DYNAMICS, RELAXATION, AND LOCAL MOTION IN DNA

有人建议研究DNA动力学，结构， 和水合作用，可能在各种生物学中发挥重要作用， 流程. 本文还研究了某些群的局部角运动的幅度， DNA提供了关于其局部变形性的信息，这可能是一种 在特定地点识别和/或各种 与DNA相互作用的蛋白质。 局部角振幅是否 在不太稳定的非标准结构中的运动，例如发夹环， 三链体的第三链，和4臂假日连接， 显著超过正常双链DNA中那些是另一个问题 地址在这里。 这样的局部角运动的幅度被确定 通过选择性标记的合成DNA的NMR弛豫测量， 溶液结合时间分辨荧光偏振 插入的乙锭的各向异性（FPA）测量（以表征 全球旋转）和最近发展的理论。 同样的理论 也将被用来估计所产生的错误时，所谓的 单分散球形扩散器的无模型公式适用于 确定非球形分子的振幅局部角运动 和明显二聚化的分子。 SP1转录激活因子可能的长期作用 其侧翼DNA二级结构上的识别序列是 通过各种物理和生物化学方法进行研究，包括 动态光散射（DLS），焦平面，圆二色性（CD） 光谱学、光学解链和对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节将 进行类似的检查。 可能的长期影响，由于一个特定的 434阻遏物识别序列的突变也进行了研究 通过物理和生物化学技术。 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 对小DNA双链体的水合作用的影响， 水动力学半径，这是由FPA测量的插层 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.