Svetlana V. Kochetkova

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Four types of polyacrylamide or polydimethyl-acrylamide gels for regioselective (by immobilization at the 3' end) of short oligonucleotides have been designed for use in manufacturing oligonucleotide microchips. Two of these supports contain amino or aldehyde groups in the gel, allowing coupling with oligonucleotides bearing aldehyde or amino groups,(More)
The mutant T7 RNA polymerase (T7 RNAP), containing two substitutions (Y639F, S641A) was earlier shown to utilize both rNTP and dNTP in a transcription-like reaction. In this report the ability of the enzyme to catalyze DNA primer extension reaction was demonstrated. The efficiency of the reaction essentially depended on the type of the primer sequence, and(More)
Oligonucleotide analogues containing one or a few glycine, L-, and D-alanine residues instead of phosphodiester internucleotide linkages were synthesized (C3′-NH-C(O)-CH(X)-NH-C(O)-C4′, where X = H, (S)-CH3, and (R)-CH3. The stability of the duplexes of modified oligonucleotides with their wild-type complements was studied. The incorporation of glycine and(More)
An improved method for the synthesis of 3-deoxy-3-carboxymethyl nucleosides was suggested. Oxidation of 5-O-benzoyl-1,2-O-isopropylidene-α-D-xylofuranose resulted in the 3-keto derivative, which was treated with triethylphosphonoacetate in the presence of sodium hydride to obtain the 3-deoxy-3-ethoxycarbonylmethylene derivative. Hydrogenation of the(More)
Earlier we showed that reported in literature nearest-neighbor thermodynamic parameters describe poorly the thermal-induced behavior of DNA duplexes immobilized in gel. Here we present a complete set of partial thermodynamic parameters for all 10 nearest-neighbor interactions specially developed for duplexes immobilized in gel. This thermodynamic library(More)
We have found that the 5'-pdGTT molecules at a concentration of 10(-4) M are oligomerized in solution in the presence of 10(-4) M tripeptide-(L-Val)3-NH-NH-DNS.CF3COOH and the condensation reagents (carbodiimide and imidazole). Oligonucleotides not less than 12 bases long were formed in the yield which was over 15%. It is known that in the absence of(More)
Binding of short fluorescently labeled AT-containing DNA duplexes with modified oligocytidylates is studied. The latter are modified to contain nonnatural α-anomers along with natural β-nucleotides; the nucleotide composition is selected according to the putative scheme of noncanonical triplex formation between duplex and oligomer bases. Nondenaturing gel(More)
Effect of attachment of 1-(2-deoxy-beta-D-ribofuranosyl)-5-nitroindole (NIDR) to the ends of target sequence of oligonucleotides immobilized on gel micromatrix on stability of duplex formed by hybridization with DNA fragment was studied. It was shown that adjunction of NIDR to 5' as well as to 3' end results in increasing stability of duplexes although in(More)
It was shown that 3'-deoxy-3'-aminothymidine and 2',3'-dideoxy-3'-aminoadenosine are effective inhibitors of DNA synthesis of sea urchin (Paracentrotus lividus) embryos during the early steps of development. The most probable mechanism of inhibition includes the blocking of the template-directed polycondensation, in which the inhibitors act as analogs of(More)