Dixit Surjit B, Pitici Felicia, Beveridge D L
Chemistry Department and Molecular Biophysics Program, Wesleyan University, Middletown, CT 06459, USA.
Biopolymers. 2004 Dec 15;75(6):468-79. doi: 10.1002/bip.20157.
Molecular dynamics (MD) simulations have been performed on the A6 containing DNA dodecamers d(GGCAAAAAACGG) solved by NMR and d(CGCAAAAAAGCG) solved by crystallography. The experimental structures differ in the direction of axis bending and in other small but important aspects relevant to the DNA curvature problem. Five nanosecond MD simulations of each sequence have been performed, beginning with both the NMR and crystal forms as well as canonical B-form DNA. The results show that all simulations converge to a common form in close proximity to the observed NMR structure, indicating that the structure obtained in the crystal is likely a strained form due to packing effects. A-tracts in the MD model are essentially straight. The origin of axis curvature is found at pyrimidine-purine steps in the flanking sequences.
已对通过核磁共振（NMR）解析的含A6的DNA十二聚体d(GGCAAAAAACGG)和通过晶体学解析的d(CGCAAAAAAGCG)进行了分子动力学（MD）模拟。实验结构在轴弯曲方向以及与DNA曲率问题相关的其他虽小但重要的方面存在差异。对每个序列进行了5纳秒的MD模拟，起始结构既有NMR形式和晶体形式，也有标准B型DNA。结果表明，所有模拟都收敛到与观察到的NMR结构非常接近的一种共同形式，这表明晶体中获得的结构可能是由于堆积效应而产生的一种应变形式。MD模型中的A序列基本是直的。轴曲率的起源位于侧翼序列中的嘧啶 - 嘌呤步。
