN1, GPR98, MY07A, PCDH15, USHIC, USHIG, and

USH2A genes can cause Usher syndrome. The genes related to Usher syndrome provide instructions for making proteins that play important roles in normal hearing, balance, and vision.

They function in the development and maintenance of hair cells, which are sensory cells in the inner ear that help transmit sound and motion signals to the brain. In the retina, these genes are also involved in determining the structure and function of light- sensing cells called rods and cones. In some cases, the exact role of these genes in hearing and vision is unknown. Most of the mutations responsible for Usher syndrome lead to a loss of hair cells in the inner ear and a gradual loss of rods and cones in the retina. Degeneration of these sensory cells causes hearing loss, balance problems, and vision loss characteristic of this condition.

Usher syndrome type I can result from mutations in the CDH23, MY07A, PCDH15,

USHIC, or USHIG gene. Usher syndrome type II can be caused by mutations in, e.g., USH2A or GPR98 (also called VLGR1) gene. Usher syndrome type III can be caused by mutations in e.g., CLRNl.

Hemoglobinopathies. Hemoglobinopathies are a group of genetic defects that result in abnormal structure of one of the globin chains of the hemoglobin molecule. Exemplary hemoglobinopathies include, e.g., sickle cell disease, alpha thalassemia, and beta thalassemia.

In an embodiment, a genetic defect in alpha globulin or beta globulin is corrected, e.g., by homologous recombination, using the Cas9 molecule and gRNA molecule described herein.

In an embodiment, a hemoglobinopathies-associated gene is targeted, using the Cas9 molecule and gRNA molecule described herein. Exemplary targets include, e.g., genes associated with control of the gamma-globin genes. In an embodiment, the target is BCL11 A. Fetal hemoglobin (also hemoglobin F or HbF or α2γ2) is a tetramer of two adult alpha- globin polypeptides and two fetal beta-like gamma-globin polypeptides. HbF is the main oxygen transport protein in the human fetus during the last seven months of development in the uterus and in the newborn until roughly 6 months old. Functionally, fetal hemoglobin differs most from adult hemoglobin in that it is able to bind oxygen with greater affinity than the adult form, giving the developing fetus better access to oxygen from the mother's bloodstream.

In newborns, fetal hemoglobin is nearly completely replaced by adult hemoglobin by approximately 6 months postnatally. In adults, fetal hemoglobin production can be reactivated pharmacologically, which is useful in the treatment of diseases such as hemoglobinopathies. For example, in certain patients with hemoglobinopathies, higher levels of gamma-globin expression can partially compensate for defective or impaired beta-globin gene production, which can ameliorate the clinical severity in these diseases. Increased HbF levels or F-cell (HbF containing erythrocyte) numbers can ameliorate the disease severity of hemoglobinopathies, e.g., beta- thalassemia major and sickle cell anemia.

Increased HbF levels or F-cell can be associated reduced BCL11A expression in cells.

The BCL11 A gene encodes a multi-zinc finger transcription factor. In an embodiment, the expression of BCL11A is modulated, e.g., down-regulated. In an embodiment, the BCL11A gene is edited. In an embodiment, the cell is a hemopoietic stem cell or progenitor cell.

Sickle cell diseases

Sickle cell disease is a group of disorders that affects hemoglobin. People with this disorder have atypical hemoglobin molecules (hemoglobin S), which can distort red blood cells into a sickle, or crescent, shape. Characteristic features of this disorder include a low number of red blood cells (anemia), repeated infections, and periodic episodes of pain.

Mutations in the HBB gene cause sickle cell disease. The HBB gene provides instructions for making beta-globin. Various versions of beta-globin result from different mutations in the HBB gene. One particular HBB gene mutation produces an abnormal version of beta-globin known as hemoglobin S (HbS). Other mutations in the HBB gene lead to additional abnormal versions of beta-globin such as hemoglobin C (HbC) and hemoglobin E (HbE). HBB gene mutations can also result in an unusually low level of beta-globin, i.e., beta thalassemia.

In people with sickle cell disease, at least one of the beta-globin subunits in hemoglobin is replaced with hemoglobin S. In sickle cell anemia, which is a common form of sickle cell disease, hemoglobin S replaces both beta-globin subunits in hemoglobin. In other types of sickle cell disease, just one beta-globin subunit in hemoglobin is replaced with hemoglobin S. The other beta-globin subunit is replaced with a different abnormal variant, such as hemoglobin C. For example, people with sickle-hemoglobin C (HbSC) disease have hemoglobin molecules with hemoglobin S and hemoglobin C instead of beta-globin. If mutations that produce hemoglobin S and beta thalassemia occur together, individuals have hemoglobin S-beta thalassemia

(HbSBetaThal) disease.

Alpha thalassemia

Alpha thalassemia is a blood disorder that reduces the production of hemoglobin. In people with the characteristic features of alpha thalassemia, a reduction in the amount of hemoglobin prevents enough oxygen from reaching the body's tissues. Affected individuals also have a shortage of red blood cells (anemia), which can cause pale skin, weakness, fatigue, and more serious complications.

Two types of alpha thalassemia can cause health problems. The more severe type is hemoglobin Bart hydrops fetalis syndrome or Hb Bart syndrome. The milder form is HbH disease. Hb Bart syndrome is characterized, e.g., by hydrops fetalis, a condition in which excess fluid builds up in the body before birth. HbH disease can cause, e.g., mild to moderate anemia, hepatosplenomegaly, and yellowing of the eyes and skin (jaundice).

Alpha thalassemia typically results from deletions involving the HBA1 and HBA2 genes. Both of these genes provide instructions for making alpha-globin, which is a subunit of hemoglobin. The different types of alpha thalassemia result from the loss of some or all of these alleles.

Hb Bart syndrome can result from the loss of all four alpha-globin alleles. HbH disease can be caused by a loss of three of the four alpha-globin alleles. In these two conditions, a shortage of alpha-globin prevents cells from making normal hemoglobin. Instead, cells produce abnormal forms of hemoglobin, i.e., hemoglobin Bart (Hb Bart) or hemoglobin H (HbH), which cannot effectively carry oxygen to the body's tissues. The substitution of Hb Bart or HbH for normal hemoglobin can cause anemia and the other serious health problems associated with alpha thalassemia.

Two additional variants of alpha thalassemia are related to a reduced amount of alpha- globin. A loss of two of the four alpha-globin alleles can result in alpha thalassemia trait. People with alpha thalassemia trait may have unusually small, pale red blood cells and mild anemia. A loss of one alpha-globin allele can be found in alpha thalassemia silent carriers.

Beta thalassemia

Beta thalassemia is a blood disorder that reduces the production of hemoglobin. In people with beta thalassemia, low levels of hemoglobin lead to a lack of oxygen in many parts of the body. Affected individuals also have a shortage of red blood cells (anemia), which can cause pale skin, weakness, fatigue, and more serious complications. People with beta thalassemia are at an increased risk of developing abnormal blood clots.

Beta thalassemia is classified into two types depending on the severity of symptoms: thalassemia major (also known as Cooley's anemia) and thalassemia intermedia. Of the two types, thalassemia major is more severe.

Mutations in the HBB gene cause beta thalassemia. The HBB gene provides instructions for making beta-globin. Some mutations in the HBB gene prevent the production of any beta- globin. The absence of beta-globin is referred to as beta-zero (B°) thalassemia. Other HBB gene mutations allow some beta-globin to be produced but in reduced amounts, i.e., beta-plus (B⁺) thalassemia. People with both types have been diagnosed with thalassemia major and thalassemia intermedia.

In an embodiment, a Cas9 molecule/gRNA molecule complex targeting a first gene is used to treat a disorder characterized by second gene, e.g., a mutation in a second gene. By way of example, targeting of the first gene, e.g., by editing or payload delivery, can compensate for, or inhibit further damage from, the affect of a second gene, e.g., a mutant second gene. In an embodiment the allele(s) of the first gene carried by the subject is not causative of the disorder.

Table IX-3. Selected Disorders and Targets for Compensatory Targeting

Up- up- down-regulate up-regulate down-regulate down- down- down-regulate regulate/ regulate regulate regulate

Down- regulate

Level of animal Factor H Eculizumab/So Rituxan Rituxan everolimus evidence: models concentrate liris c5Ab (Genentech) (Genentech)

Market (Alexion) CD20 CD20

proxy or successful in antibody antibody

animal decreasing

model mortality

Comment Muti-genetic origin. Factor H aHUS due to fH deficiency.

deficiency is a risk factor. C5 antibody has been shown

Controlling the complement to vastly improve prognosis.

cascade, through fH Can approach disease directly

upregulation or C5 through increasing fH levels

downregulation, may have a or controlling complement

beneficial effect. through C5 downregulation.

Indication Devices: Graft orthopedics- Parkinson's Allergic Epilepsy Barrett's stent, healing/wou articular Disease rhinitis esophagus, pacemaker, nd cartilage Stomach hernia mesh- healing/prev repair, ulcer, gastritis local delivery ention of arthritis

to prevent fibrosis

restenosis/

fibrosis Target mTORC2, VEGF IL-11 SNCA, HI HI receptors H2 receptor others LRRK2, Receptors CNS pylorus,

EIF4GI nasal esophagus mucosa

Upregulate down- up-regulate up-regulate up-regulate down- up-regulate down-regulate

/ regulate or fix regulate

Downregul mutations

ate

Level of everolimus VEGF local animal model HI -antianimal H2-specific evidence: administratio of cartilage histamines, models antihistamines,

Market n aids in repair e.g. Zyrtec e-g.

proxy or tracheal omeprazole, animal transplant etc.

model animal

models

Comment Embodiments Useful, e.g., In an In an

include, e.g., in the embodiment, embodiment, local delivery promoting the subject the subject is to tissue via wound sufferes from treated for device or healing arthritis or is late-stage injection to (burns, etc); in need of barrett's. prevent Embodiments healing after

fibrosis, include, e.g., injury. In

restenosis local delivery embodiments,

of growth chondrocytes

factors are targeted

post-injury to

promote

healing.

In an embodiment, Cas9 molecules, gRNA molecules, and/or Cas9 molecule/gRNA molecule complexes can be used to activate genes that regulate growth factors, such as up

regulation of Epo to drive RBC production.

5 In an embodiment, Cas9 molecules, gRNA molecules, and/or Cas9 molecule/gRNA

molecule complexes can be used to target, e.g., result in repression of, knockout of, or alteration of promoter for key transcription factors, such as BCL11A and KLF1 for up-regulating of fetal hemoglobin, e.g., for cure for sickle cell anemia and thalassemia.

Candidate Cas9 molecules, candidate gRNA molecules, and/or candidate Cas9 molecule/gRNA molecule complexes, as described herein, can be used to edit/correct a target gene or to deliver a regulator/effector inside cells, e.g., as described herein, at various subcellular locations. In an embodiment, the location is in the nucleus. In an embodiment, the location is in a sub-nuclear domain, e.g., the chromosome territories, nucleolus, nuclear speckles, Cajal bodies, Gems (gemini of Cajal bodies), or promyelocytic leukemia (PML) nuclear bodies. In an embodiment, the location is in the mitochondrion.

Candidate Cas9 molecules, candidate gRNA molecules, and/or candidate Cas9 molecule/gRNA molecule complexes, as described herein, can be used to edit/correct a target gene or to deliver a regulator/effector inside cells, as described herein, at various time points

For example, the editing/correction or delivery can occur at different phases of cell cycle, e.g., GO phase, Interphase (e.g., Gl phase, S phase, G2 phase), or M phase. As another example, the editing/correction or delivery can occur at different stages of disease progression, e.g., at latent stage or active stage of a disorder (e.g., viral infection), or at any stage or subclassification of a disorder (e.g., cancer).

Methods of the invention allow for the treatment of a disorder characterized by unwanted cell proliferation, e.g., cancer. In an embodiment, cancer cells are manipulated to make them more susceptible to treatment or to endogenous immune surveillance. In an embodiment a cancer cell is modulated to make it more susceptible to a therapeutic. In an embodiment, a cancer cell is manipulated so as to increase the expression of a gene that increases the ability of the immune system to recognize or kill the cancer cell. E.g., a Cas9 molecule/gRNA molecule complex can be used to deliver a payload, or edit a target nucleic acid so as to increase the expression of an antigen, e.g., in the case where the cancer cell has downregulated expression of the antigen. In an embodiment, a payload, e.g., a payload comprising a transcription factor or other activator of expression is delivered to the cancer cell. In an embodiment, an increase in expression is effected by cleavage of the target nucleic acid, e.g., cleavage and correction or alteration of the target nucleic acid by a template nucleic acid. In an embodiment, a payload that overrides epigenetic silencing, e.g., a modulator of methylation, is delivered. In an embodiment, the treatment further comprises administering a second anti-cancer therapy, e.g., immunotherapy, e.g., an antibody that binds the upregulated antigen.

In an embodiment, methods described herein, e.g., targeting of a genomic signature, e.g., a somatic translocation, can be used to target the Cas9 molecule/gRNA molecule to a cancer cell.

In another aspect, the invention features a method of immunizing a subject against an antigen. The method comprises using a method described herein to promote the expression of the antigen from a cell, e.g., a blood cell, such that the antigen promotes an immune response. In an embodiment, the cell is manipulated ex vivo and then returned or introduced into the subject.

X. Modified Nucleosides, Nucleotides, and Nucleic Acids

Modified nucleosides and modified nucleotides can be present in nucleic acids, e.g., particularly gRNA, but also other forms of RNA, e.g., mRNA, RNAi, or siRNA. As described herein "nucleoside" is defined as a compound containing a five-carbon sugar molecule (a pentose or ribose) or derivative thereof, and an organic base, purine or pyrimidine, or a derivative thereof. As described herein, "nucleotide" is defined as a nucleoside further comprising a phosphate group.

Modified nucleosides and nucleotides can include one or more of:

(i) alteration, e.g., replacement, of one or both of the non-linking phosphate oxygens and/or of one or more of the linking phosphate oxygens in the phosphodiester backbone linkage;

(ii) alteration, e.g., replacement, of a constituent of the ribose sugar, e.g., of the 2' hydroxyl on the ribose sugar;

(iii) wholesale replacement of the phosphate moiety with "dephospho" linkers;

(iv) modification or replacement of a naturally occurring nucleobase;

(v) replacement or modification of the ribose-phosphate backbone;

(vi) modification of the 3' end or 5' end of the oligonucleotide, e.g., removal,

modification or replacement of a terminal phosphate group or conjugation of a moiety; and

(vii) modification of the sugar.

The modifications listed above can be combined to provide modified nucleosides and nucleotides that can have two, three, four, or more modifications. For example, a modified nucleoside or nucleotide can have a modified sugar and a modified nucleobase. In an embodiment, every nucleotide of a gRNA or template nucleic acid is modified, e.g., all nucleotides have a modified phosphate group, e.g., all are phosphorothioate groups. In an embodiment, all, or substantially all, of the phosphate groups of a unimolecular or modular gRNA molecule or template nucleic acid are replaced with phosphorothioate groups.

In an embodiment, modified nucleotides, e.g., nucleotides having modifications as described herein, can be incorporated into a nucleic acid, e.g., a "modified nucleic acid." In an embodiment, the modified nucleic acids comprise one, two, three or more modified nucleotides. In an embodiment, at least 5% (e.g., at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or about 100%) of the positions in a modified nucleic acid are a modified nucleotides.

Unmodified nucleic acids can be prone to degradation by, e.g., cellular nucleases. For example, nucleases can hydrolyze nucleic acid phosphodiester bonds. Accordingly, in one aspect the modified nucleic acids described herein can contain one or more modified nucleosides or nucleotides, e.g., to introduce stability toward nucleases.

In an embodiment, the modified nucleosides, modified nucleotides, and modified nucleic acids described herein can exhibit a reduced innate immune response when introduced into a population of cells, both in vivo and ex vivo. The term "innate immune response" includes a cellular response to exogenous nucleic acids, including single stranded nucleic acids, generally of viral or bacterial origin, which involves the induction of cytokine expression and release, particularly the interferons, and cell death. In an embodiment, the modified nucleosides, modified nucleotides, and modified nucleic acids described herein can disrupt binding of a major groove interacting partner with the nucleic acid. In an embodiment, the modified nucleosides, modified nucleotides, and modified nucleic acids described herein can exhibit a reduced innate immune response when introduced into a population of cells, both in vivo and ex vivo, and also disrupt binding of a major groove interacting partner with the nucleic acid.

In an embodiment, a governing gRNA comprises modifications, e.g., modified nucleotides, modifications to the backbone, and other modifications described herein. In an embodiment, a template nucleic acid comprises modifications, e.g., modified nucleotides, modifications to the backbone, and other modifications described herein. In an embodiment, the modification improves the stability of the template nucleic acid, e.g., by increasing its resistance to endonucleases and/or exonucleases.

In an embodiment, a template nucleic acid that comprises modifications is double stranded, e.g., is double stranded DNA. In such embodiment, all the modifications are confined to one strand. In an embodiment, modifications are present on both strands. Modifications may be present in the 5' homology arm, the 3' homology arm, or the replacement sequence, or any combination thereof. In an embodiment, modifications are present in one or both homology arms but not the replacement sequence.

In an embodiment, a template nucleic acid that comprises modifications is single stranded, e.g., is single stranded DNA.

Definitions of Chemical Groups

As used herein, "alkyl" is meant to refer to a saturated hydrocarbon group which is straight-chained or branched. Example alkyl groups include methyl (Me), ethyl (Et), propyl (e.g. , n-propyl and isopropyl), butyl (e.g. , n-butyl, isobutyl, t-butyl), pentyl (e.g. , n-pentyl, isopentyl, neopentyl), and the like. An alkyl group can contain from 1 to about 20, from 2 to about 20, from 1 to about 12, from 1 to about 8, from 1 to about 6, from 1 to about 4, or from 1 to about 3 carbon atoms.

As used herein, "aryl" refers to monocyclic or polycyclic (e.g. , having 2, 3 or 4 fused rings) aromatic hydrocarbons such as, for example, phenyl, naphthyl, anthracenyl,

phenanthrenyl, indanyl, indenyl, and the like. In an embodiment, aryl groups have from 6 to about 20 carbon atoms.

As used herein, "alkenyl" refers to an aliphatic group containing at least one double bond.

As used herein, "alkynyl" refers to a straight or branched hydrocarbon chain containing 2-12 carbon atoms and characterized in having one or more triple bonds. Examples of alkynyl groups include, but are not limited to, ethynyl, propargyl, and 3-hexynyl.

As used herein, "arylalkyl" or "aralkyl" refers to an alkyl moiety in which an alkyl hydrogen atom is replaced by an aryl group. Aralkyl includes groups in which more than one hydrogen atom has been replaced by an aryl group. Examples of "arylalkyl" or "aralkyl" include benzyl, 2-phenylethyl, 3-phenylpropyl, 9-fluorenyl, benzhydryl, and trityl groups.

As used herein, "cycloalkyl" refers to a cyclic, bicyclic, tricyclic, or polycyclic non- aromatic hydrocarbon groups having 3 to 12 carbons. Examples of cycloalkyl moieties include, but are not limited to, cyclopropyl, cyclopentyl, and cyclohexyl.

As used herein, "heterocyclyl" refers to a monovalent radical of a heterocyclic ring system. Representative heterocyclyls include, without limitation, tetrahydrofuranyl,

tetrahydrothienyl, pyrrolidinyl, pyrrolidonyl, piperidinyl, pyrrolinyl, piperazinyl, dioxanyl, dioxolanyl, diazepinyl, oxazepinyl, thiazepinyl, and morpholinyl.

As used herein, "heteroaryl" refers to a monovalent radical of a heteroaromatic ring system. Examples of heteroaryl moieties include, but are not limited to, imidazolyl, oxazolyl, thiazolyl, triazolyl, pyrrolyl, furanyl, indolyl, thiophenyl pyrazolyl, pyridinyl, pyrazinyl, pyridazinyl, pyrimidinyl, indolizinyl, purinyl, naphthyridinyl, quinolyl, and pteridinyl. Phosphate Backbone Modifications

The Phosphate Group

In an embodiment, the phosphate group of a modified nucleotide can be modified by replacing one or more of the oxygens with a different substituent. Further, the modified nucleotide, e.g., modified nucleotide present in a modified nucleic acid, can include the wholesale replacement of an unmodified phosphate moiety with a modified phosphate as described herein. In an embodiment, the modification of the phosphate backbone can include alterations that result in either an uncharged linker or a charged linker with unsymmetrical charge distribution.

Examples of modified phosphate groups include, phosphorothioate, phosphoroselenates, borano phosphates, borano phosphate esters, hydrogen phosphonates, phosphoroamidates, alkyl or aryl phosphonates and phosphotriesters. In an embodiment, one of the non-bridging phosphate oxygen atoms in the phosphate backbone moiety can be replaced by any of the following groups: sulfur (S), selenium (Se), BR₃ (wherein R can be, e.g., hydrogen, alkyl, or aryl), C (e.g., an alkyl group, an aryl group, and the like), H, NR₂ (wherein R can be, e.g., hydrogen, alkyl, or aryl), or OR (wherein R can be, e.g., alkyl or aryl). The phosphorous atom in an unmodified phosphate group is achiral. However, replacement of one of the non-bridging oxygens with one of the above atoms or groups of atoms can render the phosphorous atom chiral; that is to say that a phosphorous atom in a phosphate group modified in this way is a stereogenic center. The stereogenic phosphorous atom can possess either the "R" configuration (herein Rp) or the "S" configuration (herein Sp).

Phosphorodithioates have both non-bridging oxygens replaced by sulfur. The phosphorus center in the phosphorodithioates is achiral which precludes the formation of oligoribonucleotide diastereomers. In an embodiment, modifications to one or both non-bridging oxygens can also include the replacement of the non-bridging oxygens with a group independently selected from S, Se, B, C, H, N, and OR (R can be, e.g., alkyl or aryl).

The phosphate linker can also be modified by replacement of a bridging oxygen, (i.e., the oxygen that links the phosphate to the nucleoside), with nitrogen (bridged phosphoroamidates), sulfur (bridged phosphorothioates) and carbon (bridged methylenephosphonates). The replacement can occur at either linking oxygen or at both of the linking oxygens. Replacement of the Phosphate Group

The phosphate group can be replaced by non-phosphorus containing connectors. In an embodiment, the charge phosphate group can be replaced by a neutral moiety.

Examples of moieties which can replace the phosphate group can include, without limitation, e.g., methyl phosphonate, hydroxylamino, siloxane, carbonate, carboxymethyl, carbamate, amide, thioether, ethylene oxide linker, sulfonate, sulfonamide, thioformacetal, formacetal, oxime, methyleneimino, methylenemethylimino, methylenehydrazo,

methylenedimethylhydrazo and methyleneoxymethylimino.

Replacement of the Ribophosphate Backbone

Scaffolds that can mimic nucleic acids can also be constructed wherein the phosphate linker and ribose sugar are replaced by nuclease resistant nucleoside or nucleotide surrogates. In an embodiment, the nucleobases can be tethered by a surrogate backbone. Examples can include, without limitation, the morpholino, cyclobutyl, pyrrolidine and peptide nucleic acid (PNA) nucleoside surrogates. Sugar Modifications

The modified nucleosides and modified nucleotides can include one or more

modifications to the sugar group. For example, the 2' hydroxyl group (OH) can be modified or replaced with a number of different "oxy" or "deoxy" substituents. In an embodiment, modifications to the 2' hydroxyl group can enhance the stability of the nucleic acid since the hydroxyl can no longer be deprotonated to form a 2' -alkoxide ion. The 2' -alkoxide can catalyze degradation by intramolecular nucleophilic attack on the linker phosphorus atom.

Examples of "oxy"-2' hydroxyl group modifications can include alkoxy or aryloxy (OR, wherein "R" can be, e.g., alkyl, cycloalkyl, aryl, aralkyl, heteroaryl or a sugar);

polyethyleneglycols (PEG), 0(CH₂CH₂0)_nCH₂CH₂OR wherein R can be, e.g., H or optionally substituted alkyl, and n can be an integer from 0 to 20 (e.g., from 0 to 4, from 0 to 8, from 0 to 10, from 0 to 16, from 1 to 4, from 1 to 8, from 1 to 10, from 1 to 16, from 1 to 20, from 2 to 4, from 2 to 8, from 2 to 10, from 2 to 16, from 2 to 20, from 4 to 8, from 4 to 10, from 4 to 16, and from 4 to 20). In an embodiment, the "oxy"-2' hydroxyl group modification can include

"locked" nucleic acids (LNA) in which the 2' hydroxyl can be connected, e.g., by a Ci_6 alkylene or Ci_6 heteroalkylene bridge, to the 4' carbon of the same ribose sugar, where exemplary bridges can include methylene, propylene, ether, or amino bridges; O-amino (wherein amino can be, e.g., NH₂; alkylamino, dialkylamino, heterocyclyl, arylamino, diarylamino, heteroarylamino, or diheteroarylamino, ethylenediamine, or polyamino) and aminoalkoxy, 0(CH₂)_n-amino, (wherein amino can be, e.g., NH₂; alkylamino, dialkylamino, heterocyclyl, arylamino, diarylamino, heteroarylamino, or diheteroarylamino, ethylenediamine, or polyamino). In an embodiment, the "oxy"-2' hydroxyl group modification can include the methoxyethyl group (MOE),

(OCH₂CH₂OCH₃, e.g., a PEG derivative).

"Deoxy" modifications can include hydrogen (i.e. deoxyribose sugars, e.g., at the overhang portions of partially ds RNA); halo (e.g., bromo, chloro, fluoro, or iodo); amino (wherein amino can be, e.g., NH₂; alkylamino, dialkylamino, heterocyclyl, arylamino, diarylamino, heteroarylamino, diheteroarylamino, or amino acid); NH(CH₂CH₂NH)_nCH₂CH₂- amino (wherein amino can be, e.g., as described herein), -NHC(0)R (wherein R can be, e.g., alkyl, cycloalkyl, aryl, aralkyl, heteroaryl or sugar), cyano; mercapto; alkyl-thio-alkyl;

thioalkoxy; and alkyl, cycloalkyl, aryl, alkenyl and alkynyl, which may be optionally substituted with e.g., an amino as described herein. The sugar group can also contain one or more carbons that possess the opposite stereochemical configuration than that of the corresponding carbon in ribose. Thus, a modified nucleic acid can include nucleotides containing e.g., arabinose, as the sugar. The nucleotide "monomer" can have an alpha linkage at the position on the sugar, e.g., alpha-nucleosides. The modified nucleic acids can also include "abasic" sugars, which lack a nucleobase at C- . These abasic sugars can also be further modified at one or more of the constituent sugar atoms. The modified nucleic acids can also include one or more sugars that are in the L form, e.g. L- nucleosides.

Generally, RNA includes the sugar group ribose, which is a 5-membered ring having an oxygen. Exemplary modified nucleosides and modified nucleotides can include, without limitation, replacement of the oxygen in ribose (e.g., with sulfur (S), selenium (Se), or alkylene, such as, e.g., methylene or ethylene); addition of a double bond (e.g., to replace ribose with cyclopentenyl or cyclohexenyl); ring contraction of ribose (e.g., to form a 4-membered ring of cyclobutane or oxetane); ring expansion of ribose (e.g., to form a 6- or 7-membered ring having an additional carbon or heteroatom, such as for example, anhydrohexitol, altritol, mannitol, cyclohexanyl, cyclohexenyl, and morpholino that also has a phosphoramidate backbone). In an embodiment, the modified nucleotides can include multicyclic forms (e.g., tricyclo; and

"unlocked" forms, such as glycol nucleic acid (GNA) (e.g., R-GNA or S-GNA, where ribose is replaced by glycol units attached to phosphodiester bonds), threose nucleic acid (TNA, where ribose is replaced with a-L-threofuranosyl-(3'→2')).

Modifications on the Nucleobase

The modified nucleosides and modified nucleotides described herein, which can be incorporated into a modified nucleic acid, can include a modified nucleobase. Examples of nucleobases include, but are not limited to, adenine (A), guanine (G), cytosine (C), and uracil

(U). These nucleobases can be modified or wholly replaced to provide modified nucleosides and modified nucleotides that can be incorporated into modified nucleic acids. The nucleobase of the nucleotide can be independently selected from a purine, a pyrimidine, a purine or pyrimidine analog. In an embodiment, the nucleobase can include, for example, naturally-occurring and synthetic derivatives of a base. Uracil

In an embodiment, the modified nucleobase is a modified uracil. Exemplary nucleobases and nucleosides having a modified uracil include without limitation pseudouridine (ψ), pyridin- 4-one ribonucleoside, 5-aza-uridine, 6-aza-uridine, 2-thio-5-aza-uridine, 2-thio-uridine (s2U), 4- thio-uridine (s4U), 4-thio-pseudouridine, 2-thio-pseudouridine, 5 -hydroxy-uridine (ho⁵U), 5- aminoallyl-uridine, 5-halo-uridine (e.g., 5-iodo-uridine or 5-bromo-uridine), 3-methyl-uridine

(m 3 U), 5-methoxy-uridine (mo 5 U), uridine 5-oxyacetic acid (cmo 5 U), uridine 5-oxyacetic acid methyl ester (mcmo⁵U), 5-carboxymethyl-uridine (cm⁵U), 1-carboxymethyl-pseudouridine, 5- carboxyhydroxymethyl-uridine (chm⁵U), 5-carboxyhydroxymethyl-uridine methyl ester

(mchm⁵U), 5-methoxycarbonylmethyl-uridine (mcm⁵U), 5-methoxycarbonylmethyl-2-thio- uridine (mcm⁵s2U), 5-aminomethyl-2-thio-uridine (nm⁵s2U), 5-methylaminomethyl-uridine (mnm⁵U), 5-methylaminomethyl-2-thio-uridine (mnm⁵s2U), 5-methylaminomethyl-2-seleno- uridine (mnm 5 se 2 U), 5-carbamoylmethyl-uridine (ncm 5 U), 5-carboxymethylaminomethyl-uridine (cmnm⁵U), 5-carboxymethylaminomethyl-2-thio-uridine (cmnm⁵s2U), 5-propynyl-uridine, 1- propynyl-pseudouridine, 5-taurinomethyl-uridine (xcm⁵U), 1-taurinomethyl -pseudouridine, 5- taurinomethyl-2-thio-uridine(Tm⁵s2U), 1 -taurinomethyl-4-thio-pseudouridine, 5-methyl-uridine (m⁵U, i.e., having the nucleobase deoxythymine), 1-methyl-pseudouridine (ηι'ψ), 5-methyl-2- thio-uridine (m⁵s2U), l-methyl-4-thio-pseudouridine (m xi/), 4-thio- 1-methyl-pseudouridine, 3- methyl-pseudouridine (m ψ), 2-thio- 1-methyl-pseudouridine, 1 -methyl- 1-deaza-pseudouridine, 2-thio- 1 -methyl- 1-deaza-pseudouridine, dihydrouridine (D), dihydropseudouridine, 5,6- dihydrouridine, 5-methyl-dihydrouridine (m⁵D), 2-thio-dihydrouridine, 2-thio- dihydropseudouridine, 2-methoxy-uridine, 2-methoxy-4-thio-uridine, 4-methoxy-pseudouridine, 4-methoxy-2-thio-pseudouridine, N 1-methyl-pseudouridine, 3-(3-amino-3- carboxypropyl)uridine (acp 3 U), l-methyl-3-(3-amino-3-carboxypropyl)pseudouridine (acp 3 ψ), 5- (isopentenylaminomethyl)uridine (inm⁵U), 5-(isopentenylaminomethyl)-2-thio-uridine

(inm⁵s2U), a-thio-uridine, 2'-0-methyl-uridine (Um), 5,2'-0-dimethyl-uridine (m⁵Um), 2'-0- methyl-pseudouridine (ψηι), 2-thio-2'-0-methyl-uridine (s2Um), 5-methoxycarbonylmethyl-2'- O-methyl-uridine (mem ⁵Um), 5-carbamoylmethyl-2'-0-methyl-uridine (ncm ⁵Um), 5- carboxymethylaminomethyl-2'-0-methyl-uridine (cmnm 5 Um), 3,2'-0-dimethyl-uridine (m 3 Um), 5-(isopentenylaminomethyl)-2'-0-methyl-uridine (inm⁵Um), 1 -thio-uridine, deoxythymidine, 2'- F-ara-uridine, 2'-F-uridine, 2'-OH-ara-uridine, 5-(2-carbomethoxyvinyl) uridine, 5-[3-(l-E- propenylamino)uridine, pyrazolo[3,4-d]pyrimidines, xanthine, and hypoxanthine.

Cytosine

In an embodiment, the modified nucleobase is a modified cytosine. Exemplary nucleobases and nucleosides having a modified cytosine include without limitation 5-aza- cytidine, 6-aza-cytidine, pseudoisocytidine, 3-methyl-cytidine (m C), N4-acetyl-cytidine (act), 5- formyl-cytidine (f⁵C), N4-methyl-cytidine (m⁴C), 5-methyl-cytidine (m⁵C), 5-halo-cytidine (e.g., 5-iodo-cytidine), 5-hydroxymethyl-cytidine (hm⁵C), 1-methyl-pseudoisocytidine, pyrrolo- cytidine, pyrrolo-pseudoisocytidine, 2-thio-cytidine (s2C), 2-thio-5-methyl-cytidine, 4-thio- pseudoisocytidine, 4-thio- 1-methyl-pseudoisocytidine, 4-thio-l -methyl- 1-deaza- pseudoisocytidine, 1 -methyl- 1-deaza-pseudoisocytidine, zebularine, 5-aza-zebularine, 5-methyl- zebularine, 5-aza-2-thio-zebularine, 2-thio-zebularine, 2-methoxy-cytidine, 2-methoxy- 5 -methyl- cytidine, 4-methoxy-pseudoisocytidine, 4-methoxy- 1-methyl-pseudoisocytidine, lysidine (k C), a-thio-cytidine, 2'-0-methyl-cytidine (Cm), 5,2'-0-dimethyl-cytidine (m⁵Cm), N4-acetyl-2'-0- methyl-cytidine (ac⁴Cm), N4,2'-0-dimethyl-cytidine (m⁴Cm), 5-formyl-2'-0-methyl-cytidine (f ⁵Cm), N4,N4,2'-0-trimethyl-cytidine (m⁴ ₂Cm), 1-thio-cytidine, 2'-F-ara-cytidine, 2'-F-cytidine, and 2'-OH-ara-cytidine.

Adenine

In an embodiment, the modified nucleobase is a modified adenine. Exemplary nucleobases and nucleosides having a modified adenine include without limitation 2-amino- purine, 2,6-diaminopurine, 2-amino-6-halo-purine (e.g., 2-amino-6-chloro-purine), 6-halo-purine (e.g., 6-chloro-purine), 2-amino-6-methyl-purine, 8-azido-adenosine, 7-deaza-adenine, 7-deaza- 8-aza-adenine, 7-deaza-2-amino-purine, 7-deaza-8-aza-2-amino-purine, 7-deaza-2,6- diaminopurine, 7-deaza-8-aza-2,6-diaminopurine, 1 -methyl- adenosine (i A), 2-methyl-adenine (m²A), N6-methyl-adenosine (m⁶A), 2-methylthio-N6-methyl-adenosine (ms2m⁶A), N6- isopentenyl-adenosine (i⁶A), 2-methylthio-N6-isopentenyl-adenosine (ms²i⁶A), N6-(cis- hydroxyisopentenyl)adenosine (io⁶A), 2-methylthio-N6-(cis-hydroxyisopentenyl)adenosine (ms2io⁶A), N6-glycinylcarbamoyl-adenosine (g⁶A), N6-threonylcarbamoyl-adenosine (t⁶A), N6- methyl-N6-threonylcarbamoyl-adenosine (m⁶t⁶A), 2-methylthio-N6-threonylcarbamoyl- adenosine (ms²g⁶A), N6,N6-dimethyl-adenosine (m⁶ ₂A), N6-hydroxynorvalylcarbamoyl- adenosine (hn⁶A), 2-methylthio-N6-hydroxynorvalylcarbamoyl-adenosine (ms2hn⁶A), N6- acetyl-adenosine (ac⁶A), 7-methyl-adenine, 2-methylthio-adenine, 2-methoxy-adenine, a-thio- adenosine, 2'-0-methyl-adenosine (Am), N⁶,2'-0-dimethyl-adenosine (m⁶Am), N⁶-Methyl-2'- deoxyadenosine, N6,N6,2'-0-trimethyl-adenosine (m⁶ ₂Am), l,2'-0-dimethyl-adenosine (i Am), 2'-0-ribosyladenosine (phosphate) (Ar(p)), 2-amino-N6-methyl-purine, 1-thio-adenosine, 8- azido-adenosine, 2'-F-ara-adenosine, 2'-F-adenosine, 2'-OH-ara-adenosine, and N6-(19-amino- pentaoxanonadecyl) - adeno sine .

Guanine

In an embodiment, the modified nucleobase is a modified guanine. Exemplary nucleobases and nucleosides having a modified guanine include without limitation inosine (I), 1- methyl-inosine (iVl), wyosine (imG), methylwyosine (mimG), 4-demethyl-wyosine (imG-14), isowyosine (imG2), wybutosine (yW), peroxywybutosine (o₂yW), hydroxy wybuto sine (OHyW), undermodified hydroxy wybuto sine (OHyW*), 7-deaza-guanosine, queuosine (Q),

epoxyqueuosine (oQ), galactosyl-queuosine (galQ), mannosyl-queuosine (manQ), 7-cyano-7- deaza-guanosine (preQo), 7-aminomethyl-7-deaza-guanosine (preQO, archaeosine (G⁺), 7-deaza- 8-aza-guanosine, 6-thio-guanosine, 6-thio-7-deaza-guanosine, 6-thio-7-deaza-8-aza-guanosine, 7-methyl-guanosine (m G), 6-thio-7-methyl-guanosine, 7-methyl-inosine, 6-methoxy-guanosine,

1 -methyl-guanosine (m'G), N2-methyl-guanosine (m 2 G), N2,N2-dimethyl-guanosine (m 2 ₂G),

N2,7-dimethyl-guanosine (m 2 ,7G), N2, N2,7-dimethyl-guanosine (m 2 ,2,7G), 8-oxo-guanosine, 7-methyl-8-oxo-guanosine, 1-meth thio-guanosine, N2-methyl-6-thio-guanosine, N2,N2- dimethyl-6-thio-guanosine, a-thio-guanosine, 2'-0-methyl-guanosine (Gm), N2-methyl-2'-0- methyl-guanosine (m 2"Gm), N2,N2-dimethyl-2'-0-methyl- guano sine (m 2 ₂Gm), l-methyl-2'-0- methyl-guanosine (m'Gm), N2,7-dimethyl-2'-0-methyl-guanosine (m",7Gm), 2'-0-methyl- inosine (Im), l,2'-0-dimethyl-inosine (m'lm), 0⁶-phenyl-2'-deoxyinosine, 2'-0-ribosylguanosine (phosphate) (Gr(p)), 1-thio-guanosine, 0⁶-methyl- guanosine, 0⁶-Methyl-2'-deoxy guanosine, Z - F-ara-guanosine, and 2'-F-guanosine.

Modified gRNAs

In an embodiment, the modified nucleic acids can be modified gRNAs. In an

embodiment, gRNAs can be modified at the 3' end. In this embodiment, the gRNAs can be modified at the 3' terminal U ribose. For example, the two terminal hydroxyl groups of the U ribose can be oxidized to aldehyde groups and a concomitant opening of the ribose ring to afford a modified nucleoside as sown below:

wherein "U" can be an unmodified or modified uridine.

In another embodiment, the 3' terminal U can be modified with a 2' 3' cyclic phosphate as shown below:

wherein "U" can be an unmodified or modified uridine.

In an embodiment, the gRNA molecules may contain 3' nucleotides which can be stabilized against degradation, e.g., by incorporating one or more of the modified nucleotides described herein. In this embodiment, e.g., uridines can be replaced with modified uridines, e.g., 5-(2-amino)propyl uridine, and 5-bromo uridine, or with any of the modified uridines described herein; adenosines and guanosines can be replaced with modified adenosines and guanosines, e.g., with modifications at the 8-position, e.g., 8-bromo guanosine, or with any of the modified adenosines or guanosines described herein. In an embodiment, deaza nucleotides, e.g., 7-deaza- adenosine, can be incorporated into the gRNA. In an embodiment, O- and N-alkylated nucleotides, e.g., N6-methyl andenosine, can be incorporated into the gRNA. In an embodiment, sugar-modified ribonucleotides can be incorporated, e.g., wherein the 2' OH-group is replaced by a group selected from H, -OR, -R (wherein R can be, e.g., alkyl, cycloalkyl, aryl, aralkyl, heteroaryl or sugar), halo, -SH, -SR (wherein R can be, e.g., alkyl, cycloalkyl, aryl, aralkyl, heteroaryl or sugar), amino (wherein amino can be, e.g., NH₂; alkylamino, dialkylamino, heterocyclyl, arylamino, diarylamino, heteroarylamino, diheteroarylamino, or amino acid); or cyano (-CN). In an embodiment, the phosphate backbone can be modified as described herein, e.g., with a phosphothioate group. In an embodiment, the nucleotides in the overhang region of the gRNA can each independently be a modified or unmodified nucleotide including, but not limited to 2'-sugar modified, such as, 2-F 2'-0-methyl, thymidine (T), 2'-0-methoxyethyl-5- methyluridine (Teo), 2'-0-methoxyethyladenosine (Aeo ), 2'-0-methoxyethyl-5-methylcytidine (m5Ceo ), and any combinations thereof.

In an embodiment, a one or more or all of the nucleotides in single stranded overhang of an RNA molecule, e.g., a gRNA molecule, are deoxynucleotides.

XI. Linkers

In an embodiment, the payload can be linked to the Cas9 molecules or the gRNA, e.g., by a covalent linker. This linker may be cleavable or non-cleavable. In an embodiment, a cleavable linker may be used to release the payload after transport to the desired target.

Linkers can comprise a direct bond or an atom such as, e.g., an oxygen (O) or sulfur (S), a unit such as -NR- wherein R is hydrogen or alkyl, -C(O)-, -C(0)0-, -C(0)NH-, SO, S0₂, - S0₂NH- or a chain of atoms, such as substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, substituted or unsubstituted alkynyl, arylalkyl, heteroarylalkyl. In an embodiment, one or more methylenes in the chain of atoms can be replaced with one or more of O, S, S(O), S0₂, -S0₂NH-, -NR-, -C(O)-, -C(0)0-, -C(0)NH-, a cleavable linking group, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, and substituted or unsubstituted heterocyclic.

Non-cleavable linkages

In an embodiment, the payload is attached to the Cas9 molecule or gRNA through a linker that is itself is stable under physiological conditions, such as an alkylene chain, and does not result in release of the payload from the Cas9 molecule and/or gRNA for at least 2, 3, 4, 5, 10, 15, 24 or 48 hours or for at least 1, 2, 3, 4, 5,or 10 days when administered to a subject. In an embodiment, the payload and the Cas9 molecule and/or gRNA comprise residues of a functional groups through which reaction and linkage of the payload to the Cas9 molecule or gRNA was achieved. In an embodiment, the functional groups, which may be the same or different, terminal or internal, of the payload or Cas9molecule and/or gRNA comprise an amino, acid, imidazole, hydroxyl, thio, acyl halide, -HC=CH-,— c≡c— group, or derivative thereof. In an embodiment, the linker comprises a hydrocarbylene group wherein one or more methylene groups is optionally replaced by a group Y (provided that none of the Y groups are adjacent to each other), wherein each Y, independently for each occurrence, is selected from, substituted or unsubstituted aryl, heteroaryl, cycloalkyl, heterocycloalkyl, or -0-, -C(=X)- (wherein X is NR_{1 ;} O or S), -NRi-, -NRiC(O)-, -C(0)NR , -S(0)_n-, -NRiS(0)_n-,- S(0)_nNRi -, -NRiC(0)-NR ; and R_{1 ;} independently for each occurrence, represents H or a lower alkyl and wherein n is 0, 1, or 2.

In an embodiment, the linker comprises an alkylene moiety or a heteroalkylene moiety (e.g., an alkylene glycol moiety such as ethylene glycol). In an embodiment, a linker comprises a poly-L-glutamic acid, polylactic acid, poly(ethyleneimine), an oligosaccharide, an amino acid (e.g., glycine), an amino acid chain, or any other suitable linkage. The linker groups can be biologically inactive, such as a PEG, polyglycolic acid, or polylactic acid chain. In an embodiment, the linker group represents a derivatized or non-derivatized amino acid (e.g., glycine).

Cleavable Linkages

A cleavable linking group is one which is sufficiently stable outside the cell, but which upon entry into a target cell is cleaved to release the two parts the linker is holding together. In one embodiment, the cleavable linking group is cleaved at least 10 times or more, or at least 100 times faster in the target cell or under a first reference condition (which can, e.g., be selected to mimic or represent intracellular conditions) than in the blood of a subject, or under a second reference condition (which can, e.g., be selected to mimic or represent conditions found in the blood or serum).

Cleavable linking groups are susceptible to cleavage agents, e.g., pH, redox potential or the presence of degradative molecules. Examples of such degradative agents include: redox agents which are selected for particular substrates or which have no substrate specificity, including, e.g., oxidative or reductive enzymes or reductive agents such as mercaptans, present in cells, that can degrade a redox cleavable linking group by reduction; esterases; endosomes or agents that can create an acidic environment, e.g., those that result in a pH of five or lower; enzymes that can hydrolyze or degrade an acid cleavable linking group by acting as a general acid, peptidases (which can be substrate specific), and phosphatases.

A cleavable linkage group, such as a disulfide bond (-S-S-) can be susceptible to pH. The pH of human serum is 7.4, while the average intracellular pH is slightly lower, ranging from about 7.1-7.3. Endosomes have a more acidic pH, in the range of 5.5-6.0, and lysosomes have an even more acidic pH at around 5.0. Some linkers will have a cleavable linking group that is cleaved at a preferred pH. A linker can include a cleavable linking group that is cleavable by a particular enzyme.

In general, the suitability of a candidate cleavable linking group can be evaluated by testing the ability of a degradative agent (or condition) to cleave the candidate linking group. The candidate cleavable linking group can also be tested for the ability to resist cleavage in the blood or when in contact with other non-target tissue. Thus one can determine the relative susceptibility to cleavage between a first and a second condition, where the first is selected to be indicative of cleavage in a target cell and the second is selected to be indicative of cleavage in other tissues or biological fluids, e.g., blood or serum. The evaluations can be carried out in cell free systems, in cells, in cell culture, in organ or tissue culture, or in whole animals. It may be useful to make initial evaluations in cell-free or culture conditions and to confirm by further evaluations in whole animals.

In an embodiment, the cleavable linkers include redox cleavable linkers, such as a disulfide group (-S-S-) and phosphate cleavable linkers, such as, e.g., -0-P(0)(OR)-0-, -O- P(S)(OR)-0-, -0-P(S)(SR)-0-, -S-P(0)(OR)-0-, -0-P(0)(OR)-S-, -S-P(0)(OR)-S-, -0- P(S)(OR)-S-, -S-P(S)(OR)-0-, -0-P(0)(R)-0-, -0-P(S)(R)-0-, -S-P(0)(R)-0-, -S-P(S)(R)-0-, - S-P(0)(R)-S-, -OP(S)(R)-S-, wherein R is hydrogen or alkyl.

Acid Cleavable Linking Groups

Acid cleavable linking groups are linking groups that are cleaved under acidic conditions. In an embodiment, acid cleavable linking groups are cleaved in an acidic environment with a pH of about 6.5 or lower (e.g., about 6.0, 5.5, 5.0, or lower), or by agents such as enzymes that can act as a general acid. Examples of acid cleavable linking groups include but are not limited to hydrazones, esters, and esters of amino acids. Acid cleavable groups can have the general formula -C(=N-)N-, -C(0)0-, or -OC(O)-.

Ester-Based Linking Groups

Ester-based cleavable linking groups are cleaved by enzymes such as esterases and amidases in cells. Examples of ester-based cleavable linking groups include but are not limited to esters of alkylene, alkenylene and alkynylene groups. Ester cleavable linking groups have the general formula -C(0)0-, or -OC(O)-. XII. Targeting of Genomic Signatures

Cas9 molecules, gRNA molecules, and in particular, Cas9 molecule/gRNA molecule complexes, can be used to target a cell by virtue of sequence specific interaction with a target nucleic acid comprising a selected genomic signature. This provides for targeted destruction of cells having a selected genomic signature. Method and compositions disclosed herein can be used to treat disorders characterized by a selected genomic signature, e.g., a genomic signature present in the germline or a genomic signature that arise as a result of a sporadic or somatic change in the genome, e.g., a germline or acquired mutation in a cancer cell, a viral infection, or other germline or acquired changes to the genome.

While not wishing to be bound by theory, it is believed that complementarity between the targeting domain of a gRNA molecule and the target sequence of a target nucleic acid mediates target sequence- specific interaction of the Cas9 molecule/gRNA molecule complex with the target sequence. This allows targeting of specific sequences or genomic signatures, e.g., rearrangements, e.g., translocations, insertions, deletions, and inversions, and other mutations. A Cas9 molecule/gRNA molecule complex can be used to target specific sequence, e.g., mutations, that are germline, mitochondrial, or somatic. Depending on the Cas9 molecule/gRNA molecule complex used, specific editing, the delivery of a payload, or both, can be effected. In an embodiment, both cleavage and delivery of a payload is effected.

In an embodiment, the Cas9 molecule/gRNA molecule complex that promotes cell death upon recognition of its target genomic sequence. In an embodiment, an eaCas9 molecule/gRNA molecule complex cleaves the target nucleic acid. In an embodiment, it does not deliver a payload. While not wishing to be bound by theory is it believed that endogenous cellular elements, e.g., elements of the DNA damage apoptosis signaling cascade promote apoptosis in these embodiments.

In an embodiment, an eaCas9 molecule/gRNA molecule complex cleaves the target nucleic acid and delivers a payload. The payload can comprises a compound that inhibits growth or cell division, or promotes apoptosis, e.g., an element of the DNA damage apoptosis signaling cascade. In an embodiment, a second Cas9 molecule/gRNA molecule complex is used to deliver a payload comprising a second compound that inhibits growth or cell division, or promotes apoptosis, e.g., an element of the DNA damage apoptosis signaling cascade. The Cas9 molecule/gRNA molecule complex that delivers the second payload can comprise an eiCas9 molecule or an eaCas9 molecule. An additional, e.g., third or fourth, Cas9 molecule/gRNA molecule complex, can be used to deliver additional payload, e.g., an additional compound that inhibits growth or cell division, or promotes apoptosis, e.g., an additional element of the DNA damage apoptosis signaling cascade promote.

In an embodiment, the Cas9 molecule/gRNA molecule complex delivers a payload comprising a compound that inhibits growth or cell division, or promotes apoptosis, e.g., an element of the DNA damage apoptosis signaling cascade, but does not cleave the target nucleic acid. While not wishing to be bound by theory is it believed that endogenous cellular elements, e.g., elements of the DNA damage apoptosis signaling cascade promote apoptosis in these embodiments.

Exemplary compounds that inhibit growth or cell division, or promote apoptosis, e.g., an element of the DNA damage apoptosis signaling cascade, are described herein, e.g., in Table XII-1.

Table XII-1

In an embodiment, a Cas9 molecule/gRNA molecule complex targets a sequence that includes or is near the breakpoint of a rearrangement, e.g., a translocation, inversion, insertion, deletion. In an embodiment, the rearrangement confers unwanted properties, e.g., unwanted proliferation, on the cell. In an embodiment, the cell harboring the rearrangement is a cancer cell. In an embodiment, the rearrangement comprises a kinase gene and results in unwanted, increased, or constitutive expression of the kinase activity. In an embodiment, the rearrangement disrupts the expression of a tumor suppressor.

In an embodiment, the Cas9 molecule/gRNA molecule complex:

specifically targets, and e.g., cleaves, the genome of a cell comprising a rearrangement, e.g., by targeting a mutation, e.g., a breakpoint or junction of a rearrangement; or

targets, e.g., for cleavage or payload delivery, a nucleotide sequence within 200, 100, 150, 100, 50, 25, 10, or 5 nucleotides of a mutation, e.g., a rearrangement breakpoint.

The invention includes a method of manipulating a cell comprising a genomic signature, comprising:

administering a Cas9 molecule/gRNA molecule complex that targets said genomic signature, thereby manipulating said cell.

In an embodiment, manipulating comprises inhibiting the growth or division of, or killing, said cell.

In an embodiment, said cell is a cancer cell or cell having a viral infection.

In an embodiment, the method comprises treating a subject, e.g., a human subject, for a disorder characterized by a cell having said genomic signature, e.g., a cancer or a viral infection.

In an embodiment, a Cas9 molecule/gRNA molecule complex disrupts a rearrangement, e.g., by introduction of a stop codon from a template nucleic acid, e.g., a stop codon is inserted into a fusion protein, e.g., a fusion protein comprising kinase activity.

The invention includes a method of treating a cancer having a translocation of a kinase gene to a non-kinase gene, which places the kinase domain under the control of the non-kinase gene control region comprising:

administering a Cas9 molecule/gRNA molecule complex that targets the translocation. In an embodiment, the control region, e.g., the promoter, or the coding sequence, of the kinase translocation, is edited to reduce expression.

XIII. Combination Therapy

The Cas9 molecules, gRNA molecules, and in particular, Cas9 molecule/gRNA molecule complexes, can be used in combination with a second therapeutic agent, e.g., a cancer drug. In an embodiment, the second therapeutic agent (e.g., a cancer drug) and the Cas9 molecule, gRNA molecule, and in particular, Cas9 molecule/gRNA molecule complex target different (e.g., non- overlapping) pathways. In an embodiment, the second therapeutic agent (e.g., a cancer drug) and the Cas9 molecule, gRNA molecule, and in particular, Cas9 molecule/gRNA molecule complex target a same or overlapping pathway.

Exemplary combination therapies include, e.g.:

mTOR inhibitors (e.g., Temsirolimus (Torisel®) or Everolimus (Afinitor®)) together with a AKT-specific Cas9/gRNA molecule;

Tyrosine kinase inhibitors such as Imatinib mesylate (Gleevec®); Dasatinib (Sprycel®); Bosutinib (Bosulif®); Trastuzumab (Herceptin®); Pertuzumab (Perjeta™); Lapatinib

(Tykerb®); Gefitinib (Iressa®); Erlotinib (Tarceva®) together with a HDAC-specific Cas9/gRNA molecule; and

Any chemotherapeutic agent together with one or more Cas9/gRNAs against multidrug resistance genes such as MDR1 gene.

XIV. Treatment of genetic disorder, e.g., Duchenne muscular dystrophy (DMD)

In another aspect, the invention features, a method of altering a cell, e.g., reducing or abolishing the effect of a genetic signature, e.g., a stop codon, e.g., a premature stop codon. The method comprises contacting said cell with:

a Cas9 molecule/gRNA molecule complex that cleaves at or upstream from the genetic signature, e.g., a premature stop codon,

thereby altering the cell.

While not wishing to be bound by theory it is believed that, in an embodiment, cleavage and subsequent exonuclease activity, and non-homologous end joining results in an altered sequence in which the genetic signature, e.g., a premature stop codon is eliminated, e.g., by being placed in a different frame. In an embodiment, the same series of events restores the proper reading frame to the sequence that follows the signature, e.g., premature stop codon.

When the method is carried out to correct a frameshift mutation in order to remove a premature stop codon, repair can be carried out at various sites in the DNA. One may direct cleavage at the mutation, thereby correcting the frameshift entirely and returning the protein to its wild-type (or nearly wild-type) sequence. One may also direct cleavage at or near the premature stop codon, so that all (or nearly all) amino acids of the protein C-terminal of the codon where repair was effected are wild-type. In the latter case, the resulting protein may have one or more frameshifted amino acids between the mutation and the repair site; however the protein may still be functional because it is full-length and has wild-type sequence across most of its length.

A genetic signature is a particular DNA sequence at a particular portion of the genome, that causes a phenotype (such as a genetic disease or a symptom thereof). For instance, the genetic signature may be a premature stop codon that prevents expression of a protein. In this scenario, the premature stop codon can arise from a mutation that directly creates a stop codon, or from a mutation that causes a frameshift leading to a premature stop codon being formed downstream. A genetic signature may also be a point mutation that alters the identity of an important amino acid in a protein, disrupting the protein's function.

In an embodiment, the Cas9 molecule/gRNA molecule complex mediates a double stranded break in said target nucleic acid.

In an embodiment, the genetic signature, e.g., a premature stop codon, results from a point mutation, an insertion, a deletion, or a rearrangement. In an embodiment, a mutation causes a frameshift, resulting in a genetic signature, e.g., a premature stop codon downstream of the mutation.

In an embodiment, the premature stop codon is within the target nucleic acid. In an embodiment, the target nucleic acid is upstream of the premature stop codon. The mutation may be upstream of the target nucleic acid, within the target nucleic acid, or downstream of the target nucleic acid.

In an embodiment the double stranded break is within 500, 200, 100, 50, 30, 20, 10, 5, or 2 nucleotides of the mutation. In an embodiment, the double stranded break is within 500, 200, 100, 50, 30, 20, 10, 5, or 2 nucleotides of the genetic signature, e.g., a premature stop codon.

In an embodiment, the Cas9 molecule/gRNA molecule complex mediates exonuclease digestion of the target nucleic acid. In an embodiment, the Cas9 molecule/gRNA molecule complex removes 1, 2, 3, 4, or 5 nucleotides at the double stranded break.

In an embodiment, the double stranded break is resolved by non-homologous end joining. In an embodiment the mutation and/or genetic signature, e.g., premature stop codon is in the dystrophin gene, e.g., in exon 51, or in the intron preceding or following exon 51. The premature stop codon may also be caused by a mutation in the dystrophin gene at one or more of codons 54, 645, 773, 3335, and 3340. In an embodiment, the premature stop codon in the dystrophin gene results from a deletion of codons 2305 through 2366.

In an embodiment, contacting the cell with a Cas9 molecule/gRNA molecule complex comprises contacting the cell with a nucleic acid encoding a Cas9 molecule. In an embodiment, contacting the cell with a Cas9 molecule/gRNA molecule complex comprises transfecting the cell with a nucleic acid, e.g., a plasmid, or using a viral vector such as adeno-associated virus (AAV).

In an embodiment, the method results in increased levels of the protein in which the genetic signature, e.g., a premature stop codon, was previously located. For instance, protein levels (e.g., dystrophin levels) may be increased by at least 3%, 4%, 5%, 10%, 15%, 20%, 25%, or 30% in a cell or in a tissue. In an embodiment, the method results in increased levels of the mRNA in which the premature stop codon was previously located, for instance by preventing the mRNA from undergoing nonsense-mediated mRNA decay.

In an embodiment, one or more of the target nucleic acid, the genetic signature, e.g., premature stop codon, and the mutation are located in the dystrophin gene (which is mutated in DMD). One or more of the target nucleic acid, the genetic signature, e.g., premature stop codon, and the mutation may also be located in the COL7A1 gene (mutated in type VH-associated dystrophic epidermolysis bullosa), the FKTN gene (mutated in Fukuyama congenital muscular dystrophy), the dysferlin gene (mutated in limb-girdle muscular dystrophy type 2B), the CFTR gene (mutated in cystic fibrosis), HEXA (mutated in Tay-Sachs disease), the IDS gene (mutated in Hunter syndrome), the FVIII gene (mutated in hemophilia), the IDUA gene (mutated in Hurler syndrome), the PPT1 gene (mutated in infantile neuronal ceroid lipofuscinosis), a tumor suppressor such as the ATM gene (mutated in cancers like gliomas and B-Cell Chronic

Lymphocytic Leukemia), RP2 (mutated in X-linked retinitis pigmentosa), the CTNS gene

(mutated in nephropathic cystinosis), and the AVPR2 gene (mutated in Congenital nephrogenic diabetes insipidus).

In an embodiment, the method is performed in cultured cells. In an embodiment, the method further comprises administering the cell to a patient. The cell may be, for example, an induced pluripotent stem cell, a bone marrow derived progenitor, a skeletal muscle progenitor, a CD 133+ cell, a mesoangioblast, or a MyoD-transduced dermal fibroblast. In an embodiment, the method comprises contacting the cell with a template nucleic acid under conditions that allow for homology-directed repair between the target nucleic acid and the template nucleic acid to correct the mutation or the premature stop codon. In another aspect, the invention features a method of treating a human subject having a disorder associated with a genetic signature, e.g., premature stop codon, e.g., DMD, comprising providing to the human subject:

1) a Cas9 molecule/gRNA molecule complex that cleaves at or upstream from the premature stop codon or

2) a cell that has been contacted with such complex,

thereby treating the subject.

In an embodiment, genetic signature, e.g., premature stop codon results from a point mutation, an insertion, a deletion, or a rearrangement. In an embodiment, a mutation causes a frameshift, resulting in a premature stop codon downstream of the mutation.

In an embodiment the double stranded break is within 500, 200, 100, 50, 30, 20, 10, 5, or 2 nucleotides of the mutation. In an embodiment the double stranded break is within 500, 200, 100, 50, 30, 20, 10, 5, or 2 nucleotides of the premature stop codon.

In an embodiment, the genetic signature, e.g., premature stop codon is within the target nucleic acid of the Cas9 molecule/gRNA molecule complex. In an embodiment, the target nucleic acid is upstream of the genetic signature, e.g., premature stop codon. The mutation may be upstream of the target nucleic acid, within the target nucleic acid, or downstream of the target nucleic acid.

In an embodiment, the double stranded break is resolved by non-homologous end joining. In an embodiment, the mutation and/or genetic signature, e.g., premature stop codon is in the dystrophin gene, e.g., in exon 51, or in the intron preceding or following exon 51. The premature stop codon may also be caused by a mutation in the dystrophin gene at one or more of codons 54, 645, 773, 3335, and 3340. In an embodiment, the premature stop codon in the dystrophin gene results from a deletion of codons 2305 through 2366.

In an embodiment, the method results in increased levels of the protein in which the genetic signature, e.g., premature stop codon was previously located. For instance, protein levels (e.g., dystrophin levels) may be increased by at least 3%, 4%, 5%, 10%, 15%, 20%, 25%, or 30% in a cell or in a tissue. In an embodiment, the method results in increased levels of the mRNA in which the premature stop codon was previously located, for instance by preventing the mRNA from undergoing nonsense-mediated mRNA decay.

Lymphocytic Leukemia), RP2 (mutated in X-linked retinitis pigmentosa), the CTNS gene (mutated in nephropathic cystinosis), and the AVPR2 gene (mutated in Congenital nephrogenic diabetes insipidus).

In an embodiment, the method is performed in cultured cells. In an embodiment, the method further comprises administering the cell to a patient. The cell may be, for example, an induced pluripotent stem cell, a bone marrow derived progenitor, a skeletal muscle progenitor, a CD 133+ cell, a mesoangioblast, or a MyoD-transduced dermal fibroblast. In an embodiment, the method comprises contacting the cell with a template nucleic acid under conditions that allow for homology-directed repair between the target nucleic acid and the template nucleic acid to correct the mutation or the premature stop codon.

In an embodiment, the subject has a disorder selected from Duchenne Muscular

Dystrophy (DMD), collagen type VH-associated dystrophic epidermolysis bullosa, Fukuyama congenital muscular dystrophy, and limb-girdle muscular dystrophy type 2B, cystic fibrosis, lysosomal storage disorders (such as Tay-Sachs disease, Hunter syndrome, and nephropathic cystinosis), hemophilia, Hurler syndrome, infantile neuronal ceroid lipofuscinosis, X-linked retinitis pigmentosa (RP2), cancers (such as gliomas and B-Cell Chronic Lymphocytic

Leukemia), and Congenital nephrogenic diabetes insipidus.

XV. Treatment of Disorders Characterized by Lack of Mature Specialized Cells, e.g..

Impaired Hearing, with Loss of Hair Cells, Supporting Cells, or Spiral Ganglion neurons; or for Diabetes, with Loss of Beta Islet Cells

In another aspect, the invention features, a method of altering a cell, e.g., to promote the development of other mature specialized cells, e.g, in regeneration therapy. For example, proliferation genes can be upregulated and/or checkpoint inhibitors can be inhibited, e.g., to drive down one or more differenation pathways.

In an embodiment, the method includes induction of proliferation and specified lineage maturation.

In an embodiment, the method comprises, e.g., for restoration or improvement of hearing, contacting said cell with:

a Cas9 molecule/gRNA molecule complex that up-regulates a gene that promotes the development of hair cells, or down-regulates a gene that inhibits the development of hair cells thereby altering the cell.

In an embodiment, the Cas9 molecule/gRNA molecule delivers a payload that up- regulates a gene that promotes hair cell development.

In an embodiment, the Cas9 molecule/gRNA molecule delivers a payload that down- regulates a gene that inhibits hair growth.

In an embodiment, the Cas9 molecule/gRNA molecule complex edits the genome of a cell to up-regulate a gene that promotes hair growth. In an embodiment, a template nucleic acid is used to effect a Cas9 molecule/gRNA molecule complex alteration to the genome that up- regulates a gene that promotes hair growth.

In an embodiment, the Cas9 molecule/gRNA molecule complex edits the genome of a cell to down-regulate a gene that inhibits hair growth. In an embodiment, a template nucleic acid is used to effect a Cas9 molecule/gRNA molecule complex alteration to the genome that down- regulates a gene that promotes hair growth.

In an embodiment, said cell is an iPS cell, a native hair cell progenitor, or a mature hair cell.

In an embodiment, the Cas9 molecule/gRNA molecule and modifies expression of a gene, e.g., by modifying the structure of the gene (e.g., by editing the genome) or by delivery of a payload that modulates a gene. In an embodiment, the gene is a transcription factor or other regulatory gene.

In an embodiment, for hair cell or other mature cell regeneration, the method includes one or more or all of the following:

contacting the cell with a Cas9 molecule/gRNA molecule complex that results in up- regulation one or more of the following for cell proliferation: c-Myc, GAT A3, Oct4, Sox2, Wnt, TCF3;

contacting the cell with a Cas9 molecule/gRNA molecule complex that results in down- regulation one or more of the following for check point: BCL2, BMP, Hesl, Hes5, Notch, p27, Pro l, TGFp; and

contacting the cell with a Cas9 molecule/gRNA molecule complex that results in turning on a maturation pathway. For hair cells this would include one or more of the following: Atohl (Mat l ), Barhll , Gfil, Myo7a, p63, PAX2, PAX8, Pou4f3 and for neurons would include one or more of the following: NEFH, Neurodl, Neurogl, POU4F1.

In an embodiment, the method comprises generation of inner ear hair cells, outer ear hair cells, spiral ganglion neurons, and ear supporting cells.

In an embodiment, one or more growth factors can be modulated, e.g., upregulated, e.g., TPO can be upregulated for production of platelets and GCSF can be upregulated for production of neutrophils.

In another aspect, the invention provides altered cell described herein, e.g., in this Section

XV. In another aspect, the invention features a method of treating impaired hearing. The method comprises administering to said subject, an altered cell described herein, e.g., in this section XV. In an embodiment, the cell is autologous. In an embodiment, the cell is allogeneic. In an embodiment, the cell is xenogeneic.

In another aspect, the invention features a method of treating subject, e.g., for impaired hearing. The method comprises administering to said subject:

a Cas9 molecule/gRNA molecule complex that up-regulates a gene that promotes the growth of hair, or down-regulates a gene that inhibits the growth of hair thereby altering the cell.

In an embodiment, the Cas9 molecule/gRNA molecule delivers a payload that up- regulates a gene that promotes hair growth.

In an embodiment, the method includes one or more or all of the following:

administering a Cas9 molecule/gRNA molecule complex that results in up-regulation one or more of the following: c-Myc, GATA3, Oct4, Sox2, Wnt, or TCF3;

administering a Cas9 molecule/gRNA molecule complex that results in turning on a maturation pathway. For hair cells this would include one or more of the following: Atohl (Mathl), Barhll, Gfil , Myo7a, p63, PAX2, PAX8, or Pou4f3 and for neurons would include one or more of the following: NEFH, Neurodl, Neurogl, or POU4F1. XVI. Governing gRNA Molecules and Their Use to Limit the Activity of a Cas9 System

As discussed herein, methods and compositions that use, or include, a nucleic acid, e.g., DNA, that encodes a Cas9 molecule or a gRNA molecule, can, in addition, use or include a governing gRNA molecule. The governing gRNA molecule can complex with the Cas9 molecule to inactivate or silence a component of the system, e.g., the nucleic acid that encodes the Cas9 molecule or the nucleic acid that encodes the gRNA molecule. In either case, the governing gRNA, e.g., a Cas9-targeting gRNA molecule, or a gRNA targeting gRNA molecule, limits the effect of the Cas9/gRNA complex mediated gene targeting, and can place temporal limits on activity or reduce off-target activity. Governing gRNA molecules can act as to inhibit, e.g., entirely or substantially inhibit, the production of a component of the Cas9 system and thereby limit, or govern, its activity.

Typically a nucleic acid sequence encoding a governing gRNA molecule, e.g., a Cas9- targeting gRNA molecule, is under the control of a different control region, e.g., promoter, than is the component it negatively modulates, e.g., a nucleic acid encoding the Cas9 molecule. In an embodiment, different refers to simply not being under the contol of one control region, e.g., promoter, that is fucntinally coupled to both controlled sequences. In an embodiment, different refers to different in kind or type. For example, the sequence encoding a governing gRNA molecule, e.g., a Cas9-targeting gRNA molecule, is under the control of a control region, e.g., a promoter, that has a lower level of expression, or is expressed later than the sequence which encodes the component it negatively modulates, e.g., a nucleic acid encoding the Cas9 molecule.

By way of example a sequence that encodes a governing gRNA molecule, e.g., a Cas9- targeting gRNA molecule, can be under the control of a control region (e.g., a promoter) described herein, e.g., humanU6 small nuclear promoter, or human HI promoter. In an embodiment, a sequence that encodes the component it negatively regulates, e.g. a nucleic acid encoding the Cas9 molecule, can be under the control of a control region (e.g., a promoter) described herein, e.g., human U6 small nuclear promoter, human HI promoter, or a PolII promoter, e.g., a CMV promoter, a CAGGS promoter, or a CB promoter. EXAMPLES

The following Examples are merely illustrative and are not intended to limit the scope or content of the invention in any way.

Example 1: In silico design of governing gRNA sequences targeting S. pyogenes and S. aureus Cas9

Governing guide RNAs (gRNAs) targeting S. pyogenes and S. aureus Cas9s were identified using a DNA sequence searching algorithm. In addition to identifying potential gRNA sites adjacent to PAM sequences, the software also identifies all PAM adjacent sequences that differ by 1, 2, 3 or more nucleotides from the selected gRNA sites in the human genome.

Genomic DNA sequence for each Cas9 gene was obtained from the UCSC Genome browser and sequences were screened for repeat elements using the publically available RepeatMasker program. RepeatMasker searches input DNA sequences for repeated elements and regions of low complexity. The output is a detailed annotation of the repeats present in a given query sequence.

Following identification, governing gRNAs were ranked into tiers based on their cleavage position within the Cas9 coding sequence, their orthogonality and presence of a 5' G (based on identification of close matches in the human genome containing a PAM).

Orthogonality refers to the number of sequences in the human genome that contain a minimum number of mismatches to the target sequence. A "high level of orthogonality" or "good orthogonality" may, for example, refer to 20-mer gRNAs that have no identical sequences in the human genome besides the intended target, nor any sequences that contain one or two mismatches in the target sequence. Targeting domains with good orthogonality are selected to minimize off-target DNA cleavage.

Tier 1 includes all gRNAs that target the first 500 nucleotides of coding sequence of Cas9, have good orthogonality, and begin with a 5' G. Tier 2 includes all gRNAs that target the first 500 nucleotides of coding sequence of Cas9, have good orthogonality, but don't begin with a 5' G. Tier 3 includes all gRNAs that target the first 500 nucleotides of coding sequence of Cas9, have poor orthogonality, and begin with a 5' G. Tier 4 includes all gRNAs that target the first 500 nucleotides of coding sequence of Cas9, have poor orthogonality, but don't begin with a 5' G. Tier 5 includes all gRNAs that target the remaining coding sequence. In the case of S. aureus, there is a 6 tier that includes all gRNAs whose targets have a non-optimal PAM of NNGRRV.

For all S. pyogenes targets, 17-mer, or 20-mer gRNAs were designed. For all S. aureus targets, 20-mer gRNAs were designed. gRNAs were identified for both single-gRNA nuclease cleavage and for a dual-gRNA paired "nickase" strategy. The designed governing gRNAs are listed in Tables E-l to E-12.

Table E-l

Table E-2

Table E-3

Table E-4

antiSPCas9-35 - GGGCACU U UCUCAUUGA 17 338 antiSPCas9-36 + GGU UAUGACAGCCCAUCCAA 20 339 antiSPCas9-37 + GUCCUCU UCGACAAGGA 17 340 antiSPCas9-38 - GUCCU UCCU UGUCGAAG 17 341 antiSPCas9-39 + GU U UCUUGUCCUCUUCGACA 20 342

Table E-5

First 500bp of coding sequence downstream of start codon, poor

S. pyogenes

orthogonality, does not start with G

4th Tier

DNA Target Site SEQ ID NO gRNA Name Targeting Domain

Strand Length antiSPCas9-40 - AAACAUAGUAGAUGAGG 17 343 antiSPCas9-41 + AAAGAAAGAAUCGUCAACUU 20 344 antiSPCas9-42 - AAAGAAAUU UAAGGUGU 17 345 antiSPCas9-43 + AACACCU UAAAUU UCUUUGA 20 346 antiSPCas9-44 - AAGAAAUU UAAGGUGUU 17 347 antiSPCas9-45 - AAGAGGACAAGAAACAUGAA 20 348 antiSPCas9-46 - AAU UU UUAGCAAUGAGA 17 349 antiSPCas9-47 + ACCU UAAAU UUCU UUGA 17 350 antiSPCas9-48 - ACCU UCAAAG AAAU U U A 17 351 antiSPCas9-49 + ACGGAACU UUAUCAUAU 17 352 antiSPCas9-50 + ACUAUGU UUCCAAAGAU 17 353 antiSPCas9-51 - AGAAAU UUAAGGUGU UG 17 354 antiSPCas9-52 - AGAAAU UU UUAGCAAUGAGA 20 355 antiSPCas9-53 - AGAGUCCUUCCUUGUCGAAG 20 356 antiSPCas9-54 - AGGACAAGAAACAUGAA 17 357 antiSPCas9-55 + AGGUACUU UGUAUUCAU 17 358 antiSPCas9-56 - AGUACCU UCAAAGAAAUUUA 20 359 antiSPCas9-57 + AGUCAACUAGCUU UUU UCUG 20 360 antiSPCas9-58 - AGU UGACUCAACUGAUAAAG 20 361 antiSPCas9-59 - AUAUGAUAAAGU UCCGU 17 362 antiSPCas9-60 + AUCUACUAUGU UUCCAAAGA 20 363 antiSPCas9-61 - AUGGAUAAAAAGUAUUCUAU 20 364 antiSPCas9-62 - AU UAAAAAGAAUCUUAU 17 365 antiSPCas9-63 - CAAAGAAAUU UAAGGUGUUG 20 366 antiSPCas9-64 + CAACUAGCU UU UUUCUG 17 367 antiSPCas9-65 - CAACUGAUAAAGCGGACCUG 20 368 antiSPCas9-66 + CAAGGAAGGACUCUUCCAAA 20 369 antiSPCas9-67 + CAAUGAGAAAGUGCCCA 17 370 antiSPCas9-68 + CACGGAACUUUAUCAUA 17 371 antiSPCas9-69 - CACUAAUUCCGUUGGAU 17 372 antiSPCas9-70 - CAUAUGAUAAAGUUCCG 17 373 antiSPCas9-71 - CAUGAACGGCACCCCAUCUU 20 374 antiSPCas9-72 + CCAAGUAGAUUAACCUC 17 375 antiSPCas9-73 + CCCACGGAACUUUAUCAUAU 20 376 antiSPCas9-74 - CCGUGGGCACUUUCUCAUUG 20 377 antiSPCas9-75 + CCUCAAUGAGAAAGUGCCCA 20 378 antiSPCas9-76 - CCUGAGGUUAAUCUACU 17 379 antiSPCas9-77 - CGAUUCUUUCUUUCACCGUU 20 380 antiSPCas9-78 - CGUGGGCACUUUCUCAUUGA 20 381 antiSPCas9-79 + CUACUAUGUUUCCAAAGAUG 20 382 antiSPCas9-80 + CUAUGUUUCCAAAGAUG 17 383 antiSPCas9-81 + CUGAGGUGAUAAAUCGU 17 384 antiSPCas9-82 - CUGAUAAAGCGGACCUG 17 385 antiSPCas9-83 + CUUGUAAGUAACAUAUU 17 386 antiSPCas9-84 + CUUGUCCUCUUCGACAAGGA 20 387 antiSPCas9-85 - CU U UGG AAACAU AG U AG AUG 20 388 antiSPCas9-86 + UACUAUGUUUCCAAAGA 17 389 antiSPCas9-87 + UAUGACAGCCCAUCCAA 17 390 antiSPCas9-88 - UAUUCUAUUGGUUUAGACAU 20 391 antiSPCas9-89 - UCAAAGAAAUUUAAGGUGUU 20 392 antiSPCas9-90 - UCGAUUAAAAAGAAUCUUAU 20 393 antiSPCas9-91 + UCUACUAUGUUUCCAAAGAU 20 394 antiSPCas9-92 - UCUAUUGGUUUAGACAU 17 395 antiSPCas9-93 + UCUUGUCCUCUUCGACA 17 396 antiSPCas9-94 + UCUUUUUAAUCGAAUGA 17 397 antiSPCas9-95 + UGAAGGUACUUUGUAUUCAU 20 398 antiSPCas9-96 - UGACUCAACUGAUAAAG 17 399 antiSPCas9-97 + UGAGGUGAUAAAUCGUU 17 400 antiSPCas9-98 - UGGAAACAUAGUAGAUG 17 401 antiSPCas9-99 - UGGAAACAUAGUAGAUGAGG 20 402 antiSPCas9-100 - UGGGCACUUUCUCAUUG 17 403 antiSPCas9-101 + UGUAUACCUUCUCCGAG 17 404 antiSPCas9-102 - UUCAAAGAAAUUUAAGGUGU 20 405 antiSPCas9-103 + UUCUGAGGUGAUAAAUCGUU 20 406 antiSPCas9-104 - UUCUUUCUUUCACCGUU 17 407 antiSPCas9-105 + UUUCUGAGGUGAUAAAUCGU 20 408 antiSPCas9-106 + UUUCUUGUAAGUAACAUAUU 20 409 Table E-6

antiSPCas9-141 - GGAACUCUCGGUUCGCA 17 444 antiSPCas9-142 - UGGCCGAAAACGGAUGU 17 445 antiSPCas9-143 + CGCGUCUAGCACCUCCU 17 446 antiSPCas9-144 + U CACCG U CGCGAAG U CC 17 447 antiSPCas9-145 - UAU UAAACGUCAGCUCG 17 448 antiSPCas9-146 - CGCUCGUAAAAAGGACU 17 449 antiSPCas9-147 + U UCCGCCUGCUCACGUA 17 450 antiSPCas9-148 + CUAGUGAGAGCGCUAUA 17 451 antiSPCas9-149 + CGUCGUAAUCAGAUAAA 17 452 antiSPCas9-150 - CUGAUCGCACAAUUACC 17 453 antiSPCas9-151 - UCGCAUACCUUACUAUG 17 454 antiSPCas9-152 - CGCCGGAGAGCUUCAAA 17 455 antiSPCas9-153 - GCUGGGGACGAU UGUCG 17 456 antiSPCas9-154 + CGCCUCAAGGAAGUCGA 17 457 antiSPCas9-155 - CUUAUAGCGCUCUCACU 17 458 antiSPCas9-156 - U UCUGUCGAGAUCUCCG 17 459 antiSPCas9-157 - CAUAUUGCGAAUCUUGC 17 460 antiSPCas9-158 - GGGCCGGGACUUCGCGA 17 461 antiSPCas9-159 - UAAACCCAUACGUGAGC 17 462 antiSPCas9-160 + U UUACGACUUCCUCGCU 17 463 antiSPCas9-161 - G CG C A U AC AAC A AG C AC 17 464 antiSPCas9-162 - GCAGGU UAUAUUGACGG 17 465 antiSPCas9-163 + U U UUCGCGAUCAUCU UA 17 466 antiSPCas9-164 - UCGUAUGGGAUAAGGGC 17 467 antiSPCas9-165 + AUAAUCCCGUGAUGGAU 17 468 antiSPCas9-166 - ACGAUACACUUCUACCA 17 469 antiSPCas9-167 + CAGU UGCUGACGGACUA 17 470 antiSPCas9-168 - GAACGAUAAGCUGAU UC 17 471 antiSPCas9-169 - UCUAAAUCCGGACAACU 17 472 antiSPCas9-170 - CAGCGGACU UUCGACAA 17 473 antiSPCas9-171 - CAUGGGACGUCACAAAC 17 474 antiSPCas9-172 + CAGGU UU UCUAGCCGUC 17 475 antiSPCas9-173 - CCGCUUCAAUGAUCAAA 17 476 antiSPCas9-174 + UAGCCAACAUCCGU UUU 17 477 antiSPCas9-175 + GGAGGAUUGCAUCGCUA 17 478 antiSPCas9-176 + CAUGCAAUUCGCCUAAG 17 479 antiSPCas9-177 - AAGUGGCGUGGAUGCGA 17 480 antiSPCas9-178 - CGUAUGGGAUAAGGGCC 17 481 antiSPCas9-179 - GACAGGUGAAAUCGUAU 17 482 antiSPCas9-180 + GAACCGAGAGUUCCCUC 17 483 antiSPCas9-181 + AAAUCGAUCUUCUACCC 17 484 antiSPCas9-182 + AAUGGGACGCUAAAUAC 17 485 antiSPCas9-183 - UAAAGUGCU UACACGCU 17 486 antiSPCas9-184 - UACGCAGGUUAUAUUGA 17 487 antiSPCas9-185 - AU UCUGUCGAGAUCUCC 17 488 antiSPCas9-186 - GAUUCUGUCGAGAUCUC 17 489 antiSPCas9-187 - GCCUCUCUAAAUCCCGA 17 490 antiSPCas9-188 + UGCAUCGCUAAGGUU UU 17 491 antiSPCas9-189 + GCAG UUGCUGACGGACU 17 492 antiSPCas9-190 - CGGGAUUAUAUGAAACU 17 493 antiSPCas9-191 - ACCCAUACGUGAGCAGG 17 494 antiSPCas9-192 + AGGGGUCCCACAUAGUA 17 495 antiSPCas9-193 + AGCCACCGUACU UUU UC 17 496 antiSPCas9-194 - AU UGGGGAUAACGAUUA 17 497 antiSPCas9-195 - UGACAAUGU UCCAAGCG 17 498 antiSPCas9-196 - GGUGUCGGACUUCAGAA 17 499 antiSPCas9-197 + UCUCCGCU UAGAAAGGC 17 500 antiSPCas9-198 + UGUAACCUU UCGCCUCA 17 501 antiSPCas9-199 - ACAGGU UUCCGGACAAG 17 502 antiSPCas9-200 - UGGGACCCGAAAAAGUA 17 503 antiSPCas9-201 + U UCAUAUAAUCCCGUGA 17 504 antiSPCas9-202 - CACAGG U U UCCGG ACAA 17 505 antiSPCas9-203 + AUAGUAAGGUAUGCGAA 17 506 antiSPCas9-204 + AACUGUCACU UUGCGGU 17 507 antiSPCas9-205 - U UACUAUGUGGGACCCC 17 508 antiSPCas9-206 + AUGCGGCUGGAGCGCCG 17 509 antiSPCas9-207 - UAAGACGGAAAUCACUC 17 510 antiSPCas9-208 + CGCCACUUGCAUU UAUA 17 511 antiSPCas9-209 - CCCCAUCGACU UCCUUG 17 512 antiSPCas9-210 + GCCUCAAGGAAGUCGAU 17 513 antiSPCas9-211 - U UGAUCAGUCGAAAAAC 17 514 antiSPCas9-212 + UCGGGAU UUAGAGAGGC 17 515 antiSPCas9-213 + CAAUGAGUCCCCUUGUC 17 516 antiSPCas9-214 + UCAGGU UU UCUAGCCGU 17 517 antiSPCas9-215 - GACCGGAGGGUUU UCAA 17 518 antiSPCas9-216 + AAGCCACCGUACUU UUU 17 519 antiSPCas9-217 + CUG UUCUCCGCUUAGAA 17 520 antiSPCas9-218 + AUCAU UG AAGCGG AU AA 17 521 antiSPCas9-219 - U UCGCCAGCCAUCAAAA 17 522 antiSPCas9-220 - GCCGG AG AGCU UCAAAA 17 523 antiSPCas9-221 - AGAACGAUAAGCUGAUU 17 524 antiSPCas9-222 - GCACAGGUU UCCGGACA 17 525 antiSPCas9-223 - UCGCCAGCCAUCAAAAA 17 526 antiSPCas9-224 + AAGGUAUGCGAAAGGUU 17 527 antiSPCas9-225 + GGCAAUACUUUUUCGUU 17 528 antiSPCas9-226 - GAGGAAGUUGUCGAUAA 17 529 antiSPCas9-227 + CUGACGUUUAAUAAAUC 17 530 antiSPCas9-228 - AAACCCGCCU U UCUAAG 17 531 antiSPCas9-229 - UAUAAAUGCAAGUGGCG 17 532 antiSPCas9-230 + CCACUACUUUGACUGUC 17 533 antiSPCas9-231 + GAGAGUUCCCUCGGGCC 17 534 antiSPCas9-232 + UAUAGGUUUGUACUAAC 17 535 antiSPCas9-233 - CAU U ACG AG AAG U U G AA 17 536 antiSPCas9-234 - GUAUGUUGAUCAGGAAC 17 537 antiSPCas9-235 + CGUAUUUCGUAUUCAUU 17 538 antiSPCas9-236 - UGAGGGUGAUCUAAAUC 17 539 antiSPCas9-237 + CCUCAAGGAAGUCGAUG 17 540 antiSPCas9-238 - GAAAUCGUAUGGGAUAA 17 541 antiSPCas9-239 + UGGAGUAAUCGUUUCUU 17 542 antiSPCas9-240 - UGCUAUACUUAGAAGGC 17 543 antiSPCas9-241 - CCGG AG AGCU UCAAAAG 17 544 antiSPCas9-242 - AGACAGGUGAAAUCGUA 17 545 antiSPCas9-243 - GAGCUAGUUAAGGUCAU 17 546 antiSPCas9-244 + GAGUUCCCUCGGGCCAG 17 547 antiSPCas9-245 + CUUUCAACUUCUCGUAA 17 548 antiSPCas9-246 + AGAGUUCCCUCGGGCCA 17 549 antiSPCas9-247 - AGAUCGGGAAAUGAUUG 17 550 antiSPCas9-248 - UGAGGCGAAAGGUUACA 17 551 antiSPCas9-249 - UGGCCCGAGGGAACUCU 17 552 antiSPCas9-250 + GUUUCUCGUUCUGCAAU 17 553 antiSPCas9-251 + ACGCCACUUGCAUUUAU 17 554 antiSPCas9-252 + CACUACUAGGACAGAAU 17 555 antiSPCas9-253 - AUCUACUGCGAAAGCAG 17 556 antiSPCas9-254 + GUCGGGAUUUAGAGAGG 17 557 antiSPCas9-255 - CCUAGCUGAUGCCAAUC 17 558 antiSPCas9-256 + UUCUCCGCUUAGAAAGG 17 559 antiSPCas9-257 - ACUGAGGUGCAGACCGG 17 560 antiSPCas9-258 - UGCAUGCUAUACUUAGA 17 561 antiSPCas9-259 - CUGAGGUGCAGACCGGA 17 562 antiSPCas9-260 + AUGCCCUUUUUGAUGGC 17 563 antiSPCas9-261 - AUUCACCAAUCCAUCAC 17 564 antiSPCas9-262 - UGGGACCCCUGGCCCGA 17 565 antiSPCas9-263 + UUUCAACUUCUCGUAAU 17 566 antiSPCas9-264 + GUAUUUCGUAUUCAUUC 17 567 antiSPCas9-265 - AGUGGAUGAGCUAGUUA 17 568 antiSPCas9-266 + GAGUAUGCCCUUUUUGA 17 569 antiSPCas9-267 - AUCAAACGACUCAGAAG 17 570 antiSPCas9-268 + CAUUCUCUUCGUUAUCC 17 571 antiSPCas9-269 - AUACACUUCUACCAAGG 17 572 antiSPCas9-270 - G ACU UCCU UGAGGCGAA 17 573 antiSPCas9-271 - ACCCCAAUCCUUUUUGA 17 574 antiSPCas9-272 + UGAAUCGUCCUUCAAAA 17 575 antiSPCas9-273 - UACCCUCUUUGAAGAUC 17 576 antiSPCas9-274 - UCUGAACUUGACAAGGC 17 577 antiSPCas9-275 + CGAUUGUCUUUGAGGAA 17 578 antiSPCas9-276 - GGACAUGUAUGUUGAUC 17 579 antiSPCas9-277 - CGCAUACAACAAGCACA 17 580 antiSPCas9-278 + UCGAUUACAAUGUUUUC 17 581 antiSPCas9-279 + CGUCCUUCAAAAAGGAU 17 582 antiSPCas9-280 + CUUACUAAGCUGCAAUU 17 583 antiSPCas9-281 - AAGAAACGAUUACUCCA 17 584 antiSPCas9-282 + CAACU U U UGCCACU ACU 17 585 antiSPCas9-283 - CUAUUCUGUCCUAGUAG 17 586 antiSPCas9-284 + CUGCAUAAAGUUCCUAU 17 587 antiSPCas9-285 - GUGGGACCCCUGGCCCG 17 588 antiSPCas9-286 - GUAUGCGGACUUAUUUU 17 589 antiSPCas9-287 + CCUAAGUGGAUUUGAUG 17 590 antiSPCas9-288 - G AU U U UCU AAAG AGCG A 17 591 antiSPCas9-289 - GGGCAGCCAG AUCU U AA 17 592 antiSPCas9-290 - CAAAUUGCAGCUUAGUA 17 593 antiSPCas9-291 - UGAAAUCGUAUGGGAUA 17 594 antiSPCas9-292 - U U U ACUCU U ACCAACCU 17 595 antiSPCas9-293 + GAUGCUCCUUUAAGAUC 17 596 antiSPCas9-294 + CUCUCAGUAUGUCAGAU 17 597 antiSPCas9-295 + AAAUACUUGAAUGCGGC 17 598 antiSPCas9-296 - ACUUAACUAAAGCUGAG 17 599 antiSPCas9-297 - CGAACAGGAGAUAGGCA 17 600 antiSPCas9-298 - GAUUCACCAAUCCAUCA 17 601 antiSPCas9-299 - U U UG AUCAG UCG AAAAA 17 602 antiSPCas9-300 - CU U AAAGG AGCAUCCUG 17 603 antiSPCas9-301 + CCUUUUGAUCAUUGAAG 17 604 antiSPCas9-302 - UGAGCUAGUUAAGGUCA 17 605 antiSPCas9-303 - AAACAUUGUAAUCGAGA 17 606 antiSPCas9-304 + CCAGAUUGGCAUCAGCU 17 607 antiSPCas9-305 + AAUUGGGUAUUUUCCAC 17 608 antiSPCas9-306 + UCAAACAGACUAUACUU 17 609 antiSPCas9-307 - CC AC AU CAAAU CC AC U U 17 610 antiSPCas9-308 - GGAUAUACAAAAGGCAC 17 611 antiSPCas9-309 - AAUCUACUGGCACAAAU 17 612 antiSPCas9-310 + UCAGUAUGUCAGAUAGG 17 613 antiSPCas9-311 - AGUUAAGUAUGUCACUG 17 614 antiSPCas9-312 + AAG U U CG ACU UAAAAU U 17 615 antiSPCas9-313 + UUCUGUUCGUUAUCUUC 17 616 antiSPCas9-314 - GAGGGUAUUAAAGAACU 17 617 antiSPCas9-315 - GUUAAGUAUGUCACUGA 17 618 antiSPCas9-316 + GCUUAACUGUCACUUUG 17 619 antiSPCas9-317 - AGAUUUGUCACAGCUUG 17 620 antiSPCas9-318 - AGACUUGACACUUCUCA 17 621 antiSPCas9-319 - CC AG ACAG U CAAAG U AG 17 622 antiSPCas9-320 + CCCCUUUUGAAGCUCUC 17 623 antiSPCas9-321 + UUAUCAGUUUCGCAUUU 17 624 antiSPCas9-322 - AAAU CAAACG ACU CAG A 17 625 antiSPCas9-323 - AAUCGAUUCUUCCAAAA 17 626 antiSPCas9-324 + UUCCCGAUCUUCAAAGA 17 627 antiSPCas9-325 - GUCAGUCAAAGAAUUAU 17 628 antiSPCas9-326 - GAUUUGUCACAGCUUGG 17 629 antiSPCas9-327 - GAAACCAAUGGGGAGAC 17 630 antiSPCas9-328 + AGGUUAAAGAGUCAUCA 17 631 antiSPCas9-329 - AGAGGGUAUUAAAGAAC 17 632 antiSPCas9-330 + ACAGAAUAGGCAACUGU 17 633 antiSPCas9-331 + UUUCACGAUUGUCUUUG 17 634 antiSPCas9-332 + GUCCUUCAAAAAGGAUU 17 635 antiSPCas9-333 + AUGCUUUGUGAUUUGGC 17 636 antiSPCas9-334 + UGAGAAGUGUCAAGUCU 17 637 antiSPCas9-335 - U AAAG AU AAGG ACU UCC 17 638 antiSPCas9-336 + UUUCUCGUUCUGCAAUU 17 639 antiSPCas9-337 + CCAUUGGUUUCAAUUAA 17 640 antiSPCas9-338 + AUCCAUCUUCUCUAAUA 17 641 antiSPCas9-339 - UAAUACUGAGAUUACCA 17 642 antiSPCas9-340 + UUCACCUGUCUCCCCAU 17 643 antiSPCas9-341 - AUAGAUUUGUCACAGCU 17 644 antiSPCas9-342 - CUUGUCUGAACUUGACA 17 645 antiSPCas9-343 - CUUAACUAAAGCUGAGA 17 646 antiSPCas9-344 - CAG U CAAAG AAU U AU U G 17 647 antiSPCas9-345 + AAAUUCACGUAUUUAGA 17 648 antiSPCas9-346 - UAGAUUUGUCACAGCUU 17 649 antiSPCas9-347 + UAAUACUUUGUCCAGAU 17 650 antiSPCas9-348 + ACUCACUUUCUAGCUUC 17 651 antiSPCas9-349 - CCUUUAAUUGAAACCAA 17 652 antiSPCas9-350 - UACUCCAUGGAAUUUUG 17 653 antiSPCas9-351 + GUCAAAAUACUUGAAUG 17 654 antiSPCas9-352 + ACUUAAAAUUUGGUGUC 17 655 antiSPCas9-353 - CUCUAUUACCUACAAAA 17 656 antiSPCas9-354 - CUCU U U AACCU UCAAAG 17 657 antiSPCas9-355 + CUUUACUAUGUUGACUU 17 658 antiSPCas9-356 + CAACAUGCUUUGUGAUU 17 659 antiSPCas9-357 - AAUUGGAGAUCAGUAUG 17 660 antiSPCas9-358 + CAUUUUGUAGGUAAUAG 17 661 antiSPCas9-359 + GACUGACUUCAGUUUCU 17 662 antiSPCas9-360 - ACUAAAGCUGAGAGGGG 17 663 antiSPCas9-361 - AAAAGCGAACAGGAGAU 17 664 antiSPCas9-362 - AACCCUAUAAAUGCAAG 17 665 antiSPCas9-363 - ACCCAU AU U AG AG AAG A 17 666 antiSPCas9-364 + GUAUUUCUUAAUGAGUG 17 667 antiSPCas9-365 + UAUGUUGACUUGGGGCA 17 668 antiSPCas9-366 - C AAA AG GCACAGGUUUC 17 669 antiSPCas9-367 + UUUCCCGAUCUUCAAAG 17 670 antiSPCas9-368 - U U ACCCUCU U UG AAG AU 17 671 antiSPCas9-369 - U AU U AG AG AAG AUGG AU 17 672 antiSPCas9-370 - UUAACUAAAGCUGAGAG 17 673 antiSPCas9-371 - AGUUAAGCAAUUGAAAG 17 674 antiSPCas9-372 - AAAGUCAAAAUUGGUGU 17 675 antiSPCas9-373 + UUCAAACAACUGAUUAU 17 676 antiSPCas9-374 - GUGGCAAAAGUUGAGAA 17 677 antiSPCas9-375 + UAAAGUAAACUGUGCUU 17 678 antiSPCas9-376 + CAUUGUCACUUUUCCCU 17 679 antiSPCas9-377 + U UCCU U UG AAAACCCUC 17 680 antiSPCas9-378 + AACUCACUUUCUAGCUU 17 681 antiSPCas9-379 - ACUGCCUGAGAAAUAUA 17 682 antiSPCas9-380 + CAUGCUUUGUGAUUUGG 17 683 antiSPCas9-381 - AGUGGCAAAAGUUGAGA 17 684 antiSPCas9-382 - CUGUUUGAGUUAGAAAA 17 685 antiSPCas9-383 - UAGAAAAUGGCCGAAAA 17 686 antiSPCas9-384 + UUUACUAUGUUGACUUG 17 687 antiSPCas9-385 - AUUACCUACAAAAUGGA 17 688 antiSPCas9-386 - GAAAGUGAGUUUGUGUA 17 689 antiSPCas9-387 + UCCAUCUUCUCUAAUAU 17 690 antiSPCas9-388 - CUUUAAUUGAAACCAAU 17 691 antiSPCas9-389 - UCAGUCAAAGAAUUAUU 17 692 antiSPCas9-390 - AAUCAAACGACUCAGAA 17 693 antiSPCas9-391 + UGUCCCUUCCAUUUUGU 17 694 antiSPCas9-392 - U U UAAU UG AAACCAAUG 17 695 antiSPCas9-393 + UAAAUUCUUGUCAAAGU 17 696 antiSPCas9-394 + UUGUAUAUCCUCUUUGA 17 697 antiSPCas9-395 + CUUUAAUUAUCUUUAGG 17 698 antiSPCas9-396 - AAAUGAAGAACUAUUGG 17 699 antiSPCas9-397 + UCUUUACUAUGUUGACU 17 700 antiSPCas9-398 - CCGGAGAGAAGAAAAAU 17 701 antiSPCas9-399 - AAUCAUAGAGCAAAUUU 17 702 antiSPCas9-400 - CCCGGAGAGAAGAAAAA 17 703 antiSPCas9-401 - U U ACCU ACAAAAUGG AA 17 704 antiSPCas9-402 + UCUCAGGCAGUUGCUGA 17 705 antiSPCas9-403 + UCCUUCAAAAAGGAUUG 17 706 antiSPCas9-404 - UUCAAUUCUAUAAAGUU 17 707 antiSPCas9-405 + U G G U AAG AG U AA AC AA A 17 708 antiSPCas9-406 - UCAAUUCUAUAAAGUUA 17 709 antiSPCas9-407 - GAAAUCACUCUGGCAAA 17 710 antiSPCas9-408 + ACUUCCUCAAAAUUCCA 17 711 antiSPCas9-409 + UUAUCACUAUUCCUUUU 17 712 antiSPCas9-410 - CACU U U AAAG UCAAAAU 17 713 antiSPCas9-411 - AU AU U AG AG AAG AUGG A 17 714 antiSPCas9-412 + CCCAUUUUUCUUCUCUC 17 715 antiSPCas9-413 - AAAAAAAC AG U CG AG AG 17 716 antiSPCas9-414 - U U AUG AAACAG U U AAAG 17 717 antiSPCas9-415 - AAGAAAAAUGGGUUGUU 17 718 antiSPCas9-416 + CCAUUUUUCUUCUCUCC 17 719 antiSPCas9-417 - CAUAGUAAAGAAAACUG 17 720 antiSPCas9-418 - AUAAGAGACAAGCAAAG 17 721 antiSPCas9-419 - GAUGAAGAGAAUAGAAG 17 722 antiSPCas9-420 + GGCUGGAGCGCCGAGGU 17 723 antiSPCas9-421 + AUUUCCUUAUAUUUCUC 17 724 antiSPCas9-422 + CAGAAUAGGCAACUGUA 17 725 antiSPCas9-423 - UAUGAAUUUCUUUAAGA 17 726 antiSPCas9-424 - AGAAAAUGAAGAACUAU 17 727 antiSPCas9-425 - UUACAAGGAAGUAAAAA 17 728 antiSPCas9-426 - AGAGAAGAUGGAUGGGA 17 729 antiSPCas9-427 - AAAACUGAGGUGCAGAC 17 730 antiSPCas9-428 + UAUCUUUAAUUAUCUUU 17 731 antiSPCas9-429 + AGAAUAAAAGAAGUAU U 17 732 antiSPCas9-430 - AUGAAGAGAAUAGAAGA 17 733 antiSPCas9-431 - AAAGAUAAU U AAAG AU A 17 734 antiSPCas9-432 - UAUACUUAGAAGGCAGG 17 735 antiSPCas9-433 - CAAAGAGGAUAUACAAA 17 736 antiSPCas9-434 - CAGUCGAAAAACGGGUACGC 20 737 antiSPCas9-435 - CACGCUCGGAUAAGAACCGA 20 738 antiSPCas9-436 + UAAGAUAAGCGUCGUGCGCA 20 739 antiSPCas9-437 - CGCUCACCUGUUCGACGAUA 20 740 antiSPCas9-438 + GAUAAGCGUCGUGCGCAUGG 20 741 antiSPCas9-439 - CGAU UCUGUCGAGAUCUCCG 20 742 antiSPCas9-440 - AGAGGCGUCGCUAUACGGGC 20 743 antiSPCas9-441 - U UAAAGAGGCGUCGCUAUAC 20 744 antiSPCas9-442 - AGGCG UCGCUAUACGGGCUG 20 745 antiSPCas9-443 + CGCU U UUCGCGAUCAUCUUA 20 746 antiSPCas9-444 - AGAGCGACGGCUUCGCCAAU 20 747 antiSPCas9-445 + UGAAGCGGAUAACGGCGCCU 20 748 antiSPCas9-446 - ACACGCUCGGAUAAGAACCG 20 749 antiSPCas9-447 - GAGGCGUCGCUAUACGGGCU 20 750 antiSPCas9-448 - GAUGAUCGCGAAAAGCGAAC 20 751 antiSPCas9-449 - UAAGGGCCGGGACU UCGCGA 20 752 antiSPCas9-450 + CGUAAUGGGACGCUAAAUAC 20 753 antiSPCas9-451 + CUCCGGGUAAUUGUGCGAUC 20 754 antiSPCas9-452 - UGUCGCGGAAACUUAUCAAC 20 755 antiSPCas9-453 + CGCUAGCCAACAUCCGUU UU 20 756 antiSPCas9-454 + AAUGAGUGCGGUCCCUACGA 20 757 antiSPCas9-455 - UACGCAGGUUAUAUUGACGG 20 758 antiSPCas9-456 - UGACGAUCUCGACAAUCUAC 20 759 antiSPCas9-457 - GU UAAAGAGGCGUCGCUAUA 20 760 antiSPCas9-458 + CGACGUCGUAAUCAGAUAAA 20 761 antiSPCas9-459 + UCAUAACCU UAUCGUCGAAC 20 762 antiSPCas9-460 - GCUUAUCUUAAUGCCGUCGU 20 763 antiSPCas9-461 - AAACGGAUGUUGGCUAGCGC 20 764 antiSPCas9-462 + U UGUCGACAUCCGAGUUGUC 20 765 antiSPCas9-463 - CAGCUCAAUCGUUCAUCGAG 20 766 antiSPCas9-464 - GAUCGAU UUAAUGCGUCACU 20 767 antiSPCas9-465 - CUUAUCUUAAUGCCGUCGUA 20 768 antiSPCas9-466 - UGACGGCGGAGCGAGUCAAG 20 769 antiSPCas9-467 + CUAGCCGUCGGGAUU UAGAG 20 770 antiSPCas9-468 - UCAUCGCUCGUAAAAAGGAC 20 771 antiSPCas9-469 - CGAGAACGAUAAGCUGAUUC 20 772 antiSPCas9-470 + AUGCGAACCGAGAGUUCCCU 20 773 antiSPCas9-471 - UAAGCUCAUCGCUCGUAAAA 20 774 antiSPCas9-472 - U UGUCGCGGAAACUUAUCAA 20 775 antiSPCas9-473 - UCGAUUCUGUCGAGAUCUCC 20 776 antiSPCas9-474 + UGUCGCGUCUAGCACCUCCU 20 777 antiSPCas9-475 - UGGGACCCGAAAAAGUACGG 20 778 antiSPCas9-476 + GGCCUAGUGAGAGCGCUAUA 20 779 antiSPCas9-477 - GGAUAAACCCAUACGUGAGC 20 780 antiSPCas9-478 + CCGUCGGGAUU UAGAGAGGC 20 781 antiSPCas9-479 + U UU UCCGCCUGCUCACGUAU 20 782 antiSPCas9-480 - CAUCGCUCGUAAAAAGGACU 20 783 antiSPCas9-481 - AACCU UAUAGCGCUCUCACU 20 784 antiSPCas9-482 - AUCGACU UCCU UGAGGCGAA 20 785 antiSPCas9-483 + CGAUCAGGU UUUCUAGCCGU 20 786 antiSPCas9-484 + CGUCGUAU UUCGUAUUCAU U 20 787 antiSPCas9-485 + UCG AAGCCACCG U ACU U U U U 20 788 antiSPCas9-486 + UGCGAACCGAGAGUUCCCUC 20 789 antiSPCas9-487 - U AGCGCCGG AG AGCU UCAAA 20 790 antiSPCas9-488 - AACCUGAUCGCACAAU UACC 20 791 antiSPCas9-489 - GGGUACGCAGGUUAUAU UGA 20 792 antiSPCas9-490 - GAGGGAACUCUCGGU UCGCA 20 793 antiSPCas9-491 - ACGAGAACGAUAAGCUGAU U 20 794 antiSPCas9-492 - CCCGCCUCUCUAAAUCCCGA 20 795 antiSPCas9-493 - CGGGCUGGGGACGAUUGUCG 20 796 antiSPCas9-494 - CGUAAACCCGCCU UUCUAAG 20 797 antiSPCas9-495 + CAUAUAAUCCCGUGAUGGAU 20 798 antiSPCas9-496 - U UCGAUUCUGUCGAGAUCUC 20 799 antiSPCas9-497 + CGAAGCCACCGUACUU UUUC 20 800 antiSPCas9-498 - CCGAAGAAACGAUUACUCCA 20 801 antiSPCas9-499 + GUCGUAUU UCGUAU UCAUUC 20 802 antiSPCas9-500 - AGCGCCGG AG AGCU UCAAA A 20 803 antiSPCas9-501 + U UCUCACCGUCGCGAAGUCC 20 804 antiSPCas9-502 - UGAUCUAAAUCCGGACAACU 20 805 antiSPCas9-503 + GAUCAGGUU UUCUAGCCGUC 20 806 antiSPCas9-504 - GGU UCGCCAGCCAU C A AA AA 20 807 antiSPCas9-505 + U UCGCCUCAAGGAAGUCGAU 20 808 antiSPCas9-506 + UCGCCUAAGUGGAUU UGAUG 20 809 antiSPCas9-507 - UGGU UCGCCAGCCAUCAAAA 20 810 antiSPCas9-508 + UCGCCUCAAGGAAGUCGAUG 20 811 antiSPCas9-509 + ACCGAGAGU UCCCUCGGGCC 20 812 antiSPCas9-510 + AUAGGAGGAU UGCAUCGCUA 20 813 antiSPCas9-511 + GCCGUCGGGAU UUAGAGAGG 20 814 antiSPCas9-512 - CAAUAAAGUGCUUACACGCU 20 815 antiSPCas9-513 + AUU UUCCGCCUGCUCACGUA 20 816 antiSPCas9-514 - GAACCCCAUCGACUUCCU UG 20 817 antiSPCas9-515 - GCGCCGG AG AGCU UCAAAAG 20 818 antiSPCas9-516 - ACGAUACACUUCUACCAAGG 20 819 antiSPCas9-517 - AAAUGGCCGAAAACGGAUGU 20 820 antiSPCas9-518 + UAGCAUGCAAU UCGCCUAAG 20 821 antiSPCas9-519 - UAAGCGCAUACAACAAGCAC 20 822 antiSPCas9-520 + U U UCGCCUCAAGGAAGUCGA 20 823 antiSPCas9-521 + UGAAUGCGGCUGGAGCGCCG 20 824 antiSPCas9-522 + GUGCAAUGAGUCCCCU UGUC 20 825 antiSPCas9-523 - UGCAAGUGGCGUGGAUGCGA 20 826 antiSPCas9-524 - AAGCAGCGGACU UUCGACAA 20 827 antiSPCas9-525 - UAAACCCAUACGUGAGCAGG 20 828 antiSPCas9-526 - CCCUAUAAAUGCAAGUGGCG 20 829 antiSPCas9-527 - U U UCGCAUACCUUACUAUGU 20 830 antiSPCas9-528 + GCGU UAUCAGUUUCGCAUU U 20 831 antiSPCas9-529 - GGUCAUGGGACGU C AC A AAC 20 832 antiSPCas9-530 + CGAGAGUUCCCUCGGGCCAG 20 833 antiSPCas9-531 + U UCU UUACGACU UCCUCGCU 20 834 antiSPCas9-532 - CAAACGAUACACUUCUACCA 20 835 antiSPCas9-533 - ACCU UACUAUGUGGGACCCC 20 836 antiSPCas9-534 + GAUUGCAUCGCUAAGGU UUU 20 837 antiSPCas9-535 - CU U UCGCAUACCU UACUAUG 20 838 antiSPCas9-536 + U UG AUCAU UG AAGCGG AU AA 20 839 antiSPCas9-537 - CUCGAUU UUCUAAAGAGCGA 20 840 antiSPCas9-538 + UCGAAGU UCGACUUAAAAU U 20 841 antiSPCas9-539 + AGGCAGU UGCUGACGGACUA 20 842 antiSPCas9-540 - UAUCCGCU UCAAUGAUCAAA 20 843 antiSPCas9-541 - GACUGGGACCCGAAAAAGUA 20 844 antiSPCas9-542 + CCGAGAGUUCCCUCGGGCCA 20 845 antiSPCas9-543 - GCAUGCUAUACU UAGAAGGC 20 846 antiSPCas9-544 - AAUCGUAUGGGAUAAGGGCC 20 847 antiSPCas9-545 + GUCCU UACUAAGCUGCAAUU 20 848 antiSPCas9-546 + UGUUCUCCGCUUAGAAAGGC 20 849 antiSPCas9-547 - CG ACCU U UAAU UG AAACCAA 20 850 antiSPCas9-548 - AAAUCGUAUGGGAUAAGGGC 20 851 antiSPCas9-549 - GAACAUAUUGCGAAUCUUGC 20 852 antiSPCas9-550 + GAGCUGACGU UUAAUAAAUC 20 853 antiSPCas9-551 + CUUAACUGUCACUU UGCGGU 20 854 antiSPCas9-552 + AU UAAAUCGAUCU UCUACCC 20 855 antiSPCas9-553 - GGCACAGGU UUCCGGACAAG 20 856 antiSPCas9-554 + CACAUAGUAAGGUAUGCGAA 20 857 antiSPCas9-555 + AGUAAGGUAUGCGAAAGGUU 20 858 antiSPCas9-556 + CCAUGGAGUAAUCGU UUCUU 20 859 antiSPCas9-557 + CGGGUAUU UCU UAAUGAGUG 20 860 antiSPCas9-558 - UAUGUGGGACCCCUGGCCCG 20 861 antiSPCas9-559 + CCU UGUAACCU UUCGCCUCA 20 862 antiSPCas9-560 + UCCACGCCACUUGCAUU UAU 20 863 antiSPCas9-561 - U CCC AU U ACG AG AAG U U G AA 20 864 antiSPCas9-562 - AUUGGUGUCGGACUUCAGAA 20 865 antiSPCas9-563 + AGUU UCAUAUAAUCCCGUGA 20 866 antiSPCas9-564 - GGUGAAAUCGUAUGGGAUAA 20 867 antiSPCas9-565 - AU UAUUGGGGAUAACGAUUA 20 868 antiSPCas9-566 - UCACGGGAU UAUAUGAAACU 20 869 antiSPCas9-567 - AAGUGACAAUGU UCCAAGCG 20 870 antiSPCas9-568 - GCGAAAAGCGAACAGGAGAU 20 871 antiSPCas9-569 - GGAGACAGGUGAAAUCGUAU 20 872 antiSPCas9-570 + ACCU U UCAACU UCUCGUAAU 20 873 antiSPCas9-571 - GCAG ACCGG AGGGU U U UCAA 20 874 antiSPCas9-572 + UGCCACUACUAGGACAGAAU 20 875 antiSPCas9-573 + CCACGCCACUUGCAUU UAUA 20 876 antiSPCas9-574 - AUU UAUUAAACGUCAGCUCG 20 877 antiSPCas9-575 + AACCUU UCAACU UCUCGUAA 20 878 antiSPCas9-576 - CG AAAAU CAAACG ACU CAG A 20 879 antiSPCas9-577 - UCU U UG AUCAG UCG AAAAAC 20 880 antiSPCas9-578 + CGGUAAAUUCU UGUCAAAGU 20 881 antiSPCas9-579 - AUGUGGGACCCCUGGCCCGA 20 882 antiSPCas9-580 - CGGAUAGAUU UGUCACAGCU 20 883 antiSPCas9-581 + UCGACUUAAAAUU UGGUGUC 20 884 antiSPCas9-582 - CAUCCUAGCUGAUGCCAAUC 20 885 antiSPCas9-583 + CAUCCACUACUU UGACUGUC 20 886 antiSPCas9-584 - AGGCACAGGU UUCCGGACAA 20 887 antiSPCas9-585 + GCCAGGGGUCCCACAUAGUA 20 888 antiSPCas9-586 + UCGUAAAGUAAACUGUGCU U 20 889 antiSPCas9-587 + CAGGCAGUUGCUGACGGACU 20 890 antiSPCas9-588 - CUGAU UCACCAAUCCAUCAC 20 891 antiSPCas9-589 - UGCCUAU UCUGUCCUAGUAG 20 892 antiSPCas9-590 - GAUGAGCUAGU UAAGGUCAU 20 893 antiSPCas9-591 + AGUAUGCCCUUU UUGAUGGC 20 894 antiSPCas9-592 - GGGAGACAGGUGAAAUCGUA 20 895 antiSPCas9-593 + GAUUGAAUCGUCCUUCAAAA 20 896 antiSPCas9-594 + CUGUUCUCCGCUUAGAAAGG 20 897 antiSPCas9-595 - AAGAUCUACUGCGAAAGCAG 20 898 antiSPCas9-596 - UUGUCUGAACUUGACAAGGC 20 899 antiSPCas9-597 + UGCGGCUGGAGCGCCGAGGU 20 900 antiSPCas9-598 - CAUGUAUGUUGAUCAGGAAC 20 901 antiSPCas9-599 - GACAAUCUACUGGCACAAAU 20 902 antiSPCas9-600 - CCUUGAGGCGAAAGGUUACA 20 903 antiSPCas9-601 + GCUUAAUACUUUGUCCAGAU 20 904 antiSPCas9-602 - AGGUGAAAUCGUAUGGGAUA 20 905 antiSPCas9-603 - AAGGCACAGGUUUCCGGACA 20 906 antiSPCas9-604 + AUCGUCCUUCAAAAAGGAUU 20 907 antiSPCas9-605 + CAGCUGCAUAAAGUUCCUAU 20 908 antiSPCas9-606 - GAUCUUAAAGGAGCAUCCUG 20 909 antiSPCas9-607 + GUACCUUUUGAUCAUUGAAG 20 910 antiSPCas9-608 - UGAAGAUCGGGAAAUGAUUG 20 911 antiSPCas9-609 - UGCCAAAUUGCAGCUUAGUA 20 912 antiSPCas9-610 - GGAUGAGCUAGUUAAGGUCA 20 913 antiSPCas9-611 + CG AU UCCU U UG AAAACCCUC 20 914 antiSPCas9-612 + CUUCUGUUCUCCGCUUAGAA 20 915 antiSPCas9-613 - UUUGAGGAAGUUGUCGAUAA 20 916 antiSPCas9-614 + UCAAAAUACUUGAAUGCGGC 20 917 antiSPCas9-615 - ACUGGGCAGCCAGAUCUUAA 20 918 antiSPCas9-616 - GAUAGAUUUGUCACAGCUUG 20 919 antiSPCas9-617 + CCUUGAGAAGUGUCAAGUCU 20 920 antiSPCas9-618 + AUCUCGAUUACAAUGUUUUC 20 921 antiSPCas9-619 + UCACGAUUGUCUUUGAGGAA 20 922 antiSPCas9-620 + CUGGAGUAUGCCCUUUUUGA 20 923 antiSPCas9-621 + AAAGUUUCUCGUUCUGCAAU 20 924 antiSPCas9-622 - UUGUUUACUCUUACCAACCU 20 925 antiSPCas9-623 - AAGCGCAUACAACAAGCACA 20 926 antiSPCas9-624 + AAUCGUCCUU C A AA AAG G A U 20 927 antiSPCas9-625 + UGCAAUUGGGUAUUUUCCAC 20 928 antiSPCas9-626 + CUCUCAGUAUGUCAGAUAGG 20 929 antiSPCas9-627 + UGCUUCUGUUCGUUAUCUUC 20 930 antiSPCas9-628 - GGAUAGAUUUGUCACAGCUU 20 931 antiSPCas9-629 - UGUACCCCAAUCCUUUUUGA 20 932 antiSPCas9-630 - UGGCUUGUCUGAACUUGACA 20 933 antiSPCas9-631 - AAGGGACAUGUAUGUUGAUC 20 934 antiSPCas9-632 + GAUUUCACCUGUCUCCCCAU 20 935 antiSPCas9-633 + UUAGGCAAUACUUUUUCGUU 20 936 antiSPCas9-634 + UAACUCUCAGUAUGUCAGAU 20 937 antiSPCas9-635 + GU UCCCCU UU UGAAGCUCUC 20 938 antiSPCas9-636 - UCAGUAUGCGGACU UAUUU U 20 939 antiSPCas9-637 + UCUCAACUU UUGCCACUACU 20 940 antiSPCas9-638 + GAU UAUAGGUU UGUACUAAC 20 941 antiSPCas9-639 - GACCU UUAAUUGAAACCAAU 20 942 antiSPCas9-640 - AGGAAUCGAU UCUUCCAAAA 20 943 antiSPCas9-641 - CU U U AAG ACGG AAAUCACUC 20 944 antiSPCas9-642 + AAGU UUCUCGUUCUGCAAUU 20 945 antiSPCas9-643 + GUGCAACAUGCU UUGUGAUU 20 946 antiSPCas9-644 - AUUGAAACCAAUGGGGAGAC 20 947 antiSPCas9-645 - ACU CC AG AC AG U CAAAG U AG 20 948 antiSPCas9-646 - AAU UGCAUGCUAUACU UAGA 20 949 antiSPCas9-647 + AACUCAAACAGACUAUACUU 20 950 antiSPCas9-648 - GAU UACUCCAUGGAAU UUUG 20 951 antiSPCas9-649 - GGAAAACAU UGUAAUCGAGA 20 952 antiSPCas9-650 - AGUAGUGGAUGAGCUAGUUA 20 953 antiSPCas9-651 + CAGGAUGCUCCUUUAAGAUC 20 954 antiSPCas9-652 - CAU UGAGGGUGAUCUAAAUC 20 955 antiSPCas9-653 - CCAAGACUUGACACUUCUCA 20 956 antiSPCas9-654 + UCCCCAUUGGUU UCAAUUAA 20 957 antiSPCas9-655 - AUAACUUAACUAAAGCUGAG 20 958 antiSPCas9-656 + CCCAUCCAUCU UCUCUAAUA 20 959 antiSPCas9-657 - GAGAACCCUAUAAAUGCAAG 20 960 antiSPCas9-658 - AAAACUGAGGUGCAGACCGG 20 961 antiSPCas9-659 - G G C A A AA AA AC AG U CG AG AG 20 962 antiSPCas9-660 + AGGAAAUUCACGUAU UUAGA 20 963 antiSPCas9-661 - AAGCGAACAGGAGAUAGGCA 20 964 antiSPCas9-662 - UCU UACCCUCUU UGAAGAUC 20 965 antiSPCas9-663 - CCCUGGCCCGAGGGAACUCU 20 966 antiSPCas9-664 - CGAAAUCAUAGAGCAAAUU U 20 967 antiSPCas9-665 - U UCUU UGAUCAGUCGAAAAA 20 968 antiSPCas9-666 - UGACUCU UUAACCU UCAAAG 20 969 antiSPCas9-667 + AGGACAGAAUAGGCAACUGU 20 970 antiSPCas9-668 - AG U U AAU ACUG AG AU U ACCA 20 971 antiSPCas9-669 - ACCUU UAAUUGAAACCAAUG 20 972 antiSPCas9-670 - AUUCCACAUCAAAUCCACUU 20 973 antiSPCas9-671 + AGCU UAUCACUAUUCCU UUU 20 974 antiSPCas9-672 + UGUCCAGAU UGGCAUCAGCU 20 975 antiSPCas9-673 - GAAAGUUAAGUAUGUCACUG 20 976 antiSPCas9-674 + AACAUGCU UUGUGAU UUGGC 20 977 antiSPCas9-675 + CAU U UCCCG AUCU UCAAAG A 20 978 antiSPCas9-676 - CCAU AU U AG AG AAG AUGG AU 20 979 antiSPCas9-677 - UACCUCUAUUACCUACAAAA 20 980 antiSPCas9-678 - AUAGAUUUGUCACAGCUUGG 20 981 antiSPCas9-679 + GGUUGGUAAGAGUAAACAAA 20 982 antiSPCas9-680 + UCAUUUCCCGAUCUUCAAAG 20 983 antiSPCas9-681 - ACGGAAAUCACUCUGGCAAA 20 984 antiSPCas9-682 + UGAAGGUUAAAGAGUCAUCA 20 985 antiSPCas9-683 + CUCUUCAAACAACUGAUUAU 20 986 antiSPCas9-684 + CUUCAUUCUCUUCGUUAUCC 20 987 antiSPCas9-685 - A U AC AAA AG GCACAGGUUUC 20 988 antiSPCas9-686 - GUAGUGGCAAAAGUUGAGAA 20 989 antiSPCas9-687 - AGUCAGUCAAAGAAUUAUUG 20 990 antiSPCas9-688 - GCAACUGCCUGAGAAAUAUA 20 991 antiSPCas9-689 - CUAGAAAGUGAGUUUGUGUA 20 992 antiSPCas9-690 + GAACAUUGUCACUUUUCCCU 20 993 antiSPCas9-691 - CCCAU AU U AG AG AAG AUGG A 20 994 antiSPCas9-692 + CAACAUGCUUUGUGAUUUGG 20 995 antiSPCas9-693 + ACAUGUCCCUUCCAUUUUGU 20 996 antiSPCas9-694 - CUCUUACCCUCUUUGAAGAU 20 997 antiSPCas9-695 - ACAAAUUGGAGAUCAGUAUG 20 998 antiSPCas9-696 - AAACUGAGGUGCAGACCGGA 20 999 antiSPCas9-697 - UACCCGGAGAGAAGAAAAAU 20 1000 antiSPCas9-698 - UUAACUAAAGCUGAGAGGGG 20 1001 antiSPCas9-699 - GAAGUCAGUCAAAGAAUUAU 20 1002 antiSPCas9-700 - AAAGUUAAGUAUGUCACUGA 20 1003 antiSPCas9-701 - UCUAUUACCUACAAAAUGGA 20 1004 antiSPCas9-702 - A AC U U AAC U AA AG C U G AG AG 20 1005 antiSPCas9-703 - AAUUAAAGAUAAGGACUUCC 20 1006 antiSPCas9-704 - AGUAGUGGCAAAAGUUGAGA 20 1007 antiSPCas9-705 - AGAGGAUAUACAAAAGGCAC 20 1008 antiSPCas9-706 + UCUUUUCACGAUUGUCUUUG 20 1009 antiSPCas9-707 - CAAACCCAU AU U AG AG AAG A 20 1010 antiSPCas9-708 + UGUGUCAAAAUACUUGAAUG 20 1011 antiSPCas9-709 - GACAGUUAAGCAAUUGAAAG 20 1012 antiSPCas9-710 - GAAGAGGGUAUUAAAGAACU 20 1013 antiSPCas9-711 + UUCCAUUUUGUAGGUAAUAG 20 1014 antiSPCas9-712 - GCGGAUGAAGAGAAUAGAAG 20 1015 antiSPCas9-713 - CUAUUACCUACAAAAUGGAA 20 1016 antiSPCas9-714 + AUUGCUUAACUGUCACUUUG 20 1017 antiSPCas9-715 - AGUCUGUUUGAGUUAGAAAA 20 1018 antiSPCas9-716 + ACAAACUCACUUUCUAGCUU 20 1019 antiSPCas9-717 - AAAAUCAAACGACUCAGAAG 20 1020 antiSPCas9-718 - AGAAGAGGGUAUUAAAGAAC 20 1021 antiSPCas9-719 + CAAACUCACUUUCUAGCUUC 20 1022 antiSPCas9-720 - U U ACCCGG AG AG AAG AAAAA 20 1023 antiSPCas9-721 + AUUUCUCAGGCAGUUGCUGA 20 1024 antiSPCas9-722 - AGUUAGAAAAUGGCCGAAAA 20 1025 antiSPCas9-723 - UAACUUAACUAAAGCUGAGA 20 1026 antiSPCas9-724 + GGACAGAAUAGGCAACUGUA 20 1027 antiSPCas9-725 - AAGUCAGUCAAAGAAUUAUU 20 1028 antiSPCas9-726 - AGGUUAUGAAACAGUUAAAG 20 1029 antiSPCas9-727 + UUUGACUGACUUCAGUUUCU 20 1030 antiSPCas9-728 + CAACCCAUUUUUCUUCUCUC 20 1031 antiSPCas9-729 + UCGUCCUUCAAAAAGGAUUG 20 1032 antiSPCas9-730 + UACUAUGUUGACUUGGGGCA 20 1033 antiSPCas9-731 - UGCUAUACUUAGAAGGCAGG 20 1034 antiSPCas9-732 + ACAACU UCCUCAAAAU UCCA 20 1035 antiSPCas9-733 - UUUAAAGUCAAAAUUGGUGU 20 1036 antiSPCas9-734 - CGGAUGAAGAGAAUAGAAGA 20 1037 antiSPCas9-735 + CUUUUGUAUAUCCUCUUUGA 20 1038 antiSPCas9-736 + AACCCAUUUUUCUUCUCUCC 20 1039 antiSPCas9-737 + CCAUCCAUCUUCUCUAAUAU 20 1040 antiSPCas9-738 - AU U AG AG AAG AUGG AUGGG A 20 1041 antiSPCas9-739 - ACUGAUUCACCAAUCCAUCA 20 1042 antiSPCas9-740 - CCUAAAGAUAAUUAAAGAUA 20 1043 antiSPCas9-741 - GGGAUAAGAGACAAGCAAAG 20 1044 antiSPCas9-742 + UUCUUUACUAUGUUGACUUG 20 1045 antiSPCas9-743 - GAAAAUCAAACGACUCAGAA 20 1046 antiSPCas9-744 + UUUCUUUACUAUGUUGACUU 20 1047 antiSPCas9-745 + CCUUAUCUUUAAUUAUCUUU 20 1048 antiSPCas9-746 - AAUCACUUUAAAGU C A A A A U 20 1049 antiSPCas9-747 - AGAAAAUGAAGAACUAUUGG 20 1050 antiSPCas9-748 + GUUAGAAUAAAAGAAGUAUU 20 1051 antiSPCas9-749 - CAACAUAGUAAAGAAAACUG 20 1052 antiSPCas9-750 - AGGUUACAAGG AAG U AAAAA 20 1053 antiSPCas9-751 + UAUCUUUAAUUAUCUUUAGG 20 1054 antiSPCas9-752 - GAGAAGAAAAAUGGGUUGUU 20 1055 antiSPCas9-753 - CAUUAUGAAUUUCUUUAAGA 20 1056 antiSPCas9-754 + UUUUCUUUACUAUGUUGACU 20 1057 antiSPCas9-755 - AUUUUCAAUUCUAUAAAGUU 20 1058 antiSPCas9-756 + AAUAUUUCCUUAUAUUUCUC 20 1059 antiSPCas9-757 - UUUUCAAUUCUAUAAAGUUA 20 1060 antiSPCas9-758 - UAAAGAAAAUGAAGAACUAU 20 1061 antiSPCas9-759 - AAGAAAACUGAGGUGCAGAC 20 1062 antiSPCas9-760 - CUUCAAAGAGGAUAUACAAA 20 1063

Table E-7

Table E-8

antiSACas9-8 - ACCGACCAUUCUGAGCUGAG 20 1071 antiSACas9-9 - UGCUGACCGACCAUUCUGAG 20 1072 antiSACas9-10 + AACAGCAGUUUCUUCACCCU 20 1073 antiSACas9-ll + AGGAUUAAUUCCACUCAGCU 20 1074 antiSACas9-12 - UACAUUCUGGGGCUGGACAU 20 1075 antiSACas9-13 - AUGAAGCCAGGGUGAAAGGC 20 1076 antiSACas9-14 - CUGAAACGACGGAGAAGGCA 20 1079 antiSACas9-15 - CGGAGAAGGCACAGAAUCCA 20 1080

Table E-10

First 500bp of coding sequence downstream of start codon,

S. aureus

poor orthogonality, starts with G

3rd Tier

Target Site

g NA Name DNA Strand Targeting Domain Length SEQ ID NO antiSACas9-16 - GAGUCAGAAGCUGUCAGAGG 20 1081 antiSACas9-17 - GAAGAAAGAUGGCGAGGUGA 20 1082 antiSACas9-18 - GGGAUUACAAGCGUGGGGUA 20 1083

Table E-ll

S. aureus Rest of gene

5th Tier

Target Site

gRNA Name DNA Strand Targeting Domain Length SEQ ID NO antiSACas9-19 - GAUACGCUACUCGCGGCCUG 20 1084 antiSACas9-20 + AUGAUCGACCUCGUAGUUGA 20 1085 antiSACas9-21 - AUGAAUGAUAAGCGCCCCCC 20 1086 antiSACas9-22 - ACGCAGAUCUGUACAACGCC 20 1087 antiSACas9-23 - ACUACAAGUACUCUCACCGG 20 1088 antiSACas9-24 + CGCCGUUGUCCAGAUAGACA 20 1089 antiSACas9-25 - UCAUUGAGAACGCCGAACUG 20 1090 antiSACas9-26 + UAAUAUGAUCGACCUCGUAG 20 1091 antiSACas9-27 + GCGUUCUCUUUCCCGGUAGU 20 1092 antiSACas9-28 - GGCGAACUGUAUAGGGUCAU 20 1093 antiSACas9-29 - GCCCGAAAUCGAGACAGAAC 20 1094 antiSACas9-30 - AUCUGCUGAACCGCAUUGAA 20 1095 antiSACas9-31 + CCG U UCAG AU UG U UCACAAU 20 1096 antiSACas9-32 + UCGGAGCUCUGGUAGAUAGU 20 1097 antiSACas9-33 + GACCACCUUGUUGCGACUGU 20 1098 antiSACas9-34 + UUUGUAUGCCACAGCUCAUC 20 1099 antiSACas9-35 + GGGCUUUUUAUCCACCCGGU 20 1100 antiSACas9-36 + GUUGAGUACUUUUUGAUACU 20 1101 antiSACas9-37 - AAGAUCAAUGGCGAACUGUA 20 1102 antiSACas9-38 - GAAAGUCAAG U CCAUCAACG 20 1103 antiSACas9-39 + GGUCCCUCAUAGUAGGUUCU 20 1104 antiSACas9-40 - CCUAUUUCCGGGUGAACAAU 20 1105 antiSACas9-41 + CGCAGCAGAUUCAUCAGGCC 20 1106 antiSACas9-42 + CAGGUUUCCCAGAAUGUCGG 20 1107 antiSACas9-43 - CGAACAGAUUAGUAAUCUGA 20 1108 antiSACas9-44 + CCAGAUUGUUCACCCGGAAA 20 1109 antiSACas9-45 + AAAUCGUCCACCAGUGUGGU 20 1110 antiSACas9-46 - CUUCGGAUGGAAAGACAUCA 20 1111 antiSACas9-47 - AAAUGCCGACUUCAUCUUUA 20 1112 antiSACas9-48 - UCAACAGAUUCUCCGUCCAG 20 1113 antiSACas9-49 + GCGUUGAUCACUUUGAUGCU 20 1114 antiSACas9-50 - AAGGACUACAAGUACUCUCA 20 1115 antiSACas9-51 + CUCCGCUUGACCACGGGUGA 20 1116 antiSACas9-52 - GGUGACAAGCACUGGAAAAC 20 1117 antiSACas9-53 - ACCUGACCAAGUAUAGCAAA 20 1118 antiSACas9-54 + GGAUGAAGCUCCGCUUGACC 20 1119 antiSACas9-55 - CCGCAUCAGCAAGACCAAAA 20 1120 antiSACas9-56 - UCCAGAAGGAUUUUAUUAAC 20 1121 antiSACas9-57 + UUGAUAUGCUUGAUCUGGUG 20 1122 antiSACas9-58 - UGUAUAAAUUUGUGACUGUC 20 1123 antiSACas9-59 - CUCACCAGAUCAAGCAUAUC 20 1124 antiSACas9-60 - UGCAGAAGGCUUACCACCAG 20 1125 antiSACas9-61 + UUGAUGUCCUCUUCGUUGAC 20 1126 antiSACas9-62 + CUAAUCUGUUCGAUCUCUUC 20 1127 antiSACas9-63 + GACCAGCACCUUGUUGUUAA 20 1128 antiSACas9-64 - GAAGAGGACAUCAAGGGCUA 20 1129 antiSACas9-65 + UAAUAAAAUCCUUCUGGACG 20 1130 antiSACas9-66 - U G G U CCC A AA AA AG G U G G AC 20 1131 antiSACas9-67 + CUCUUCAUAGUACUUAUACA 20 1132 antiSACas9-68 - AAUCUGCUGCGAUCCUAUUU 20 1133 antiSACas9-69 + GAACUAGACAGGUACUGGAA 20 1134 antiSACas9-70 + AAAGGUUUCGUAAGAGAUCU 20 1135 antiSACas9-71 + CCCUUUCCUUUGGCCAGAUU 20 1136 antiSACas9-72 + UCGUCUUUUCUUGUACUAUA 20 1137 antiSACas9-73 + AGGAGUCCUAUUGCCCUUUU 20 1138 antiSACas9-74 - U AUG AU UG ACAUCACU U ACC 20 1139 antiSACas9-75 + UUCACCUCAUACAGGUUUCC 20 1140 antiSACas9-76 + CUCCAGGGGGAUGGCCUCCA 20 1141 antiSACas9-77 - UGAAAGCUAUCAAUCUGAUU 20 1142 antiSACas9-78 - UCAAGUACUAUGGGAACAAG 20 1143 antiSACas9-79 - UGAACAACCUGGUCAUCACC 20 1144 antiSACas9-80 + UUGUUCAGCAGGUCCUCCAG 20 1145 antiSACas9-81 - ACCGAGAGUAUCUGGAAAAC 20 1146 antiSACas9-82 - GUUUAAAAAGGAGCGCAACA 20 1147 antiSACas9-83 + CUUCAGUUUCUGAUAUGUCU 20 1148 antiSACas9-84 - AAACAAUUGCCUCUAAGACU 20 1149 antiSACas9-85 - GAAAAAGAUUAGCAACCAGG 20 1150 antiSACas9-86 - CAGGGAUGAAAACGAGAAAC 20 1151 antiSACas9-87 + UUCAGGUUAGUCAGCUCUUC 20 1152 antiSACas9-88 + UUGUCGAAGGACACGCUUCU 20 1153 antiSACas9-89 - AA ACC U U U A AA AAG C AC A U U 20 1154 antiSACas9-90 - ACCAGGAGAAGGGAGCCCCU 20 1155 antiSACas9-91 - GUACAAGAAAAGACGAUAAG 20 1156 antiSACas9-92 - GAUGUUCGAAGAGAAGCAGG 20 1157 antiSACas9-93 - AAAAGGAGAACUACUAUGAA 20 1158 antiSACas9-94 - AAUUUGUGACUGUCAAGAAU 20 1159

Table E-12

S. aureus Suboptimal PAM - NNGRRV

6th Tier

Target Site

g NA Name DNA Strand Targeting Domain Length SEQ ID NO antiSACas9-95 + GAAGCAGGCCGAAUCUAUGC 20 1160 antiSACas9-96 + AGGAAUGGUACGAGAUGCUG 20 1161 antiSACas9-97 + UCCGGGUGAACAAUCUGGAU 20 1162 antiSACas9-98 + AGACUCGGAGAACCUACUAU 20 1163 antiSACas9-99 + GGACGCACAGAAGAUGAUCA 20 1164 antiSACas9-100 - UCACAUCCAGAUUGUUCACC 20 1165 antiSACas9-101 + GGAGAAGGGAGCCCCUUCGG 20 1166 antiSACas9-102 + CCGGCAACGAGCUGUCUACA 20 1167 antiSACas9-103 + AAGUACUCAACCGACAUUCU 20 1168 antiSACas9-104 + AAUGACACCCUGUAUAGUAC 20 1169 antiSACas9-105 + ACUGUUCAAGGAGGCCAACG 20 1170 antiSACas9-106 + CCGACUUCAUCUUUAAGGAG 20 1171 antiSACas9-107 - GAAUCUGAACUAGACAGGUA 20 1172 antiSACas9-108 + CGGGUGGAUAAAAAGCCCAA 20 1173 antiSACas9-109 + ACCAGAGCUCCGAGGACAUC 20 1174 antiSACas9-110 - GGUGGUACAUCAGCAGCUUC 20 1175 antiSACas9-lll + CCGGAACACACAACCUGUCC 20 1176 antiSACas9-112 - GUGCUU UU UAAAGGUU UCGU 20 1177 antiSACas9-113 - UUCACAUCCAGAU UGU UCAC 20 1178 antiSACas9-114 - UUCCAGAGCU UUGCUAU UGC 20 1179 antiSACas9-115 + ACAUCU UU UCUGAGGCGCAA 20 1180 antiSACas9-116 + A AAG C U G A U C AAC A AA AG U C 20 1181 antiSACas9-117 + GAAUCUGGAUGUCAUCAAAA 20 1182 antiSACas9-118 + UAUAAGUACUAUGAAGAGAC 20 1183 antiSACas9-119 + CAUCACUUACCGAGAGUAUC 20 1184 antiSACas9-120 + UAUCAUUAUCGAGCUGGCUA 20 1185 antiSACas9-121 + CAAGGUGCUGGUCAAGCAGG 20 1186 antiSACas9-122 + AAAGUACUCAACCGACAU UC 20 1187 antiSACas9-123 - AUUGUCGAAGGACACGCUUC 20 1188 antiSACas9-124 + GAGUGCAUAACGUCAAUGAG 20 1189 antiSACas9-125 + AGUAUGUCGCAGAGCUGCAG 20 1190 antiSACas9-126 - GAAAUCGUCCACCAGUGUGG 20 1191 antiSACas9-127 + ACCAUGAUCCUCAGACAUAU 20 1192 antiSACas9-128 - CUUGACGCU UCUCAGCUCU U 20 1193 antiSACas9-129 + GUAUAAGUACUAUGAAGAGA 20 1194 antiSACas9-130 + GGGGUAUGGGAU UAUUGACU 20 1195 antiSACas9-131 + CCCACUGUAUAAGUACUAUG 20 1196 antiSACas9-132 + U CGAAAACG U G U U UAAGCAG 20 1197 antiSACas9-133 + AGACCAAAAAGGAGUACCUG 20 1198 antiSACas9-134 - U UAAACACG UU UUCGAUGAU 20 1199 antiSACas9-135 - GCU UGACCACGGGUGACAGA 20 1200 antiSACas9-136 - U UAAACU UCCAU UUGCGCCU 20 1201 antiSACas9-137 + AUGAGGGACGGAGAAGCAAG 20 1202 antiSACas9-138 - CUGACUCAGGUCCACCUUU U 20 1203 antiSACas9-139 + GAAAGACAUCAAGGAAUGGU 20 1204 antiSACas9-140 + UAAGGACAUCACAGCACGGA 20 1205 antiSACas9-141 + AAAAGGUGGACCUGAGUCAG 20 1206 antiSACas9-142 + AAUAUGAU UGACAUCACUUA 20 1207 antiSACas9-143 + GAGAAGGGAGCCCCUUCGGA 20 1208 antiSACas9-144 + GAU UAUCCGAACUACCGGGA 20 1209 antiSACas9-145 + UCAAAGAAGCCAAGCAGCUG 20 1210 antiSACas9-146 - GGUGAGAGUACUUGUAGUCC 20 1211 antiSACas9-147 + ACCUGAACAGCGAGCUGACC 20 1212 antiSACas9-148 + GACCGACCAU UCUGAGCUGA 20 1213 antiSACas9-149 - GCUUGAUCUGGUGAGGAGUG 20 1214 antiSACas9-150 - UGACCAGCACCUUGUUGUUA 20 1215 antiSACas9-151 + CAAGCUGCACGAUAUGCAGG 20 1216 antiSACas9-152 - UAAAGGUUUCGUAAGAGAUC 20 1217 antiSACas9-153 + GCACCU AU U U UCCAG AAGAG 20 1218 antiSACas9-154 + AAACGAGAAACUGGAAUACU 20 1219 antiSACas9-155 + UGAAGAGAUUAUCCGAACUA 20 1220 antiSACas9-156 + GGCUGAAGAAAGAUGGCGAG 20 1221 antiSACas9-157 + GUCCAGAAGGAUUUUAUUAA 20 1222 antiSACas9-158 + GAACAGCGAGCUGACCCAGG 20 1223 antiSACas9-159 + AGAACCUACUAUGAGGGACC 20 1224 antiSACas9-160 - AGCCAGGUGCAGCAGAGCUG 20 1225 antiSACas9-161 + CUACUAUGAGGGACCAGGAG 20 1226 antiSACas9-162 + G AAAACCAG AG U U CACCAAU 20 1227 antiSACas9-163 + AC AAC A AG GUGCUGGU C AAG 20 1228 antiSACas9-164 + GCAGACCAAUGAACGCAUUG 20 1229 antiSACas9-165 + GGAAAAAGCUGGACAAAGCC 20 1230 antiSACas9-166 + U UCAG AU UCCAAG AUCUCU U 20 1231 antiSACas9-167 + AGCUGCAGCUGGAACGGCUG 20 1232 antiSACas9-168 + GAUUAUGGAGCAGUACGGCG 20 1233 antiSACas9-169 - AGAAUCAGAUUGAUAGCUUU 20 1234 antiSACas9-170 - UCCUCCAGGGGGAUGGCCUC 20 1235 antiSACas9-171 + GGG AU U AU UG ACU AUG AAAC 20 1236 antiSACas9-172 + UCUCACGCAAUAGCAAAGCU 20 1237 antiSACas9-173 + ACGUGGAAAACAAUGAGGGA 20 1238 antiSACas9-174 - UUGACGCUUCUCAGCUCUUC 20 1239 antiSACas9-175 + GAUAUCAUUAUCGAGCUGGC 20 1240 antiSACas9-176 - GUUAAUAAAAUCCUUCUGGA 20 1241 antiSACas9-177 + CAACCUGGUCAUCACCAGGG 20 1242 antiSACas9-178 + GCACAUUCUGAAUCUGGCCA 20 1243 antiSACas9-179 + GGUGGACCUGAGUCAGCAGA 20 1244 antiSACas9-180 + AUAUUAAGGACAUCACAGCA 20 1245 antiSACas9-181 + CUACAUUCUGGGGCUGGACA 20 1246 antiSACas9-182 + GCAAGAGGGGAGCCAGGCGC 20 1247 antiSACas9-183 + CCAGGGAUGAAAACGAGAAA 20 1248 antiSACas9-184 - UAGCCAGGUGCAGCAGAGCU 20 1249 antiSACas9-185 + GGGCUACCGGGUGACAAGCA 20 1250 antiSACas9-186 + GGUCAUCACCAGGGAUGAAA 20 1251 antiSACas9-187 + GAGCCAGGCGCCUGAAACGA 20 1252 antiSACas9-188 + GCUACGAAGAGGCUAAAAAG 20 1253 antiSACas9-189 + GGACAAAGCCAAGAAAGUGA 20 1254 antiSACas9-190 - UUGGGCUUUUUAUCCACCCG 20 1255 antiSACas9-191 + GACUGUUCAAGGAGGCCAAC 20 1256 antiSACas9-192 + AAAAGUACUCAACCGACAUU 20 1257 antiSACas9-193 + UAGUAAUCUGAAGGGGUACA 20 1258 antiSACas9-194 + GGCCGAAUCUAUGCCCGAAA 20 1259 antiSACas9-195 + UCAAGCUGCACGAUAUGCAG 20 1260 antiSACas9-196 + CUGAACAACCUGGUCAUCAC 20 1261 antiSACas9-197 + GGCACAGAAUCCAGAGGGUG 20 1262 antiSACas9-198 + ACGCAAUAGCAAAGCUCUGG 20 1263 antiSACas9-199 + AGAGAACGCAAAGUACCUGA 20 1264 antiSACas9-200 + UCAUCACCAGGGAUGAAAAC 20 1265 antiSACas9-201 + AAGGAGUACCUGCUGGAAGA 20 1266 antiSACas9-202 + AGCAGAAGAAAAAGCCUACA 20 1267 antiSACas9-203 + ACAUCACUUACCGAGAGUAU 20 1268 antiSACas9-204 + CACAGCACGGAAAGAAAUCA 20 1269 antiSACas9-205 + AGAAGAUGAUCAAUGAGAUG 20 1270 antiSACas9-206 + AAGCUGCACGAUAUGCAGGA 20 1271 antiSACas9-207 - AUUGUUCAGCAGGUCCUCCA 20 1272 antiSACas9-208 + GAUAUUAAGGACAUCACAGC 20 1273 antiSACas9-209 + CUAUGAGAAGUUCCAGAUCA 20 1274 antiSACas9-210 + GAAGAGAUUAUCCGAACUAC 20 1275 antiSACas9-211 + UACACUGAAACAGAUUGCUA 20 1276 antiSACas9-212 + AGUACAAGAAAAGACGAUAA 20 1277 antiSACas9-213 + CGGGAUUACAAGCGUGGGGU 20 1278 antiSACas9-214 + GGCUACCGGGUGACAAGCAC 20 1279 antiSACas9-215 + AUAUCGACCUGCUGGAGACU 20 1280 antiSACas9-216 + UUAAUCCUUAUGAAGCCAGG 20 1281 antiSACas9-217 + CGAGACAGAACAGGAGUACA 20 1282 antiSACas9-218 + GAUCAAGAAGAUCAAGUACU 20 1283 antiSACas9-219 + GCCGACUUCAUCUUUAAGGA 20 1284 antiSACas9-220 + AAGAGAUUAUCCGAACUACC 20 1285 antiSACas9-221 + AUGAUCAAUGAGAUGCAGAA 20 1286 antiSACas9-222 + AGGCCAACGUGGAAAACAAU 20 1287 antiSACas9-223 + AUCAAGAAGAUCAAGUACUA 20 1288 antiSACas9-224 + CACAUUCUGAAUCUGGCCAA 20 1289 antiSACas9-225 + ACGACAAAGAUAAUGACAAG 20 1290 antiSACas9-226 - AAUCUGAACUAGACAGGUAC 20 1291 antiSACas9-227 + GCCUGAGUCAGAAGCUGUCA 20 1292 antiSACas9-228 + CGAUACUUAUAUCGACCUGC 20 1293 antiSACas9-229 + UAGUACAAGAAAAGACGAUA 20 1294 antiSACas9-230 + CCUUCGGAUGGAAAGACAUC 20 1295 antiSACas9-231 + GAUGGAGAACCAGAUGUUCG 20 1296 antiSACas9-232 - CGGCGCUUAGCCAGGUGCAG 20 1297 antiSACas9-233 + AGUAAUCUGAAGGGGUACAC 20 1298 antiSACas9-234 + CGACCUGAUUAAGAUCAAUG 20 1299 antiSACas9-235 + AGCUAUCAAUCUGAUUCUGG 20 1300 antiSACas9-236 + AAAGGAACUACAUUCUGGGG 20 1301 antiSACas9-237 + GGCCAACGUGGAAAACAAUG 20 1302 antiSACas9-238 + UCUUUAAGGAGUGGAAAAAG 20 1303 antiSACas9-239 + AGGAGUACCUGCUGGAAGAG 20 1304 antiSACas9-240 + UGACUAUCUACCAGAGCUCC 20 1305 antiSACas9-241 - GUGGUACAUCAGCAGCUUCU 20 1306 antiSACas9-242 + AGGAGAUCCUGGUCAACGAA 20 1307 antiSACas9-243 - UGUUGUUAAAGGAAUUGUCG 20 1308 antiSACas9-244 + ACAU UGCACCU AU U U UCCAG 20 1309 antiSACas9-245 + GAGAACUCUAAAAAGGGCAA 20 1310 antiSACas9-246 + AGAGCUGACUAACCUGAACA 20 1311 antiSACas9-247 + CAUACAGAUUCGAUGUCUAU 20 1312 antiSACas9-248 + UUCUGAAUCUGGCCAAAGGA 20 1313 antiSACas9-249 - UGACUCAGGUCCACCUUUUU 20 1314 antiSACas9-250 + AACUGUAUAGGGUCAUCGGG 20 1315 antiSACas9-251 - GAAUCAGAUUGAUAGCUUUC 20 1316 antiSACas9-252 + UGGCUAGGGAGAAGAACAGC 20 1317 antiSACas9-253 + UCCAGGAAGAGCUGACUAAC 20 1318 antiSACas9-254 - CUUUGACGUAGUCGCUUGUC 20 1319 antiSACas9-255 + AUAAGUACUAUGAAGAGACU 20 1320 antiSACas9-256 - UUCCGGUUAAUAAAAUCCUU 20 1321 antiSACas9-257 + UGAAGCUGGUCCCAAAAAAG 20 1322 antiSACas9-258 - UAGAUUCGGCCUGCUUCUCU 20 1323 antiSACas9-259 + UCAAGAAGAUCAAGUACUAU 20 1324 antiSACas9-260 + AUUUUAUUAACCGGAAUCUG 20 1325 antiSACas9-261 + UGGGAAACCUGUAUGAGGUG 20 1326 antiSACas9-262 + UCAGAAACUGAAGCUGAUUA 20 1327 antiSACas9-263 + AGGCUUACCACCAGCUGGAU 20 1328 antiSACas9-264 + UGCUGCGAUCCUAUUUCCGG 20 1329 antiSACas9-265 + AUAACGUCAAUGAGGUGGAA 20 1330 antiSACas9-266 + GAACGCAUUGAAGAGAUUAU 20 1331 antiSACas9-267 + UUCUGUCACCCGUGGUCAAG 20 1332 antiSACas9-268 + GCGCAAAUGGAAGUUUAAAA 20 1333 antiSACas9-269 - UAAACACGUUUUCGAUGAUC 20 1334 antiSACas9-270 - GUACUUGAUCUUCUUGAUCA 20 1335 antiSACas9-271 - AAGUCGGCAUUUGCGAUAAU 20 1336 antiSACas9-272 + CGAGCUGACCCAGGAAGAGA 20 1337 antiSACas9-273 + UCAAGCAUAUCAAGGAUUUC 20 1338 antiSACas9-274 + AGGUGCUGGUCAAGCAGGAA 20 1339 antiSACas9-275 + CUCUGGAGGCCAUCCCCCUG 20 1340 antiSACas9-276 + ACUAUGAGGGACCAGGAGAA 20 1341 antiSACas9-277 + GAGCUCCGAGGACAUCCAGG 20 1342 antiSACas9-278 + CAAAAAGGAGUACCUGCUGG 20 1343 antiSACas9-279 + AUACCCUGAUUGUGAACAAU 20 1344 antiSACas9-280 + UCUGGAAGAGAAGUAUGUCG 20 1345 antiSACas9-281 + AUAAGGGGAAUACCCUGAUU 20 1346 antiSACas9-282 - CCAGCUCGAUAAUGAUAUCA 20 1347 antiSACas9-283 + GG AU U AU UG ACU AUG AAACA 20 1348 antiSACas9-284 + GAGGGACGGAGAAGCAAGAG 20 1349 antiSACas9-285 - CAGCUCUUCCUGGAUGUCCU 20 1350 antiSACas9-286 + G AAAG AAAU CAU U G AG AACG 20 1351 antiSACas9-287 + CAGCACGGAAAGAAAUCAUU 20 1352 antiSACas9-288 + GACUCGGAGAACCUACUAUG 20 1353 antiSACas9-289 - AAGAUGUGAACCCGCCGUUG 20 1354 antiSACas9-290 + GGUGGAUAAAAAGCCCAACA 20 1355 antiSACas9-291 + UCGGGGUGAACAAUGAUCUG 20 1356 antiSACas9-292 + UGUACAACGCCCUGAAUGAC 20 1357 antiSACas9-293 - ACUCCUGUUCUGUCUCGAUU 20 1358 antiSACas9-294 + AUCUAUGCCCGAAAUCGAGA 20 1359 antiSACas9-295 + GGAACAAGCUGAAUGCCCAU 20 1360 antiSACas9-296 - ACCAGGUUGUUCAGGUCAUU 20 1361 antiSACas9-297 + ACAAAGCCAAGAAAGUGAUG 20 1362 antiSACas9-298 + CAACCUGCUGACCGACCAUU 20 1363 antiSACas9-299 + AUCUGGAUGUCAUCAAAAAG 20 1364 antiSACas9-300 + CCAUCCCCCUGGAGGACCUG 20 1365 antiSACas9-301 - GGUCGGUCAGCAGGUUGUAA 20 1366 antiSACas9-302 + UGAAAGUGUAUCACGAUAUU 20 1367 antiSACas9-303 + CUAAGAUCCUGACUAUCUAC 20 1368 antiSACas9-304 + UGGUCAAGCGGAGCUUCAUC 20 1369 antiSACas9-305 + CGGCAACGAGCUGUCUACAA 20 1370 antiSACas9-306 + AGCAGGAAGAGAACUCUAAA 20 1371 antiSACas9-307 + GAAACGAAACCGGCAGACCA 20 1372 antiSACas9-308 - CUUGAUGUCUUUCCAUCCGA 20 1373 antiSACas9-309 + CCUGAUUGUGAACAAUCUGA 20 1374 antiSACas9-310 + UUAUCGAGCUGGCUAGGGAG 20 1375 antiSACas9-311 - CGUGAUACACUUUCAGAUUG 20 1376 antiSACas9-312 + AAGAGAUCCCAACCACACUG 20 1377 antiSACas9-313 - UUCGUAAGAGAUCUUGGAAU 20 1378 antiSACas9-314 + CCUGCCCAAUGAUAUCAUUA 20 1379 antiSACas9-315 + AUCGACCUGCUGGAGACUCG 20 1380 antiSACas9-316 - UGUCAUUGAUCAGCUCUCUG 20 1381 antiSACas9-317 + UGGAGCAGUACGGCGACGAG 20 1382 antiSACas9-318 - AUUUGCGCCUCAGAAAAGAU 20 1383 antiSACas9-319 - UGUUUUCCACGUUGGCCUCC 20 1384 antiSACas9-320 - CGUUGUUGUAAAAGGAGGCG 20 1385 antiSACas9-321 + AGCACCCUCAGAUUAUCAAA 20 1386 antiSACas9-322 - UCUGCGACAUACUUCUCUUC 20 1387 antiSACas9-323 + GGAAUGGUACGAGAUGCUGA 20 1388 antiSACas9-324 + GUAUGUCGCAGAGCUGCAGC 20 1389 antiSACas9-325 + UGGUCAACGAAGAGGACAUC 20 1390 antiSACas9-326 + GGUGGAAGAGGACACCGGCA 20 1391 antiSACas9-327 - UAAUCGUCUGUGAUGUCCAG 20 1392 antiSACas9-328 + UUAUCCGAACUACCGGGAAA 20 1393 antiSACas9-329 - AAUUGUUUUGAUAAUUCGAG 20 1394 antiSACas9-330 + GACCAAAAAGGAGUACCUGC 20 1395 antiSACas9-331 + CAUCAAAAAGGAGAACUACU 20 1396 antiSACas9-332 + AGUGAAUAGCAAGUGCUACG 20 1397 antiSACas9-333 + CGACAUUCUGGGAAACCUGU 20 1398 antiSACas9-334 + CCGAGGAGUGCAUAACGUCA 20 1399 antiSACas9-335 + AGGCCUGAGUCAGAAGCUGU 20 1400 antiSACas9-336 + GCAAUAGCAAAGCUCUGGAA 20 1401 antiSACas9-337 + ACCUAUUUUCCAGAAGAGCU 20 1402 antiSACas9-338 - UCAGCUCUUCCUGGAUGUCC 20 1403 antiSACas9-339 - GCAGGUCGAUAUAAGUAUCG 20 1404 antiSACas9-340 - CUUGAUAUGCUUGAUCUGGU 20 1405 antiSACas9-341 + AGUGCAUAACGUCAAUGAGG 20 1406 antiSACas9-342 - AGCUUCAGUUUCUGAUAUGU 20 1407 antiSACas9-343 - GGCAAUUGUUUUGAUAAUUC 20 1408 antiSACas9-344 + CAACAAGGUGCUGGUCAAGC 20 1409 antiSACas9-345 + AGUGAUGGAGAACCAGAUGU 20 1410 antiSACas9-346 + GGGAAAGUGUCUGUAUUCUC 20 1411 antiSACas9-347 + AGGGAAAGUGUCUGUAUUCU 20 1412 antiSACas9-348 + AGAUCGAACAGAUUAGUAAU 20 1413 antiSACas9-349 - GAUUGUUCAGCAGGUCCUCC 20 1414 antiSACas9-350 + AAUCAAGCUGCACGAUAUGC 20 1415 antiSACas9-351 + GUGGAAAACAAUGAGGGACG 20 1416 antiSACas9-352 + GCCAGGCGCCUGAAACGACG 20 1417 antiSACas9-353 + UCGAUACUUAUAUCGACCUG 20 1418 antiSACas9-354 + AGGAUAAUGGCCCCGUGAUC 20 1419 antiSACas9-355 + UCAUUAUCGAGCUGGCUAGG 20 1420 antiSACas9-356 + AACCUACUAUGAGGGACCAG 20 1421 antiSACas9-357 + ACAAUGAGGGACGGAGAAGC 20 1422 antiSACas9-358 + UGAAGUGAAUAGCAAGUGCU 20 1423 antiSACas9-359 + AUUCUCUGGAGGCCAUCCCC 20 1424 antiSACas9-360 + CUGAAGAAAGAUGGCGAGGU 20 1425 antiSACas9-361 + UGGCGAACUGUAUAGGGUCA 20 1426 antiSACas9-362 + UACUAUGAGGGACCAGGAGA 20 1427 antiSACas9-363 - CAAUUGUUUUGAUAAUUCGA 20 1428 antiSACas9-364 + GCUGAGUGGAAUUAAUCCUU 20 1429 antiSACas9-365 + CUGCUGCACCUGGCUAAGCG 20 1430 antiSACas9-366 + CCAGAGCUCCGAGGACAUCC 20 1431 antiSACas9-367 - AAU UG UCG AAGG ACACGCU U 20 1432 antiSACas9-368 + UAUAUCGACCUGCUGGAGAC 20 1433 antiSACas9-369 + AGCUGAUCAACAAAAGUCCC 20 1434 antiSACas9-370 + AGAAGAACAGCAAGGACGCA 20 1435 antiSACas9-371 + UGGAGAACCAGAUGUUCGAA 20 1436 antiSACas9-372 + AGAUUGCAAUCUUUAACCGG 20 1437 antiSACas9-373 + UUCUCUGGAGGCCAUCCCCC 20 1438 antiSACas9-374 + AAUGAGGGACGGAGAAGCAA 20 1439 antiSACas9-375 - UCCUUGAUAUGCUUGAUCUG 20 1440 antiSACas9-376 + GGGACAUUGCACCUAUUUUC 20 1441 antiSACas9-377 + AAGUGAUCAACGCCAUCAUC 20 1442 antiSACas9-378 + GCUGCACCUGGCUAAGCGCC 20 1443 antiSACas9-379 + GGAACGGCUGAAGAAAGAUG 20 1444 antiSACas9-380 - CCUUGAUGUCUUUCCAUCCG 20 1445 antiSACas9-381 + GGAGGCCAACGUGGAAAACA 20 1446 antiSACas9-382 + ACGGCGGGUUCACAUCUUUU 20 1447 antiSACas9-383 + GAGGUCGAUCAUAUUAUCCC 20 1448 antiSACas9-384 + UCGAACAGAUUAGUAAUCUG 20 1449 antiSACas9-385 + CAAUGAUCUGCUGAACCGCA 20 1450 antiSACas9-386 + CCUGACUAUCUACCAGAGCU 20 1451 antiSACas9-387 + ACGAGAAACUGGAAUACUAU 20 1452 antiSACas9-388 + CGCAGGCGUCAGACUGUUCA 20 1453 antiSACas9-389 - AUUCCUUGAUGUCUUUCCAU 20 1454 antiSACas9-390 + CCGGCAGACCAAUGAACGCA 20 1455 antiSACas9-391 + AGAAUCUGGAUGUCAUCAAA 20 1456 antiSACas9-392 + UGCUAAGGAGAUCCUGGUCA 20 1457 antiSACas9-393 - AGUACUUGAUCUUCUUGAUC 20 1458 antiSACas9-394 + AUAUCAUUAUCGAGCUGGCU 20 1459 antiSACas9-395 + AAAUCAAGCUGCACGAUAUG 20 1460 antiSACas9-396 + CAGAGCUGCAGCUGGAACGG 20 1461 antiSACas9-397 + GAACCCACUGUAUAAGUACU 20 1462 antiSACas9-398 - UGAUCACUUUGAUGCUCUGG 20 1463 antiSACas9-399 + GCUGAACAAUCCAUUCAACU 20 1464 antiSACas9-400 + CAUCUUUUCUGAGGCGCAAA 20 1465 antiSACas9-401 + GCCGCAUCAGCAAGACCAAA 20 1466 antiSACas9-402 + AUCAGAAACUGAAGCUGAUU 20 1467 antiSACas9-403 + AUCCUCAGACAUAUCAGAAA 20 1468 antiSACas9-404 + ACGCAGGCGUCAGACUGUUC 20 1469 antiSACas9-405 - CCUUGUUGUUAAAGGAAUUG 20 1470 antiSACas9-406 + CUCACGCAAUAGCAAAGCUC 20 1471 antiSACas9-407 + CAAAUGCCGACUUCAUCUUU 20 1472 antiSACas9-408 + UUAUGGAGCAGUACGGCGAC 20 1473 antiSACas9-409 - GCUUUUUCCACUCCUUAAAG 20 1474 antiSACas9-410 + UCAUCGAAAACGUGUUUAAG 20 1475 antiSACas9-411 + CCAGGGUGAAAGGCCUGAGU 20 1476 antiSACas9-412 - GGUUAAUAAAAUCCUUCUGG 20 1477 antiSACas9-413 + ACAAGGUGGUCAAGCUGUCA 20 1478 antiSACas9-414 + GAGAACCUACUAUGAGGGAC 20 1479 antiSACas9-415 + CAAAGGGUACAAGCACCAUG 20 1480 antiSACas9-416 + AACGUGGAAAACAAUGAGGG 20 1481 antiSACas9-417 + UUCUGGGAAACCUGUAUGAG 20 1482 antiSACas9-418 + UGAGGGACGGAGAAGCAAGA 20 1483 antiSACas9-419 + CAAGACAAGCGACUACGUCA 20 1484 antiSACas9-420 + GGAGCCAGGCGCCUGAAACG 20 1485 antiSACas9-421 + ACAUCAACAGAUUCUCCGUC 20 1486 antiSACas9-422 - UGAACUAGACAGGUACUGGA 20 1487 antiSACas9-423 + CUACACUGAAACAGAUUGCU 20 1488 antiSACas9-424 + GACGGAGAAGGCACAGAAUC 20 1489 antiSACas9-425 - CUUUUUGAUACUCUGAGUCU 20 1490 antiSACas9-426 + UGGACAAAGCCAAGAAAGUG 20 1491 antiSACas9-427 + AUUCUGUCACCCGUGGUCAA 20 1492 antiSACas9-428 + AUAGUACAAGAAAAGACGAU 20 1493 antiSACas9-429 + CCUGAACAGCGAGCUGACCC 20 1494 antiSACas9-430 - GAGGCAAUUGUUUUGAUAAU 20 1495 antiSACas9-431 - AAUCAGGUCGUUGUUGUAAA 20 1496 antiSACas9-432 - GCAAUUGUUUUGAUAAUUCG 20 1497 antiSACas9-433 + GGCGCAAAUGGAAGUUUAAA 20 1498 antiSACas9-434 + UCGAGACAGAACAGGAGUAC 20 1499 antiSACas9-435 + CCAAGCAGCUGC U G AA AG U G 20 1500 antiSACas9-436 + UGGACAUCGGGAUUACAAGC 20 1501 antiSACas9-437 + GAAGGCACAGAAUCCAGAGG 20 1502 antiSACas9-438 + UAAGGAGAUCCUGGUCAACG 20 1503 antiSACas9-439 - UAAUCAGGUCGUUGUUGUAA 20 1504 antiSACas9-440 - GGAUUGUUCAGCAGGUCCUC 20 1505 antiSACas9-441 + GCAUAACGUCAAUGAGGUGG 20 1506 antiSACas9-442 + GGAGACUCGGAGAACCUACU 20 1507 antiSACas9-443 + CCUGAGUCAGAAGCUGUCAG 20 1508 antiSACas9-444 + UGCCCGAAAUCGAGACAGAA 20 1509

Example 2: Efficacy of governing gRNAs targeting Cas9 co-transfected with a gRNA targeting VEGF in 293T cells

In this study, 293T cells (120,000 cells per well in a 24 well plate) were transfected with 750 ng of a plasmid expressing epitope-tagged (3X Flag-tagged) S. pyogenes Cas9 together with 125 ng of a construct expressing a gRNA targeting the VEGF gene (gRNA sequence

GGTGAGUGAGUGUGUGCGUG (SEQ ID NO: 1510), see the 20mer of VEGFA Site 3 (Target Site 3) from Figure Id of Fu et al, Improving CIRSPR-Cas nuclease specificity using truncated guide RNAs. Nat Biotechnol 32, 279-284 (2014)). Simultaneously, the cells were transfected with 125 ng of one of three gRNA expression constructs: a construct expressing a gRNA targeting the CCR5 gene (serving as a control), a construct expressing governing gRNA anti-SPCas9-175 (see Example 1) targeting S. pyogenes Cas9, or a construct expressing governing gRNA anti-SPCas9- 1 (see Example 1) targeting S. pyogenes Cas9. Cells were harvested for analysis one day, two days, three days, six days and nine days after transfection.

To quantify mutation rates of the endogenous VEGF and plasmid-borne Cas9 genes, total genomic DNA was isolated at each time point, and regions encompassing the VEGF gRNA and Cas9 governing gRNA targeting sequences were amplified by PCR. Amplified PCR products were denatured and re-annealed, followed by treatment with T7E1 nuclease. Mutation rates (indel frequency) were measured using a capillary electrophoresis instrument as described in Reyon, D. et al, FLASH assembly of TALENs for high-throughput genome editing. Nat

Biotechnol 30, 460-465 (2012). Mutation frequencies (% indels+standard deviation) of VEGF and Cas9 for the three treatment groups are shown in Table E-13. These results confirm that both Cas9-targeted governing gRNAs induce mutations in the Cas9 gene, and that the endogenous VEGF locus is mutated to a similar extent in the presence or absence of a co- transfected Cas9-targeted governing gRNA.

To assess levels of Cas9 protein during the time course of the experiment, total protein lysates were prepared from each treatment group at each time point. Protein samples (15 ug) were separated by SDS-PAGE, blotted to PVDF membrane, and probed with an antibody specific for the 3XFlag epitope tag. An antibody specific for cytoskeletal actin was used as a loading control. As shown in FIG. 7, co-transfection with each of the Cas9-targeted governing gRNAs leads to reduced levels of Cas9 protein, especially at six and nine days following transfection.

Table E-13. VEGF and Cas9 mutation rates

Example 3: Activity comparison of S. aureus gRNAs of various lengths

In this study, HEK-293T cells stably expressing GFP were co-transfected with constructs expressing gRNAs with targeting domains of various lengths (from 15-20 nucleotides) together with a construct expressing S. aureus Cas9. The gRNAs targeted several different genes: VEGF (total of 22 gRNAs), CCR5 (total of 15 gRNAs) and GFP (total of 10 gRNAs). The targeting domains of all the tested gRNAs initiated with a G nucleotide, and all of the gRNA target sites were associated with NNGRRT PAM sequences.

To quantify activity of the VEGF and CCR5 targeting gRNAs, total genomic DNA was isolated from cells two days following transfection and regions encompassing the VEGF and CCR5 gRNA target sites were amplified by PCR. Amplified PCR products were denatured and re-annealed, followed by treatment with T7E1 nuclease. Mutation rates (indel frequency) were measured using a capillary electrophoresis instrument as described in Reyon, D. et ah, FLASH assembly of TALENs for high-throughput genome editing. Nat Biotechnol 30, 460-465 (2012). To quantify activity of the GFP targeting gRNAs, cells were harvested three days following transfection and the percentage of GFP-negative cells (indicating mutation of the GFP gene) were measured by flow cytometry. The mean activity of all gRNAs of each targeting domain length was calculated and compared to the mean activity of the gRNAs with 20 nucleotide targeting domains. As shown in Table E-14, gRNAs with shorter targeting domains have lower average activity than those with 20 nucleotide targeting domains.

Table E-14. Mean activity of S. aureus gRNAs with various length targeting domains compared to gRNAs with 20 nucleotide targeting domains.

18 0.244 0.087

17 0.028 0.014

16 0.012 0.005

15 0.005 0.004

INCORPORATION BY REFERENCE

All publications, patents, and patent applications mentioned herein are hereby incorporated by reference in their entirety as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated by reference. In case of conflict, the present application, including any definitions herein, will control.

EQUIVALENTS

Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. While this invention has been disclosed with reference to specific aspects, it is apparent that other aspects and variations of this invention may be devised by others skilled in the art without departing from the true spirit and scope of the invention. The appended claims are intended to be construed to include all such aspects and equivalent variations.

Other embodiments are within the following claims.

Claims

CLAIMS What is claimed is:

1. A gRNA molecule that targets a Cas9 molecule.

2. The gRNA molecule of claim 1, wherein the gRNA molecule targets a nucleic acid sequence that encodes the Cas9 molecule, wherein the nucleic acid sequence that encodes the Cas9 molecule comprises one or more of: a sequence encoding the amino acid sequence of the Cas9 molecule, a sequence encoding the amino acid sequence of the Cas9 molecule comprising non- translated sequence, or a sequence encoding the amino acid sequence of the Cas9 molecule comprising non-transcribed sequence.

3. The gRNA molecule of claims 1 or 2, wherein the Cas9 molecule is an eaCas9 molecule.

4. The gRNA molecule of claims 1 or 2, wherein the Cas9 molecule is an eiCas9 molecule.

5. The gRNA molecule of any of claims 1-4, wherein the gRNA molecule is configured to provide a Cas9 molecule-mediated cleavage event in the nucleic acid sequence that encodes the Cas9 molecule.

6. The gRNA molecule of any of claims 1-5, wherein the gRNA molecule comprises a targeting domain configured to provide a Cas9 molecule-mediated cleavage event in the nucleic acid sequence that encodes the Cas9 molecule.

7. The gRNA molecule of any of claims 1-6, wherein the gRNA molecule:

targets the Cas9 molecule-amino acid coding sequence of the nucleic acid sequence; is configured to provide a Cas9 molecule-mediated cleavage event in the Cas9 molecule- amino acid coding sequence of the nucleic acid sequence; or

8. The gRNA molecule of any of claims 1-6, wherein the gRNA molecule:

targets a non-coding sequence of the nucleic acid sequence;

9. The gRNA molecule of any of claims 1-6, wherein the gRNA molecule:

targets an untranslated sequence of the nucleic acid sequence;

comprises a targeting domain configured to provide a Cas9 moleucle-mediated cleavage event in an untranslated sequence of the nucleic acid sequence.

10. The gRNA molecule of any of claim 1-6, wherein the gRNA molecule:

11. The gRNA molecule of any of claim 1-6, wherein the gRNA molecule:

12. The gRNA molecule of any of claims 1-6, wherein the gRNA molecule:

targets the promoter region of the nucleic acid sequence, is configured to provide a Cas9 molecule-mediated cleavage event in the promoter region of nucleic acid sequence; or

wherein the promoter region is functionally linked to the Cas9 molecule amino acid coding region

13. The gRNA molecule of any of claims 1-6, wherein the gRNA molecule:

targets Cas9 molecule intronic sequence of the nucleic acid sequence;

14. The gRNA molecule of any of claims 1-13, wherein the Cas9 molecule is a S. pyogenes Cas9 molecule.

15. The gRNA molecule of any of claims 1-13, wherein the Cas9 molecule is a S. aureus Cas9 molecule.

16. The gRNA molecule of any of claim 1-15, wherein the gRNA is a chimeric gRNA.

17. The gRNA molecule of any of claim 1-15, wherein the gRNA is a modular gRNA.

18. A nucleic acid comprising a sequence that encodes a governing gRNA molecule.

19. The nucleic acid of claim 18, wherein the governing gRNA molecule comprises a Cas9 molecule-targeting gRNA molecule.

20. A nucleic acid comprising a sequence that encodes a gRNA molecule of any of claims 1-17.

21. The nucleic acid of claim 20, wherein the nucleic acid is purified.

22. A vector comprising the nucleic acid of any of claims 18-21.

23. The vector of claim 22, wheren the vector is a viral vector.

24. The vector of claim 23, wherein the viral vector is an AAV vector.

25. A nucleic acid comprising:

a) a first nucleic acid sequence that encodes a governing gRNA molecule; and b) a second nucleic acid sequence that encodes a Cas9 molecule.

26. The nucleic acid of claim 25, wherein the governing gRNA molecule comprises a Cas9 molecule-targeting gRNA molecule.

27. The nucleic acid of claim 26, wherein the Cas9 molecule-targeting gRNA molecule targets the second nucleic acid sequence that encodes the Cas9 molecule.

28. The nucleic acid of any of claims 25-27, wherein the Cas9 molecule is an eaCas9 molecule.

29. The nucleic acid of any of claims 25-27, wherein the Cas9 molecule is an eiCas9 molecule.

30. The nucleic acid of any of claims 25-29, wherein the gRNA molecule is configured to provide a Cas9 molecule-mediated cleavage event in the second nucleic acid sequence.

31. The nucleic acid of any of claim 25-30, wherein the gRNA molecule comprises a targeting domain configured to provide a Cas9 molecule-mediated cleavage event in the second nucleic acid sequence.

32. The nucleic acid of any of claim 25-31, wherein the gRNA molecule is a gRNA molecule of any of claims 7-19 and targets the second nucleic acid sequence.

33. The nucleic acid of any of claims 25-32, wherein component a) and component b) are provided on the same nucleic acid molecule.

34. The nucleic acid of any of claims 25-32, wherein component a) and component b) are provided on different nucleic acid molecules.

35. The nucleic acid of any of claims 25-34, configured such that a Cas9-targeting gRNA transcribed from the nucleic acid forms a complex with a Cas9 molecule produced from the nucleic acid.

36. The nucleic acid of claim 35, wherein the complex is capable of inactivating the nucleic acid sequence that comprises or encodes the Cas9 molecule sequence.

37. The nucleic acid of claim 36, wherein the inactivating comprises cleaving.

38. The nucleic acid of any of claims 25-37, wherein the first nucleic acid sequence is under the control of a first control region and the second nucleic acid sequence is under the control of a second control region and the first and second control regions are different.

39. The nucleic acid of claim 38, wherein one of the first and second control regions is a constitutive promoter and one is an inducible promoter.

40. The nucleic acid of any of claims 25-39, wherein the first nucleic acid sequence and the second nucleic acid sequence are differentially expressed.

41. The nucleic acid of claim 40, wherein the differential expression is differential expression in terms of level of expression or temporal differential expression.

42. The nucleic acid of any of claims 25-41, further comprising: c) a third nucleic acid sequence that encodes a second gRNA molecule comprising a targeting domain which is complementary with a target nucleic acid, wherin the second gRNA does not target b).

43. The nucleic acid of claim 42, wherein

the first nucleic acid sequence is under the control of a first control region;

the second nucleic acid sequence is under the control of a second control region; and the third nucleic acid sequence is under the control of a third control region, wherein, the first control region is different from the second and/or the third control region.

44. The nucleic acid of any of claims 25-43, further comprising a template nucleic acid sequence.

45. The nucleic acid of any of claims 25-44, wherein the nucleic acid is purified.

46. A vector comprising a nucleic acid of any of claims 25-45.

47. The vector of claim 46, wheren the vector is a viral vector.

48. The vector of claim 47, wherein the viral vector is an AAV vector.

49. A composition, comprising:

a) a governing gRNA molecule or a nucleic acid that encodes a governing gRNA molecule.

50. The composition of claim 49, comprising one or more of;

b) a Cas9 molecule or a nucleic acid sequence that encodes the Cas9 molecule;

c) a second gRNA molecule or a nucleic acid encoding the second gRNA molecule; and d) a template nucleic acid.

51. The composition of claim 49 or 50, wherein the governing gRNA molecule comprises a Cas9 molecule-targeting gRNA molecule.

52. The composition of claim 51, wherein the Cas9 molecule-targeting gRNA comprises a gRNA molecule of any of claims 1-17.

53. The composition of any of claims 50-52, wherein the governing gRNA molecule is configured to provide a Cas9 molecule-mediated cleavage event in the nucleic acid sequence that encodes the Cas9 molecule.

54. The composition of any of claims 49-53, comprising a Cas9 molecule-targeting gRNA molecule and a nucleic acid encoding the Cas9 molecule.

55. The composition of any of claims 49-54, comprising a Cas9 molecule-targeting gRNA molecule and the Cas9 molecule.

56. The composition of any of claims 49-55, further comprising:

c) a second gRNA molecule or a nucleic acid encoding the second gRNA molecule.

57. The composition of claim 56, wherein the second gRNA targets a Cas9 molecule to a target nucleic acid.

58. The composition of any of claims 49-57, further comprising:

d) a template nucleic acid.

59. The composition of claim 58, wherein the template nucleic acid is configured to mediate repair of a break positioned by the second gRNA.

60. The composition of any of claims 49-59, wherein each of a), b), c) and d) is present as a nucleic acid and are encoded on the same nucleic acid molecule.

61. The composition of any of claims 49-60, wherein a first sequence selected from a), b), c) and d) is encoded on a first nucleic acid molecule and a second sequence selected from a), b), c), and d) is encoded on a second nucleic acid molecule.

62. A pharmaceutical preparation comprising:

a gRNA molecule of any of claims 1-17;

a nucleic acid of any of claims 18-21 or 25-45;

a vector of any of claims 22-24 or 46-48; or

a composition of any of claims 49-61.

63. A cell comprising:

a gRNA molecule of any of claims 1-17;

a nucleic acid of any of claims 18-21 or 25-45;

a vector of any of claims 22-24 or 46-48; or

a composition of any of claims 49-61.

64. The cell of claim 63, comprising:

a nucleic acid sequence that encodes the Cas9 molecule, wherein the sequence that encodes the Cas9 molecule comprises one or more of: a sequence encoding the amino acid sequence of the Cas9 molecule, a sequence encoding the amino acid sequence of the Cas9 molecule comprising non-translated sequence, and a sequence encoding the amino acid sequence of the Cas9 molecule comprising non-transcribed sequence; and

a governing gRNA molecule.

65. The cell of claim 64, wherein the governing gRNA molecule comprises a gRNA molecule that targets the nucleic acid sequence that encode the Cas 9 molecule.

66. The cell of any of claims 63-65, wherein the gRNA molecule is a gRNA molecule of any of claims 1-19.

67. The cell of any of claims 63-66, further comprising a Cas9 molecule.

68. The cell of any of claims 63-67, further comprising a second gRNA molecule or a nucleic acid encoding the second gRNA molecule.

69. The cell of claim 68, wherein the second gRNA targets a Cas9 molecule to a target nucleic acid.

70. The cell of any of claims 63-69, further comprising: a template nucleic acid.

71. The cell of claim 70, wherein the template nucleic acid is configured to mediate repair of a break in the target nucleic acid positioned by the second gRNA molecule.

72. The cell of any of claims 68-71, comprising a target nucleic acid cleaved by second gRNA molecule mediated targeting of the Cas9 molecule.

73. The cell of any of claim 63-72, comprising a target nucleic acid that has been cleaved and repaired.

74. The cell of claim 73, wherein the repair comprises template nucleic acid mediated repair.

75. The cell of any of claims 63-74, wherein the nucleic acid sequence encoding the Cas9 molecule has not been cleaved.

76. The cell of any of claims 75, wherein the nucleic acid sequence encoding the Cas9 molecule expresses Cas9 molecule.

77. The cell of any of claims 63-74, wherein the nucleic acid sequence encoding the Cas9 molecule has been cleaved by gRNA mediated targeting of Cas 9 molecule.

78. The cell of claim 77, wherein the cleaved nucleic acid sequence encoding the Cas9 molecule has reduced ability to express Cas 9 molecule, as compared to the same molecule not having been cleaved.

79. The cell of claim 77, wherein the cleaved nucleic acid sequence encoding the Cas9 molecule is substantially incapable of expressing Cas 9 molecule.

80. The cell of claim 79, comprising:

a cleaved nucleic acid sequence encoding the Cas9 molecule; and

a target nucleic acid having a repaired Cas9 molecule-mediated cleavage event.

81. The cell of any of claims 63-80, wherein the cell is a vertebrate, mammalian, rodent, goat, pig, bird, chicken, turkey, cow, horse, sheep, fish, primate, or human cell.

82. The cell of any of claims 63-80, wherein the cell is a plant cell.

83. The cell of claim 82, wherein the plant cell is a monocot or a dicot.

84. The cell of any of claims 63-80, wherein the cell is a human cell.

85. The cell of claim 81, wherein the cell is a somatic cell, germ cell, or prenatal cell.

86. The cell of claim 81, wherein the cell is a zygotic, blastocyst or embryonic cell, a stem cell, a mitotically competent cell, a meiotically competent cell.

87. A method of altering a cell or a target nucleic acid of a cell, comprising contacting the cell with an effective amount of:

a gRNA molecule of any of claims 1-17;

a nucleic acid of any of claims 18-21 or 25-45;

a vector of any of claims 22-24 or 46-48; or

a composition of any of claims 49-61.

88. The method of claim 87, wherein the altering comprises altering the structure of the target nucleic acid.

89. The method of claim 88, wherein the altering comprises altering the sequence of the target nucleic acid.

90. A method of treating a subject, the method comprising contacting a cell or a subject, with an effective amount of:

a gRNA molecule of any of claims 1-17;

a nucleic acid of any of claims 18-21 or 25-45;

a vector of any of claims 22-24 or 46-48; or

a composition of any of claims 49-61.

91. The method of claim 90, comprising altering the structure of a target nucleic acid in the cell or the subject.

92. The method of claim 91, comprising altering the sequence of the target nucleic acid.

93. The method of any of claims 87-92, wherein the cell is a vertebrate, mammalian, rodent, goat, pig, bird, chicken, turkey, cow, horse, sheep, fish, primate, or human cell.

94. The method of any of claims 87-92, wherein the cell is a plant cell.

95. The method of claim 94, wherein the plant cell is a monocot or a dicot.

96. The method of any of claims 87-92, wherein the cell is a human cell.

97. The method of claim 93, wherein the cell is a somatic cell, germ cell, or prenatal cell.

98. The method of claim 93, wherein the cell is a zygotic, blastocyst or embryonic cell, a stem cell, a mitotically competent cell, a meiotically competent cell.

99. The method of any of claims 90-99, wherein the subject is a mammal, primate, or human.

100. The method of any of claims 87-99, wherein the target nucleic acid is a chromosomal nucleic acid.

101. A reaction mixture comprising a cell and:

a gRNA molecule of any of claims 1-17;

a nucleic acid of any of claims 18-21 or 25-45;

a vector of any of claims 22-24 or 46-48; or

a composition of any of claims 49-61.

102. A kit comprising:

a gRNA molecule of any of claims 1-17;

a nucleic acid of any of claims 18-21 or 25-45;

a vector of any of claims 22-24 or 46-48; or

a composition of any of claims 49-61.