The evolution of 5S RNA secondary structures

Abstract

The Pipas-McMahon algorithm based on free energy calculations was applied to the search for a 5S RNA base-pair structure common to all known sequences. A Y-shaped model is found consistently among the structures having the lowest free energy using 5S RNA sequences from either eukaryotic or prokaryotic sources. Comparison of this Y structure with models which have recently been proposed show these models to be remarkably similar, and the minor differences are explicable based on the technique used to obtain the model. That prokaryotic and eukaryotic 5S RNA can adopt a similar secondary structure is strong support for its resistance to change during evolution. [5S RNA from Escherichia coli, Bacillus megaterium, B. stearothermophilus, Anacystis nidulans, Chlorella, Xenopus, Torulopsis utilis, Drosophila, Saccharomyces cerevisiae, S. carlsbergensis, chicken, rye, bean and KB cells was studied.].