Ribonuclease V1

Not to be confused with Ribonuclease V.

Ribonuclease V1 (RNase V1) is a ribonuclease enzyme found in the venom of the Caspian cobra (Naja oxiana).^[1] It cleaves double-stranded RNA in a non-sequence-specific manner, usually requiring a substrate of at least six stacked nucleotides.^[2] Like many ribonucleases, the enzyme requires the presence of magnesium ions for activity.^[3]

A Caspian cobra

Laboratory use

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

Structural discoveries

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]