Rangel David P, Fujimoto Bryant S, Schurr J Michael
Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA.
J Phys Chem B. 2008 Oct 23;112(42):13359-66. doi: 10.1021/jp801526w. Epub 2008 Aug 22.
Two different methods are proposed to estimate the persistence length ( P) of DNA from the measured torsion elastic constant (alpha) and the twist energy parameter ( E T ) that governs the supercoiling free energy. The first method involves Monte Carlo simulations and reversible-work calculations of E T for model DNAs that possess the measured alpha and selected trial values of P. Comparison of the computed E T values with the experimental value allows estimation of P (or equivalently the bending elastic constant (kappa beta)) by interpolation. A far simpler, though less accurate, alternative is to solve a previously conjectured analytical relation connecting E T , alpha, kappa beta (or P), and an unknown "constant" ( B). The present simulations are used to ascertain the optimum value of B and to assess the validity and accuracy of that relation. Within the simulation errors, P values obtained from the measured alpha and E T via this analytical expression agree with those determined from the simulations and E T values reckoned from the input alpha and kappa beta by this analytical expression agree with the corresponding simulated values. Although B is found to be insensitive to variation in alpha, it appears to decline slightly with increasing kappa beta. The original analytical expression is modified to take this apparent variation of B with kappa beta into account. By using this modified analytical relation to estimate P (from the measured alpha and E T ) or E T (from the input alpha and kappa beta), much closer agreement is obtained respectively with the values of P or E T obtained from the simulations. As specific examples, these methods are applied to determine P in 0 and 20 w/v % ethylene glycol, which has been shown to induce a structural transition in duplex DNA.
提出了两种不同的方法，用于根据测得的扭转弹性常数（α）和控制超螺旋自由能的扭曲能量参数（ET）来估算DNA的持久长度（P）。第一种方法涉及对具有测得的α和选定的P试验值的模型DNA进行蒙特卡罗模拟和ET的可逆功计算。将计算得到的ET值与实验值进行比较，通过插值法可以估算出P（或等效的弯曲弹性常数κβ）。另一种更简单但不太准确的方法是求解一个先前推测的解析关系式，该关系式将ET、α、κβ（或P）与一个未知的“常数”（B）联系起来。目前的模拟用于确定B的最佳值，并评估该关系式的有效性和准确性。在模拟误差范围内，通过该解析表达式从测得的α和ET获得的P值与从模拟中确定的值一致，并且通过该解析表达式根据输入的α和κβ计算得到的ET值与相应的模拟值一致。尽管发现B对α的变化不敏感，但它似乎随着κβ的增加而略有下降。对原始解析表达式进行了修改，以考虑B随κβ的这种明显变化。通过使用这个修改后的解析关系式来估算P（从测得的α和ET）或ET（从输入的α和κβ），分别与从模拟中获得的P或ET值取得了更接近的一致性。作为具体例子，这些方法被应用于确定在0和20 w/v%乙二醇中的P，已证明乙二醇会诱导双链DNA发生结构转变。
