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Nucleic Acids Research 2005 33(4):1201-1212; doi:10.1093/nar/gki264
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Published online 24 February 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

Enhanced RNA cleavage within bulge-loops by an artificial ribonuclease

Irina L. Kuznetsova, Marina A. Zenkova*, Hans J. Gross1 and Valentin V. Vlassov

Institute of Chemical Biology and Fundamental Medicine SB RAS Lavrentiev Avenue 8, Novosibirsk 630090, Russia 1 Institute of Biochemistry, Biocenter Am Hubland, D-97074 Würzburg, Germany

*To whom correspondence should be addressed. Tel: +7 3832 333761; Fax: +7 3832 333761; Email: marzen{at}niboch.nsc.ru

Received November 25, 2004. Revised February 2, 2005. Accepted February 2, 2005.

Cleavage of phosphodiester bonds by small ribonuclease mimics within different bulge-loops of RNA was investigated. Bulge-loops of different size (1–7 nt) and sequence composition were formed in a 3' terminal fragment of influenza virus M2 RNA (96 nt) by hybridization of complementary oligodeoxynucleotides. Small bulges (up to 4 nt) were readily formed upon oligonucleotide hybridization, whereas hybridization of the RNA to the oligonucleotides designed to produce larger bulges resulted in formation of several alternative structures. A synthetic ribonuclease mimic displaying Pyr–Pu cleavage specificity cleaved CpA motifs located within bulges faster than similar motifs within the rest of the RNA. In the presence of 10 mM MgCl2, 75% of the cleavage products resulted from the attack of this motif. Thus, selective RNA cleavage at a single target phosphodiester bond was achieved by using bulge forming oligonucleotides and a small ribonuclease A mimic.


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