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Control of DNA minor groove width and Fis protein binding by the purine 2-amino group.

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Hancock SP, Ghane T, Cascio D, Rohs R, Di Felice R, Johnson RC
OpenAccess logo Nucleic Acids Res 41 6750-60 (2013)
Related entries: 4ihw, 4ihx, 4ihy

Cited: 49 times
EuropePMC logo PMID: 23661683

Abstract

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.

Articles - 4ihv mentioned but not cited (2)

  1. Control of DNA minor groove width and Fis protein binding by the purine 2-amino group. Hancock SP, Ghane T, Cascio D, Rohs R, Di Felice R, Johnson RC. Nucleic Acids Res 41 6750-6760 (2013)
  2. Energy Transfer as A Driving Force in Nucleic Acid⁻Protein Interactions. Zavyalova E, Kopylov A. Molecules 24 1443 (2019)


Reviews citing this publication (5)

  1. Absence of a simple code: how transcription factors read the genome. Slattery M, Zhou T, Yang L, Dantas Machado AC, Gordân R, Rohs R. Trends Biochem Sci 39 381-399 (2014)
  2. The λ Integrase Site-specific Recombination Pathway. Landy A. Microbiol Spectr 3 MDNA3-0051-2014 (2015)
  3. How motif environment influences transcription factor search dynamics: Finding a needle in a haystack. Dror I, Rohs R, Mandel-Gutfreund Y. Bioessays 38 605-612 (2016)
  4. Post-translational modification of nucleoid-associated proteins: an extra layer of functional modulation in bacteria? Dilweg IW, Dame RT. Biochem Soc Trans 46 1381-1392 (2018)
  5. Noncanonical binding of transcription factors: time to revisit specificity? Samee MAH. Mol Biol Cell 34 (2023)

Articles citing this publication (42)



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