DYNAMICS, RELAXATION, AND LOCAL MOTION IN DNA

DNA 中的动力学、放松和局部运动

• 批准号: 6240436
• 负责人: J M SCHURR
• 金额: $ 11.79万
• 依托单位: UNIVERSITY OF WASHINGTON
• 依托单位国家: 美国
• 财政年份: 1997
• 资助国家: 美国
• 起止时间: 1997-01-01 至 1997-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6240436
• 关键词: DNA; anions; carbon; cations; chemical hydration; circular dichroism; endonuclease; ethidium; fluorescence polarization; fluorescent dye /probe; gel electrophoresis; lasers; light scattering; molecular dynamics; molecular energy level; nuclear magnetic resonance spectroscopy; nucleic acid sequence; nucleic acid structure; protonation; stable isotope; synthetic nucleic acid; temperature; time resolved data

It is proposed to investigate certain aspects of DNA dynamics, structure, and hydration that may have significant roles in various biological processes. The amplitudes of local angular motion of selected groups in DNA provide information about its local deformability, which may be a significant factor in site-specific recognition and/or action of various proteins that interact with DNA. Whether the amplitudes of local angular motions in less stable non-standard structures, such as a hairpin loop, the third strand of a triplex, and a 4-arm Holiday junction, significantly exceed those in a normal duplex DNA is another question addressed here. Such amplitudes of local angular motion are determined by NMR relaxation measurements of selectively labelled synthetic DNAs in solution in conjunction with time-resolved fluorescence polarization anisotropy (FPA) measurements of intercalated ethidium (to characterize the global rotations) and recently developed theory. That same theory will also be used to estimate the errors incurred when the so-called model-free formulas for monodisperse spherical diffusors are applied to determine the amplitudes local angular motion of non-spherical molecules and molecules that dimerize appreciably. Possible long range effects of the SP1 transcriptional activator recognition sequence on the secondary structure of its flanking DNA are investigated by a variety of physical and biochemical methods, including dynamic light scattering (DLS), FPA, circular dichroism (CD) spectroscopy, optical melting and susceptibility to S1 nuclease. Any modulation of such long range effects upon binding the Sp1 protein will be similarly examined. Possible long range effects due to a particular mutation in the 434 repressor recognition sequence are also investigated by physical and biochemical techniques. The intrinsic twist and twist energy parameter are determined from measured topoisomer ratios after circularizing in the presence of various amounts of ethidium, again using recently developed theory. The effects of particular cations, anions, temperature, and other agents on the hydration of small DNA duplexes are examined via their effects on the hydrodynamic radius, which is measured by FPA of intercalated ethidium.

建议研究 DNA 动力学、结构、 和水合作用可能在各种生物中发挥重要作用 流程。 所选组的局部角运动的幅度 DNA 提供有关其局部变形能力的信息，这可能是 各种特定位点识别和/或行动的重要因素 与 DNA 相互作用的蛋白质。 是否局部角的幅值 不太稳定的非标准结构中的运动，例如发夹环， 三联体的第三条链和四臂假日交汇处， 另一个问题是显着超过正常双链 DNA 在此提出。 确定局部角运动的这种幅度 通过 NMR 弛豫测量选择性标记的合成 DNA 与时间分辨荧光偏振相结合的解决方案 插层乙锭的各向异性 (FPA) 测量（以表征 全球旋转）和最近发展的理论。 同样的理论 也将用于估计所谓的 单分散球形扩散器的无模型公式适用于 确定非球形分子的局部角运动幅度 和明显二聚化的分子。 SP1 转录激活剂可能的远距离影响 其侧翼DNA二级结构上的识别序列是 通过多种物理和生化方法进行研究，包括 动态光散射 (DLS)、FPA、圆二色性 (CD) 光谱、光学熔解和对 S1 核酸酶的敏感性。任何 结合 Sp1 蛋白后调节这种长距离效应将 进行类似的检查。 由于特定的原因可能产生长期影响 还研究了 434 阻遏物识别序列中的突变 通过物理和生化技术。 内在的扭曲和扭曲 能量参数由测量的拓扑异构体比率确定 在不同量的乙锭存在下进行环化，再次使用 最近发展的理论。 特定阳离子、阴离子、温度和其他因素的影响 通过对小 DNA 双链体水合的影响来检查 流体动力学半径，由插层的 FPA 测量 乙锭。