模拟DNA的极端拉伸。
Modelling extreme stretching of DNA.
作者信息
Lebrun A, Lavery R
机构信息
Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Paris, France.
出版信息
Nucleic Acids Res. 1996 Jun 15;24(12):2260-7. doi: 10.1093/nar/24.12.2260.
Abstract
Molecular modelling with Jumna is used to study extreme stretching of the DNA double helix. The results, which correlate well with recent nanomanipulation experiments, show how the double helix can be extended to twice its normal length before its base pairs break. Depending on the way the duplex is stretched two types of conformation can occur, either an unwound flat ribbon or a narrow fibre with negatively inclined base pairs. The energetics of both types of deformation are similar and existing structures show that at least the flat ribbon form can exist locally under biological conditions.
摘要
使用Jumna进行分子建模来研究DNA双螺旋的极限拉伸。这些结果与最近的纳米操作实验相关性良好，显示了双螺旋在其碱基对断裂之前如何能够扩展到其正常长度的两倍。根据双链拉伸的方式，会出现两种构象类型，要么是展开的扁平带，要么是碱基对呈负倾斜的窄纤维。两种变形类型的能量学相似，现有结构表明至少扁平带形式在生物学条件下可以局部存在。
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本文引用的文献
1
Physical studies of nucleic acid.核酸的物理研究。
Nature. 1951 May 12;167(4254):759-60. doi: 10.1038/167759a0.
2
Stretching DNA with a receding meniscus: Experiments and models.用后退弯月面拉伸DNA：实验与模型
Phys Rev Lett. 1995 Jun 5;74(23):4754-4757. doi: 10.1103/PhysRevLett.74.4754.
3
Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules.过度拉伸B型DNA：单个双链和单链DNA分子的弹性响应
Science. 1996 Feb 9;271(5250):795-9. doi: 10.1126/science.271.5250.795.
4
DNA: an extensible molecule.DNA：一种可延展的分子。
Science. 1996 Feb 9;271(5250):792-4. doi: 10.1126/science.271.5250.792.
5
Intercalation, DNA kinking, and the control of transcription.嵌入作用、DNA 扭结与转录调控
Science. 1996 Feb 9;271(5250):778-84. doi: 10.1126/science.271.5250.778.
6
A novel form of the DNA double helix imposed on the TATA-box by the TATA-binding protein.一种由TATA结合蛋白施加于TATA框上的新型DNA双螺旋结构。
Nat Struct Biol. 1996 Jan;3(1):32-7. doi: 10.1038/nsb0196-32.
7
Looking into the grooves of DNA.深入探究DNA的凹槽结构。
Biopolymers. 1993 Mar;33(3):479-90. doi: 10.1002/bip.360330314.
8
Crystal structure of a yeast TBP/TATA-box complex.酵母TBP/TATA盒复合物的晶体结构。
Nature. 1993 Oct 7;365(6446):512-20. doi: 10.1038/365512a0.
9
Modelling DNA conformational mechanics.
Biophys Chem. 1994 May;50(1-2):33-45. doi: 10.1016/0301-4622(94)85018-6.
10
Molecular basis of human 46X,Y sex reversal revealed from the three-dimensional solution structure of the human SRY-DNA complex.从人类SRY-DNA复合物的三维溶液结构揭示人类46,X,Y性反转的分子基础。
Cell. 1995 Jun 2;81(5):705-14. doi: 10.1016/0092-8674(95)90532-4.
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