Biophysics Program, Stanford University, Stanford, California, USA.
Biophys J. 2011 Aug 17;101(4):856-65. doi: 10.1016/j.bpj.2011.06.066.
Access to genetically encoded data depends on the dynamics of DNA-binding proteins searching for specific target sites in the genome. This search process is thought to occur by facilitated diffusion-a combination of three-dimensional diffusion and one-dimensional sliding. Although facilitated diffusion is capable of significantly speeding up the search in vitro, the importance of this mechanism in vivo remains unclear. We use numeric simulations and analytical theory to model the target-search dynamics of DNA-binding proteins under a wide range of conditions. Our models reproduce experimental measurements of search-rate enhancement within bulk in vitro experiments, as well as the target search time for transcription factors measured in vivo. We find that facilitated diffusion can accelerate the search process only for a limited range of parameters and only under dilute DNA conditions. We address the role of DNA configuration and confinement, demonstrating that facilitated diffusion does not speed up the search on coiled versus straight DNA. Furthermore, we show that, under in vivo conditions, the search process becomes effectively diffusive and is independent of DNA configuration. We believe our results cast in a new light the role of facilitated diffusion in DNA targeting kinetics within the cell.
获取基因编码数据取决于 DNA 结合蛋白在基因组中搜索特定靶位的动力学。这种搜索过程被认为是通过易化扩散来实现的，即三维扩散和一维滑动的组合。尽管易化扩散能够显著加快体外搜索速度，但该机制在体内的重要性仍不清楚。我们使用数值模拟和分析理论，在广泛的条件下对 DNA 结合蛋白的靶标搜索动力学进行建模。我们的模型再现了体内实验中测量的转录因子的靶标搜索时间，以及在体外 bulk 实验中测量的搜索速率增强。我们发现，易化扩散只能在有限的参数范围内并在稀 DNA 条件下加速搜索过程。我们探讨了 DNA 构象和限制的作用，表明易化扩散不会加速卷曲 DNA 与直链 DNA 之间的搜索。此外，我们表明，在体内条件下，搜索过程变得有效扩散，与 DNA 构象无关。我们认为，我们的研究结果为易化扩散在细胞内 DNA 靶向动力学中的作用提供了新的认识。
