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DNA Nanotweezers Studied with a Coarse-Grained Model of DNA
Open accessAbstract
We introduce a coarse-grained rigid nucleotide model of DNA that reproduces the basic thermodynamics of short strands, duplex hybridization, single-stranded stacking, and hairpin formation, and also captures the essential structural properties of DNA: the helical pitch, persistence length, and torsional stiffness of double-stranded molecules, as well as the comparative flexibility of unstacked single strands. We apply the model to calculate the detailed free-energy landscape of one full cycle of DNA "tweezers," a simple machine driven by hybridization and strand displacement.
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Citations
Cited by
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
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
On the biophysics and kinetics of toehold-mediated DNA strand displacement
Srinivas, N., Ouldridge, T. E., Šulc, P., Schaeffer, J. M., Yurke, B., Louis, A. A., Doye, J. P. K., & Winfree, E. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt801 · Cited by 506
Self-citationStructural, mechanical, and thermodynamic properties of a coarse-grained DNA model
Ouldridge, T. E., Louis, A. A., & Doye, J. P. K. (2011) · The Journal of Chemical Physics · doi:10.1063/1.3552946 · Cited by 462
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Metadata
- Authors
- Ouldridge, T. E., Louis, A. A., & Doye, J. P. K.
- Venue
- Physical Review Letters
- Publisher
- American Physical Society (APS)
- Published
- 2010-04-26
- Volume
- 104
- Issue
- 17
- Pages
- 178101-178101
- ISSN
- 0031-9007 (ISSN-L)
- 1079-7114
- OpenAlex
- W2050103377
- Cited by
- 192
- References
- 0
- FWCI
- 5.43
- Type
- journal article
- Language
- en
- Open access
- green
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