title: [Comparison of the conformation of RNA from phage MS2 and 16S rRNA. Interaction with dyes specific for the secondary structure of native RNA and RNA subjected to hydrolysis by nuclease S1].
abstract: The interaction of ethidium bromide (EtBr) with double-stranded (ds), and acridine orange (AO) with single-stranded (ss) fragments of 16S rRNA Escherichia coli in a wide range of ionic strength, at various pH, Zn2+ ion concentrations and partial hydrolysis by nuclease S1 was investigated. It was shown that about 90% of the RNA molecule is accessible to both dyes, when the ionic strength is near of 0.01 (pH 7). Approximately half of the RNA becomes inaccessible to dyes, when the ionic strength was increased up to 0.08-0.24 (pH 4.7-7), independent on the presence of Zn2+ ions (10(-3) M). About a half of the ds-, and a quarter of the ss-segments of the RNA, deduced from the secondary structure model were protected from the interaction with EtBr and AO. The hydrolysis of about a half of ss-segments upon addition of the Zn2+ (10(-3) M) ions did not affect the RNA tertiary structure. The experimental data obtained confirm the idea of the existence of some "nucleus" (or "nuclei") within the 16S rRNA molecule. The "nucleus" seems to be inaccessible to the dyes and is very stable to heat denaturation. It was supposed that this structure is organized by means of interaction of some of the parallelly oriented ds-segments, as it was suggested earlier for the phage MS2 RNA structure.
authors.forename: O F
authors.initials: OF
authors.lastname: Borisova
authors.forename: V V
authors.initials: VV
authors.lastname: Grechko
authors.forename: N V
authors.initials: NV
authors.lastname: Kuznetsova
authors.forename: N K
authors.initials: NK
authors.lastname: Sakharova
authors.forename: G I
authors.initials: GI
authors.lastname: Timokhina
mesh_terms: D000165:Acridine Orange / Q000494:pharmacology; D003090:Coliphages / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics; D004996:Ethidium / Q000494:pharmacology; D006868:Hydrolysis; D007700:Kinetics; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D012330:RNA, Double-Stranded / Q000187:drug effects; D012335:RNA, Ribosomal / Q000187:drug effects; D012367:RNA, Viral / Q000187:drug effects
chemical_list: D012330:RNA, Double-Stranded; D012335:RNA, Ribosomal; D012367:RNA, Viral; D004996:Ethidium; D000165:Acridine Orange
vernacular_title: Sravnenie prostranstvennoĭ organizatsii RNK faga MS2 i 16S rRNK. Vzaimodeĭstvie s krasiteliami, spetsifichnymi ko vtorichnoĭ strukture, nativnoĭ RNK i posle ee gidroliza nukleazoĭ S1.