Ensemble-based RNA secondary structure characterization (Engineering in Genomics)

We have presented here a method of characterizing the expected secondary structure or structures from a Boltzmann-weighted ensemble of such structures. In several applications of this method, the results provided structural insight not attainable by the use of free energy minimization methods. Previous approaches to characterizing the Boltzmann ensemble of structures have included the base-pairing probability profile as represented in the base pairing "dot plot" chart, the generation and examination of "suboptimal" structures and the visual examination of the Boltzmann ensemble of 1,000 structures. This method may be generally applicable to RNA secondary structure prediction and characterization and especially useful in automated applications