RNA Secondary Structures

The central dogma of molecular biology states that the flow of information is from DNA, through RNA, to proteins. What this means is that DNA is the storage medium of genomic information, while proteins are the molecules with functional and structural rôles. In this view, RNA is mostly considered a ‘supporting actor’, being the medium used for transporting information from storage to where it is activated. RNA is short for RiboNucleic Acid, and DNA is short for 2′-DeoxyriboNucleic Acid (capitalisation just to indicate acronym). It should thus be of no surprise that the two types of molecules are similar. Both molecules consists of long chains of nucleotides, where a nucleotide is a combination of a phosphate group, a ringformed pentose (i.e. carbohydrate with five carbon atoms), and a nitrogenous base (either a purine which consists of two aromatic ring structures and can be either adenine or guanine, or a pyrimidine that consists of a single aromatic ring structure and can be either cytosine, thymine (DNA), or uracil (RNA)). Good desriptions of RNA, DNA, nucleotides, and the central dogma are available at http://en. wikipedia.org/. Where DNA molecules usually consist of two complementary strands forming the famous Watson-Crick double helix Watson and Crick [1953], RNA molecules usually just consist of a single strand. However, this strand can fold back against itself, so that local helices of consecutive base pairs are formed. Apart from the standard Watson-Crick pairings of C(ytosine) with G(uanine) and A(denine) with (U)racil, also the (G)uanine-(U)racil wobble base pairing is commonly observed in RNA structures. The function of an RNA molecule is predominantly determined by the threedimensional structure it forms, and information about this can therefore be very useful for studying a particular RNA. Knowing which bases form base pairs reveals a lot of information about the overall structure, so the set of base pairs is