PHYSICAL STUDIES OF RNA STRUCTURAL MOTIFS

Rna分子是许多细胞过程的积极参与者，但 对它们的结构、动力学或基本方面知之甚少 折叠机制；只详细了解转移RNA。四 较大的RNA的不同片段已被鉴定为含有 与其生物学作用相关的有趣结构和潜在的 说明较大的RNAs用于实现特定目标的策略 功能。它们是： I.复杂的信使核糖核酸假结作为一种 翻译抑制子；它还具有实质性的三级结构 到已知的二级结构，必须在过程中展开和重新折叠 翻译，并可能采用另一种构象。 二、带有凸起环的保守rRNA发夹显示了 由凸起和发夹环形成的伪结结构，以及 结构在发夹环内。 三、逆转录病毒的信使核糖核酸假结导致STOP通读 密码子；结构上和一个环内的5‘序列可形成 附加结构。 四、大亚基核糖体RNA的三个螺旋的连接 包含由特定结构稳定的实质性三级结构 单一的镁离子和氨离子的结合。 我们将使用几种实验方法来阐明 它们中每一个的折叠三级结构的热力学，并 进一步探讨折叠的动力学以及特异性和非特异性的作用 特定的阳离子。我们将特别注意“构象” 开关“，这可能是RNA功能的共同特征。 在一系列合作实验中，瞬变电双折射 将用于确定每个碱基对的持续长度和漂洗 随机序列双链RNA在溶液中的作用，并考察了 RNA弯曲和柔韧性上的凸起环。

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.