Chargaff's second parity rule and the kinetics of DNA replication

Abstract: A model of DNA replication is investigated, which is based on the biochemical kinetics of DNA polymerases, copying a DNA strand into its complement, except for rare point-like mutations due to nucleotide substitutions. Numerical simulations of many successive replications starting from an initial DNA sequence show that the fractions of mono- and oligonucleotides converge toward compliance with Chargaff's second parity rule. The theory of this multireplication process reveals that the approximate equalities between the fractions of complementary nucleotides are the consequence of (1) the dominant role of complementarity in the DNA replication kinetic process and (2) the smallness of the polymerase error probability. These two features lead to a robust mechanism underlying Chargaff's second parity rule.