title: Cooperative interactions in the tandem of oligonucleotide derivatives arranged at complementary target. Quantitative estimates and contribution of the target secondary structure.
abstract: The intraduplex reaction of the alkylating reagent CIRCH2NHpd(TTCCCA) (X, ClR is p-(N-2-chloroethyl-N-methylaminophenyl) residue) with the target 26-mer d(TTGCCTTGAATGGGAAGAGGGTCATT) (P) in the presence of effectors was studied. The effectors used were Phn-L-pd(TTCAAGGC)p-L-Phn (E1) and Phn-L-pd(TGACCCTC)p-L-Phy (E2), where Phn is N-(2-hydroxyethyl)-phenazinium residue and L is NHCH2CH2NH spacer. The dependence of the alkylation extent of the target on the reagent concentration was treated using the equation derived earlier for the two-component system (reagent + target) to calculate association constants of X with P, PE1, PE2 and PE1E2. The latter were found to be Kxe1 = 6.75 x 10(5) M-1, Kxe2 = 4.15 x 10(4) M-1 and Kxe12 = 5.87 x 10(6) M-1 as compared with the affinity of X to P Kx = 2.16 x 10(4) M-1 in the absence of effectors. Taking into account the internal structure of the target, co-operativity parameters describing interactions in the tandem E1 x X x E2 arranged at the target were calculated as alpha 1 = 16, alpha 2 = 10 and alpha 12 = 139 for the duplexes PXE1, PXE2 and PXE1E2.
authors.affiliation: Institute of Bioorganic Chemistry, Siberian Division of Russian Academy of Sciences, Novosibirsk.
authors.forename: O S
authors.initials: OS
authors.lastname: Fedorova
authors.forename: A
authors.initials: A
authors.lastname: Adeenah-Zadah
authors.forename: D G
authors.initials: DG
authors.lastname: Knorre
mesh_terms: D000477:Alkylating Agents; D001483:Base Sequence; D018076:DNA, Complementary / Q000737:chemistry* / Q000378:metabolism*; D007700:Kinetics; D008969:Molecular Sequence Data; D009150:Mustard Compounds / Q000737:chemistry; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry / Q000378:metabolism*; D010619:Phenazines / Q000737:chemistry
chemical_list: D000477:Alkylating Agents; D018076:DNA, Complementary; D009150:Mustard Compounds; D009838:Oligodeoxyribonucleotides; D010619:Phenazines; C076555:10-(2-hydroxyethyl)phenazine; C025881:4(N)-(2-chloroethyl-N-methylamino)benzylamine