DYNAMICS, RELAXATION, AND LOCAL MOTION IN DNA

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。中选定组的局部角运动的振幅 DNA提供了有关其局部变形性的信息，这可能是一种 在特定地点识别和/或行动各种 与DNA相互作用的蛋白质。无论局部角度的幅值 在不太稳定的非标准结构中的运动，如发夹环， 三链的第三股，和一个四臂Holiday连接， 显著超过正常双链DNA则是另一个问题 地址在这里。这种局部角运动的幅度是确定的 选择性标记合成DNA的核磁共振弛豫测量 结合时间分辨荧光偏振的解 插层乙锭的各向异性(FPA)测量(以表征 全球旋转)和最近发展起来的理论。同样的理论 还将被用来估计所谓的 将单分散球形扩散器的无模型公式应用于 确定非球形分子局部角运动的振幅 以及明显二聚化的分子。 SP1转录激活子可能的长程效应 其侧翼DNA二级结构的识别序列为 通过各种物理和生化方法进行研究，包括 动态光散射(DLS)、焦平面阵列(FPA)、圆二色谱(CD) 光谱、光学熔融和对S1核酸酶的敏感性。任何 对结合Sp1蛋白的这种长程效应的调制将 接受同样的检查。由于特定的原因，可能产生的长期影响 此外，还研究了434抑制物识别序列的突变 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 在不同数量的乙锭存在的情况下循环，再次使用 最近发展起来的理论。 特定阳离子、阴离子、温度和其他因素的影响 关于小DNA双链的水合作用，通过它们对 用夹层FPA测得的水动力半径 乙锭。

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.