NMR STUDY OF SLIPPED LOOP DNA STRUCTURE

滑环DNA结构(SLS-DNA)是一种新的假说类型 核酸的折叠。它可能形成于DNA序列，具有 短的直接重复序列(大约5-6个碱基对长)，当一个链 DNA相对于另一个DNA发生了移位。两个环路，形成于 这样的转变，有可能形成三级碱基对。使用 将DNA微型卡罗计划和与 MidasPlus分子图形学，我们建立了SLS的模型。我们 对一种25核苷酸DNA模型进行了高分辨核磁共振研究 序列，该序列被设计成形成固定的SLS作为同源二聚体。 然而，我们发现这种分子折叠成一个明显的，尽管 与SLS相关的拓扑。这是一种新型的三重核酸， 我们称之为伪方结(PSQ)。我们计算了一个 溶液中DNA假平方结的高分辨结构， 基于核奥豪泽效应数据。SLS和PSQ序列 基序在单链DNA和RNA基因组中很常见；它们可能 扮演结构和/或功能角色。目前我们正在确认 这种来自病毒RNA基因组的适合高分辨率的基序 结构研究。交互式计算机图形软件 由计算机图形实验室开发，用于所有阶段的 精炼：检验实验的自我一致性 约束，以监控改进的过程，最后， 可视化并分析最终的结构。

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.