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通过核磁共振和分子力学确定的含有三个胸腺嘧啶环的DNA发夹的溶液结构。

The solution structure of a DNA hairpin containing a loop of three thymidines determined by nuclear magnetic resonance and molecular mechanics.

作者信息

Boulard Y, Gabarro-Arpa J, Cognet J A, Le Bret M, Guy A, Téoule R, Guschlbauer W, Fazakerley G V

机构信息

Département de Biologie Cellulaire et Moléculaire, Centre d'Etudes de Saclay, Gif-sur-Yvette, France.

出版信息

Nucleic Acids Res. 1991 Oct 11;19(19):5159-67. doi: 10.1093/nar/19.19.5159.

DOI:10.1093/nar/19.19.5159
PMID:1923802
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC328870/
Abstract

We have determined by two-dimensional nuclear magnetic resonance studies and molecular mechanics calculations the three-dimensional solution structure of a 21 residue oligonucleotide capable of forming a hairpin structure with a loop of three thymidine residues. This structure is in equilibrium with a duplex form. At 33 degrees C, low ionic strength and in the presence of MgCl2 the hairpin form dominates in solution. Six Watson-Crick base pairs are formed topped by the loop structure. The residues 1-3 and 18-21 are not complementary and form dangling ends. Distance constraints have been derived from nuclear Overhauser enhancement measurements. These, together with molecular mechanics calculations, have been used to determine the structure. We do not observe stacking of thymidine residues either over the 3' or the 5' end of the stem.

摘要

我们通过二维核磁共振研究和分子力学计算，确定了一个由21个残基组成的寡核苷酸的三维溶液结构，该寡核苷酸能够形成一个带有三个胸腺嘧啶残基环的发夹结构。这种结构与双链体形式处于平衡状态。在33℃、低离子强度且存在MgCl2的情况下，发夹形式在溶液中占主导地位。形成了六个沃森-克里克碱基对，顶部为环结构。残基1-3和18-21不互补，形成悬垂末端。距离限制是通过核Overhauser增强测量得出的。这些限制与分子力学计算一起被用于确定结构。我们在茎的3'或5'末端均未观察到胸腺嘧啶残基的堆积。

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本文引用的文献

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Cruciform structures in supercoiled DNA.超螺旋DNA中的十字形结构。
Nature. 1981 Feb 5;289(5797):466-70. doi: 10.1038/289466a0.
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Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG.B-DNA十二聚体中的可逆弯曲和螺旋几何结构：CGCGAATTBrCGCG
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Cruciform structures in palindromic DNA are favored by DNA supercoiling.回文DNA中的十字形结构受DNA超螺旋的青睐。
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Hairpin-loop formation by inverted repeats in supercoiled DNA is a local and transmissible property.超螺旋DNA中反向重复序列形成发夹环是一种局部且可传递的特性。
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