Alvarez-Salgado Francisco, Desvaux Hervé, Boulard Yves
Laboratoire du Contrôle du Cycle Cellulaire, DSV/DBJC, Service de Biochimie et de Génétique Moléculaire, CEA-Saclay, 91191 Gif-sur-Yvette Cedex, France.
Magn Reson Chem. 2006 Dec;44(12):1081-9. doi: 10.1002/mrc.1902.
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.
我们通过核磁共振（NMR）对两条未标记的自互补DNA十二聚体d(GACTGTACAGTC)2和d(GACTGTGCAGTC)2进行了溶液研究，第二条序列由两个G-T错配组成。结构是通过单独从核Overhauser效应（NOE）中提取的距离，或使用在三种不同液晶介质中测量的NOE和残余偶极耦合（RDC）约束来确定的。我们确保了关于液晶元对DNA结构影响的数据，以及RDC作为约束条件纳入协议优化的方式是一致的。我们还测试了不同组RDC的影响以及优化D(a)和R计算的最佳方法。比较了十个最佳能量最终结构的分辨率和准确性。添加一小组RDC约束显著改善了最终确定的结构。我们利用了RDC的特异性，即它包含取向信息，并探索了DNA双链体的整体形状；发现双链体没有大的曲率。对于G-T碱基对，在这个特定序列（G-T错配串联）中，我们观察到了一种新的碱基配对模式，其中涉及形成一个分叉氢键。
