Introduction to Computational Biology Lecture # 32: RNA secondary structure predication

Today we are going to learn about prediction of RNA folding. RNA is a polymer of four types of nucleotides subunits ACGU. C-G and A-U form hydrogen bonded base pairs, and are said to be complementary. G-C pairs form three hydrogen bonds and tend to be more stable than the A-U pairs, which form only two. In addition to the canonical A-U and G-C pairs, non canonical pairs can also occur in RNA secondary structure. The most common non-canonical pair is the G-U pair which is almost thermodynamically favorable as Watson-Crick pairs. Base pairs are almost always stacked onto other base pairs in a RNA structure. Unlike DNA, RNA is typically produced as a single stranded molecule which then folds intramulecularly to form a number of short base paired stems. This base paired structure is called the RNA secondary structure. Why is RNA folding important? Many interesting RNAs conserve a secondary structure of base-pairing interactions more than they conserve sequence. This makes RNA sequence analysis more complicated and difficult than protein or DNA sequence analysis. An example of a secondary structure of RNA is illustrated in Figure ??.