The DOI matches its Crossref record; 51 of the 51 references it cites were found in a registry or an index.
The role of DNA shape in protein–DNA recognition
Open accessAbstract
The recognition of specific DNA sequences by proteins is thought to depend on two types of mechanism: one that involves the formation of hydrogen bonds with specific bases, primarily in the major groove, and one involving sequence-dependent deformations of the DNA helix. By comprehensively analysing the three-dimensional structures of protein-DNA complexes, here we show that the binding of arginine residues to narrow minor grooves is a widely used mode for protein-DNA recognition. This readout mechanism exploits the phenomenon that narrow minor grooves strongly enhance the negative electrostatic potential of the DNA. The nucleosome core particle offers a prominent example of this effect. Minor-groove narrowing is often associated with the presence of A-tracts, AT-rich sequences that exclude the flexible TpA step. These findings indicate that the ability to detect local variations in DNA shape and electrostatic potential is a general mechanism that enables proteins to use information in the minor groove, which otherwise offers few opportunities for the formation of base-specific hydrogen bonds, to achieve DNA-binding specificity.
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“Twisting, bending, and shearing of DNA influence local binding in a TF-specific fashion (Rohs et al., 2009).”
From WILDS: A Benchmark of in-the-Wild Distribution Shifts (2020) · cites this paper as Rohs et al., 2009
Experimental — accuracy not yet measuredIn the citing paper
“The L1 loop formed contacts with DNA in the minor groove (shape readout) 24 .”
From Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator (2015) · cites this paper as [24]
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Cites
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 13,111
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Classical Electrostatics in Biology and Chemistry
Honig, B. H., & Nicholls, A. O. (1995) · Science · doi:10.1126/science.7761829 · Cited by 2,891
Self-citationSatisfying Hydrogen Bonding Potential in Proteins
McDonald, I. K., & Thornton, J. M. (1994) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.1334 · Cited by 2,136
A genomic code for nucleosome positioning
Segal, E., Fondufe‐Mittendorf, Y. N., Chen, L., Thåström, A., Field, Y., Moore, I. K., Wang, J.-P. Z., & Widom, J. (2006) · Nature · doi:10.1038/nature04979 · Cited by 1,492
Solvent Mediated Interactions in the Structure of the Nucleosome Core Particle at 1.9Å Resolution
Davey, C. A., Sargent, D. F., Luger, K., Mäder, A. W., & Richmond, T. J. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00386-8 · Cited by 1,490
The structure of DNA in the nucleosome core
Richmond, T. J., & Davey, C. A. (2003) · Nature · doi:10.1038/nature01595 · Cited by 1,287
Sequence-specific recognition of double helical nucleic acids by proteins.
Seeman, N. C., Rosenberg, J. M., & Rich, A. (1976) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.73.3.804 · Cited by 1,125
Crystal structure of a yeast TBP/TATA-box complex
Kim, Y., Geiger, J. H., Hahn, S., & Sigler, P. B. (1993) · Nature · doi:10.1038/365512a0 · Cited by 1,085
Co-crystal structure of TBP recognizing the minor groove of a TATA element
Kim, J. L., Nikolov, D. B., & Burley, S. K. (1993) · Nature · doi:10.1038/365520a0 · Cited by 1,065
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The Human Transcription Factors
Lambert, S. A., Jolma, A., Campitelli, L. F., Das, P. K., Yin, Y., Albu, M., Chen, X., Taipale, J., Hughes, T. R., & Weirauch, M. T. (2018) · Cell · doi:10.1016/j.cell.2018.01.029 · Cited by 3,399
Crystal structure of Cas9 in complex with guide RNA and target DNA
Nishimasu, H., Ran, F. A., Hsu, P. D., Konermann, S., Shehata, S. I., Dohmae, N., Ishitani, R., Zhang, F., & Nureki, O. (2014) · Cell · doi:10.1016/j.cell.2014.02.001 · Cited by 2,306
DNA-Binding Specificities of Human Transcription Factors
Jolma, A., Yan, J., Whitington, T., Toivonen, J., Nitta, K. R., Rastas, P. M. A., Morgunova, E. Y., Enge, M., Taipale, M., Wei, G., et al. (2013) · Cell · doi:10.1016/j.cell.2012.12.009 · Cited by 1,262
Kelley, D. R., Snoek, J., & Rinn, J. L. (2016) · Genome Research · doi:10.1101/gr.200535.115 · Cited by 1,048
Origins of Specificity in Protein-DNA Recognition
Rohs, R., Jin, X., West, S. M., Joshi, R., Honig, B. H., & Mann, R. S. (2010) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-060408-091030 · Cited by 902
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Metadata
- Authors
- Rohs, R., West, S. M., Sosinsky, A., Liu, P., Mann, R. S., & Honig, B.
- Affiliations
- Howard Hughes Medical Institute (US)
- Columbia University (US)
- Corresponding author
- Mann, Richard S.
- Honig, Barry
- Venue
- Nature
- Published
- 2009-10
- Volume
- 461
- Issue
- 7268
- Pages
- 1248-1253
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC2793086
- OpenAlex
- W2012627860
- Cited by
- 1,096
- References
- 51
- Citations by year
- 2026: 51 · 2025: 68 · 2024: 73 · 2023: 66 · 2022: 77 · 2021: 76 · 2020: 58 · 2019: 57 · 2018: 55 · 2017: 65 · 2016: 52 · 2015: 76 · 2014: 72 · 2013: 74 · 2012: 64
- FWCI
- 23.46
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- BIROn (Birkbeck, University of London) (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- National Cancer Institute (U54CA121852)
- National Institute of General Medical Sciences (GM54510, R01GM030518, R01GM054510)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Diffusion and Search Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- protein-DNA recognition, DNA shape, minor groove, major groove, arginine binding, nucleosome core particle, A-tracts, sequence-specific DNA-binding proteins, DNA binding specificity, protein-DNA complex, hydrogen bonding
- MeSH terms
- Animals, Arginine, Base Sequence, DNA, DNA-Binding Proteins, Hydrogen Bonding, Lysine, Nucleic Acid Conformation, Nucleosomes, Protein Binding, Saccharomyces cerevisiae, Databases, Factual, AT Rich Sequence, Static Electricity
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