STRUCTURE AND FUNCTION OF RNA LOOPS AND DUPLEXES

这项工作的最终目标是了解RNA结构， 函数关系 尽管有生物学上的例子证明了RNA的重要性 结构，很少有物理研究描述的影响， RNA：蛋白质复合物或RNA：RNA 交互. 这里提出的工作有两个组成部分：1） 调查的生化和生物物理参数的 序列特异性RNA结合蛋白，人U1 A，与 RNA底物。 U1 A是U1 snRNP的蛋白质之一，其结合 到U1 snRNA茎/环II。 U1 A蛋白含有一个结构和 序列依赖性基序是许多RNA结合蛋白共有的， 所谓的“RNP保守基序”，或者“RRM”。 了解这个系统的相互作用将提供更多 不仅是关于snRNP的蛋白质和RNA如何组装的信息， 但也应该作为这个类的一般属性的模型 RNA结合蛋白。2)RNA：RNA相互作用包括碱基配对， 双链体和含有不成对碱基的结构基序中，三级 循环结构中的交互，以及使用 修改基地 含有这些元素的RNA将在这里进行研究 确定它们的热力学和结构性质， 理解RNA的这些特征的目标是，当它们被发现时， 生物序列。 所有的RNA都将通过NMR和化学方法进行研究， 酶探测，以确定其结构，以及表征 是精神上的 RNA分子将被酶促合成或 化学上;当使用酶促合成时，将有可能 掺入同位素标记核苷酸以促进NMR 结构分析

The ultimate goal of this work is to understand RNA structure and function relations. Despite biological examples of the importance of RNA structure, there are few physical studies which describe the influence of RNA structure on systems such as RNA:protein complexes or RNA:RNA interactions. The work proposed here has two components: 1) investigation of the biochemical and biophysical parameters of the association of a sequence-specific RNA binding protein, human U1A, with its RNA substrate. U1A is one of the proteins of U1 snRNP, which binds to the U1 snRNA stem/loop II. The U1A protein contains a structural and sequence-dependent motif which is common to many RNA binding proteins, the so-called "RNP conserved motif", or alternatively, "RRM". Understanding the interactions of this system will provide more information not only on how the proteins and RNA of the snRNP assemble, but should also serve as a model for the general properties of this class of RNA binding protein. 2) RNA:RNA interactions include base pairing in duplexes and in structural motifs containing unpaired bases, tertiary interactions in loop structures, and nonstandard interactions using modified bases. RNAs containing these elements will be investigated here to determine their thermodynamic and structural properties, again with the goal of understanding these features of RNA when they are found in biological sequences. All RNAs will be studied by NMR and chemical and enzymatic probing to determine their structure, as well as characterized thermodynamically. RNA molecules will be synthesized enzymatically or chemically; when enzymatic synthesis is used, it will be possible to incorporate isotopically labelled nucleotides to facilitate NMR structural analysis.