The DOI matches its Crossref record; 88 of the 88 references it cites were found in a registry or an index.
Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model
Open accessAbstract
We explore in detail the structural, mechanical, and thermodynamic properties of a coarse-grained model of DNA similar to that recently introduced in a study of DNA nanotweezers [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, Phys. Rev. Lett. 134, 178101 (2010)]. Effective interactions are used to represent chain connectivity, excluded volume, base stacking, and hydrogen bonding, naturally reproducing a range of DNA behavior. The model incorporates the specificity of Watson–Crick base pairing, but otherwise neglects sequence dependence of interaction strengths, resulting in an “average base” description of DNA. We quantify the relation to experiment of the thermodynamics of single-stranded stacking, duplex hybridization, and hairpin formation, as well as structural properties such as the persistence length of single strands and duplexes, and the elastic torsional and stretching moduli of double helices. We also explore the model's representation of more complex motifs involving dangling ends, bulged bases and internal loops, and the effect of stacking and fraying on the thermodynamics of the duplex formation transition.
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Cites
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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
Principles and Applications of Nucleic Acid Strand Displacement Reactions
Simmel, F. C., Yurke, B., & Singh, H. R. (2019) · Chemical Reviews · doi:10.1021/acs.chemrev.8b00580 · Cited by 792
Martini coarse-grained force field: Extension to RNA
Uusitalo, J. J., Ingólfsson, H. I., Marrink, S. J., & Faustino, I. (2017) · Biophysical Journal · doi:10.1016/j.bpj.2017.05.043 · Cited by 259
Metadata
- Authors
- Ouldridge, T. E., Louis, A. A., & Doye, J. P. K.
- Venue
- The Journal of Chemical Physics
- Publisher
- AIP Publishing
- Published
- 2011-02-22
- Volume
- 134
- Issue
- 8
- Pages
- 085101-085101
- ISSN
- 0021-9606 (ISSN-L)
- 1089-7690
- OpenAlex
- W2065996552
- Cited by
- 462
- References
- 88
- FWCI
- 6.70
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Ouldridge, T. E., Louis, A. A., & Doye, J. P. K. (2011). Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model. The Journal of Chemical Physics. https://doi.org/10.1063/1.3552946
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
