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本文引用的文献

1
Sequence-Dependent Effects in the Cyclization of Short DNA.短DNA环化中的序列依赖性效应
J Chem Theory Comput. 2006 May;2(3):685-95. doi: 10.1021/ct060025+.
2
Structure based sequence dependent stiffness scale for trinucleotides: a direct method.基于结构的三核苷酸序列依赖性刚度标度:一种直接方法。
J Biol Phys. 2000 Mar;26(1):43-50. doi: 10.1023/A:1005250718139.
3
High local concentration: a fundamental strategy of life.高局部浓度:生命的基本策略。
J Mol Biol. 2010 Jan 15;395(2):242-53. doi: 10.1016/j.jmb.2009.10.056. Epub 2009 Oct 31.
4
The role of DNA shape in protein-DNA recognition.DNA形状在蛋白质-DNA识别中的作用。
Nature. 2009 Oct 29;461(7268):1248-53. doi: 10.1038/nature08473.
5
Comprehensive mapping of long-range interactions reveals folding principles of the human genome.远距离相互作用的全面图谱揭示了人类基因组的折叠原理。
Science. 2009 Oct 9;326(5950):289-93. doi: 10.1126/science.1181369.
6
Counterion atmosphere and hydration patterns near a nucleosome core particle.核小体核心颗粒附近的反离子气氛和水合模式。
J Am Chem Soc. 2009 Oct 21;131(41):15005-13. doi: 10.1021/ja905376q.
7
Probing the conformational distributions of subpersistence length DNA.探究亚持久长度DNA的构象分布。
Biophys J. 2009 Sep 2;97(5):1408-17. doi: 10.1016/j.bpj.2009.06.031.
8
A translational signature for nucleosome positioning in vivo.体内核小体定位的翻译特征
Nucleic Acids Res. 2009 Sep;37(16):5309-21. doi: 10.1093/nar/gkp574. Epub 2009 Jul 13.
9
In the absence of writhe, DNA relieves torsional stress with localized, sequence-dependent structural failure to preserve B-form.在没有扭曲的情况下,DNA通过局部的、序列依赖性的结构破坏来缓解扭转应力,以保持B型结构。
Nucleic Acids Res. 2009 Sep;37(16):5568-77. doi: 10.1093/nar/gkp556. Epub 2009 Jul 8.
10
Concentration and length dependence of DNA looping in transcriptional regulation.转录调控中DNA环化的浓度和长度依赖性
PLoS One. 2009 May 25;4(5):e5621. doi: 10.1371/journal.pone.0005621.

体外和体内的 DNA 弯曲和柔韧性。

DNA curvature and flexibility in vitro and in vivo.

机构信息

Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.

出版信息

Q Rev Biophys. 2010 Feb;43(1):23-63. doi: 10.1017/S0033583510000077. Epub 2010 May 18.

DOI:10.1017/S0033583510000077
PMID:20478077
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4190679/
Abstract

It has been more than 50 years since the elucidation of the structure of double-helical DNA. Despite active research and progress in DNA biology and biochemistry, much remains to be learned in the field of DNA biophysics. Predicting the sequence-dependent curvature and flexibility of DNA is difficult. Applicability of the conventional worm-like chain polymer model of DNA has been challenged. The fundamental forces responsible for the remarkable resistance of DNA to bending and twisting remain controversial. The apparent 'softening' of DNA measured in vivo in the presence of kinking proteins and superhelical strain is incompletely understood. New methods and insights are being applied to these problems. This review places current work on DNA biophysics in historical context and illustrates the ongoing interplay between theory and experiment in this exciting field.

摘要

自双螺旋 DNA 结构阐明以来已经超过 50 年。尽管 DNA 生物学和生物化学领域的研究和进展十分活跃,但在 DNA 生物物理学领域仍有许多需要学习的地方。预测 DNA 的序列依赖性曲率和柔韧性具有挑战性。传统的 DNA 类似蠕虫链聚合物模型的适用性受到了挑战。导致 DNA 对弯曲和扭曲具有显著抵抗力的基本力仍然存在争议。在存在扭结蛋白和超螺旋应变的情况下,在体内测量到的 DNA 明显“软化”现象尚未被完全理解。目前正在将新的方法和见解应用于这些问题。本综述将 DNA 生物物理学的当前工作置于历史背景下,并说明了该令人兴奋的领域中理论和实验之间的持续相互作用。