Salt concentration modulates the DNA target search strategy of NdeI
Salt concentration modulates the DNA target search strategy of NdeI
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DOI：
10.1016/j.bbrc.2020.10.036
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发表时间：
2021-01-01
影响因子：
3.1
通讯作者：
Price, Allen C.
中科院分区：
文献类型：
--
作者：
Ferreira, Raquel M.;Ware, Anna D.;Price, Allen C.
DNA目标搜索是获取基因组信息的细胞交易中的关键步骤。DNA结合蛋白如何将联合收割机3D扩散、滑动和跳跃结合成一个整体搜索策略，目前还知之甚少。在这里，我们报告使用单分子DNA拴系方法来表征II型限制性内切酶NdeI的目标搜索动力学。测量的搜索速率强烈地依赖于DNA长度以及作为盐浓度。使用路障，我们表明，在我们的研究中，在盐浓度的DNA滑动长度有显着的变化。为了解释我们的结果，我们提出了一个模型，包括3D和1D搜索的周期，其中盐浓度通过改变每个1D扫描探测的DNA长度来调节策略。在低盐条件下，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。在更高的盐，NdeI必须执行多个周期的目标搜索，由于一维搜索的效率降低。(C)2020爱思唯尔公司All rights reserved.
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. (C) 2020 Elsevier Inc. All rights reserved.