NMR STUDIES OF VACCINIA VIRUS DNA SEQUENCES

痘苗病毒 DNA 序列的 NMR 研究

• 批准号: 6347975
• 负责人: NIKOLAI B ULYANOV
• 金额: $ 0.61万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2000
• 资助国家: 美国
• 起止时间: 2000-07-01 至 2001-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6347975
• 关键词: bacteria; biomedical resource; environmental toxicology; enzymes

The DNA of vaccinia virus is a large (180 kbp) linear duplex with cross-linked termini, such that a single strand circle forms upon denaturation. The terminal 10 kbp are inverted repeats, and the ultimate 106 nucleotides at each end form incompletely base paired hairpins; they are involved in the formation of replicative intermediates of vaccinia virus. The terminal hairpins are extremely AT-rich (96% AT) and contain an asymmetric internal loop and a number of single base bulges. We are interested in a structure of a vaccinia virus DNA fragment which contains two unpaired residues (G and C) within the context of a 100% AT-rich duplex. We designed a construct containing this sequence (a 29-mer hairpin loop DNA) and a corresponding control construct lacking the unpaired residues (a 27-mer hairpin loop DNA), and acquired sets of 2D proton NMR data for high-resolution structure calculations. We have nearly completed proton resonance assignments for both molecules, and currently we are carrying out structure calculations for the control 27-mer sequence. The interactive computer graphics software developed at the Computer Graphics Laboratory is used at all stages of the refinement: firstly, to examine the self-consistency of the experimental restraints, then, to monitor the course of the refinement, and finally, to visualize and analyze the final structure.

牛痘病毒的DNA是一个大的（180 kbp）线性双链体， 交联的末端，使得单链环在 变性 末端10 kbp是反向重复序列， 最后每端106个核苷酸形成不完全碱基配对 发夹;它们参与复制的形成 牛痘病毒的中间体。 末端的发夹结构 AT丰富（96% AT），包含一个不对称的内环和一个数字 一个单一的基地隆起。 我们感兴趣的是牛痘的结构 含有两个未配对残基（G和C）的病毒DNA片段 在100%AT富集双链体的情况下。 我们设计了一个结构 含有该序列（29-mer发夹环DNA）和 缺少未配对残基的相应对照构建体（a 27-mer发夹环DNA），并获得了2D质子NMR数据集，用于 高分辨率结构计算。 我们几乎完成了 两种分子的质子共振分配，目前我们正在 对对照27-mer序列进行结构计算。 在计算机开发的交互式计算机图形软件 图形实验室用于细化的所有阶段：首先， 来检验实验约束的自洽性，那么， 监控提炼过程，最后，可视化， 分析最终结构。