Compositions and methods of nucleic acid-targeting nucleic acids

A method for detecting if two complexes are in proximity to one another comprising:

• providing a first complex, wherein the first complex comprises a first site-directed polypeptide comprising a first non-native sequence that comprises a first portion of an endonuclease split system and a first nucleic acid-targeting nucleic acid comprising a first nucleic acid sequence complementary to a first target nucleic acid, wherein the first complex contacts the first target nucleic acid;
• providing a second complex, wherein the second complex comprises a second site-directed polypeptide comprising a second non-native sequence that comprises a second portion of an endonuclease split system and a second nucleic acid-targeting nucleic acid comprising a second nucleic acid sequence complementary to a second target nucleic acid, wherein the second complex contacts the second target nucleic acid;
• and
• detecting an interaction between the first portion and the second portion, wherein (i) the endonuclease split system forms an active endonuclease when the first portion of the endonuclease split system and the second portion of the endonuclease split system are in proximity, (ii) the interaction results in cleavage of the first target sequence and the second target sequence by the active endonuclease, and (iii) the detecting indicates the first complex and the second complex are in proximity to one another.