Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics

摘要: The thermodynamics of RNA-RNA interaction consists two components: the energy necessary to make a potential binding region accessible, i.e. unpaired, and gained from base pairing partners. We show here that both components can be efficiently computed using an improved variant RNAup. method is then applied set bacterial small RNAs involved in translational control. In all cases biologically active sRNA target interactions, sites predicted by RNAup are perfect agreement with literature. addition prediction site location, also used determine mode action. Using information about location accessibility change resulting we discriminate between positive negative regulators translation.