Experimental and Numerical Studies on B-DNA Overstretching Transition in Presence of Sodium Ions at Physiological Temperature

Abstract:

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.

• Periodical: Solid State Phenomena (Volumes 121-123)
• Pages: 1093-1096
• DOI: https://doi.org/10.4028/www.scientific.net/SSP.121-123.1093
• Online since: March 2007
• Authors: Hong Xia Fu, Chan Ghee Koh, Hu Chen, Chwee Teck Lim
• Keywords: Metropolis Monte Carlo Method, Na⁺ Concentration , Optical Tweezer, Overstretching Transition, Three-Dimensional Model

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