The evolution of 5S RNA secondary structures

Abstract

We have applied the Pipas–McMahon algorithm based on free energy calculations to the search for a 5S RNA base-pair structure common to all known sequences. We find that a 'Y'-shaped model is 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.