Inverse folding of RNA

The aim of the inverse folding problem for RNA is, given a target structure like e.g. the one depicted in Fig. 1, find a sequence that folds into this structure. In this project we will exclusively focus on the secondary structure. The main driving force behind RNA structure formation is the creation of base pairs similar to the ones observed in the DNA double helical structure. In RNA thymine is replaced with uracil, so the Watson-Crick base pairs of RNA are between C and G, and between A and U. Additionally the so-called wobble base pair between G and U is commonly observed, and these six (when accounting for ordering) types of base pairs are known as the canonical base pairs of RNA. The main difference between DNA and RNA is that where the DNA helix is formed between complementary strands, an RNA molecule consists of just a single strand, or sequence, and the helices are formed locally between different parts of the sequence. The secondary structure of an RNA molecule is the set of base pair interactions observed in the full three dimensional structure. In lieu of costly experiments to determine the true structure, the secondary structure predicted by standard methods is usually used to determine the fold of proposed sequences. RNA secondary structure prediction is one of the classical problems in computational biology [12]. For decades it has been applied to make inferences about the structure of sequenced RNA, and more recently as an integral part of non-coding RNA gene finding [27, 21]. One standard method is based on a model assigning free energies to secondary structures [26, 19].