Coarse-Grained DNA model

A simple coarse-grained model of single-stranded DNA (ssDNA) was developed, featuring only two sites per nucleotide that represent the centers of mass of the backbone and sugar/base groups. Interactions between sites are described using tabulated bonded potentials optimized to reproduce the solution structure of DNA observed in atomistic molecular dynamics simulations. Isotropic potentials describe nonbonded interactions, implicitly taking into account the solvent conditions to match the experimentally determined radius of gyration of ssDNA. The model reproduces experimentally measured force–extension dependence of an unstructured DNA strand across 2 orders of magnitude of the applied force. A complete description of the model was published in the Journal of Chemical Theory and Computation.

All required configuration files can be downloaded. To use the model, a custom version of NAMD must be compiled using a patch provided in the archive. For questions, contact Christopher Maffeo.

Christopher Maffeo, Thuy T. M. Ngo, Taekjip Ha, and Aleksei Aksimentiev Journal of Chemical Theory and Computation (2014)

Every cell contains a blueprint for life in the form of DNA, a polymeric molecule with unique physical and chemical properties. Despite its prominent role in central biological processes such as replication, transcription and repair, single-stranded DNA has been the subject of few studies compared to double-stranded DNA. It is desirable to have accurate computational models of ssDNA to assist in the interpretation of experimental results. However, the gold-standard of biomolecular computational modeling—all-atom molecular dynamics simulation—is too computationally demanding to simulate even short (<100 nt) DNA fragments. A simpler coarse-grained model is needed. Stimulated by the dirth of reliable coarse-grained single-stranded DNA models, a the Aksimentiev and Ha groups collaborated to create the first computational model of DNA specifically optimized for single-stranded DNA using. Parameterized against a combination of structural properties extracted from all-atom simulation and from experiment, the model reproduces experimentally measured force-extension dependence of a poly(dT) strand across two orders of magnitude of the applied force. The accuracy of the model was confirmed by measuring the end-to-end distance of a dT14 fragment via FRET while stretching the molecules using optical tweezers. The low computational demands and high accuracy of the model enable its use in the design of new DNA nanotechnology devices and the interpretation of single-molecule experiments.