Clore G M, Oschkinat H, McLaughlin L W, Benseler F, Happ C S, Happ E, Gronenborn A M
Max-Planck-Institut für Biochemie, Martinsried bei München, FRG.
Biochemistry. 1988 May 31;27(11):4185-97. doi: 10.1021/bi00411a042.
The solution structure of the self-complementary dodecamer 5'd(CGCGPATTCGCG)2, containing a purine-thymine base pair within the hexameric canonical recognition site GAATTC for the restriction endonuclease EcoRI, is investigated by nuclear magnetic resonance spectroscopy and restrained molecular dynamics. Nonexchangeable and exchangeable protons are assigned in a sequential manner. A set of 228 approximate interproton distance restraints are derived from two-dimensional nuclear Overhauser enhancement spectra recorded at short mixing times. These distances are used as the basis for refinement using restrained molecular dynamics in which the interproton distance restraints are incorporated into the total energy function of the system in the form of effective potentials. Eight calculations are carried out, four starting from classical A-DNA and four from classical B-DNA. In all cases convergence to very similar B-type structures is achieved with an average atomic root mean square (rms) difference between the eight converged structures of 0.7 +/- 0.2 A, compared to a value of 6.5 A for that between the two starting structures. It is shown that the introduction of the purine-thymine mismatch does not result in any significant distortion of the structure. The variations in the helical parameters display a clear sequence dependence. The variation in helix twist and propeller twist follows Calladine's rules and can be attributed to the relief of interstrand purine-purine clash at adjacent base pairs. Overall the structure is straight. Closer examination, however, reveals that the central 5 base pair steps describe a smooth bend directed toward the major groove with a radius of curvature of approximately 38 A, which is compensated by two smaller kinks in the direction of the minor groove at base pair steps 3 and 9. These features can be explained in terms of the observed variation in roll and slide.
通过核磁共振光谱法和受限分子动力学研究了自互补十二聚体5'd（CGCGPATTCGCG）2的溶液结构，该十二聚体在限制性内切酶EcoRI的六聚体经典识别位点GAATTC内含有一个嘌呤 - 胸腺嘧啶碱基对。不可交换和可交换质子以序列方式进行归属。一组228个近似质子间距离约束来自在短混合时间记录的二维核Overhauser增强光谱。这些距离用作使用受限分子动力学进行精修的基础，其中质子间距离约束以有效势的形式纳入系统的总能量函数。进行了八次计算，四次从经典A - DNA开始，四次从经典B - DNA开始。在所有情况下都收敛到非常相似的B型结构，八个收敛结构之间的平均原子均方根（rms）差异为0.7±0.2 Å，而两个起始结构之间的该值为6.5 Å。结果表明，嘌呤 - 胸腺嘧啶错配的引入不会导致结构的任何显著扭曲。螺旋参数的变化显示出明显的序列依赖性。螺旋扭曲和螺旋桨扭曲的变化遵循卡拉丁规则，可归因于相邻碱基对间链间嘌呤 - 嘌呤冲突的缓解。总体而言，结构是直的。然而，更仔细的检查表明，中央5个碱基对步长描述了一个朝向大沟的平滑弯曲，曲率半径约为38 Å，这由碱基对步长3和9处小沟方向的两个较小扭结补偿。这些特征可以根据观察到的滚动和滑动变化来解释。
