Secondary structure in formylmethionine tRNA 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, T psi C loop, anticodon stem, and acceptor stem were investigated. Virtually unique hydrolyses with RNase H were observed at the T psi C 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 T psi C 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.
Hayase
Y
Y
Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
Inoue
H
H
Ohtsuka
E
E
D000926:Anticodon / Q000378:metabolism; D001483:Base Sequence; D004722:Endoribonucleases / Q000378:metabolism*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000138:chemical synthesis / Q000378:metabolism*; D012358:RNA, Transfer, Met / Q000378:metabolism*; D016914:Ribonuclease H; D013329:Structure-Activity Relationship
D000926:Anticodon; D009841:Oligonucleotides; D012358:RNA, Transfer, Met; D004722:Endoribonucleases; D016914:Ribonuclease H