Kinetics of target site localization of a protein on DNA:: A stochastic approach
Kinetics of target site localization of a protein on DNA:: A stochastic approach
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DOI：
10.1529/biophysj.104.045773
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发表时间：
2004-09-01
影响因子：
3.4
通讯作者：
Moreau, M
中科院分区：
文献类型：
--
作者：
Coppey, M;Bénichou, O;Moreau, M
人们普遍认为，限制性内切酶对靶DNA序列的切割速率比从扩散限制理论计算的最大切割速率快几个数量级。因此，通常认为限制性内切酶与DNA的靶位点相互作用必须通过两个步骤发生：沿DNA片段沿着的一维扩散，以及来自缔合-解离事件的长程跳跃。在这里，我们提出了一个随机模型，该反应包括一系列的一维扩散的限制性内切酶对非特异性DNA序列中断的三维漂移的解决方案，直到达到的目标序列。该模型提供了一个最佳的发现策略，解释了快速的关联率。通过不相关的随机跳跃对漂移进行建模，我们恢复了贝格等人在1981年给出的靶位点缔合发生所需的平均时间的表达式，并且我们明确给出了描述酶的随机途径的几个物理量。对于竞争性目标位点，我们计算两个量：持续合成能力和偏好。通过将这些理论表达式与最近获得的EcoRV-DNA相互作用的实验数据进行比较，我们量化了：1）对于代表性的一维扩散系数，EcoRV在DNA上的每个结合事件的平均停留时间; 2）在一维扩散期间扫描的DNA的平均长度（在一个结合事件期间和整个过程期间）;和3），从一个靶位点到另一个靶位点所需的平均时间和平均访问次数。此外，我们评估的DNA切割的动力学方面的限制性内切酶进行另一个一维扩散后，在同一个DNA基板的三维偏移的概率。
It is widely recognized that the cleaving rate of a restriction enzyme on target DNA sequences is several orders-of-magnitude faster than the maximal one calculated from the diffusion-limited theory. It was therefore commonly assumed that the target site interaction of a restriction enzyme with DNA has to occur via two steps: one-dimensional diffusion along a DNA segment, and long-range jumps coming from association-dissociation events. We propose here a stochastic model for this reaction which comprises a series of one-dimensional diffusions of a restriction enzyme on nonspecific DNA sequences interrupted by three-dimensional excursions in the solution until the target sequence is reached. This model provides an optimal finding strategy which explains the fast association rate. Modeling the excursions by uncorrelated random jumps, we recover the expression of the mean time required for target site association to occur given by Berg et al. in 1981, and we explicitly give several physical quantities describing the stochastic pathway of the enzyme. For competitive target sites we calculate two quantities: processivity and preference. By comparing these theoretical expressions to recent experimental data obtained for EcoRV-DNA interaction, we quantify: 1), the mean residence time per binding event of EcoRV on DNA for a representative one-dimensional diffusion coefficient; 2), the average lengths of DNA scanned during the one-dimensional diffusion ( during one binding event and during the overall process); and 3), the mean time and the mean number of visits needed to go from one target site to the other. Further, we evaluate the dynamics of DNA cleavage with regard to the probability for the restriction enzyme to perform another one-dimensional diffusion on the same DNA substrate following a three-dimensional excursion.