Cited by 1,096DNA and Nucleic Acid ChemistryDiffusion and Search DynamicsGenomics and Chromatin Dynamics

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The role of DNA shape in protein–DNA recognition

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Rohs, Remo, West, Sean M., Sosinsky, Alona, Liu, Peng, Mann, Richard S., Honig, Barry·2009·Nature

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Abstract

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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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
ORCID: Rohs, Remo
West, Sean M.
Sosinsky, Alona
Liu, Peng
Mann, Richard S.
Honig, Barry
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2009-10
Volume: 461
Issue: 7268
Pages: 1248-1253
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature08473
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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The role of DNA shape in protein–DNA recognition

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