Genes and the physics of the DNA double-helix.
The processing of the genetic information stored in the double-helical DNA implies the separation of the two strands, the physics of which is described by the helix-coil transition model. Is there a relationship between genetic maps and DNA physical stability maps that plot the sequence-specific propensity for the thermal disruption of the double-helix? Here, with appropriate methodological formulations, such maps are derived for a large set of sequences, including complete genomes. The superposition of the two maps leads to a contrasted picture with correlations ranging between two extremes: from almost perfect (with the genes precisely delineated as stable regions) to more or less complete unrelatedness. The simplest explanation for the results is that the observed striking correlations correspond to the relics of a primeval organisation of the genetic message, with the physics of DNA playing a role in the delimitation of coding regions. In order to trace the evolutionary fate of this signal further, a detailed study of the yeast complete genome is performed. In this study, the superposition of the genetic and physical stability maps is examined in the light of information concerning gene duplication. On the basis of this analysis it is concluded that the 'signature' associated with the supposed archaic signal is in the process of being erased, most probably because the underlying feature is no longer under selective pressure. There are many evolutionary implications for the results presented and for their proposed interpretations, notably concerning models of mutational dynamics in relation to erasure processes.
Yeramian
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Unité de Physico-Chimie des Macromolécules Biologiques (URA 1773 du CNRS), Institut Pasteur, 75724 Cedex 15, Paris, France. yeramian@pasteur.fr
D000465:Algorithms; D001482:Base Composition; D004271:DNA, Fungal / Q000737:chemistry* / Q000235:genetics; D020440:Gene Duplication; D005800:Genes, Fungal / Q000235:genetics*; D016681:Genome, Fungal; D008954:Models, Biological; D009690:Nucleic Acid Conformation; D055585:Physical Phenomena; D010825:Physics; D012441:Saccharomyces cerevisiae / Q000235:genetics; D013816:Thermodynamics
D004271:DNA, Fungal