The DOI matches its Crossref record; 46 of the 46 references it cites were found in a registry or an index.
Transient Hoogsteen base pairs in canonical duplex DNA
Open accessAbstract
Sequence-directed variations in the canonical DNA double helix structure that retain Watson–Crick base-pairing have important roles in DNA recognition, topology and nucleosome positioning. By using nuclear magnetic resonance relaxation dispersion spectroscopy in concert with steered molecular dynamics simulations, we have observed transient sequence-specific excursions away from Watson–Crick base-pairing at CA and TA steps inside canonical duplex DNA towards low-populated and short-lived A•T and G•C Hoogsteen base pairs. The observation of Hoogsteen base pairs in DNA duplexes specifically bound to transcription factors and in damaged DNA sites implies that the DNA double helix intrinsically codes for excited state Hoogsteen base pairs as a means of expanding its structural complexity beyond that which can be achieved based on Watson–Crick base-pairing. The methods presented here provide a new route for characterizing transient low-populated nucleic acid structures, which we predict will be abundant in the genome and constitute a second transient layer of the genetic code.
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UCSF Chimera—A visualization system for exploratory research and analysis
Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004) · Journal of Computational Chemistry · doi:10.1002/jcc.20084 · Cited by 45,828
Canonical dynamics: Equilibrium phase-space distributions
Hoover, W. G. (1985) · Physical Review A · doi:10.1103/physreva.31.1695 · Cited by 23,465
A unified formulation of the constant temperature molecular dynamics methods
Nosé, S. (1984) · The Journal of Chemical Physics · doi:10.1063/1.447334 · Cited by 19,152
NMRPipe: A multidimensional spectral processing system based on UNIX pipes
Delaglio, F., Grzesiek, S., Vuister, G., Zhu, G., Pfeifer, J., & Bax, A. (1995) · Journal of Biomolecular NMR · doi:10.1007/bf00197809 · Cited by 15,965
Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid
WATSON, J. D., & CRICK, F. H. C. (1953) · Nature · doi:10.1038/171737a0 · Cited by 13,584
Dynamic personalities of proteins
Henzler-Wildman, K., & Kern, D. (2007) · Nature · doi:10.1038/nature06522 · Cited by 2,545
Molecular structure of a left-handed double helical DNA fragment at atomic resolution
Wang, A. H.-J., Quigley, G. J., Kolpak, F. J., Crawford, J. L., van Boom, J. H., van der Marel, G., & Rich, A. (1979) · Nature · doi:10.1038/282680a0 · Cited by 2,118
The role of dynamic conformational ensembles in biomolecular recognition
Boehr, D. D., Nussinov, R., & Wright, P. E. (2009) · Nature Chemical Biology · doi:10.1038/nchembio.232 · Cited by 2,008
A genomic code for nucleosome positioning
Segal, E., Fondufe-Mittendorf, Y., Chen, L., Thåström, A., Field, Y., Moore, I. K., Wang, J.-P. Z., & Widom, J. (2006) · Nature · doi:10.1038/nature04979 · Cited by 1,499
The structure of DNA in the nucleosome core
Richmond, T. J., & Davey, C. A. (2003) · Nature · doi:10.1038/nature01595 · Cited by 1,286
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Self-citationHow DNA polymerases catalyse replication and repair with contrasting fidelity
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Representing structures of the multiple conformational states of proteins
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Lifetime of ground conformational state determines the activity of structured RNA
Thompson, R. D., Carbaugh, D. L., Nielsen, J. R., Witt, C. M., Faison, E. M., Meganck, R. M., Rangadurai, A., Zhao, B., Bonin, J. P., Nicely, N. I., et al. (2025) · Nature Chemical Biology · doi:10.1038/s41589-025-01843-1 · Cited by 7
Metadata
- Authors
- Nikolova, E. N., Kim, E., Wise, A. A., O’Brien, P. J., Andricioaei, I., & Al-Hashimi, H. M.
- Venue
- Nature
- Published
- 2011-01-26
- Volume
- 470
- Issue
- 7335
- Pages
- 498-502
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W2052246375
- Cited by
- 344
- References
- 46
- FWCI
- 11.17
- Type
- journal article
- Language
- en
- Open access
- green
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