Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation.
Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation.
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DOI：
10.1093/nar/gkw815
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发表时间：
2016-11-02
影响因子：
14.9
通讯作者：
Harris SA
中科院分区：
文献类型：
--
作者：
Sutthibutpong T;Matek C;Benham C;Slade GG;Noy A;Laughton C;K Doye JP;Louis AA;Harris SA
已经确定的是，基因调控可以通过与DNA结合并打开或关闭特定基因的激活蛋白和阻遏蛋白来实现，并且复杂的代谢网络决定给定基因在给定时间的转录水平。使用三种互补的计算技术来研究DNA微环内DNA变性的序列依赖性，我们观察到，无论何时DNA的末端受到约束，信息都可以通过DNA本身的机械应力传输直接进行长距离传输，而不需要任何外部信号因素。我们的模型结合了联合收割机原子分子动力学（MD）与粗粒度模拟和统计力学计算，跨越三个不同的空间分辨率和时间尺度制度。虽然他们给出了高度弯曲和超螺旋DNA环中序列依赖性变性的非局部性的共识，但每个人也揭示了由于将DNA限制在微环的闭环内而发生的远程信息传递的独特方面。
It is well established that gene regulation can be achieved through activator and repressor proteins that bind to DNA and switch particular genes on or off, and that complex metabolic networks determine the levels of transcription of a given gene at a given time. Using three complementary computational techniques to study the sequence-dependence of DNA denaturation within DNA minicircles, we have observed that whenever the ends of the DNA are constrained, information can be transferred over long distances directly by the transmission of mechanical stress through the DNA itself, without any requirement for external signalling factors. Our models combine atomistic molecular dynamics (MD) with coarse-grained simulations and statistical mechanical calculations to span three distinct spatial resolutions and timescale regimes. While they give a consensus view of the non-locality of sequence-dependent denaturation in highly bent and supercoiled DNA loops, each also reveals a unique aspect of long-range informational transfer that occurs as a result of restraining the DNA within the closed loop of the minicircles.
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影响因子：
16.6
作者：
Irobalieva RN;Fogg JM;Catanese DJ Jr;Sutthibutpong T;Chen M;Barker AK;Ludtke SJ;Harris SA;Schmid MF;Chiu W;Zechiedrich L
通讯作者：
Zechiedrich L
DOI：
10.1038/nrg3454
发表时间：
2013-06
期刊：
Nature reviews. Genetics
影响因子：
--
作者：
通讯作者：
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转录依赖性动态超串联是一种短距离基因组力。
影响因子：
16.8
作者：
Kouzine, Fedor;Gupta, Ashutosh;Baranello, Laura;Wojtowicz, Damian;Ben-Aissa, Khadija;Liu, Juhong;Przytycka, Teresa M.;Levens, David
通讯作者：
Levens, David
影响因子：
11.4
作者：
He, LS;Liu, JH;Levens, D
通讯作者：
Levens, D
影响因子：
2.4
作者：
Fye, RM;Benham, CJ
通讯作者：
Benham, CJ