RNA Structure and Modeling: Progress and Techniques

Abstract

Publisher Summary This chapter discusses the progress and techniques of RNA structure and modeling. To understand the structure of RNA, it is necessary to first understand some of the unique biochemical properties associated with RNA and its structural elements. These properties directly lead to the formation of structural elements and motifs in tertiary structures. These include not only basic structure elements like helices, loops, bulges, and junctions but also less common elements like ribose zipper and tetraloop-receptor that contribute to the difficulty of tertiary structure prediction. The study of RNA structure started later than protein structure research, people followed the path of protein studies for experience and methods, such as crystallography and molecular dynamic simulation. A group of RNA molecules that have been used for structural studies are the ribozymes. A ribozyme is an RNA molecule that has the ability to catalyze a reaction. The characterization of RNA structure and structural dynamics is greatly enhanced by the application of chemical and enzymatic probes of RNA structure in solution. These probes enable to study RNA structures in conditions that are physiologically relevant and to investigate their interactions with partner molecules and to detect enzymatic active sites.