Empirical validation of a two-state kinetic model for the B-Z transition of double-stranded poly[d(G-m5C)]

A formula based on a first-order kinetic equation is derived to evaluate the rate constant of the B-Z transition of a synthetic double-stranded poly[d(G-m5C)] in terms of the salt concentration, the absolute temperature, and the cooperativity index. The validity of the formula was tested using circular dichroism spectroscopy after variation of the type of salt (NaCl, MgCl2), the salt concentration, and the temperature of the polynucleotide solution. A consequence of the proposed function is that in conditions of high salt there is a predictable salt threshold which determines the particular molecular mechanism of the B-Z transition. The paper also describes the way in which this threshold level is temperature dependent. A detailed comparison of our data with the experimental data found by other authors is given. The function agrees quantitatively with the experiments and explains the contrasting results found in the literature about the influence in the B-Z transition of both the temperature and the polymer size.