  Locations of DNA replication initiation in prokaryotes, called "origins of
replication", are well-characterized. However, a mechanistic understanding of
the sequence-dependence of the local unzipping of double-stranded DNA, the
first step towards replication initiation, is lacking. Here, utilizing a Markov
chain model that was created to address the directional nature of DNA unzipping
and replication, we model the sequence dependence of local melting of
double-stranded linear DNA segments. We show that generalized palindromic
sequences with high nucleotide skews have a low kinetic barrier for local
melting near melting temperatures. This allows for such sequences to function
as replication origins. We support our claim with evidence for high-skew
palindromic sequences within the replication origins of mitochondrial DNA,
bacteria, archaea and plasmids.
