Nucleic Acids Research, 1990, Vol. 18, No. 16 4809-4815
© 1990
ENZYMOLOGY |
The cleavage specificity of RNase III
Department of Biological Sciences, State University of New York at Albany Albany, NY 12222, USA
*To whom correspondence should be addressed
Received April 23, 1990. Revised July 23, 1990. Accepted July 23, 1990.
We determined sites in 
cll mRNA that are cleaved by RNase III in the presence of OOP antisense RNA, using a series of OOP RNAs with different internal deletions. In OOP RNA-cll mRNA structures containing a potential region of continuous double-stranded RNA bounded by a non-complementary unpaired region, RNase III cleaved the ell mRNA at one or more preferred sites located 10 to 14 bases from the 3'-end of the region of continuous complementarity. Cleavage patterns were almost identical when the presumptive structure was the same continuously double-stranded region followed by a single-stranded bulge and a second short region of base pairing. The sequences of the new cleavage sites show generally good agreement with a consensus sequence derived from thirty-five previously determined cleavage sequences. In contrast, four ‘non-sites’ at which cleavage is never observed show poor agreement with this consensus sequence. We conclude that RNase III specificity is determined both by the distance from the end of continuous pairing and by nucleotide sequence features within the region of pairing.
+Present address: Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
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