In studies of transcriptional regulation, it is often necessary to determine the structure and/or amount of a given RNA species. Several techniques have been developed making use of the fact that some nucleases will only digest single-stranded nucleic acids (ssDNA or ssRNA). Duplexes, whether DNA: DNA, RNA: RNA, or DNA: RNA, are resistant to digestion. By hybridizing samples with labeled single-stranded probes, the amount of probe complementary material in the sample mixture can be assayed, as well as the probe sequence involved. Such assays can be carried out on complex mixtures of RNA, as the labeled probe will only hybridize to the target RNA sequence. The most common uses for these techniques are to find transcription start sites and splice sites, and to quantitate specific RNA.

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