title: Enhanced RNA cleavage within bulge-loops by an artificial ribonuclease.
abstract: 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.
authors.affiliation: Institute of Chemical Biology and Fundamental Medicine SB RAS Lavrentiev Avenue 8, Novosibirsk 630090, Russia.
authors.forename: Irina L
authors.initials: IL
authors.lastname: Kuznetsova
authors.forename: Marina A
authors.initials: MA
authors.lastname: Zenkova
authors.forename: Hans J
authors.initials: HJ
authors.lastname: Gross
authors.forename: Valentin V
authors.initials: VV
authors.lastname: Vlassov
mesh_terms: D001483:Base Sequence; D002021:Buffers; D007093:Imidazoles / Q000737:chemistry; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D012313:RNA / Q000737:chemistry* / Q000378:metabolism*; D012367:RNA, Viral / Q000737:chemistry / Q000378:metabolism; D012259:Ribonuclease, Pancreatic / Q000737:chemistry / Q000378:metabolism*; D013379:Substrate Specificity
chemical_list: D002021:Buffers; D007093:Imidazoles; D009838:Oligodeoxyribonucleotides; D012367:RNA, Viral; D012313:RNA; C029899:imidazole; D012259:Ribonuclease, Pancreatic
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