How to rely correctly on experimental data when parameterizing simple DNA models

A. S. Shigaev, V. D. Lakhno


Abstract: Correct parameterization of simple mechanical models of DNA is one of the most important tasks in theoretical studies of this macromolecule. One of the main obstacles to solving this problem is the incorrect interpretation of many experimental data when compared with simple DNA models. The present study is devoted to ways of solving this problem. We consider the problems of taking account of degrees of freedom in a mechanical model of DNA using the example of the Peyrard-Bishop-Dauxois model. It has been shown that the discrepancies between theory and experiments are orders of magnitude smaller than previously believed if interpretations of the experimental data are correct. The main concepts of comparison of theory with experiment was formulated – the concept of local cooperativity in radial opening of the duplex and the concept of an effective threshold coordinate in describing the open state of DNA in radial mechanical models. The interpretation of experimental data is shown to be practically correct within the framework of these concepts.

Keywords: DNA open states, mechanical models of DNA, Peyrard-Bishop-Dauxois model, parametrization of models, local cooperativity, radial DNA model.