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 sugarrepuckering 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 solventapproach 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 .
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 .
R
We propose a "sugar"
More than twenty
R
model capable of simulating both biologically significant B- and A-DNA. The model also demonstrates both the A to B and
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
R
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 sugarrepuckering between C2'-endo and C3'-endo by the use of one nonharmonic potential
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
R
(2
the forms of both the potentials being different from the ones generally used. The model also includes (i
R
in solution around the DNA, (3) implicit solventapproach and (4
(in an implicit solvent) and (ii
R
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
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