A method of identifying a facilitator nucleic acid comprising: (a) hybridizing a first component oligonucleotide and a second component oligonucleotide to a facilitator nucleic acid and a substrate nucleic acid to form a catalytically active nucleic acid enzyme, wherein the first component oligonucleotide comprises a facilitator-specific sequence, a substrate-specific sequence, and a partial catalytic core sequence disposed between the facilitator-specific sequence and the substrate-specific sequence, wherein the second component oligonucleotide comprises a facilitator-specific sequence, a substrate-specific sequence, and a partial catalytic core sequence disposed between the facilitator-specific sequence and the substrate-specific sequence and wherein the substrate nucleic acid comprises one or more labels; (b) cleaving the substrate nucleic acid with the catalytically active nucleic acid enzyme at a cleavage site to form a 5' fragment and a 3' fragment of the substrate nucleic acid; (c) hybridizing the 5' fragment of the substrate nucleic acid to a capture probe, wherein the capture probe comprises a first region that is complementary to the 5'-fragment of the substrate nucleic acid, a second region that provides a mismatch to the 3'-terminal nucleotide of the 5'-fragment of the substrate nucleic acid, and a third region that provides a template sequence for nucleic acid synthesis from the 3'-end of the 5'-fragment of the substrate nucleic acid; (d) removing the 3'-terminal nucleotide from the 5'-fragment of the substrate nucleic acid to form an extendable 5'-fragment of the substrate nucleic acid; (e) extending the extendable 5'-fragment of the substrate nucleic acid along the capture probe; and (f) performing melt analysis on a double-stranded extension product formed by extending the extendable 5'-fragment of the substrate nucleic acid along the capture probe, to identify the facilitator nucleic acid. (a) hybridizing a first component oligonucleotide and a second component oligonucleotide to a facilitator nucleic acid and a substrate nucleic acid to form a catalytically active nucleic acid enzyme, wherein the first component oligonucleotide comprises a facilitator-specific sequence, a substrate-specific sequence, and a partial catalytic core sequence disposed between the facilitator-specific sequence and the substrate-specific sequence, wherein the second component oligonucleotide comprises a facilitator-specific sequence, a substrate-specific sequence, and a partial catalytic core sequence disposed between the facilitator-specific sequence and the substrate-specific sequence and wherein the substrate nucleic acid comprises one or more labels; (b) cleaving the substrate nucleic acid with the catalytically active nucleic acid enzyme at a cleavage site to form a 5' fragment and a 3' fragment of the substrate nucleic acid; (c) hybridizing the 5' fragment of the substrate nucleic acid to a capture probe, wherein the capture probe comprises a first region that is complementary to the 5'-fragment of the substrate nucleic acid, a second region that provides a mismatch to the 3'-terminal nucleotide of the 5'-fragment of the substrate nucleic acid, and a third region that provides a template sequence for nucleic acid synthesis from the 3'-end of the 5'-fragment of the substrate nucleic acid; (d) removing the 3'-terminal nucleotide from the 5'-fragment of the substrate nucleic acid to form an extendable 5'-fragment of the substrate nucleic acid; (e) extending the extendable 5'-fragment of the substrate nucleic acid along the capture probe; and (f) performing melt analysis on a double-stranded extension product formed by extending the extendable 5'-fragment of the substrate nucleic acid along the capture probe, to identify the facilitator nucleic acid.