The DOI matches its Crossref record; 66 of the 66 references it cites were found in a registry or an index.
Introducing improved structural properties and salt dependence into a coarse-grained model of DNA
Open accessAbstract
We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na+] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.
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Cites
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Song, X., & Reif, J. (2019) · ACS Nano · doi:10.1021/acsnano.9b02562 · Cited by 73
Multi-resolution simulation of DNA transport through large synthetic nanostructures
Choudhary, A., Maffeo, C., & Aksimentiev, A. (2022) · Physical Chemistry Chemical Physics · doi:10.1039/d1cp04589j · Cited by 22
Metadata
- Authors
- 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., & Doye, J. P. K.
- Venue
- The Journal of Chemical Physics
- Publisher
- AIP Publishing
- Published
- 2015-06-15
- Volume
- 142
- Issue
- 23
- Pages
- 234901-234901
- ISSN
- 0021-9606 (ISSN-L)
- 1089-7690
- OpenAlex
- W1568631168
- Cited by
- 381
- References
- 66
- FWCI
- 8.62
- Type
- journal article
- Language
- en
- Open access
- bronze
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- 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., & Doye, J. P. K. (2015). Introducing improved structural properties and salt dependence into a coarse-grained model of DNA. The Journal of Chemical Physics. https://doi.org/10.1063/1.4921957
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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