title: [Complementary addressed alkylation of 16S rRNA of Escherichia coli by 2',3'-O-[4-N-methyl-N-(2-chloroethyl)-amino]benzylidene derivatives of oligodeoxyribonucleotides. V. Study of the factors affecting selectivity of modification].
abstract: We studied the effect of different factors (reagent concentration, temperature, presence of oligonucleotide-effector (3',5'-diphenazinium derivative of oligodeoxyribonucleotide) stabilizing duplex RNA.reagent) on the selectivity of the site-directed modification of 16S rRNA with 2,3'-O-[4-N-methyl-N-(2-chloroethyl)-amino]-benzylidene derivative of oligonucleotide p(dTTTGCTCCCC)rA (reagent I) under conditions of secondary structure stability. The constant of cooperative binding of the reagent and oligonucleotide-effector with 16s rRNA was determined. The temperature rise from 20 to 40 degrees C brought about a 1.5-fold increase in the relative extent of modification at the target site 771-781. In the presence of oligonucleotide-effector, which is a full complementary copy of the 782-789 fragment of 16S rRNA (reagent concentration is 1 x 10(-6) M), the selectivity of the RNA modification at the target site is doubled and a high level of the modification is retained. When the reagent concentration in the reaction mixture was decreased down to 1 x 10(-7) M, the same level of selectivity was achieved without the oligonucleotide-effector. Under these conditions, however, a drastic (20-fold) drop of the level of the 16S rRNA alkylation was observed.
authors.forename: M A
authors.initials: MA
authors.lastname: Zenkova
authors.forename: G G
authors.initials: GG
authors.lastname: Karpova
authors.forename: A S
authors.initials: AS
authors.lastname: Levina
authors.forename: S V
authors.initials: SV
authors.lastname: Mamaev
authors.forename: Iu N
authors.initials: IuN
authors.lastname: Pazarova
authors.forename: O S
authors.initials: OS
authors.lastname: Fedorova
mesh_terms: D000478:Alkylation; D001483:Base Sequence; D001597:Benzylidene Compounds / Q000737:chemistry*; D004926:Escherichia coli / Q000378:metabolism*; D007202:Indicators and Reagents; D008969:Molecular Sequence Data; D009588:Nitrogen Mustard Compounds / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D012329:RNA, Bacterial / Q000737:chemistry*; D012336:RNA, Ribosomal, 16S / Q000737:chemistry*; D013696:Temperature
chemical_list: D001597:Benzylidene Compounds; D007202:Indicators and Reagents; D009588:Nitrogen Mustard Compounds; D009838:Oligodeoxyribonucleotides; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S
vernacular_title: Komplementarno adresovannoe alkilirovanie 16S rRNK Escherichia coli 2',3'-O-[4-N-metil-N-(2-khlorétil)-oligodezoksiribonukleotidov. V. Issledovanie faktorov, vliiaiushchikh na selektivnots' modifikatsii.