  Chargaff's second parity rule holds empirically for most types of DNA that
along single strands of DNA the base contents are equal for complimentary
bases, A = T, G = C. A Markov chain model is constructed to track the evolution
of any single base position along single strands of genomes whose organisms are
equipped with replication mismatch repair. Under the key assumptions that
mismatch error rates primarily depend the number of hydrogen bonds of
nucleotides and that the mismatch repairing process itself makes strand
recognition error, the model shows that the steady state probabilities for any
base position to take on one of the 4 nucleotide bases are equal for
complimentary bases. As a result, Chargaff's second parity rule is the
manifestation of the Law of Large Number acting on the steady state
probabilities. More importantly, because the model pinpoints mismatch repair as
a basis of the rule, it is suitable for experimental verification.
