RNA STRUCTURE IN AGILE LOCI OF RIBOSOME AND RETROVIRUSES

加州大学旧金山分校和莫斯科俄罗斯科学院恩格尔哈特分子生物学研究所在RNA构象领域提出了一个合作项目。本建议的父母补助金为GM39247(7/1/98-6/30/02)。对于具有重要功能的序列，我们将研究RNA的替代构象。具体地说，将研究两种情况，其中RNA的构象转换可能发挥重要的功能作用：(1)在禽反转录病毒基因组RNA二聚化过程中形成的结构。(2)基于核糖体RNA序列的系统发育分析，莫斯科小组最近提出了核糖体肽转移酶癌的一个假想的瞬时RNA假结。一组RNA寡核苷酸(长度为40到50个核苷酸)将在溶液中进行研究，包括来自一些禽类逆转录病毒的序列、人和细菌的rRNA序列、一些突变的序列。在这个项目中，莫斯科小组将通过物理化学方法表征RNA寡核苷酸，并使用化学物质和酶探测绘制单链和双链区域的地图。基于这些数据，将为所涉及的结构计算三维模型，并由加州大学旧金山分校的研究小组使用高分辨率核磁共振研究合适的序列。在核糖体操作的某些阶段，假结结构的可逆形成可能是蛋白质合成过程中大规模动力学的原因。了解这一过程的详细机制以及逆转录病毒二聚体的详细机制和所涉及的结构知识，可能会为设计新的细菌和抗病毒治疗药物开辟新的视角。

A collaborative project is proposed between UCSF and the Engelhardt Institute of Molecular Biology, Russian Academy of Science, Moscow, in the area of RNA conformations. The parent grant for the present proposal is GM39247 (7/1/98-6/30/02). Alternative conformations of RNA will be studied for functionally important sequences. Specifically, two cases will be investigated where conformation switching of RNA may play an important functional role: (1) structures that are formed during the dimerization of genomic RNA of avian retroviruses. (2) a hypothetical transient RNA psuedoknot at the ribosomal peptidyl transferase cancer, proposed recently by the Moscow group based on phylogenetic analysis of ribosomal RNA sequences. A set of RNA oligonucleotides (40 to 50 nucleotides in length) will be studied in solution, including sequences from a number of avian retroviruses, human and bacterial rRNA sequences, a number of mutated sequences. In this project, the Moscow group will characterize the RNA oligonucleotides by physicochemical methods and map the single- and double-stranded regions using chemicals and enzymatic probing. Based on these data, three-dimensional models will be calculated for the structures involved, and suitable sequences will be studied by UCSF groups using high resolution NMR. A reversible formation of a pseudoknot structure at certain stages of the ribosome operation may be responsible for the large-scale dynamics during protein synthesis. Understanding the detailed mechanisms of this process as well as that of the retroviral dimerization and knowledge of the structures involved may open new perspectives in designing new bacterial and antiviral therapeutic agents.