  More than twenty coarse-grained (CG) DNA models have been developed for
simulating the behavior of this molecule under various conditions, including
those required for nanotechnology. However, none of these models reproduces the
DNA polymorphism associated with conformational changes in the ribose rings of
the DNA backbone. These changes make an essential contribution to the DNA local
deformability and provide the possibility of the transition of the DNA double
helix from the B-form to the A-form during interactions with biological
molecules. We propose a CG representation of the ribose conformational
flexibility. We substantiate the choice of the CG sites (6 per nucleotide)
needed for the "sugar" GC DNA model, and obtain the potentials of the CG
interactions between the sites by the "bottom-up" approach using the all-atom
AMBER force field. We show that the representation of the ribose flexibility
requires one non-harmonic and one three-particle potential, the forms of both
the potentials being different from the ones generally used. The model also
includes (i) explicit representation of ions (in an implicit solvent) and (ii)
sequence dependence. With these features, the sugar CG DNA model reproduces
(with the same parameters) both the B- and A- stable forms under corresponding
conditions and demonstrates both the A to B and the B to A phase transitions.
