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J. Biol. Chem., Vol. 261, Issue 12, 5396-5403, 04, 1986
HB Lowman and DE Draper
The V1 nuclease from cobra venom preferentially hydrolyzes double helical
RNA and has been used extensively for detecting RNA secondary structure. To
increase the utility of this enzyme as an RNA structure probe, we have
investigated its properties and substrate specificity, using assays for
polynucleotide hydrolysis based on fluorescent polynucleotide derivatives.
Enzymatic activity requires both Na+ and Mg2+, with optima at 100 and 0.3
mM, respectively. From the sharp decrease in enzyme activity above 100 mM
Na+ we estimate that 3-4 ionic interactions between the protein and
polynucleotide phosphates take place. Analysis of products remaining after
extensive V1 digestion also shows that the minimum size substrate is 4-6
nucleotides long. Helical RNAs and DNAs have Michaelis constants a factor
of 3-10 times lower than most single-stranded RNAs. However, poly(epsilon
A) has a Michaelis constant equal to the best synthetic double helices
tested and is hydrolyzed at a rate comparable to helical RNA. The major V1
cutting sites in yeast tRNAPhe have Michaelis constants lower than any
synthetic polymers. These data suggest that V1 nuclease recognizes any
4-6-nucleotide segment of polynucleotide backbone with an approximately
helical conformation, but does not require that the bases be paired in a
helix. A few single-stranded V1 cleavage sites are known in tRNA and rRNA,
and their structures are consistent with the suggested V1 recognition site.
On the recognition of helical RNA by cobra venom V1 nuclease
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