Abstract: This application describes a fluorogenic nucleic acid kit or composition for quantitative detection of a target ribonucleic acid (RNA) sequence in a test sample comprising at least one pair of oligonucleotide probes comprising a photocatalyst probe and a profluorophore probe, wherein one of the photocatalyst probe and the profluorophore probe is complementary to and capable of specifically binding an upstream portion of the target RNA sequence, and the other probe is complementary to and capable of specifically binding to a downstream portion of the target RNA sequence, the photocatalyst probe comprises a first oligonucleotide covalently bound to a photocatalyst, the profluorophore probe comprises a second oligonucleotide covalently bound to a profluorophore, and the photocatalyst is activatable by exposure to light and a reducing agent to form a reduced, activated photocatalyst that, when both probes of the pair are hybridized to the target RNA sequence, is capable of photoreducing the profluorophore to form

Abstract: Disclosed are compositions, reagents, methods, assays, and kits for quantitative and sensitive detection of target ribonucleic acid (RNA) sequences, particularly target RNA sequences that contain RNA spliced sites, hairpin stem-loops or other topological configurations of RNA secondary, tertiary, and quaternary structure, as well as linear RNA sequences. In some embodiments, fluorogenic modified-backbone oligonucleotide probes are employed for specific sequence hybridization across the target site, followed by chemical autoligation to produce a fluorescent molecule within the ligated probes. The autoligation detection reaction is performed isothermally or through thermocycling.