The DOI matches its Crossref record; 60 of the 60 references it cites were found in a registry or an index.
Sequence-dependent thermodynamics of a coarse-grained DNA model
Open accessAbstract
We introduce a sequence-dependent parametrization for a coarse-grained DNA model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134, 085101 (2011)]10.1063/1.3552946 originally designed to reproduce the properties of DNA molecules with average sequences. The new parametrization introduces sequence-dependent stacking and base-pairing interaction strengths chosen to reproduce the melting temperatures of short duplexes. By developing a histogram reweighting technique, we are able to fit our parameters to the melting temperatures of thousands of sequences. To demonstrate the flexibility of the model, we study the effects of sequence on: (a) the heterogeneous stacking transition of single strands, (b) the tendency of a duplex to fray at its melting point, (c) the effects of stacking strength in the loop on the melting temperature of hairpins, (d) the force-extension properties of single strands, and (e) the structure of a kissing-loop complex. Where possible, we compare our results with experimental data and find a good agreement. A simulation code called oxDNA, implementing our model, is available as a free software.
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Cites
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., & Karplus, M. (1983) · Journal of Computational Chemistry · doi:10.1002/jcc.540040211 · Cited by 14,944
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., & Kollman, P. A. (1995) · Journal of the American Chemical Society · doi:10.1021/ja00124a002 · Cited by 13,103
Folding DNA to create nanoscale shapes and patterns
Rothemund, P. W. K. (2006) · Nature · doi:10.1038/nature04586 · Cited by 7,354
Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
Torrie, G. M., & Valleau, J. P. (1977) · Journal of Computational Physics · doi:10.1016/0021-9991(77)90121-8 · Cited by 6,091
Understanding Molecular Simulation: From Algorithms to Applications
Frenkel, D., Smit, B., & Ratner, M. A. (1997) · Physics Today · doi:10.1063/1.881812 · Cited by 5,059
Principles of Nucleic Acid Structure
(2008) · Elsevier eBooks · doi:10.1016/b978-0-12-369507-9.x5001-8 · Cited by 4,504
Molecular Computation of Solutions to Combinatorial Problems
Adleman, L. M. (1994) · Science · doi:10.1126/science.7973651 · Cited by 4,474
Design and self-assembly of two-dimensional DNA crystals
Winfree, E., Liu, F., Wenzler, L. A., & Seeman, N. C. (1998) · Nature · doi:10.1038/28998 · Cited by 2,857
A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
SantaLucia, J. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.4.1460 · Cited by 2,793
Smith, S. B., Cui, Y., & Bustamante, C. (1996) · Science · doi:10.1126/science.271.5250.795 · Cited by 2,770
Cited by
Thompson, A. P., Aktulga, H. M., Berger, R., Bolintineanu, D. S., Brown, W. M., Crozier, P. S., in 't Veld, P. J., Kohlmeyer, A., Moore, S. G., Nguyen, T. D., et al. (2022) · Computer Physics Communications · doi:10.1016/j.cpc.2021.108171 · Cited by 12,598
Perspective: Coarse-grained models for biomolecular systems
Noid, W. G. (2013) · The Journal of Chemical Physics · doi:10.1063/1.4818908 · Cited by 893
The power of coarse graining in biomolecular simulations
Ingólfsson, H. I., Lopez, C. A., Uusitalo, J. J., de Jong, D. H., Gopal, S. M., Periole, X., & Marrink, S. J. (2014) · WIREs Computational Molecular Science · doi:10.1002/wcms.1169 · Cited by 572
Introducing improved structural properties and salt dependence into a coarse-grained model of DNA
Snodin, B. E. K., Randisi, F., Mosayebi, M., Šulc, P., Schreck, J. S., Romano, F., Ouldridge, T. E., Tsukanov, R., Nir, E., Louis, A. A., et al. (2015) · The Journal of Chemical Physics · doi:10.1063/1.4921957 · Cited by 381
Self-citation
Metadata
- Authors
- Šulc, P., Romano, F., Ouldridge, T. E., Rovigatti, L., Doye, J. P. K., & Louis, A. A.
- Venue
- The Journal of Chemical Physics
- Publisher
- AIP Publishing
- Published
- 2012-10-01
- Volume
- 137
- Issue
- 13
- Pages
- 135101-135101
- ISSN
- 0021-9606 (ISSN-L)
- 1089-7690
- OpenAlex
- W2026285337
- Cited by
- 338
- References
- 60
- FWCI
- 6.39
- Type
- journal article
- Language
- en
- Open access
- bronze
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