Transcription factor (TF) molecules translocate by facilitated diffusion (a combination of 3D diffusion around and 1D random walk on the DNA). Despite the attention this mechanism received in the last 40 years, only a few studies investigated the influence of the cellular environment on the facilitated diffusion mechanism and, in particular, the influence of `other' DNA binding proteins competing with the TF molecules for DNA space. Molecular crowding on the DNA is likely to influence the association rate of TFs to their target site and the steady state occupancy of those sites, but it is still not clear how it influences the search in a genome-wide context, when the model includes biologically relevant parameters (such as: TF abundance, TF affinity for DNA and TF dynamics on the DNA). We performed stochastic simulations of TFs performing the facilitated diffusion mechanism, and considered various abundances of cognate and non-cognate TFs. We show that, for both obstacles that move on the DNA and obstacles that are fixed on the DNA, changes in search time are not statistically significant in case of biologically relevant crowding levels on the DNA. In the case of non-cognate proteins that slide on the DNA, molecular crowding on the DNA always leads to statistically significant lower levels of occupancy, which may confer a general mechanism to control gene activity levels globally. When the `other' molecules are immobile on the DNA, we found a completely different behaviour, namely: the occupancy of the target site is always increased by higher molecular crowding on the DNA. Finally, we show that crowding on the DNA may increase transcriptional noise through increased variability of the occupancy time of the target sites.
All-or-none switching of transcriptional activity on single DNA molecules caused by a discrete conformational transition
最近，它已被证实，长的双链DNA分子的大小大于几十个千碱基对（kbp），表现出离散的构象转变，从一个细长的螺旋状态的紧凑的小球状态时，添加各种化学物质，通常会引起DNA缩合。在这项研究中，我们对一个大的DNA进行了单分子观察，Lambda ZAP II DNA（约。41 kbp），在含有RNA聚合酶和底物以及不同浓度的精胺（四价阳离子）的溶液中，通过使用DNA和RNA的荧光染色。我们发现，转录，或RNA的生产，是完全抑制在紧凑的状态，但积极进行在未折叠的螺旋状态。这种全或无的影响，转录活性诱导的离散构象转变的单个DNA分子进行了讨论有关的机制，大规模的遗传活动的调节。
