DNA环化时间的半经验计算方法

A Method for Calculating the Time Required for DNA Looping

DNA分子是生命遗传信息的主要物质载体。DNA环化是DNA不同位置所携带信息的一种协同实现方式。典型的例子是转录调控,增强子通过DNA环化与启动子相互作用,从而实现了对基因表达水平的调控。因此,破译DNA的环化动力学是解读基础生命过程的重要课题。本文在介绍DNA结构和力学性质的基础上,综述DNA环化时间的计算方法。在生理条件下,DNA的主要性质特点是弯折柔性强,而扭转和拉伸刚性强;据此,DNA环化可视作自发的熵减过程。运用热力学统计理论,可获得计算DNA环化时间的半经验公式。公式中的参数可由单分子光谱共聚焦技术测得的数据确定。该公式表明,空间拓扑决定了环化概率,DNA长度决定了环化时间。该公式适用于计算DNA上的顺式元件之间、顺式元件与启动子之间的相互作用。其优点在于避开了DNA结构和细胞核环境的复杂性。

The formation of a DNA loop takes a crucial role in transcriptional regulation, where the enhancer is tethered to its promoter. This step is a time-limiting step for activating transcriptional initiation.Here, We review a formula that is appropriate for computing the time required for formatting such a loop, or other DNA loops at the similar length scale where the looping can be attributed to a spontaneous decrease in conformation entropy. The formula shows that topological structure due to the orientation of two big grooves where a protein binds primarily determines whether two sites could be looped, and that the intervening DNA length defines the looping time. This method takes the advantages of bypassing the complexity of DNA structure and cellular circumstances,but requiring some parameters to be measured experimentally.