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.
Highlights
Protein binding to DNA is central to all aspects of chromosome function
All of the Fis–DNA contacts present in the F1 structure are maintained in the F28 structure, and the protein backbone atoms of the F1 and F28 structures align with a root-mean-square deviation (RMSD) of 0.27 A
We show that the exocyclic 2-amino group on guanine is the key determinant responsible for modulating minor groove geometry
Summary
Protein binding to DNA is central to all aspects of chromosome function. Proteins can bind DNA over a range of affinities and specificities that are fine-tuned through multiple mechanisms depending on the individual protein and its function at particular binding sites. Shape recognition can contribute in essential ways to DNA site selection by DNAbinding proteins that display both stringent and relaxed sequence specificity [4,5]. An important subset of sequence-dependent DNA conformation is the shape of the minor groove. DNA segments with subtle variations in minor groove widths can direct Hox proteins to their different target sites with exquisite specificity [7]. In these and other examples, basic side chain residues, most often arginines, selectively insert into the minor grooves because of shape-dependent differences in electrostatic potential [8]. Similar principals contribute to the phasing of nucleosomes and selective binding of abundant nucleoid-associated proteins in bacteria [8,9,10,11,12]
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