Experimental and Numerical Studies on B-DNA Overstretching Transition in Presence of Sodium Ions at Physiological Temperature
In this paper, the effects of Na+ concentration on the overstretching transition of B-DNA molecule at physiological temperature are studied by both experimental and numerical methods. Using optical tweezers, the relationship of external force and relative extension is obtained by stretching single B-DNA molecule at 37°C. As the concentration increases from 0.909mM to 909mM, the overstretching transition force increases from 65.65 ± 1.2pN to 43.07 ± 1.2pN. An analytical expression is derived, which shows that overstretching transition force is linear with the natural logarithm of salt concentration. Based on a previous model, a three-dimensional model is proposed herein and solved by Metropolis Monte Carlo method. The bending deformation of DNA backbones, cooperativity of base-stacking interactions, electrostatic interactions, and spatial effects of DNA double helix structure are taken into account. Our key contribution is that the electrostatic energy is explicitly given as a function of folding angle and Na+ concentration. A new parameter is also introduced to account for the cooperativity of base-stacking interactions. The numerical results of this model are in good agreement with our experimental results.
Chunli BAI, Sishen XIE, Xing ZHU
H. X. Fu et al., "Experimental and Numerical Studies on B-DNA Overstretching Transition in Presence of Sodium Ions at Physiological Temperature", Solid State Phenomena, Vols. 121-123, pp. 1093-1096, 2007