DNA的各向异性柔韧性与核小体结构
Anisotropic flexibility of DNA and the nucleosomal structure.
作者信息
Zhurkin V B, Lysov Y P, Ivanov V I
出版信息
Nucleic Acids Res. 1979 Mar;6(3):1081-96. doi: 10.1093/nar/6.3.1081.
Abstract
Potential energy calculations of the DNA duplex dimeric subunit show that the double helix may be bent in the direction of minor and major grooves much more easily than in other directions. It is found that the total winding angle of DNA decreases upon such bending. A new model for DNA folding in the nucleosome is proposed on the basis of these findings according to which the DNA molecule is kinked each fifth base pair to the side of the minor and major grooves alternatively. The model explains the known contradiction between a C-like circular dichroism for the nucleosomal DNA and the nuclease digestion data, which testify to the B-form of DNA.
摘要
对DNA双链二聚体亚基的势能计算表明，双螺旋向小沟和大沟方向弯曲可能比向其他方向弯曲更容易。研究发现，DNA的总缠绕角在这种弯曲时会减小。基于这些发现，提出了一种核小体中DNA折叠的新模型，根据该模型，DNA分子每隔五个碱基对交替向小沟和大沟一侧弯折。该模型解释了核小体DNA的C类圆二色性与核酸酶消化数据之间已知的矛盾，核酸酶消化数据证明DNA为B型。
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本文引用的文献
1
Stereochemistry of nucleic acids and polynucleotides. 3. Electronic charge distribution.核酸与多核苷酸的立体化学。3. 电子电荷分布。
Biopolymers. 1971;10(7):1159-67. doi: 10.1002/bip.360100707.
2
The geometry of nucleic acids.核酸的几何学
Prog Biophys Mol Biol. 1970;21:265-319. doi: 10.1016/0079-6107(70)90027-1.
3
Flexibility of DNA.DNA的柔韧性
Biopolymers. 1974 Jan;13(1):217-26. doi: 10.1002/bip.1974.360130115.
4
Different conformations of double-stranded nucleic acid in solution as revealed by circular dichroism.圆二色光谱揭示溶液中双链核酸的不同构象。
Biopolymers. 1973;12(1):89-110. doi: 10.1002/bip.1973.360120109.
5
Mixed conformations of deoxyribonucleic acid in intact chromatin isolated by various preparative methods.通过各种制备方法分离得到的完整染色质中脱氧核糖核酸的混合构象。
Biochemistry. 1972 Nov 7;11(23):4347-58. doi: 10.1021/bi00773a023.
6
Subunit structure of chromatin.染色质的亚基结构。
Nature. 1974 Sep 20;251(5472):249-51. doi: 10.1038/251249a0.
7
Determination of the activation energy for pseudorotation of the furanose ring in nucleosides by 13-C nuclear-magnetic-resonance relaxation.通过碳-13核磁共振弛豫测定核苷中呋喃糖环假旋转的活化能。
Eur J Biochem. 1975 May 6;53(2):517-24. doi: 10.1111/j.1432-1033.1975.tb04094.x.
8
Kinky helix.卷曲螺旋
Nature. 1975 Jun 12;255(5509):530-3. doi: 10.1038/255530a0.
9
Conformational structure of polynucleotides around the O-P bonds: refined parameters for CPF calculations.
Biopolymers. 1976 Nov;15(11):2303-7. doi: 10.1002/bip.1976.360151119.
10
The flexibility of low molecular weight double-stranded DNA as a function of length. I. Light scattering measurements and the estimation of persistence lengths from light scattering, sedimentation and viscosity.低分子量双链DNA的柔韧性与长度的关系。I. 光散射测量以及通过光散射、沉降和粘度估算持久长度
Biophys Chem. 1976 Sep;5(3):301-18. doi: 10.1016/0301-4622(76)80042-7.
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