Strahan G D, Shafer R H, Keniry M A
Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco 94143.
Nucleic Acids Res. 1994 Dec 11;22(24):5447-55. doi: 10.1093/nar/22.24.5447.
Two-dimensional 1H NMR studies on the dimeric hairpin quadruplex formed by d(G3T4G3) in the presence of either NaCl or KCl are presented. In the presence of either salt, the quadruplex structure is characterized by half the guanine nucleosides in the syn conformation about the glycosidic bond, the other half in the anti conformation, as reported for other similar sequences. However, 1H NOESY and 1H-31P heteronuclear correlation experiments demonstrate that the deoxyguanosines do not strictly alternate between syn and anti along individual strands. Thus we find the following sequences with regard to glycosidic bond conformation: 5'-G1SG2SG3AT4AT5A-T6AT7AG8SG9AG10A-3' and 5'-G11SG12AG13AT14AT1 5AT16AT17AG18SG19SG20A-3', where S and A denote syn and anti, respectively. This represents the first experimental evidence for a nucleic acid structure containing two sequential nucleosides in the syn conformation. The stacking interactions of the resulting quadruplex quartets and their component bases have been evaluated using unrestrained molecular dynamics calculations and energy component analysis. These calculations suggest that the sequential syn-syn/anti-anti and syn-anti quartet stacks are almost equal in energy, whereas the anti-syn stack, which is not present in our structure, is energetically less favorable by about 4 kcal/mol. Possible reasons for this energy difference and its implications for the stability of quadruplex structures are discussed.
本文展示了在NaCl或KCl存在下，由d(G3T4G3)形成的二聚体发夹四链体的二维1H NMR研究。与其他类似序列的报道一样，在任何一种盐存在的情况下，四链体结构的特征是，糖苷键周围约一半的鸟嘌呤核苷处于顺式构象，另一半处于反式构象。然而，1H NOESY和1H-31P异核相关实验表明，脱氧鸟苷在单链上并非严格地在顺式和反式之间交替。因此，我们发现了以下关于糖苷键构象的序列：5'-G1SG2SG3AT4AT5A-T6AT7AG8SG9AG10A-3'和5'-G11SG12AG13AT14AT1 5AT16AT17AG18SG19SG20A-3'，其中S和A分别表示顺式和反式。这是核酸结构中含有两个连续顺式构象核苷的首个实验证据。利用无约束分子动力学计算和能量成分分析，对所得四链体四重奏及其组成碱基的堆积相互作用进行了评估。这些计算表明，连续的顺-顺/反-反和顺-反四重奏堆积在能量上几乎相等，而我们结构中不存在的反-顺堆积在能量上不利约4 kcal/mol。讨论了这种能量差异的可能原因及其对四链体结构稳定性的影响。
