Methods and compositions for detecting polynucleotides and fragments thereof

A method for detecting a target polynucleotide having a length of about 10 to about 250 nucleotides, comprising:

• a. hybridizing the target polynucleotide with a target specific oligonucleotide (TSO)
• to produce a TSO-hybridized target polynucleotide, wherein the TSO comprises:
• i. a first TSO region that hybridizes to a first target polynucleotide region;
• ii. a second TSO region that hybridizes to a second target polynucleotide region;
• and
• iii. a third TSO region that hybridizes to a third target polynucleotide region;
• wherein the second TSO region connects the first and third TSO regions;
• and wherein upon hybridization of the TSO to the target polynucleotide, the first and third of target polynucleotide regions become substrates for cleavage by a cleaving agent, and the second target polynucleotide region is not a substrate for cleavage by the cleaving agent;
• b. cleaving the target polynucleotide at a first site within the first target polynucleotide region and a second site within the third target polynucleotide region to generate a TSO-hybridized processed target polynucleotide,
• c. amplifying the TSO-hybridized processed target polynucleotide to produce an amplified processed polynucleotide, wherein amplifying the TSO-hybridized processed target polynucleotide comprises circularizing the processed target polynucleotide to produce a circular processed target polynucleotide and amplifying the circular processed target polynucleotide:
• and
• d. detecting the amplified processed polynucleotide, thereby detecting the target polynucleotide.