title: Translocation properties of primitive molecular machines and their relevance to the structure of the genetic code.
abstract: We address the question, related with the origin of the genetic code, of why are there three bases per codon in the translation to protein process. As a follow-up to our previous work (Aldana et al., 1998, Martínez-Mekler et al., 1999a,b), we approach this problem by considering the translocation properties of primitive molecular machines, which capture basic features of ribosomal/messenger RNA interactions, while operating under prebiotic conditions. Our model consists of a short one-dimensional chain of charged particles (rRNA antecedent) interacting with a polymer (mRNA antecedent) via electrostatic forces. The chain is subject to external forcing that causes it to move along the polymer which is fixed in a quasi-one-dimensional geometry. Our numerical and analytic studies of statistical properties of random chain/polymer potentials suggest that, under very general conditions, a dynamics is attained in which the chain moves along the polymer in steps of three monomers. By adjusting the model in order to consider present-day genetic sequences, we show that the above property is enhanced for coding regions. Intergenic sequences display a behavior closer to the random situation. We argue that this dynamical property could be one of the underlying causes for the three-base codon structure of the genetic code
authors.affiliation: The James Franck Institute, The University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637-1467, USA. maximino@control.uchicago.edu
authors.forename: M
authors.initials: M
authors.lastname: Aldana-González
authors.forename: G
authors.initials: G
authors.lastname: Cocho
authors.forename: H
authors.initials: H
authors.lastname: Larralde
authors.forename: G
authors.initials: G
authors.lastname: Martínez-Mekler
mesh_terms: D000818:Animals; D003062:Codon; D019143:Evolution, Molecular; D005815:Genetic Code; D008957:Models, Genetic; D000069497:Origin of Life; D014178:Translocation, Genetic
chemical_list: D003062:Codon