Ribonuclease V1

Purified RNase V1 is a commonly used reagent in molecular biology experiments. In conjunction with other ribonucleases that cleave single-stranded RNA after specific nucleotides or sequences – such as RNase T1 and RNase I – it can be used to map internal interactions in large RNA molecules with complex secondary structure or to perform footprinting experiments on macromolecular complexes containing RNA.[3]

RNase V1 is the only commonly used laboratory RNase that provides positive evidence for the presence of double-stranded helical conformations in target RNA.[4] Because RNase V1 has some activity against RNA that is base-paired but single-stranded,[5] dual susceptibility to both RNase V1 and RNase I at a single site in a target RNA molecule provides evidence of this relatively unusual conformation found in RNA loops.[6]

The distinctive secondary structure of transfer RNA, containing a series of double helices separated by flexible loops

RNase V1 played a particularly important role in the elucidation of the distinctive stem-loop structure of transfer RNA.[1][7] It has also been extensively used to study the highly structured RNA genomes of retroviruses, such as hepatitis C,[8] dengue virus,[9] and HIV.[10] Together with S1 nuclease, which specifically cleaves single-stranded RNA, it can be used to profile the secondary structure propensities of messenger RNA molecules, a procedure that can be applied to whole transcriptomes when paired with deep sequencing.[11][12]