We propose a "sugar" coarse-grained (CG) DNA model capable of simulating both biologically significant B- and A-DNA forms. The number of degrees of freedom is reduced to six grains per nucleotide. We show that this is the minimal number sufficient for this purpose. The key features of the sugar CG DNA model are : (1) simulation of sugar repuckering between C2'-endo and C3'-endo by the use of one non-harmonic potential and one three-particle potential, (2) explicit representation of sodium counterions and (3) implicit solvent approach . Effects of solvation and of partial charge screening at small distances are taken into account through the shape of potentials of interactions between charged particles . We obtain parameters of the sugar CG DNA model from the all-atom AMBER model. The suggested model allows adequate simulation of the transitions between A- and B-DNA forms, as well as of large deformations of long DNA molecules , for example, in binding with proteins . Small modifications of the model can provide the possibility of introducing sequence dependence, as well as of modeling base pairs openings . One can also study other, than sodium, ions as well as different solvents, and model the corresponding electrostatic effects .
We propose a "sugar" coarse-grained (CG) DNA model capable of simulating both biologically significant B- and A-DNA . The model also demonstrates both the A to B and the B to A transitions. The number of degrees of freedom is reduced to six grains per nucleotide. We show that this is the minimal number sufficient for this purpose. The key features of the model are (1) simulation of sugar repuckering between C2'-endo and C3'-endo by the use of one nonharmonic potential and one three-particle potential, (2) explicit representation of ions in solution around the DNA, (3) implicit solvent approach and (4) sequence dependence . We obtain parameters of the model from the all atom AMBER force field. The model can be used to study large local deformations of long DNA molecules ( for example, in binding with proteins ). Small modification of the model can provide the possibility of modeling base pairs openings in melting, transcription and replication. And one can also simulate the interactions of the DNA molecule with different types of ions in different kinds of solutions .
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