Fujimoto Bryant S, Schurr J Michael
Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA.
Biophys J. 2002 Feb;82(2):944-62. doi: 10.1016/S0006-3495(02)75455-6.
Recent advances in atomic force microscopy (AFM) have enabled researchers to obtain images of supercoiled DNAs deposited on mica surfaces in buffered aqueous milieux. Confining a supercoiled DNA to a plane greatly restricts its configurational freedom, and could conceivably alter certain structural properties, such as its twist and writhe. A program that was originally written to perform Monte Carlo simulations of supercoiled DNAs in solution was modified to include a surface potential. This potential flattens the DNAs to simulate the effect of deposition on a surface. We have simulated transfers of a 3760-basepair supercoiled DNA from solution to a surface in both 161 and 10 mM ionic strength. In both cases, the geometric and thermodynamic properties of the supercoiled DNAs on the surface differ significantly from the corresponding quantities in solution. At 161 mM ionic strength, the writhe/twist ratio is 1.20-1.33 times larger for DNAs on the surface than for DNAs in solution and significant differences in the radii of gyration are also observed. Simulated surface structures in 161 mM ionic strength closely resemble those observed by AFM. Simulated surface structures in 10 mM ionic strength are similar to a minority of the structures observed by AFM, but differ from the majority of such structures for unknown reasons. In 161 mM ionic strength, the internal energy (excluding the surface potential) decreases substantially as the DNA is confined to the surface. Evidently, supercoiled DNAs in solution are typically deformed farther from the minimum energy configuration than are the corresponding surface-confined DNAs. Nevertheless, the work (Delta A(int)) done on the internal coordinates, which include uniform rotations at constant configuration, during the transfer is positive and 2.6-fold larger than the decrease in internal energy. The corresponding entropy change is negative, and its contribution to Delta A(int) is positive and exceeds the decrease in internal energy by 3.6 fold. The work done on the internal coordinates during the solution-to-surface transfer is directed primarily toward reducing their entropy. Evidently, the number of configurations available to the more deformed solution DNA is vastly greater than for the less deformed surface-confined DNA.
原子力显微镜（AFM）的最新进展使研究人员能够获取沉积在缓冲水溶液环境中的云母表面上的超螺旋DNA的图像。将超螺旋DNA限制在一个平面内会极大地限制其构象自由度，并可能改变某些结构特性，例如其扭曲和缠绕。一个最初编写用于对溶液中的超螺旋DNA进行蒙特卡罗模拟的程序被修改为包含表面势。这个势使DNA变平以模拟沉积在表面上的效果。我们已经模拟了在161和10 mM离子强度下，一个3760个碱基对的超螺旋DNA从溶液转移到表面的过程。在这两种情况下，表面上超螺旋DNA的几何和热力学性质与溶液中的相应量有显著差异。在161 mM离子强度下，表面上的DNA的缠绕/扭曲比是溶液中DNA的1.20 - 1.33倍，并且还观察到回转半径有显著差异。在161 mM离子强度下模拟的表面结构与通过AFM观察到的结构非常相似。在10 mM离子强度下模拟的表面结构与通过AFM观察到的少数结构相似，但出于未知原因与大多数此类结构不同。在161 mM离子强度下，当DNA被限制在表面时，内能（不包括表面势）会大幅降低。显然，溶液中的超螺旋DNA通常比相应的表面限制DNA更远离最低能量构型而发生变形。然而，在转移过程中对内部坐标（包括在恒定构型下的均匀旋转）所做的功（ΔA(int)）是正的，并且比内能的降低大2.6倍。相应的熵变是负的，并且其对ΔA(int)的贡献是正的，并且比内能的降低超过3.6倍。在从溶液到表面的转移过程中对内部坐标所做的功主要用于降低它们的熵。显然，变形更大的溶液DNA可用的构象数量比变形较小的表面限制DNA多得多。
