Designing RNA secondary structures in coding regions

Sophisticated regulatory structures appear within highly-constrained coding regions of genes. We study the extent to which such structures can be constructed. Can such stem loops appear essentially anywhere within coding regions, or is the potential restricted to rare amino acid sequences? While predicting secondary structures of an RNA sequence is an extensively studied problem in computational biology, the inverse problem, designing sequences based on a known structure is also important. We work on a particular version of the inverse RNA folding problem, where our goal is to achieve a targeted energy level. For a particular RNA structure, we design sequences with the maximum and minimum folding energy while maintaining desired codon distribution. Our major contributions in work is to optimize RNA secondary structure under codon constraints via fast estimation of folding energies following local modification.