Elcock A H, Rodger A, Richards W G
Physical and Theoretical Chemistry Laboratory, University of Oxford, United Kingdom.
Biopolymers. 1996 Sep;39(3):309-26. doi: 10.1002/(SICI)1097-0282(199609)39:3%3C309::AID-BIP4%3E3.0.CO;2-S.
Extensive molecular dynamics (MD) simulations have been used to investigate the intercalative binding of 9-hydroxyellipticine to the DNA oligonucleotide d(ATATATATATAT)2. Four independent simulations differing in the initial orientation of the drug at the intercalation site were carried out, and compared both with each other and a control simulation of the free DNA sequence. The structure of the latter was compared with structures obtained from x-ray crystallography and nmr spectroscopy, as well as the theoretically derived "alternating B-DNA" model [A. Klug et al. (1979), Journal of Molecular Biology, Vol. 131, p. 669]. The alternation of twist angles observed in experimental structures was reproduced in the simulation. All four independent simulations of the drug-DNA intercalation complex converged in placing the pyridine ring of the ellipticine chromophore in the major groove; in one case this involved a 180 degrees rotation of the drug at the intercalation site. At a more detailed level, the drug is seen to be capable of adopting several distinct orientations, each stable over a period of hundreds of pico-seconds. Despite the presence of several polar groups in the drug, however, no direct hydrogen bonding to the DNA occurs; instead, interactions between the methyl groups of the drug and the thymine bases at the intercalation site appear important in determining the orientational preferences of the drug. Comparison of the intercalation complexes with the free DNA sequence shows a degree of unwinding resulting from intercalation, in good agreement with experimental results, but spread over the three central base-pair steps, not confined to the intercalation site itself. Measurements of torsional rigidity indicate only a slight stiffening of the DNA restricted to the immediate site of intercalation. The structures obtained from the MD simulations were used to calculate theoretical CD spectra, with separate simulations giving very different results. This appears to indicate that given an accurate assignment of the main electronic transition dipole moment of the ellipticine chromophore, discrimination of the more realistic binding geometries may be possible. The relative merits of the various drug orientations observed in the simulations are discussed and a perpendicular orientation of the drug at the intercalation site is considered to be the most consistent with experimental data. While the simulations themselves represent a total of over 2 ns, however, the differences apparent between independent runs indicate that longer simulation times will be required before a complete, unequivocal view of DNA intercalation is obtained.
广泛的分子动力学（MD）模拟已被用于研究9-羟基玫瑰树碱与DNA寡核苷酸d(ATATATATATAT)2的嵌入结合。进行了四个在嵌入位点药物初始取向不同的独立模拟，并将它们相互比较，同时与自由DNA序列的对照模拟进行比较。将后者的结构与通过X射线晶体学和核磁共振光谱获得的结构，以及理论推导的“交替B-DNA”模型[ A. Klug等人（1979年），《分子生物学杂志》，第131卷，第669页]进行了比较。模拟中重现了实验结构中观察到的扭曲角的交替。药物-DNA嵌入复合物的所有四个独立模拟在将玫瑰树碱发色团的吡啶环置于大沟中时都收敛；在一种情况下，这涉及药物在嵌入位点的180度旋转。在更详细的层面上，可以看到药物能够采取几种不同的取向，每种取向在数百皮秒的时间内都是稳定的。然而，尽管药物中有几个极性基团，但没有与DNA直接形成氢键；相反，药物的甲基与嵌入位点的胸腺嘧啶碱基之间的相互作用在确定药物的取向偏好方面似乎很重要。将嵌入复合物与自由DNA序列进行比较表明，嵌入导致了一定程度的解旋，这与实验结果非常一致，但这种解旋分布在三个中心碱基对步骤上，而不限于嵌入位点本身。扭转刚度的测量表明，DNA仅在嵌入的直接位点有轻微的变硬。从MD模拟获得的结构用于计算理论圆二色光谱，不同的模拟给出了非常不同的结果。这似乎表明，给定玫瑰树碱发色团主要电子跃迁偶极矩的准确赋值，可能能够区分更现实的结合几何结构。讨论了模拟中观察到的各种药物取向的相对优点，并且认为药物在嵌入位点的垂直取向与实验数据最一致。然而，虽然模拟本身总共超过2纳秒，但独立运行之间明显的差异表明，在获得DNA嵌入的完整、明确的观点之前，需要更长的模拟时间。
