de Souza O N, Goodfellow J M
Department of Crystallography, Birkbeck College, London, U.K.
J Comput Aided Mol Des. 1994 Jun;8(3):307-22. doi: 10.1007/BF00126748.
We have undertaken molecular dynamics simulations on the d(CGCAAAAAAGCG).d(CGCTTTTTTGCG) dodecamer in solution. In this study, we focus on aspects of conformation and dynamics, including the possibility of cross-strand hydrogen bonds. We compare our results with those from crystallography as well as infrared, Raman and NMR spectroscopy and cyclization kinetics. Our method of analysis allows us to visualise the curvature of the helix as a function of time during the simulation. We find that the major distortions of the helix axis path occur at the junctions between the (essentially straight) A-tract and the CG- and GC-tracts, although at one junction this is due to hyperflexibility (i.e., regions of high flexibility with no preferred direction of curvature), while at the other junction a static curvature is found (i.e., a preferred, sustained direction of curvature).
我们对溶液中的d(CGCAAAAAAGCG).d(CGCTTTTTTGCG)十二聚体进行了分子动力学模拟。在本研究中，我们关注构象和动力学方面，包括跨链氢键的可能性。我们将我们的结果与来自晶体学以及红外、拉曼和核磁共振光谱和环化动力学的结果进行比较。我们的分析方法使我们能够在模拟过程中可视化螺旋曲率随时间的变化。我们发现，螺旋轴路径的主要扭曲发生在（基本为直线的）A序列与CG和GC序列的交界处，不过在一个交界处这是由于超柔性（即具有高灵活性且无优先曲率方向的区域），而在另一个交界处则发现了静态曲率（即优先的、持续的曲率方向）。
