Experimental and Numerical Studies on B-DNA Overstretching Transition in Presence of Sodium Ions at Physiological Temperature |
| Journal |
Solid State Phenomena (Volumes 121 - 123) |
| Volume |
Nanoscience and Technology |
| Edited by |
Chunli BAI, Sishen XIE, Xing ZHU |
| Pages |
1093-1096 |
| DOI |
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 |
| 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. |
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