Control of DNA minor groove width and Fis protein binding by the purine 2-amino group.
Publication Type:Journal Article
Source:Nucleic Acids Res, Volume 41, Issue 13, p.6750-60 (2013)
Keywords:Base Pairing, DNA, Factor For Inversion Stimulation Protein, Molecular Dynamics Simulation, Nucleic Acid Conformation, Phosphates, Protein Binding, Purines
<p>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. </p>