Chary K V, Hosur R V, Govil G, Tan Z K, Miles H T
Biochemistry. 1987 Mar 10;26(5):1315-22. doi: 10.1021/bi00379a017.
Resonance assignments of nonexchangeable base and sugar protons of the self-complementary dodecanucleotide d(GAATTCGAATTC) have been obtained by using the two-dimensional Fourier transform NMR methods correlated spectroscopy and nuclear Overhauser effect spectroscopy. Conformational details about the sugar pucker, the glycosidic dihedral angle, and the overall secondary structure of the molecule have been derived from the relative intensities of cross peaks in the two-dimensional NMR spectra in aqueous solution. It is observed that d(GAATTCGAATTC) assumes a novel double-helical structure. The solution conformations of the two complementary strands are identical, unlike those observed in a related sequence in the solid state. Most of the five-membered sugar rings adopt an unusual O1'-endo geometry. All the glycosidic dihedral angles are in the anti domain. The AATT segments A2-T5 and A8-T11 show better stacking compared to the rest of the molecule. These features fit into a right-handed DNA model for the above two segments, with the sugar geometries different from the conventional ones. There are important structural variations in the central TCG portion, which is known to show preferences for DNase I activity, and between G1-A2 and G7-A8, which are cleavage points in the EcoRI recognition sequence. The sugar puckers for G1 and G7 are significantly different from the rest of the molecule. Further, in the three segments mentioned above, the sugar phosphate geometry is such that the distances between protons on adjacent nucleotides are much larger than those expected for a right-handed DNA. We suggest that such crevices in the DNA structure may act as "hot points" in initiation of protein recognition.
通过使用二维傅里叶变换核磁共振方法，即相关谱和核Overhauser效应谱，已获得了自互补十二聚体核苷酸d(GAATTCGAATTC)中不可交换碱基和糖质子的共振归属。关于糖环构象、糖苷二面角以及分子整体二级结构的详细信息，是从水溶液中二维核磁共振谱交叉峰的相对强度推导出来的。观察到d(GAATTCGAATTC)呈现出一种新颖的双螺旋结构。两条互补链的溶液构象是相同的，这与在固态下相关序列中观察到的情况不同。大多数五元糖环采用不寻常的O1'-内向构象。所有糖苷二面角都处于反式区域。与分子的其余部分相比，AATT片段A2 - T5和A8 - T11显示出更好的堆积。这些特征符合上述两个片段的右手DNA模型，其糖的几何形状与传统的不同。在已知对DNase I活性有偏好的中央TCG部分，以及在EcoRI识别序列中的切割点G1 - A2和G7 - A8之间，存在重要的结构差异。G1和G7的糖环构象与分子的其余部分有显著不同。此外，在上述三个片段中，糖磷酸酯的几何形状使得相邻核苷酸上质子之间的距离比右手DNA预期的距离大得多。我们认为，DNA结构中的这种缝隙可能在蛋白质识别起始过程中充当“热点”。
