In living systems, RNAs play important biological functions. The functional form of an RNA frequently requires a specific tertiary structure. The scaffold for this structure is provided by secondary structural elements that are hydrogen bonds within the molecule. Here, we concentrate on the inverse RNA folding problem. In this problem, an RNA secondary structure is given as a target structure a...

MOTIVATION The structure of RNA molecules is often crucial for their function. Therefore, secondary structure prediction has gained much interest. Here, we consider the inverse RNA folding problem, which means designing RNA sequences that fold into a given structure. RESULTS We introduce a new algorithm for the inverse folding problem (INFO-RNA) that consists of two parts; a dynamic programmi...

MOTIVATION RNA sequence design is studied at least as long as the classical folding problem. Although for the latter the functional fold of an RNA molecule is to be found ,: inverse folding tries to identify RNA sequences that fold into a function-specific target structure. In combination with RNA-based biotechnology and synthetic biology ,: reliable RNA sequence design becomes a crucial step t...