Levene S D, Crothers D M
J Mol Biol. 1986 May 5;189(1):61-72. doi: 10.1016/0022-2836(86)90381-5.
The rate of ligation of DNA molecules into circular forms depends on the ring closure probability, commonly called the j-factor, which is a sensitive measure of the extent to which thermal fluctuations contribute to bending and twisting of DNA molecules in solution. We present a theoretical treatment of the cyclization equilibria of DNA that employs a special Monte Carlo method for generating large ensembles of model DNA chains. Using this method, the chain length dependence of the j-factor was calculated for molecules. in the size range 250 to 2000 base-pairs. The Monte Carlo results are compared with recent analytical theory and experimental data. We show that a value of 475 A for the persistence length of DNA, close to values measured by a number of other methods, is in excellent agreement with the cyclization results. Preliminary applications of the Monte Carlo method to the problem of systematically bent DNA molecules are presented. The calculated j-factor is shown to be very sensitive to the amount of bending in these fragments. This fact suggests that ligase closure measurements of systematically bent DNA molecules should be a useful method for studying sequence-directed bending in DNA.
DNA分子连接成环状的速率取决于环化概率，通常称为j因子，它是衡量热涨落对溶液中DNA分子弯曲和扭转影响程度的一个灵敏指标。我们提出了一种DNA环化平衡的理论处理方法，该方法采用一种特殊的蒙特卡罗方法来生成大量的模型DNA链系综。利用这种方法，计算了250至2000个碱基对大小范围内分子的j因子对链长的依赖性。将蒙特卡罗结果与最近的解析理论和实验数据进行了比较。我们表明，DNA的持久长度为475 Å，这一数值与其他多种方法测得的值相近，与环化结果非常吻合。文中还介绍了蒙特卡罗方法在系统弯曲DNA分子问题上的初步应用。计算得到的j因子对这些片段中的弯曲量非常敏感。这一事实表明，对系统弯曲的DNA分子进行连接酶封闭测量应该是研究DNA中序列导向弯曲的一种有用方法。
