PHYSICAL STUDIES OF RNA STRUCTURAL MOTIFS

RNA分子是许多细胞过程的积极参与者，然而， 关于它们的结构、动力学或 折叠机制;只有转移RNA被详细理解。四 已经鉴定出较大RNA的不同片段含有 与其生物学作用相关的有趣结构， 说明了较大RNA用于实现特定 功能协调发展的它们是： I.一个复杂的mRNA假结作为一个调控位点， 翻译阻遏物;它具有大量的三级结构，此外 已知的二级结构，必须展开和重新折叠， 翻译，并可能采用替代构象。 二.一个保守的带有凸起环的rRNA发夹显示了 由凸起和发夹环形成的假结结构，以及 发夹环内的结构。 三.来自逆转录病毒的mRNA假结导致停止的通读 密码子;结构的5'端和一个环内的序列可以形成 额外的结构。 四.大亚基核糖体RNA的三个螺旋的连接 含有大量的三级结构， 单个Mg 2+和NH 4+离子的结合。 几种实验方法将用于阐明 折叠三级结构的热力学， 进一步探索折叠的动力学以及特异性和非特异性的作用， 特定阳离子。将特别注意“构象”。 开关”，这可能是RNA功能的共同特征。 在一组合作实验中，瞬态电双折射 将用于确定每个碱基对的持续长度和冲洗 随机序列双链RNA在溶液中，并研究的影响， 凸起环对RNA弯曲和柔性的影响。

RNA molecules are active participants in many cellular processes, yet little is known about fundamental aspects of their structure, dynamics, or folding mechanisms; only transfer RNAs are understood in detail. Four different fragments of larger RNAs have been identified as containing interesting structure relevant to their biological roles and potentially illustrative of strategies used by larger RNAs to achieve specific functions. They are: i. A complex mRNA pseudoknot serves as a regulatory site for a translational repressor; it has substantial tertiary structure in addition to the known secondary structure, must unfold and refold during translation, and probably adopts alternative conformations. ii. A conserved rRNA hairpin with bulge loop shows competition between a pseudoknot structure formed by the bulge and hairpin loops, and a structure within the hairpin loop. iii. An mRNA pseudoknot from a retrovirus causes readthrough of stop codons; sequences 5' to the structure and within one loop may form additional structure. iv. A junction of three helices from the large subunit ribosomal RNA contains substantial tertiary structure that is stabilized by specific binding of single Mg2+ and NH4+ ions. Several experimental approaches will be used to elucidate the thermodynamics of folding tertiary structure in each of these, and to further explore the kinetics of folding and the roles of specific and non- specific cations. Particular attention will be paid to "conformational switches", which may be a common feature of RNA function. In a set of collaborative experiments, transient electric birefringence will be used to determine the persistence length and rinse per base pair of random sequence duplex RNA in solution, and investigate the effects of bulge loops on RNA bending and flexibility.