Sokolov Igor M, Metzler Ralf, Pant Kiran, Williams Mark C
Institut für Physik, Humboldt Universität zu Berlin, Germany.
Biophys J. 2005 Aug;89(2):895-902. doi: 10.1529/biophysj.104.057612. Epub 2005 May 20.
At low to moderate ambient salt concentrations, DNA-binding proteins bind relatively tightly to DNA, and only very rarely detach. Intersegmental transfer due to DNA-looping can be excluded by applying an external pulling force to the DNA molecule. Under such conditions, we explore the targeting dynamics of N proteins sliding diffusively along DNA in search of their specific target sequence. At lower densities of binding proteins, we find a reduction of the characteristic search time proportional to N(-2), with corrections at higher concentrations. Rates for detachment and attachment of binding proteins are incorporated in the model. Our findings are in agreement with recent single molecule studies in the presence of bacteriophage T4 gene 32 protein for which the unbinding rate is much lower than the specific binding rate.
在低至中等环境盐浓度下，DNA结合蛋白与DNA结合相对紧密，且极少分离。通过对DNA分子施加外部拉力，可以排除由于DNA环化导致的片段间转移。在这种条件下，我们探究了N蛋白沿DNA进行扩散滑动以寻找其特定靶序列的靶向动力学。在结合蛋白密度较低时，我们发现特征搜索时间的减少与N的-2次方成正比，在较高浓度时有修正。结合蛋白的分离和附着速率被纳入模型。我们的发现与最近在噬菌体T4基因32蛋白存在下的单分子研究一致，其解离速率远低于特异性结合速率。
