Biopolym. Cell. 2000; 16(6):495-504.
http://dx.doi.org/10.7124/bc.00058F
Structure and Function of Biopolymers
Conformational transitions of poly(C) and poly(dC): study by the proton buffer capacity method
1Zarudnaya M. I., 1Potyahaylo A. L., 1Hovorun D. M.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680

Abstract

On the basis of the literature data the pH-dependencies of proton buffer capacity ofpoly(C) (at 0,1 M Na+ ) and poly(dC) (at 0,05 M Na+ ) are computed. These dependencies are expanded into basic functions corresponding to ionized groups of equal pK. It is found that the buffer capacity curve of poly(C) has four peaks: two narrow and two wide ones. The first narrow peak (pK-5,6) reflects the process of cooperative formation of double helices, which is induced by the profanation of the N3 atom of the nucleotide bases partly exposed in the solution. The second narrow peak (pK-2,9) is assigned to the cooperative dissociation of these helices. The first wide peak (pK–5,3) corresponds to the noncooperative process of the poly(C) double helices profanation at the N3 nitrogen atom. The second wide peak (pK – 3,1) is assigned to the noncooperative profanation of electroneutral cytidine bases at the oxygen atom with cis-orientation of added proton about glycoside bond. This reaction leads to the decrease of thermodynamic stability of the poty(C) double helices and finally results in their dissociation. The confor-mational transitions of the poly(dC) induced by its protonation are discussed as well.
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