SOLUTION STRUCTURE OF 2 DNA OLIGONUCLEOTIDES: HIV

我们正致力于解决两个DNA的溶液结构 寡核苷酸：乙肝病毒DR1片段和GERE 识别碎片。这些是宿主识别的DNA片段 细胞RNA聚合酶II和枯草芽孢杆菌Gere蛋白， 分别进行了分析。这些化合物的NOESY和COSY核磁共振谱 寡核苷酸是以前获得的。随后， 分配共振并测量峰值音量。我们已经提炼了 这些数据使用Amber 4.1分子动力学包并使用 图形模型来生成PDB文件，我们使用该文件来运行这些 分子动力学计算。 我们已经制作了轨迹的电影来评估薄弱的部分 结构，并确定给定的运行是否在物理上 合情合理。

We are working on solving the solution structure of two DNA oligonucleotides: the Hepatitis B Dr1 fragment, and the gerE recognition fragment. These are the DNA fragments recognized by host cell RNA Polymerase II, and by the Bacillus subtilis protein gerE, respectively. The NOESY and COSY NMR spectra of these oligonucleotides were obtained previously. Subsequently, the resonances were assigned and peak volumes measured. We have refined these data using Amber 4.1 molecular dynamics package and used the graphics model to produce a pdb file which we used to run these molecular dynamics calculations. We have produced movies of trajectories to assess weak portions of the structure, and to determine whether a given run is physically reasonable.