单链DNA“A”和“B”型的螺旋几何结构源自二聚体亚基的最低能量构象。
Helix geometry of single stranded DNA 'A' and 'B' forms from minimum energy conformations of dimeric subunits.
作者信息
Hingerty B, Broyde S
出版信息
Nucleic Acids Res. 1978 Jan;5(1):127-37. doi: 10.1093/nar/5.1.127.
Abstract
Low energy conformations with dihedral angles similar to those occurring in fibers of the 'A' and 'B' forms of DNAs have been calculated for the deoxydinucleoside phosphates dApdA, dCpdC, dTpdT, dGpdG and dGpdC (1-3). These conformers have been used as building blocks for generating larger single stranded polymers, whose helical parameters we have calculated. We find that single stranded 'A' and 'B' form helices tend to be narrower and more tightly wound than the duplexes obtained in fibers (4,5). This is consistent with experimental observations on single stranded fibers of poly (rC) (6). We also find that the different sequences have different helix geometries. In addition, it is observed that large variations in helix geometry for a given sequence are achievable at little energetic cost.
摘要
已针对脱氧二核苷磷酸dApdA、dCpdC、dTpdT、dGpdG和dGpdC（1 - 3）计算出具有与DNA“A”和“B”形式纤维中出现的二面角相似的低能构象。这些构象异构体已被用作构建更大单链聚合物的结构单元，我们已计算出其螺旋参数。我们发现，单链“A”和“B”形式的螺旋往往比纤维中获得的双链体更窄且缠绕更紧密。这与聚（rC）单链纤维的实验观察结果一致（6）。我们还发现不同的序列具有不同的螺旋几何形状。此外，观察到对于给定序列，在几乎不消耗能量的情况下可实现螺旋几何形状的巨大变化。
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本文引用的文献
1
Possible polypeptide configurations of proteins from the viewpoint of internal rotation potential.
Adv Enzymol Relat Subj Biochem. 1961;23:1-27. doi: 10.1002/9780470122686.ch1.
2
The molecular structure of polyadenylic acid.聚腺苷酸的分子结构。
J Mol Biol. 1961 Feb;3:71-86. doi: 10.1016/s0022-2836(61)80009-0.
3
Interactions contributing to the stability of a polynucleotide helical chain role of the 2'-hydroxyl and of the phosphate groups.对多核苷酸螺旋链稳定性有贡献的相互作用：2'-羟基和磷酸基团的作用。
Biochim Biophys Acta. 1969 Jul 22;186(1):110-23. doi: 10.1016/0005-2787(69)90493-6.
4
Molecular and crystal structure of the polynucleotide complex: polyinosinic acid plus polydeoxycytidylic acid.多核苷酸复合物的分子结构与晶体结构：聚肌苷酸加聚脱氧胞苷酸
J Mol Biol. 1970 Mar 14;48(2):243-61. doi: 10.1016/0022-2836(70)90159-2.
5
The structure of a DNA-RNA hybrid.DNA-RNA杂交体的结构。
Proc Natl Acad Sci U S A. 1967 Jun;57(6):1804-10. doi: 10.1073/pnas.57.6.1804.
6
Optimised parameters for A-DNA and B-DNA.A-DNA和B-DNA的优化参数。
Biochem Biophys Res Commun. 1972 Jun 28;47(6):1504-9. doi: 10.1016/0006-291X(72)90243-4.
7
Conformational analysis of the sugar ring in nucleosides and nucleotides. Improved method for the interpretation of proton magnetic resonance coupling constants.核苷和核苷酸中糖环的构象分析。解释质子磁共振耦合常数的改进方法。
J Am Chem Soc. 1973 Apr 4;95(7):2333-44. doi: 10.1021/ja00788a038.
8
The dimensions and shapes of the furanose rings in nucleic acids.核酸中呋喃糖环的尺寸和形状。
Biochem J. 1972 Nov;130(2):453-65. doi: 10.1042/bj1300453.
9
Structural details of double-helix observed for DNAs containing alternating purine and pyrimidine sequences.在含有交替嘌呤和嘧啶序列的DNA中观察到双螺旋的结构细节。
J Mol Biol. 1974 Sep 15;88(2):523-33. doi: 10.1016/0022-2836(74)90499-9.
10
Structures for the polynucleotide complexes poly(dA) with poly (dT) and poly(dT) with poly(dA) with poly (dT).聚（dA）与聚（dT）以及聚（dT）与聚（dA）和聚（dT）形成的多核苷酸复合物的结构
J Mol Biol. 1974 Sep 15;88(2):509-21. doi: 10.1016/0022-2836(74)90498-7.
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