Methods for cleaving dna and rna molecules

A genetically modified cell comprising at least one exogenous coding region encoding

• a) a CRISPR-RNA (crRNA), wherein the crRNA is a single stranded RNA comprising:
• a tag region comprising at least 5 to no greater than 12 nucleotides, and a guide region comprising a nucleotide sequence of at least 15 nucleotides, wherein the tag region is immediately upstream of the guide region;
• or
• b) a Cmr complex, wherein the Cmr complex comprises at least 4 proteins comprising Cmr2, Cmr3, Cmr4, and Cmr5,
• wherein the Cmr2 protein comprises a mutation of the HD superfamily hydrolase domain to reduce RNA-activated DNAse activity of the Cmr complex.

A method for determining whether a predetermined RNA is present or absent in a sample, comprising:

• incubating a composition with a sample,
• wherein the composition comprises
• a) a CRISPR-RNA (crRNA), wherein the crRNA is a single stranded RNA comprising:
• a tag region comprising at least 5 to no greater than 12 nucleotides, and a guide region comprising a nucleotide sequence of at least 15 nucleotides, wherein the tag region is immediately upstream of the guide region;
• b) a Cmr complex, wherein the Cmr complex comprises at least 4 proteins comprising Cmr2, Cmr3, Cmr4, and Cmr5,
• c) a substrate DNA,
• wherein the sample is suspected of including a predetermined RNA that comprises a nucleotide sequence that is substantially complementary to at least a portion of the guide region of the crRNA, and
• wherein the incubating comprises incubating the sample under suitable conditions for cleavage of the substrate DNA when the predetermined RNA is present.

A method for cleaving a predetermined RNA molecule, comprising:

• incubating a composition with a sample,
• wherein the composition comprises
• a) a CRISPR-RNA (crRNA), wherein the crRNA is a single stranded RNA comprising:
• a tag region comprising at least 5 to no greater than 12 nucleotides, and a guide region comprising a nucleotide sequence of at least 15 nucleotides, wherein the tag region is immediately upstream of the guide region;
• b) a Cmr complex, wherein the Cmr complex comprises at least 6 proteins comprising Cmr1, Cmr2, Cmr3, Cmr4, Cmr5, and Cmr6,
• wherein the sample is suspected of comprising a predetermined RNA molecule that comprises a nucleotide sequence that is substantially complementary to at least a portion of the guide region of the crRNA,
• wherein the Cmr2 protein comprises a mutation that reduces RNA-activated DNAse activity of the Cmr complex, and
• wherein the incubating comprises incubating the sample under suitable conditions for cleavage of the predetermined RNA molecule.