Protonated polynucleotide structures. Sequence-dependent and protonation-sensitive metastable states in DNA premelting.

Abstract

Circular dichroism and absorbance‐difference spectra of polydeoxynucleotides and DNAs of various base composition have been measured at different submelting temperatures. The following results were obtained. The changes observed by both techniques correlate poorly with (G + C) content, but follow the normalized YpY, i.e. (fCpC+fTpT)/xG+C, and not the mixed RpY, i.e. (fApT+fTpA)/yA+T, nearest‐neighbour frequencies. Small pH changes have considerable effect on the difference spectra. The metastable protonated form of poly(dG) · poly(dC) Correlates better with the circular dichroism spectra than the non‐protonated form. It is concluded that dC clusters may be at the origin of DNA premelting, especially if they are in the metastable protonated form.