The RNase H digestion of the addressed alkylated, with derivatives of oligodeoxyribonucleotides, 16S rRNA at the reagent's binding sites

M. A. Zenkova, G. G. Karpova, A. S. Levina

Novosibirsk Institute of Bioorganic Chemistry, Siberian Division, Academy of Sciences of the USSR

Abstract: It is demonstrated that 16S rRNA, complementary-addressed labeled with 2',3'-O-[4-N-methyl-N-(2-chloroethyl)-amino]benzylidene derivatives of oligonucleotides d(pACCTTGTT)rA and d(pTTTGCTCCCC)rA, can be cleaved by RNase H within the ad-ducts, resulted from the modification. Comparative study of the 16S rRNA cleavage with RNase H within the above mentioned covalent adducts, on the one hand, and within heteroduplexes with the same oligodeoxyribonucleotides, on the other, showed that(i) the complementary-addressed modification proceeds both in perfect and non-perfect complexes; (ii) 16S rRNA is cleaved by RNase H within both perfect and non-perfect complexes resulted from the alkylation, non-perfect complexes being considerably stabilized by the covalent bond between the reagent and the RNA; (iii) non-perfect complexes of 16S rRNA with the free oligodeoxyribonucleotides are unstable even at the high oligonucleo-tide concentration, so that no cleavage of 16S rRNA in such duplexes is observed. The approach based on cleavage of RNA within covalent adducts resulted from the complementary-addressed RNA modification may be used for fragmentation of RNA molecule in the addressed reagent's binding site.

Russian Journal of Bioorganic Chemistry 1990, 16 (6):780-787

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