Summary: PRIMITIVE MOLECULAR MACHINE SCENARIO FOR THE ORIGIN
OF THE THREE BASE CODON COMPOSITION
G. MARTÍNEZ-MEKLERa, M. ALDANAb, F. CÁZAREZ-BUSHb, R.
GARCÍA-PELAYOb and G. COCHOb
a Laboratorio de Cuernavaca, Instituto de Física, UNAM, Apdo. Postal 48-3, 62251 Cuernavaca,
b Instituto de Física, UNAM, Apdo. Postal 20-364, 01000 México, D.F., México
(Received 18 December, 1996)
Abstract. We set up a scenario for the operation of primordial synthesis machines operating in outer
space quasi one dimensional channels, where polymers interact with fixed particles. The scheme
allows for polymerization, translocation and translation. We will show that under very general con-
ditions the particle/polymer interaction potential has spatial regularities with an average distance
of three between neighboring minima. We present a model that exhibits how primitive molecular
machines may convert the structural properties of the potential into locomotion regularities. On
average, polymer movement takes place by shifts with long time intervals every three displacements.
We argue that this feature is generic and lies at the origin of the three base codon composition.
In this work we address the fundamental question, associated with the origin of
the genetic code: why are there three bases per codon in the translation to protein
process? We shall refer to this as the n = 3 problem. We present a primitive mole-