The “sugar” coarse-grained DNA model

• Published in: Journal of molecular modeling Vol. 23; no. 2; pp. 66 - 16
• Main Authors: Kovaleva, N. A., Koroleva (Kikot), I. P., Mazo, M. A., Zubova, E. A.
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01.02.2017; Springer Nature B.V
• Subjects: Characterization and Evaluation of Materials; Chemistry; Chemistry and Materials Science; Computer Appl. in Life Sciences; Computer Applications in Chemistry; DNA, A-Form - chemistry; DNA, B-Form - chemistry; Flexibility; Formability; Models, Chemical; Molecular Dynamics Simulation; Molecular Medicine; Nucleic Acid Denaturation; Nucleotides; Original Paper; Phase transitions; Polymorphism; Polymorphism, Single Nucleotide - genetics; Representations; Ribose; Ribose - chemistry; Ribose - metabolism; Static Electricity; Sugar; Theoretical and Computational Chemistry; Thermodynamics; Coarse graining; DNA; Phase transition
• ISSN: 1610-2940; 0948-5023
• DOI: 10.1007/s00894-017-3209-z

More than 20 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 (six 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. Graphical Abstract The proposed coarse-grained DNA model allows to reproduce both the B- and A- DNA forms and the transitions between them under corresponding conditions.