Lecture Notes

Ribonucleic acid, or RNA, is as the name suggests a molecule very similar to 2′-deoxyribonucleic acid, or DNA. The two differences are an extra hydroxyl group on the ringformed ribose sugar on the backbone, and the substitution of thymine with uracil as one of the four possible side chain bases. According to the central dogma, DNA → RNA → protein, RNA is restricted to a role as an intermediate messenger between the hereditary genetic medium of DNA and the biochemically active molecules of proteins. However, numerous known examples exist of RNAs with structural and catalytic importance, cf. e.g. [3, Section 10.1]. Recent discoveries even seem to indicate that RNA may play a pivotal role in gene regulation [9]. It is therefore of interest to be able to infer the structure, or structural features, for an RNA sequence. An understanding of the types of constraints determining RNA structure can also assist in better modeling of RNA sequence evolution.