Evolutionary expansion of structurally complex DNA sequences

Abstract

The observed number per base pair (i.e. the frequency) of G(3+)N(1-7)G(3+)N(1-7)G(3+)N(1-7)G(3+) motifs has increased rapidly in the eumetazoa for which complete genomic sequences are available. This increase appears to be under positive selective pressure since it exceeds the frequency expected for a random sequence genome in every case. Since the motif is capable of forming several non-B DNA structures including quadruplexes, triplexes and hairpins, the expansion has been enabled by the presence of systems capable of suppressing non-B DNA conformations during normal replication and repair and by the emergence of proteins that promote the formation of unusual structures at these sites. Positive selection for these motifs suggests that they are not merely associated with their negative effects on genome stability, but may be useful in increasing the number of structural states in nucleic acids that are available for the elaboration of epigenetic states.