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Abstract
Details of the reaction coordinate for DNA melting are fundamental to much of biology
and biotechnology. Recently, it has been shown experimentally that there are at least
three states involved. To clarify the reaction mechanism of the melting transition
of DNA, we perform 100-ns molecular dynamics simulations of a homo-oligomeric, 12-basepair
DNA duplex, d(A(12)).d(T(12)), with explicit salt water at 400 K. Analysis of the
trajectory reveals the various biochemically important processes that occur on different
timescales. Peeling (including fraying from the ends), searching for Watson-Crick
complements, and dissociation are recognizable processes. However, we find that basepair
searching for Watson-Crick complements along a strand is not mechanistically tied
to or directly accessible from the dissociation steps of strand melting. A three-step
melting mechanism is proposed where the untwisting of the duplex is determined to
be the major component of the reaction coordinate at the barrier. Though the observations
are limited to the characteristics of the system being studied, they provide important
insight into the mechanism of melting of other more biologically relevant forms of
DNA, which will certainly differ in details from those here.