Methods and compositions for detection of specific nucleotide sequences

A method for detecting specific nucleic acid sequences, comprising

• a) obtaining isolated nucleic acid sequences from a sample suspected of containing a target nucleic acid sequence;
• b) contacting a target-protection molecule that specifically binds to the target nucleic acid sequence with the nucleic acid sequences of step a) under hybridizing conditions sufficient to form a protected target nucleic acid sequence (PNAS);
• c) digesting the isolated nucleic acids containing one or more PNAS of step b) with enzymes to form a PNAS structure having at least one 5' single-stranded region generated by enzymatic digestion (PNAS/tail);
• e) hybridizing a capture molecule to a single-stranded region of the PNAS/tail;
• f) hybridizing a reporter molecule to a single-stranded region of the PNAS/tail;
• and
• g) detecting the PNAS/tail as indicative of the presence of the target nucleic acid sequence.