Selective pressures on RNA hairpins in vivo and in vitro

Comparison of the most stable potential hairpins in the sequences of natura l ribozymes with those in the randomized sequences has revealed that the ha irpin loop energies are lower than expected by chance. Although these hairp ins are not necessarily parts of functional structures, there is a selectiv e pressure to diminish the destabilizing free energies of the hairpin loops . In contrast, no significant bias is observed in the stacking values of th e most stable stems. In the ribozymes isolated in vitro the loops of potent ial hairpins are closer to random values, which can result in less efficien t folding rates. Furthermore, the effects of kinetic traps seem to be more significant in the folding pathways of the in vitro isolates due to a poten tial to form stable stacks incompatible with the functional folds. Similarl y to natural ribozyme sequences, the untranslated regions of viral RNAs als o form hairpins with relatively low loop free energies. These evolutionary trends suggest ways for efficient engineering of improved RNA constructs on the basis of analysis of in vitro isolates and approaches for the search o f regions coding for functional RNA structures in large genome sequences.