  In this paper, we show that the coarse grain model for DNA, which has been
proposed recently by Knotts, Rathore, Schwartz and de Pablo (J. Chem. Phys.
126, 084901 (2007)), can be adapted to describe the thermal and mechanical
denaturation of long DNA sequences by adjusting slightly the base pairing
contribution. The adjusted model leads to (i) critical temperatures for long
homogeneous sequences that are in good agreement with both experimental ones
and those obtained from statistical models, (ii) a realistic step-like
denaturation behaviour for long inhomogeneous sequences, and (iii) critical
forces at ambient temperature of the order of 10 pN, close to measured values.
The adjusted model furthermore supports the conclusion that the thermal
denaturation of long homogeneous sequences corresponds to a first-order phase
transition and yields a critical exponent for the critical force equal to
sigma=0.70. This model is both geometrically and energetically realistic, in
the sense that the helical structure and the grooves, where most proteins bind,
are satisfactorily reproduced, while the energy and force required to break a
base pair lie in the expected range. It therefore represents a promising tool
for studying the dynamics of DNA-protein specific interactions at an
unprecedented detail level.
