MWSU Different Riboswitches

May 21, 2014

Software UNAFold has been created that can predict the folding or hybridization of one or two single-stranded RNA or DNA molecules using free energy parameters. Partition function calculations predict base pair probabilities , stochastic samples of foldings or hybridization, and melting profiles as a function of increasing temperature. This software may be useful in predicting how the known riboswitches (AddA, M6, etc.) fold up when the ligand binds to the aptamer. With this knowledge we might be able to construct alternate riboswitches that function better in the melamine to ammeline system. Hopefully, we can get current riboswitches to show programmed evolution and will not need this software, but future experiments might benefit from its use. The UNAFold Academic License costs $50.00. We should use known riboswitches from Dixon's article (File:504635230beb8b07ce.pdf" (AddA, M6, M6C, M6', M6", M6C', M6C") with melamine deaminase before experimenting with new riboswitches.