[Chemical reactions in double-helical nucleic acids. XV. The effect of local DNA structure on the efficacy of chemical ligation].

A series of model DNA-duplexes with a single break in one of the chains were studied. The efficiency of the new internucleotide bond formation by means of chemical ligation was shown to depend on the DNA structure in the nick site, decreasing in the following order: pyrimidine-pyrimidine > purine-pyrimidine > pyrimidine-purine > > purine-purine. This relationship is the most pronounced in duplexes with 5'-hydroxyl group as 3'-phosphate acceptor. For duplexes, containing non-complementary base pairs in the reaction centre, the yield of ligation products also depends on the nature of the interacting nucleotides.