Snap-back primers and detectable hairpin structures

A kit for forming an invasive cleavage structure from a target nucleic acid, selected from the group consisting of:

• I) a first kit, comprising a snap-back primer and a reverse primer configured to amplify a target sequence, and a downstream probe,
• wherein said snap-back primer comprises:
• i) a 3′ region configured to hybridize to said target nucleic acid such that it can be extended by a polymerase to generate a first amplification product, and
• ii) a 5′ region configured to not hybridize to said target nucleic when said 3′ region of said snap-back primer is hybridized to said target nucleic acid;
• wherein said reverse primer comprises a 3′ region configured to hybridize to said first amplification product such that it can be extended by a polymerase to generate a second amplification product having a 3′ hairpin structure;
• and
• wherein said downstream probe is configured to form an invasive cleavage structure with said 3′ hairpin structure of said second amplification product, wherein said downstream probe comprises a 3′ region configured to hybridize to second amplification product, and a 5′ region configured to not hybridize to second amplification product;
• and
• II) a second kit, comprising a snap-back primer and an upstream probe, wherein said snap-back primer comprises:
• i) a 5′ region configured to not hybridize to said target nucleic when said 3′ region of said snap-back primer is hybridized to said target nucleic acid, and
• ii) a 3′ region configured to hybridize to said target nucleic acid such that it can be extended by a polymerase to generate an amplification product comprising a 5′ hairpin structure;
• wherein said upstream probe is configured to form an invasive cleavage structure with said 5′ hairpin structure of said amplification product, wherein said upstream probe comprises a 5′ region configured to hybridize to said amplification product and a 3′ region configured to not hybridize to said amplification product.