title: Evolution and RNA relics. a systems biology view.
abstract: The genetic code has evolved from its initial non-degenerate wobble version until reaching its present state of degeneracy. By using the stereochemical hypothesis, we revisit the problem of codon assignations to the synonymy classes of amino-acids. We obtain these classes with a simple classifier based on physico-chemical properties of nucleic bases, like hydrophobicity and molecular weight. Then we propose simple RNA (or more generally XNA, with X for D, P or R) ring structures that present, overlap included, one and only one codon by synonymy class as solutions of a combinatory variational problem. We compare these solutions to sequences of present RNAs considered as relics, with a high interspecific invariance, like invariant parts of (t)RNAs and micro-RNAs. We conclude by emphasizing some optimal properties of the genetic code.
authors.affiliation: TIMC-IMAG, UMR CNRS 5525, Faculty of Medicine of Grenoble, University J. Fourier, 38 700 La Tronche, France. Jacques.Demongeot@imag.fr
authors.forename: Jacques
authors.initials: J
authors.lastname: Demongeot
authors.forename: Nicolas
authors.initials: N
authors.lastname: Glade
authors.forename: Andrés
authors.initials: A
authors.lastname: Moreira
mesh_terms: D000818:Animals; D001483:Base Sequence; D019143:Evolution, Molecular; D005815:Genetic Code; D006801:Humans; D008297:Male; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry / Q000235:genetics*; D013045:Species Specificity; D049490:Systems Biology
chemical_list: D012313:RNA