  We develop a robust coarse-grained model for single and double stranded DNA
by representing each nucleotide by three interaction sites (TIS) located at the
centers of mass of sugar, phosphate, and base. The resulting TIS model includes
base-stacking, hydrogen bond, and electrostatic interactions as well as
bond-stretching and bond angle potentials that account for the polymeric nature
of DNA. The choices of force constants for stretching and the bending
potentials were guided by a Boltzmann inversion procedure using a large
representative set of DNA structures extracted from the Protein Data Bank. Some
of the parameters in the stacking interactions were calculated using a learning
procedure, which ensured that the experimentally measured melting temperatures
of dimers are faithfully reproduced. Without any further adjustments, the
calculations based on the TIS model reproduces the experimentally measured salt
and sequence dependence of the size of single stranded DNA (ssDNA), as well as
the persistence lengths of poly(dA) and poly(dT) chains. Interestingly, upon
application of mechanical force the extension of poly(dA) exhibits a plateau,
which we trace to the formation of stacked helical domains. In contrast, the
force-extension curve (FEC) of poly(dT) is entropic in origin, and could be
described by a standard polymer model. We also show that the persistence length
of double stranded DNA is consistent with the prediction based on the worm-like
chain. The persistence length, which decreases with increasing salt
concentration, is in accord with the Odijk-Skolnick-Fixman theory intended for
stiff polyelectrolyte chains near the rod limit. The range of applications,
which did not require adjusting any parameter after the initial construction
based solely on PDB structures and melting profiles of dimers, attests to the
transferability and robustness of the TIS model for ssDNA and dsDNA.
