Biology:Ribonuclease V1

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Short description: Ribonuclease enzyme found in the venom of the Caspian cobra
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] 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]

References

  1. 1.0 1.1 "Partial digestion of tRNA--aminoacyl-tRNA synthetase complexes with cobra venom ribonuclease". Biochemistry 20 (4): 1006–11. February 1981. doi:10.1021/bi00507a055. PMID 7011369. 
  2. Ying, Shao Yao, ed (2006-01-01). MicroRNA Protocols. Humana Press. p. 23. ISBN 9781597451239. https://archive.org/details/micrornaprotocol00ying_0. 
  3. 3.0 3.1 "RNA structure determination using nuclease digestion". Cold Spring Harbor Protocols 2013 (4): 379–82. April 2013. 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. https://books.google.com/books?id=KV7nBQAAQBAJ&pg=PA32. 
  5. "On the recognition of helical RNA by cobra venom V1 nuclease". The Journal of Biological Chemistry 261 (12): 5396–403. April 1986. doi:10.1016/S0021-9258(19)57229-5. PMID 2420800. 
  6. "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): 5234–44. April 2014. doi:10.1093/nar/gku133. PMID 24520115. 
  7. "Mapping tRNA structure in solution using double-strand-specific ribonuclease V1 from cobra venom". Nucleic Acids Research 9 (19): 5125–40. October 1981. doi:10.1093/nar/9.19.5125. PMID 7031604. 
  8. "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. October 1997. doi:10.1128/JVI.71.10.7345-7352.1997. PMID 9311812. 
  9. "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): 1161–6. January 2009. doi:10.1128/JVI.01362-08. PMID 19004957. 
  10. "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. July 1992. doi:10.1128/JVI.66.7.4144-4153.1992. PMID 1602537. .
  11. "Genome-wide measurement of RNA secondary structure in yeast". Nature 467 (7311): 103–7. September 2010. doi:10.1038/nature09322. PMID 20811459. Bibcode2010Natur.467..103K. 
  12. Silverman, Ian M.; Berkowitz, Nathan D.; Gosai, Sager J.; Gregory, Brian D. (2016). "Genome-Wide Approaches for RNA Structure Probing". in Yeo, Gene W.. RNA Processing. Springer. pp. 29–59. ISBN 978-3-319-29071-3.