CATION-BINDING ENVIRONMENTS ON DEOXYOLIGONUCLEOTIDES

脱氧寡糖核苷酸的阳离子结合环境

• 批准号: 2180333
• 负责人: WILLIAM H BRAUNLIN
• 金额: $ 13.03万
• 依托单位: UNIVERSITY OF NEBRASKA LINCOLN
• 依托单位国家: 美国
• 财政年份: 1988
• 资助国家: 美国
• 起止时间: 1988-09-20 至 1996-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/2180333
• 关键词: DNA; X ray crystallography; biophysics; cadmium; calcium; cations; chemical binding; chemical chain length; circular dichroism; cobalt; computer program /software; computer simulation; conformation; crystallization; hydrogen bond; ionic bond; ionic strengths; magnesium; molecular dynamics; nuclear magnetic resonance spectroscopy; nucleic acid sequence; nucleic acid structure; oligonucleotides; physical model; polyamines; stereochemistry; stereoisomer; thermodynamics; water solution

The local structure of oligonucleotides can be exquisitely sensitive to the presence of multivalent cations in solution. This structural variability depends significantly on oligonucleotide sequence as well as cation type, and hence does not result from nonspecific cation associations. The goal of the proposed work is to clarify the origins of these structural effects. The dynamic behavior of bound cations is sensitive to the relative contributions of specific and nonspecific cation binding. These dynamics will be monitored by the nmr of the bound cations. The structural consequences of cation binding will in turn be determined by two-dimensional proton nmr. Multinuclear nmr and equilibrium binding studies are proposed in order to examine the roles of simple cations in stabilizing oligonucleotide conformations and in promoting oligonucleotide structural transitions. Circular dichroism will provide an initial characterization of cation-induced structural perturbations. Cation nmr relaxation and pulsed field gradient diffusion experiments will be used to monitor the mobility (translational, rotational and internal) of cations in oligonucleotide solution. Cation nmr experiments will also be used to examine the effect of DNA length and salt concentration on specific and nonspecific cation associations. These studies will be complemented by thermodynamic binding measurements of Donnan equilibria. Proton nmr, x-ray diffraction studies and molecular modelling will provide additional information regarding the nature of cation-induced structural perturbations, and the geometry of cation binding sites. The primary focus of the proposed work will be on double-helical oligonucleotide structures involving Watson-Crick base-pairing. However, exploratory work is also proposed to examine cation effects on unusual structures that may be important for homologous recombination (e.g. junction structures), regulation of transcription (e.g. triple helical structures) and for the stabilization of the ends of chromosomes (e.g. G-rich telomeric sequences). Specifically, experiments are proposed in order (1) To define cation effects on the overall geometry of selected oligonucleotides. (2) To characterize the local environment of specifically bound cations. (3) To correlate the dynamics of bound cations to cation-induced oligonucleotide structural transitions. (4) To determine experimentally the effect of DNA length on local and global cation binding to short oligonucleotides. (5) To explore cation binding to unusual oligonucleotide structures.

寡核苷酸的局部结构可以对 溶液中存在多价阳离子。 这种结构性 变异性显著取决于寡核苷酸序列， 阳离子类型，因此不是由非特异性阳离子引起的 协会. 拟议工作的目标是澄清的起源 这些结构效应。 结合阳离子的动力学行为是 对特异性和非特异性的相对贡献敏感 阳离子结合 这些动力学将由束缚的NMR监测 阳离子。 阳离子结合的结构后果反过来将是 通过二维质子NMR测定。 多核核磁共振和平衡结合研究的建议，以 检查简单阳离子在稳定寡核苷酸中的作用 构象和促进寡核苷酸结构转变。 圆二色性将提供一个初步的表征 阳离子诱导的结构扰动。 阳离子核磁共振弛豫和 脉冲场梯度扩散实验将用于监测 流动性（平移，旋转和内部）的阳离子在 寡核苷酸溶液。 阳离子核磁共振实验也将用于 研究DNA长度和盐浓度对特异性和 非特异性阳离子缔合。 这些研究将得到以下方面的补充： Donnan平衡的热力学结合测量。 质子核磁共振， X射线衍射研究和分子模型将提供更多的 关于阳离子诱导的结构的性质的信息 扰动和阳离子结合位点的几何形状。 拟议工作的主要重点将是双螺旋 涉及沃森-克里克碱基配对的寡核苷酸结构。 然而，在这方面， 还提出了探索性工作，以检查阳离子对异常 对于同源重组可能重要的结构（例如， 连接结构）、转录调节（例如三螺旋 结构）和用于稳定染色体末端（例如， 富含G的端粒序列）。 具体地，实验在以下文献中提出： 顺序（1）定义阳离子对所选材料的整体几何形状的影响 寡核苷酸(2)描述当地的环境 特异性结合阳离子。(3)将束缚的动力学 阳离子到阳离子诱导的寡核苷酸结构转变。(4)到 通过实验确定DNA长度对局部和全局的影响， 阳离子与短寡核苷酸结合。(5)探索阳离子结合 不寻常的寡核苷酸结构