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Title: Experimental and numerical studies on B-DNA overstretching transition in presence of sodium ions at physiological temperature
Authors: Hongxia, F. 
Chan, G.K. 
Hu, C. 
Chwee, T.L. 
Keywords: Metropolis Monte Carlo method
Na+ concentration
Optical tweezers
Overstretching transition
Three-dimensional model
Issue Date: 2007
Citation: Hongxia, F.,Chan, G.K.,Hu, C.,Chwee, T.L. (2007). Experimental and numerical studies on B-DNA overstretching transition in presence of sodium ions at physiological temperature. Diffusion and Defect Data Pt.B: Solid State Phenomena 121-123 (PART 2) : 1093-1096. ScholarBank@NUS Repository.
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.
Source Title: Diffusion and Defect Data Pt.B: Solid State Phenomena
ISBN: 3908451302
ISSN: 10120394
Appears in Collections:Staff Publications

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