NMR structure of a cyclic polyamide-DNA complex.
NMR structure of a cyclic polyamide-DNA complex.
复制标题
DOI：
10.1021/ja0373622
复制
发表时间：
2004-06
影响因子：
15
通讯作者：
Qing Zhang;T. J. Dwyer;V. Tsui;D. Case;Junhyeong Cho;P. Dervan;D. Wemmer
中科院分区：
文献类型：
--
作者：
Qing Zhang;T. J. Dwyer;V. Tsui;D. Case;Junhyeong Cho;P. Dervan;D. Wemmer
由核磁共振限制的分子力学推导出了一种环状聚酰胺配体与DNA低聚物络合的溶液结构。聚酰胺，环-γ-ImPyPy-γ-PyPyPy-，结合到靶DNA与纳摩尔的解离常数，其特征在于通过定量足迹先前报道。2D（1）H NMR数据用于产生距离限制，该距离限制限定了具有DNA双链体d（5 ′-GCCTGTTAGCG-3 ′）：d（5 ′-CGCTAACAGGC-3 ′）的该环状聚酰胺的结构。数据解释使用完整的松弛矩阵分析的NOESY交叉峰强度与程序MARDIGRAS。基于NMR的距离限制（共276个）应用于使用溶剂模型的受限制分子动力学计算中，得到配体和结合位点的rmsd约为1 A的结构。所得的结构表明结合位点的DNA发生了一些变形。来自环化的约束导致相对于未连接的复合物，环状配体的一半中的环的堆叠改变。尽管如此，与DNA的相互作用与在未连接的复合物中发现的非常相似。配体酰胺和DNA亚氨基质子交换率的测量表明配体的解离非常缓慢，并表明DNA可以经历开放的波动，而配体是绑定的，虽然配体的存在降低了它们的频率相对于游离DNA。
The solution structure of a cyclic polyamide ligand complexed to a DNA oligomer, derived from NMR restrained molecular mechanics, is presented. The polyamide, cyclo-gamma-ImPyPy-gamma-PyPyPy-, binds to target DNA with a nanomolar dissociation constant as characterized by quantitative footprinting previously reported. 2D (1)H NMR data were used to generate distance restraints defining the structure of this cyclic polyamide with the DNA duplex d(5'-GCCTGTTAGCG-3'):d(5'-CGCTAACAGGC-3'). Data interpretation used complete relaxation matrix analysis of the NOESY cross-peak intensities with the program MARDIGRAS. The NMR-based distance restraints (276 total) were applied in restrained molecular dynamics calculations using a solvent model, yielding structures with an rmsd for the ligand and binding site of approximately 1 A. The resulting structures indicate some distortion of the DNA in the binding site. The constraints from cyclization lead to altered stacking of the rings in the halves of the cyclic ligand relative to unlinked complexes. Despite this, the interactions with DNA are very similar to what has been found in unlinked complexes. Measurements of ligand amide and DNA imino proton exchange rates indicate very slow dissociation of the ligand and show that the DNA can undergo opening fluctuations while the ligand is bound although the presence of the ligand decreases their frequency relative to the free DNA.