A stem-loop "kissing" model for the initiation of recombination and the origin of introns

Mutations which improve the efficiency of recombination should affect either the proteins which mediate recombination or their substrate, DNA itself. The former mutations would be localized to a few sites. The latter would be dispersed. Studies of hybridization between RNA molecules have suggested that recombination may be initiated by a homology search involving the "kissing" of the tips of stem loops. This predicts that, in the absence of other constraints, mutations which assist the formation of stem loops would be favored. From comparisons of the folding of normal and shuffled DNA sequences, I present evidence for an evolutionary selection pressure to distribute stem loops generally throughout genomes. I propose that this early pressure came into conflict with later local pressures to impose information concerning specific function. The conflict was accommodated by permitting sections of DNA concerned with a specific function to evolve in dispersed segments. Traces of the conflict seem to be present in some modern intron-containing genes. Thus, introns may have allowed the interspersing of selectively advantageous stem loops in coding regions of DNA.