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Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications by Albert Y. Zomaya, Mourad Elloumi

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CHAPTER 24

AN INTRODUCTION TO RNA STRUCTURE AND PSEUDOKNOT PREDICTION

Jana Sperschneider and Amitava Datta

If 10% of protein fold researchers switched to RNA, the problem could be solved in one or two years.

—Tinoco and Bustamante, 1999 [39]

24.1 INTRODUCTION

For nearly a century, the view most researchers had on RNA did not reach beyond the central dogma of molecular biology: DNA is transcribed to messenger RNA, which in turn is translated to proteins. Consequently, RNA was seen solely as the passive carrier of genetic information from DNA to proteins and not much else. In the 1980s, the field of RNA experienced major turbulences with the discovery of the ability of RNA to act as a catalyst. Numerous noncoding RNAs that are not translated to proteins have been discovered, and the prevailing view among scientists is that these functional RNAs no longer have to hide behind proteins. Unlike DNA with its famous double helix structure, RNA exhibits diverse three-dimensional folds and is an extremely versatile molecule. For example, RNA is known to take part in translational regulation, intron splicing, and gene expression. Novel functional RNAs are discovered continuously, and many more breakthroughs in this exciting area can be expected in the foreseeable future.

One of the central paradigms in molecular biology states that structure is related strongly to function. Laboratory structure prediction is intricate and costly. Therefore, computational structure prediction from sequence ...

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