Translational control by RNA-RNA interaction: Improved computation of RNA-RNA binding thermodynamics

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