CASZ COMPOSITIONS AND METHODS OF USE

1 . A method of guiding a class 2 CRISPR/Cas endonuclease to a target sequence of a target nucleic acid, the method comprising contacting the target nucleic acid with a non-naturally occurring complex comprising:

(a) the class 2 CRISPR/Cas endonuclease, wherein the class 2 CRISPR/Cas endonuclease has a length of 350-900 amino acids and includes 3 partial RuvC subdomains that are not contiguous with respect to the primary amino acid sequence of the protein, but form a RuvC domain when the protein is produced and folds; and

(b) a guide RNA that comprises a guide sequence that hybridizes to a target sequence of the target nucleic acid and comprises a region that binds to the class 2 CRISPR/Cas endonuclease.

2 . The method of claim 1 , wherein the method results in modification of the target nucleic acid, modulation of transcription from the target nucleic acid, or modification of a polypeptide associated with a target nucleic acid,

3 . The method of claim 2 , wherein the target nucleic acid is modified by being cleaved.

4 . The method of claim 1 , wherein the target nucleic acid is selected from: double stranded DNA, single stranded DNA, RNA, genomic DNA, and extrachromosomal DNA.

5 . The method of claim 1 , wherein the guide sequence and the region that binds to the class 2 CRISPR/Cas endonuclease are heterologous to one another.

6 . The method of claim 1 , wherein said contacting results in genome editing.

7 . The method of claim 1 , wherein said contacting takes place:

a) outside of a bacterial cell and outside of an archaeal cell; or

b) in vitro outside of a cell; or

c) inside of a target cell.

8 . The method of claim 7 , wherein said contacting comprises: introducing into the target cell at least one of:

(a) the class 2 CRISPR/Cas endonuclease, or a nucleic acid encoding the class 2 CRISPR/Cas endonuclease; and

(b) the guide RNA, or a nucleic acid encoding the guide RNA.

9 . The method of claim 8 , wherein the nucleic acid encoding the class 2 CRISPR/Cas endonuclease is a non-naturally occurring sequence that is codon optimized for expression in the target cell.

10 . The method of claim 7 , wherein the target cell is a eukaryotic cell.

11 . The method of claim 7 , wherein the target cell is:

a) in culture in vitro; or

b) in vivo; or

c) ex vivo.

12 . The method of claim 10 , wherein the eukaryotic cell is selected from the group consisting of: a plant cell, a fungal cell, a single cell eukaryotic organism, a mammalian cell, a reptile cell, an insect cell, an avian cell, a fish cell, a parasite cell, an arthropod cell, a cell of an invertebrate, a cell of a vertebrate, a rodent cell, a mouse cell, a rat cell, a primate cell, a non-human primate cell, and a human cell.

13 . The method of claim 7 , wherein said contacting further comprises: introducing a DNA donor template into the target cell.

14 . The method of claim 1 , wherein the method comprises contacting the target nucleic acid with a transactivating noncoding RNA (trancRNA).

15 . A composition comprising a non-naturally occurring complex comprising:

(a) a class 2 CRISPR/Cas endonuclease, or a nucleic acid encoding said class 2 CRISPR/Cas endonuclease; and

(b) a guide RNA, or a nucleic acid encoding said guide RNA, wherein said guide RNA comprises a guide sequence that is complementary to a target sequence of a target nucleic acid, and comprises a region that can bind to the class 2 CRISPR/Cas endonuclease;

wherein the class 2 CRISPR/Cas endonuclease:

i) has a length of 350-900 amino acids;

ii) includes 3 partial RuvC subdomains that are not contiguous with respect to the primary amino acid sequence of the protein, but form a RuvC domain when the protein is produced and folds; and

iii) interacts with the guide RNA to form a ribonucleoprotein complex that is targeted to the target sequence via base pairing between the guide RNA and the target sequence.

16 . The composition of claim 15 , further comprising a transactivating noncoding RNA (trancRNA), or a nucleic acid encoding said trancRNA.

17 . A kit comprising a non-naturally occurring complex comprising:

(a) a class 2 CRISPR/Cas endonuclease, or a nucleic acid encoding said class 2 CRISPR/Cas endonuclease; and

(b) a guide RNA, or a nucleic acid encoding said guide RNA, wherein said guide RNA comprises a guide sequence that is complementary to a target sequence of a target nucleic acid, and comprises a region that can bind to the class 2 CRISPR/Cas endonuclease;

wherein the class 2 CRISPR/Cas endonuclease:

i) has a length of 350-900 amino acids;

ii) includes 3 partial RuvC subdomains that are not contiguous with respect to the primary amino acid sequence of the protein, but form a RuvC domain when the protein is produced and folds; and

iii) interacts with the guide RNA to form a ribonucleoprotein complex that is targeted to the target sequence via base pairing between the guide RNA and the target sequence.

18 . The kit of claim 17 , further comprising a transactivating noncoding RNA (trancRNA), or a nucleic acid encoding said trancRNA.

19 . A genetically modified eukaryotic cell, comprising:

(a) a class 2 CRISPR/Cas endonuclease, or a nucleic acid encoding said class 2 CRISPR/Cas endonuclease; and

(b) a guide RNA, or a nucleic acid encoding said guide RNA, wherein said guide RNA comprises a guide sequence that is complementary to a target sequence of a target nucleic acid, and comprises a region that can bind to the class 2 CRISPR/Cas endonuclease;

wherein the class 2 CRISPR/Cas endonuclease:

i) has a length of 350-900 amino acids;

ii) includes 3 partial RuvC subdomains that are not contiguous with respect to the primary amino acid sequence of the protein, but form a RuvC domain when the protein is produced and folds; and

iii) interacts with the guide RNA to form a ribonucleoprotein complex that is targeted to the target sequence via base pairing between the guide RNA and the target sequence.

20 . The eukaryotic cell of claim 19 , further comprising a transactivating noncoding RNA (trancRNA), or a nucleic acid encoding said trancRNA.

21 . A method of detecting a target DNA in a sample, the method comprising:

(a) contacting the sample with:

(i) a class 2 CRISPR/Cas endonuclease, wherein the class 2 CRISPR/Cas endonuclease has a length of 350-900 amino acids and includes 3 partial RuvC subdomains that are not contiguous with respect to the primary amino acid sequence of the protein, but form a RuvC domain when the protein is produced and folds;

(ii) a guide RNA comprising: a region that binds to the class 2 CRISPR/Cas endonuclease, and a guide sequence that hybridizes with the target DNA; and

(iii) a detector DNA that is single stranded and does not hybridize with the guide sequence of the guide RNA; and

(b) measuring a detectable signal produced by cleavage of the single stranded detector DNA by the class 2 CRISPR/Cas endonuclease, thereby detecting the target DNA.

22 . A kit for detecting a target DNA in a sample, the kit comprising:

(a) a guide RNA, or a nucleic acid encoding the guide RNA; wherein the guide RNA comprises: a region that binds to a class 2 CRISPR/Cas endonuclease, and a guide sequence that is complementary to a target DNA;

(b) a labeled detector DNA that is single stranded and does not hybridize with the guide sequence of the guide RNA; And

(c) the class 2 CRISPR/Cas endonuclease, wherein the class 2 CRISPR/Cas endonuclease:

i) has a length of 350-900 amino acids;

ii) includes 3 partial RuvC subdomains that are not contiguous with respect to the primary amino acid sequence of the protein, but form a RuvC domain when the protein is produced and folds; and

iii) interacts with the guide RNA to form a ribonucleoprotein complex that is targeted to the target sequence via base pairing between the guide RNA and the target sequence.

23 . A method of cleaving single stranded DNAs (ssDNAs), the method comprising:

contacting a population of nucleic acids, wherein said population comprises a target DNA and a plurality of non-target ssDNAs, with:

(i) a class 2 CRISPR/Cas endonuclease, wherein the class 2 CRISPR/Cas endonuclease has a length of 350-900 amino acids and includes 3 partial RuvC subdomains that are not contiguous with respect to the primary amino acid sequence of the protein, but form a RuvC domain when the protein is produced and folds; and

(ii) a guide RNA comprising: a region that binds to the class 2 CRISPR/Cas endonuclease, and a guide sequence that hybridizes with the target DNA,

wherein the class 2 CRISPR/Cas endonuclease cleaves non-target ssDNAs of said plurality.