Free Energy Landscape of A-DNA to B-DNA Conversion in Aqueous Solution

随机六聚体 化学 分子动力学 结晶学 水溶液 DNA 伞式取样 最大值和最小值 计算化学 热力学 物理 物理化学 数学 生物化学 数学分析
作者
Nilesh K. Banavali,Benoı̂t Roux
出处
期刊:Journal of the American Chemical Society [American Chemical Society]
卷期号:127 (18): 6866-6876 被引量:123
标识
DOI:10.1021/ja050482k
摘要

The interconversion between the well-characterized A- and B-forms of DNA is a structural transition for which the intermediate states and the free energy difference between the two endpoints are not known precisely. In the present study, the difference between the Root Mean Square Distance (RMSD) from canonical A-form and B-form DNA is used as an order parameter to characterize this free energy difference using umbrella sampling molecular dynamics (MD) simulations with explicit solvent. The constraint imposed along this order parameter allows relatively unrestricted evolution of the intermediate structures away from both canonical A- and B-forms. The free energy difference between the A- and B-forms for the hexamer DNA sequence CTCGAG in aqueous solution is conservatively estimated to be at least 2.8 kcal/mol. A continuum of intermediate structures with no well-defined local minima links the two forms. The absence of any major barriers in the free energy surface is consistent with spontaneous conversion of the A-form DNA to B-form DNA in unconstrained simulations. The extensive sampling in the MD simulations (>0.1 μs) also allowed quantitative energetic characterization of local backbone conformational variables such as sugar pseudorotation angles and BI/BII state equilibria and their dependence on base identity. The absolute minimum in the calculated free energy profile corresponds closely to the crystal structure of the hexamer sequence, indicating that the present method has the potential to identify the most stable state for an arbitrary DNA sequence in water.
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