Control of DNA minor groove width and Fis protein binding by the purine 2-amino group
Open accessAbstract
The width of the DNA minor groove varies with sequence and can be a major determinant of DNA shape recognition by proteins. For example, the minor groove within the center of the Fis-DNA complex narrows to about half the mean minor groove width of canonical B-form DNA to fit onto the protein surface. G/C base pairs within this segment, which is not contacted by the Fis protein, reduce binding affinities up to 2000-fold over A/T-rich sequences. We show here through multiple X-ray structures and binding properties of Fis-DNA complexes containing base analogs that the 2-amino group on guanine is the primary molecular determinant controlling minor groove widths. Molecular dynamics simulations of free-DNA targets with canonical and modified bases further demonstrate that sequence-dependent narrowing of minor groove widths is modulated almost entirely by the presence of purine 2-amino groups. We also provide evidence that protein-mediated phosphate neutralization facilitates minor groove compression and is particularly important for binding to non-optimally shaped DNA duplexes.
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AT-rich sequences tend to form a narrow minor groove because of negative propeller twisting, which is stabilized by inter-base-pair hydrogen bonds in the major groove.
“AT-rich sequences tend to form a narrow minor groove because of negative propeller twisting, which is stabilized by inter-base-pair hydrogen bonds in the major groove 31 .”
From Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator (2015) · cites this paper as [31]
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- Authors
- Hancock, S. P., Ghane, T., Cascio, D., Rohs, R., Di Felice, R., & Johnson, R. C.
- Affiliations
- University of Southern California (US)
- Corresponding author
- Johnson, Reid C.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-05-09
- Volume
- 41
- Issue
- 13
- Pages
- 6750-6760
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC3711457
- OpenAlex
- W2117314105
- Cited by
- 83
- References
- 73
- Citations by year
- 2026: 2 · 2025: 4 · 2024: 5 · 2023: 7 · 2022: 3 · 2021: 3 · 2020: 3 · 2019: 7 · 2018: 9 · 2017: 5 · 2016: 5 · 2015: 15 · 2014: 11 · 2013: 4
- FWCI
- 5.22
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nucleic Acids Research (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion, other-oa)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Funders
- U.S. Department of Energy (DE‐ AC02‐06CH11357, AC02‐06CH11357, P41 GM103403, 06CH11357, FC02-02ER63421, DE-AC02-)
- Istituto Italiano di Tecnologia
- National Institutes of Health (DE-AC02–06CH11357, GM103403, GM038509)
- National Institute of General Medical Sciences (GM038509, R37GM038509, P41GM103403)
- National Center for Research Resources (GM103403, P41RR015301)
- 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 › Protein Structure and Dynamics
- Keywords
- Fis protein, AT-rich sequences, GC base pairs, protein-DNA binding affinity, DNA duplex conformation
- MeSH terms
- DNA, Nucleic Acid Conformation, Phosphates, Protein Binding, Purines, Base Pairing, Factor For Inversion Stimulation Protein, Molecular Dynamics Simulation
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