Detection of nucleic acid sequences using endonuclease

A method of detecting a nucleic acid sequence, comprising:

• creating a plurality of double-stranded nucleic acids by hybridizing a plurality of single-stranded nucleic acids within a sample with a plurality of probe nucleic acids, each double-stranded nucleic acid of the plurality of double-stranded nucleic acids comprising a first strand including one of the single-stranded nucleic acids of the plurality of single-stranded nucleic acids within the sample and second strand including one of the plurality of probe nucleic acids;
• exposing the plurality of double-stranded nucleic acids to a digestive protein, the digestive protein comprising an endonuclease domain functionally equivalent to SEQ ID NO:1, wherein said exposure digests at least one of the first strand and the second strand of a double-stranded nucleic acid of the plurality of double-stranded nucleic acids comprising at least one of a bulge and a Y-junction;
• and
• detecting a presence of the plurality of double-stranded nucleic acids following said exposure to the digestive protein.