Quantitative parameters of cooperative interactions of oligonucleotides within tandem complexes

Author： Timofeeva N. A. Koval V. V. Fedorova O. S.

ISSN： 1066-5285

Source： Russian Chemical Bulletin, Vol.52, Iss.11, 2003-11, pp. : 2507-2516

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Abstract

Quantitative parameters of cooperative interactions of deoxyribooligonucleotides within perfect complementary complexes with a nick in one strand and imperfect complexes containing one mismatched base pair in the nick were obtained. One complementary strand was represented by 22-mer oligonucleotides, while the other, by two short 8-mer oligonucleotides forming a tandem complex with the central part of the 22-mer. In the tandem complexes, the 8-mers form contacts of the following types: 5"-Py*pPy-3", 5"-Pu*pPy-3", and 5"-Pu*pPu-3", where p is phosphate, Py and Pu are pyrimidine and purine nucleosides, respectively, and * stands for a nick. In each incompletely complementary complex, the mismatched base pair in the nick is formed by the 3"-end nucleoside of the 8-mer oligonucleotide and by the nucleoside located in the middle of the 22-mer oligonucleotide. The alkylating {4-[N-(2-chloroethyl)-N-methylamino]phenyl}methylamino group (RCl) is linked through the 5"-end phosphate of the 8-mers (reagents) close to 3"-ends of the 22-mers. The dependences of the limit extents of alkylation of 22-mers (targets) at zero and saturating concentrations of the neighbor oligonucleotides (effectors) on the initial concentration of RCl-derivatives of oligonucleotides (reagents) were used to calculate the association constants K_X of the reagent with the target. The ratio of these constants was used to determine the parameters of contact cooperativity α, which characterize the interactions at the junction of two oligonucleotides within the tandem complexes.