B型DNA中的BII转变
BI-BII transitions in B-DNA.
作者信息
Hartmann B, Piazzola D, Lavery R
机构信息
Laboratoire de Biochimie Théorique, CNRS URA77, Paris, France.
出版信息
Nucleic Acids Res. 1993 Feb 11;21(3):561-8. doi: 10.1093/nar/21.3.561.
Abstract
Molecular modelling is used to study the conformational and energetic aspects of BI-BII transitions within the backbone of a B-DNA dodecamer d(CATGACGTCATG) whose fine structure has previously been determined by molecular modelling combined with NMR spectroscopy. It is shown that while the dodecamer under investigation does not contain any BII junctions, the central CpG step can most easily undergo the transition. More generally, it is also found that the base sequence and hence the backbone geometry of a DNA segment, strongly influences both the conformational impact of the transition, the associated energy barrier and the stability of the resulting BII state.
摘要
分子建模用于研究B-DNA十二聚体d(CATGACGTCATG)主链内BI-BII转变的构象和能量方面，该十二聚体的精细结构先前已通过分子建模与核磁共振光谱相结合的方法确定。结果表明，虽然所研究的十二聚体不包含任何BII连接，但中央的CpG步最容易发生转变。更普遍地，还发现DNA片段的碱基序列以及因此其主链几何结构，强烈影响转变的构象影响、相关的能量屏障以及所得BII状态的稳定性。
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本文引用的文献
1
Conformational flexibility of DNA: polymorphism and handedness.DNA的构象灵活性：多态性与螺旋方向
Proc Natl Acad Sci U S A. 1980 Nov;77(11):6486-90. doi: 10.1073/pnas.77.11.6486.
2
Helix geometry, hydration, and G.A mismatch in a B-DNA decamer.B型DNA十聚体中的螺旋几何结构、水合作用及G·A错配
Science. 1987 Oct 23;238(4826):498-504. doi: 10.1126/science.3310237.
3
A general approach to the optimization of the conformation of ring molecules with an application to valinomycin.一种优化环状分子构象的通用方法及其在缬氨霉素中的应用。
J Biomol Struct Dyn. 1986 Dec;4(3):443-62. doi: 10.1080/07391102.1986.10506361.
4
The flexibility of the nucleic acids: (II). The calculation of internal energy and applications to mononucleotide repeat DNA.核酸的柔韧性：（II）。单核苷酸重复DNA的内能计算及应用
J Biomol Struct Dyn. 1986 Apr;3(5):989-1014. doi: 10.1080/07391102.1986.10508478.
5
Energetic coupling between DNA bending and base pair opening.DNA弯曲与碱基对打开之间的能量耦合。
Proc Natl Acad Sci U S A. 1988 Oct;85(19):7231-5. doi: 10.1073/pnas.85.19.7231.
6
Definitions and nomenclature of nucleic acid structure parameters.
J Mol Biol. 1989 Feb 20;205(4):787-91. doi: 10.1016/0022-2836(89)90324-0.
7
Identification of a cyclic-AMP-responsive element within the rat somatostatin gene.大鼠生长抑素基因中环磷酸腺苷反应元件的鉴定。
Proc Natl Acad Sci U S A. 1986 Sep;83(18):6682-6. doi: 10.1073/pnas.83.18.6682.
8
Theoretical prediction of base sequence effects in DNA. Experimental reactivity of Z-DNA and B-Z transition enthalpies.
J Mol Biol. 1989 May 20;207(2):433-44. doi: 10.1016/0022-2836(89)90265-9.
9
10
Defining the structure of irregular nucleic acids: conventions and principles.
J Biomol Struct Dyn. 1989 Feb;6(4):655-67. doi: 10.1080/07391102.1989.10507728.
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