Ribonuclease V1

Not to be confused with ribonuclease V.
A Caspian cobra

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]

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] Used 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]

References

  1. 1 2 Favorova, O. O.; Fasiolo, F; Keith, G; Vassilenko, S. K.; Ebel, J. P. (1981). "Partial digestion of tRNA--aminoacyl-tRNA synthetase complexes with cobra venom ribonuclease". Biochemistry 20 (4): 1006–11. doi:10.1021/bi00507a055. PMID 7011369.
  2. ↑ Ying, Shao Yao, ed. (2006-01-01). MicroRNA Protocols. Humana Press. p. 23. ISBN 9781597451239.
  3. 1 2 Nilsen, TW (2013). "RNA Structure Determination Using Nuclease Digestion". Cold Spring Harbor Protocols 2013 (4): 379–82. doi:10.1101/pdb.prot072330. PMID 23547152.
  4. ↑ Duval, Melodie; Romilly, Cedric; Helfer, Anne-Catherine; Fuchsbauer, Olivier; Romby, Pascale; Marzi, Stefano (2013). Klostermeier, Dagmar; Hammann, Christian, eds. RNA Structure and Folding: Biophysical Techniques and Prediction Methods. Walter de Gruyter. p. 32. ISBN 9783110284959.
  5. ↑ Lowman, H. B.; Draper, D. E. (1986). "On the recognition of helical RNA by cobra venom V1 nuclease". The Journal of Biological Chemistry 261 (12): 5396–403. PMID 2420800.
  6. ↑ Chaulk, S. G.; Xu, Z.; Glover, M. J. N.; Fahlman, R. P. (2014). "MicroRNA miR-92a-1 biogenesis and mRNA targeting is modulated by a tertiary contact within the miR-17 92 microRNA cluster". Nucleic Acids Research 42 (8): 5234–5244. doi:10.1093/nar/gku133.
  7. ↑ Lockard, R. E.; Kumar, A (1981). "Mapping tRNA structure in solution using double-strand-specific ribonuclease V1 from cobra venom". Nucleic Acids Research 9 (19): 5125–40. doi:10.1093/nar/9.19.5125. PMC 327503. PMID 7031604.
  8. ↑ Blight, K. J.; Rice, C. M. (1997). "Secondary structure determination of the conserved 98-base sequence at the 3' terminus of hepatitis C virus genome RNA". Journal of Virology 71 (10): 7345–52. PMC 192079. PMID 9311812.
  9. ↑ Polacek, C.; Foley, J. E.; Harris, E. (2008). "Conformational Changes in the Solution Structure of the Dengue Virus 5' End in the Presence and Absence of the 3' Untranslated Region". Journal of Virology 83 (2): 1161–1166. doi:10.1128/JVI.01362-08.
  10. ↑ Harrison, G. P.; Lever, A. M. (1992). "The human immunodeficiency virus type 1 packaging signal and major splice donor region have a conserved stable secondary structure". Journal of Virology 66 (7): 4144–53. PMC 241217. PMID 1602537..
  11. ↑ Kertesz, M; Wan, Y; Mazor, E; Rinn, J. L.; Nutter, R. C.; Chang, H. Y.; Segal, E (2010). "Genome-wide measurement of RNA secondary structure in yeast". Nature 467 (7311): 103–7. doi:10.1038/nature09322. PMC 3847670. PMID 20811459.
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