Polymer transport in random potentials and the genetic code: The waltz of life

Abstract

We address the question of why the translation from nucleic acids to protein forming amino acids is carried out by triplets known as codons. We approach this problem from a dynamical point of view by considering the translocation properties of primitive molecular machines operating under prebiotic conditions [1, 2, 3, 4]. Our model captures some basic ribosome-mRNA interaction features. We consider short chains of charged particles interacting with polymers via electrostatic forces, constrained to move in quasi one dimensional geometries, subject to external forcing. 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, traversing swiftly two monomers and lingering on the third one as in a waltz. This behavior is enhanced when we consider present day protein coding sequences. We also comment on noncoding sequences. We argue that this property could be one of the underlying causes for the three base codon structure of the genetic code.