NMR assessment of the global shape of a non-labelled DNA dodecamer containing a tandem of G-T mismatches
NMR assessment of the global shape of a non-labelled DNA dodecamer containing a tandem of G-T mismatches
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DOI：
10.1002/mrc.1902
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发表时间：
2006-12-01
影响因子：
2
通讯作者：
Boulard, Yves
中科院分区：
文献类型：
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作者：
Alvarez-Salgado, Francisco;Desvaux, Herve;Boulard, Yves
我们用核磁共振对两个非标记自互补DNA十二聚体d(GACTGTACAGTC)(2)和d(GACTGTGCAGTC)(2)进行了溶液研究，第二个序列由两个G-T错配组成。使用从NOE效应单独提取的距离或使用NOE和RDC约束来确定结构，在三种不同的液晶介质中测量。我们确保了我们关于介元对DNA结构的影响的数据，以及RDC作为约束被纳入到协议精化中的方式，是一致的。我们还测试了不同的RDC组的影响，以及优化D-a和R计算的最佳方法，并比较了十种最佳能量最终结构的分辨率和精度。添加一小组RDC约束显著改进了最终确定的结构。我们利用RDC的特殊性，即它包含方向信息，探索了DNA双链的整体形状；发现双链没有很大的曲率。对于G-T碱基对，我们在这个特殊的序列(G-T错配的串联)中观察到了一种新的碱基配对模式，其中包括形成一个分叉的氢键。版权所有(C)2006 John Wiley&Sons，Ltd.
We have carried out a solution study of two non-labelled self-complementary DNA dodecamers d(GACTGTACAGTC)(2) and d(GACTGTGCAGTC)(2) by NMR, the second sequence composed of two G-T mismatches. Structures were determined using distances extracted from NOE effects alone or using both NOE and RDC constraints, measured in three different liquid crystalline media. We ensured that our data on the influence of the mesogen on the DNA structures, and the way in which the RDCs were incorporated as constraints in the protocol refinement, were consistent. We also tested the influence of different sets of RDCs and the best means of optimizing the calculation of D-a and R. Resolution and accuracy of the ten best energy final structures were compared. The addition of a small set of RDC constraints significantly improves the final determined structures. We took advantage of the specificity of the RDC, i.e. it contains orientational information, and explored the global shape of the DNA duplexes; it was found that the duplexes do not have a large curvature. For the G-T base pair, we observed, in this particular sequence (tandem of G-T mismatches), a new pattern of base pairing, which involved the formation of a bifurcated hydrogen bond. Copyright (C) 2006 John Wiley & Sons, Ltd.