DNA target search is a key step in cellular transactions that access genomic information. How DNA binding proteins combine 3D diffusion, sliding and hopping into an overall search strategy remains poorly understood. Here we report the use of a single molecule DNA tethering method to characterize the target search kinetics of the type II restriction endonuclease NdeI. The measured search rate depends strongly on DNA length as well as salt concentration. Using roadblocks, we show that there are significant changes in the DNA sliding length over the salt concentrations in our study. To explain our results, we propose a model including cycles of 3D and 1D search in which salt concentration modulates the strategy by varying the length of DNA probed per 1D scan. At low salt NdeI makes a single non-specific encounter with DNA followed by an effective and complete 1D scan. At higher salt, NdeI must execute multiple cycles of target search due to the reduced efficacy of 1D search.

DNA靶标搜索是访问基因组信息的细胞交易中的关键步骤。DNA结合蛋白如何将3D扩散，滑动和跳跃结合成一个整体搜索策略仍然知之甚少。在这里我们报告使用单分子DNA束缚方法来表征II型限制性核酸内切酶NdeI的目标搜索动力学。测得的搜索速率在很大程度上取决于DNA长度以及盐浓度。使用障碍物，我们表明在我们的研究中，DNA滑动长度随盐浓度的变化很大。为了解释我们的结果，我们提出了一个包括3D和1D搜索循环的模型，其中盐浓度通过改变每次1D扫描探测到的DNA的长度来调节策略。在低盐下，NdeI与DNA进行一次非特异性接触，然后进行有效而完整的一维扫描。在高盐含量下，由于一维搜索的效率降低，NdeI必须执行多个目标搜索循环。