NMR STUDY OF SLIPPED LOOP DNA STRUCTURE

Slipped Loop DNA Structure（SLS-DNA）是一种新的DNA结构类型 of folding折叠for nucleic核酸. 它可以形成DNA序列， 短的直接重复序列（约5-6个碱基对长），当一条链的 DNA是相对于另一个转移的。 两个循环，形成的结果， 这种移位具有形成三级碱基对潜力。 使用 结合DNAminiCarlo程序和交互式工作， MidasPlus分子图形，我们建立了一个模型的SLS。 我们 进行了一个高分辨率的核磁共振研究的模型25个核苷酸的DNA 序列，其被设计为形成作为同源二聚体的固定SLS。 然而，我们发现这种分子以不同的方式折叠， SLS相关拓扑。 这是一种新的核酸三级折叠， 我们称之为伪方结（PSQ）。 我们计算出 高分辨率结构的DNA伪方结在溶液中， 基于核奥弗豪泽效应数据。 SLS和PSQ序列 基序在单链DNA和RNA基因组中很常见，它们可能 发挥结构和/或功能作用。 目前，我们正在确定 这种来自病毒RNA基因组的基序适合于高分辨率 结构研究。 交互式计算机图形软件 在计算机图形实验室开发的用于所有阶段的 精炼：检验实验的自洽性 限制，以监测细化的过程，最后， 可视化并分析最终结构。

Slipped Loop DNA Structure (SLS-DNA) is a novel hypothetical type of folding for nucleic acids. It may form for DNA sequences with short direct repeats (about 5-6 base pairs long), when one strand of DNA is shifted relative to another. Two loops, formed as a result of such a shift, have a potential to form tertiary base pairs. Using a combination of the DNAminiCarlo program and interactive work with the MidasPlus molecular graphics, we built a model for the SLS. We carried out a high resolution NMR study of a model 25-nucleotide DNA sequence, which was designed to form an immobile SLS as a homodimer. However, we showed that this molecule folds in a distinct, albeit SLS-related topology. This is a novel tertiary fold of nucleic acids, which we call a Pseudosquare Knot (PSQ). We calculated a high-resolution structure for the DNA Pseudosquare Knot in solution, based on nuclear Overhauser effect data. Both SLS and PSQ sequence motifs are frequent in single-stranded DNA and RNA genomes; they may play structural and/or functional roles. Presently we are identifying such motifs from viral RNA genomes suitable for high-resolution structural studies. The interactive computer graphics software developed at the Computer Graphics Laboratory is used at all stages of the refinement: to examine the self-consistency of the experimental restraints, to monitor the course of the refinement, and finally, to visualize and analyze the final structure.