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

Abstract:

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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.

Info:

Periodical:

Solid State Phenomena (Volumes 121-123)

Edited by:

Chunli BAI, Sishen XIE, Xing ZHU

Pages:

1093-1096

DOI:

10.4028/www.scientific.net/SSP.121-123.1093

Citation:

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

Online since:

March 2007

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$35.00

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