The biological significance of G-T/G-U mispairing in nucleic acid secondary structure

We have computed the expected distribution of the potential for hairpin-like secondary structures with small loops (3-20 bases) and uninterrupted stems and compared that to the distribution observed in the complete genomes of seven DNA viruses from animals, plants and bacteria, as well as a bacterial plasmid. The formation of G-T mismatches in the stems of these structures was allowed. Furthermore we have analyzed the distribution of the potential for such structures along the genetic maps of these genomes, specifically around the start sites of known genes. Our data reveal that the potential for mismatch containing structures with stem length exceeding eight base pairs is over-represented and non-randomly distributed, but to a much lesser degree than that for perfect structures of equal size. Moreover, the potential for both types of structures is preferentially located near functional start codons. From this we deduce that in general G-T/G-U containing nucleic acid secondary structures are biologically relevant, though possibly less significant than perfect ones.