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

Mutations which improve the efficiency of recombination should affecteither the proteins which mediate recombination or their substrate, DNAitself. The former mutations would be localized to a few sites. The latterwould be dispersed. Studies of hybridization between RNA molecules havesuggested that recombination may be initiated by a homology searchinvolving the "kissing" of the tips of stem loops. This predicts that, inthe absence of other constraints, mutations which assist the formation ofstem loops would be favored. From comparisons of the folding of normal andshuffled DNA sequences, I present evidence for an evolutionary selectionpressure to distribute stem loops generally throughout genomes. I proposethat this early pressure came into conflict with later local pressures toimpose information concerning specific function. The conflict wasaccommodated by permitting sections of DNA concerned with a specificfunction to evolve in dispersed segments. Traces of the conflict seem to bepresent in some modern intron-containing genes. Thus, introns may haveallowed the interspersing of selectively advantageous stem loops in codingregions of DNA.