Trotta E, D'Ambrosio E, Ravagnan G, Paci M
Consiglio Nazionale Ricerche, Istituto di Medicina Sperimentale, Viale Marx 15, I-00137 Rome, Italy.
J Biol Chem. 1996 Nov 1;271(44):27608-14. doi: 10.1074/jbc.271.44.27608.
The solution structure of the complex between 4', 6-diamidino-2-phenylindole (DAPI) and DNA oligomer (d(CGATCG))2 at a 2:1 drug/duplex ratio has been characterized by combined use of proton one- and two-dimensional NMR spectroscopy, molecular mechanics, and molecular dynamics computations. Intermolecular nuclear Overhauser effects (NOEs), DNA structure perturbations, and resonance shifts induced by binding provide evidence that DAPI interacts with DNA hexamer by two different binding mechanisms, in fast exchange on the NMR time scale, without any significant distortion of the B-type conformation of DNA hexamer. The results indicate that the ligand binds into the minor groove of the central 5'-ATC-3' region of the hexamer and on the outside of the oligomer by a pi,pi-stacking interaction with the terminal C1:G6 base pairs. A model for both binding mechanisms that accounts for all experimental data was generated by molecular mechanics and dynamics calculations based on experimental NOEs. In the minor groove binding, N2 amino group of G2 precludes a deep insertion of phenyl ring of DAPI into the groove. Position and orientation of the drug in the external stacking interaction resemble those suggested for intercalation of DAPI between C:G base pairs.
通过联合使用质子一维和二维核磁共振光谱、分子力学以及分子动力学计算，表征了在药物/双链体比例为2:1时，4',6-二脒基-2-苯基吲哚（DAPI）与DNA寡聚物（d(CGATCG)）2形成的复合物的溶液结构。分子间核Overhauser效应（NOE）、DNA结构扰动以及结合诱导的共振位移提供了证据，表明DAPI通过两种不同的结合机制与DNA六聚体相互作用，在核磁共振时间尺度上快速交换，且DNA六聚体的B型构象没有任何明显变形。结果表明，配体通过与末端C1:G6碱基对的π,π-堆积相互作用，结合到六聚体中央5'-ATC-3'区域的小沟以及寡聚物外部。基于实验NOE，通过分子力学和动力学计算生成了一个解释所有实验数据的两种结合机制的模型。在小沟结合中，G2的N2氨基阻止了DAPI苯环深入插入小沟。药物在外部堆积相互作用中的位置和取向类似于DAPI插入C:G碱基对之间所暗示的情况。
