SECONDARY STRUCTURE IN FORMYLMETHIONINE TRANSFER-RNA INFLUENCES THE SITE-DIRECTED CLEAVAGE OF RIBONUCLEASE-H USING CHIMERIC 2'-O-METHYL OLIGODEOXYRIBONUCLEOTIDES

In order to cleave RNA at specific positions in Escherichia coli formylmethionine tRNA, RNase H and complementary chimeric oligonucleotides consisting of DNA and 2′-O-methyl-RNA (Inoue et al. (1987) FEBS Lett. 215, 327] were used. Specific cleavages in the D loop, anticodon loop, TΨC loop, anticodon stem, and acceptor stem were investigated. Virtually unique hydrolyses with RNase H were observed at the TΨC loop, anticodon stem, and acceptor stem when relatively longer chimeric oligonucleotides (20-mer) were used. An efficient cleavage at the anticodon was obtained with a chimeric 13-mer when the higher structure of the tRNA was broken by hybridization with a 20-mer at the acceptor as well as the TΨC stem region. It was found that stabilities of hybrids with chimeric oligonucleotides and the presence of minor nucleosides affect the cleavage of tRNA by this approach. © 1990, American Chemical Society. All rights reserved.