NMR Structure and Dynamics and Computational Studies of RNA

两个RNA发夹，铁响应RNA发夹，具有6个核苷酸环，和UUCG四环，具有C:G或G:C环闭合碱基对，在这里用作模型系统来探测结构，稳定性和动力学。采用15N/13C/1H/31P异质核磁共振法测定了RNA的结构，并用紫外吸收热熔法对其进行了热力学表征。13C和31P核磁共振弛豫测量分别用于确定单个碱基和核糖以及磷酸二酯主链的动力学。为了独立测量RNA碱基的动态运动，在RNA的特定位置引入2-氨基嘌呤，并测量时间分辨荧光寿命和各向异性。这些实验结果与溶剂连续体（GB/SA）中随机动力学的分子结构和动力学模拟结果进行了比较。RNA分子的结构和灵活性将决定它如何与其他细胞成分（如蛋白质或其他核酸）相互作用。现在有几种光谱方法可用于描述小RNA分子的结构和运动特性：核磁共振（NMR）提供了结构信息以及结构灵活性的描述，荧光也提供了运动时间尺度上的窗口。这些方法应用于两种RNA分子，这两种RNA分子预计具有明显不同的特性，反映了它们的生物学功能：一种结合蛋白质，另一种作为主食限制较大RNA的结构。然后使用计算方法来模拟它们的结构和内在运动。

HallMCB 9816906Two RNA hairpins, the Iron Responsive RNA hairpin, with a six-nucleotide loop, and a UUCG tetraloop with either a C:G or G:C loop-closing base pair, are used here as model systems to probe structure, stability, and dynamics. The RNA structures are determined by 15N/13C/1H/31P heteronuclear NMR methods, and characterized thermodynamically using thermal melting monitored by ultraviolet absorption. 13C and 31P NMR relaxation measurements are used to determine the dynamics of the individual base and ribose, and phosphodiester backbone, respectively. To independently measure the dynamic motions of the RNA bases, 2-amino-purine is introduced at specific positions in the RNA, and the time-resolved fluorescence lifetimes and anisotropy are measured. These experimental results are compared with simulations of molecular structure and dynamics, using stochastic dynamics in a solvent continuum (GB/SA).The structure and flexibility of an RNA molecule will determine how it interacts with other cellular components, such as proteins or other nucleic acids. Several spectroscopic methods are now available to describe the structure and motional properties of small RNA molecules: nuclear magnetic resonance (NMR) provides structural information as well as a description of the flexibility of the structure, and fluorescence also provides a window on the time scales of the motion. These methods are applied to two RNA molecules which are anticipated to have distinctly different properties, reflecting their biological functions: one binds a protein, and the other acts as a staple to confine the structures of larger RNAs. Computational methods are then used to model their structures and intrinsic motions.