title: Interference between Triplex and Protein Binding to Distal Sites on Supercoiled DNA.
abstract: We have explored the interdependence of the binding of a DNA triplex and a repressor protein to distal recognition sites on supercoiled DNA minicircles using MD simulations. We observe that the interaction between the two ligands through their influence on their DNA template is determined by a subtle interplay of DNA mechanics and electrostatics, that the changes in flexibility induced by ligand binding play an important role and that supercoiling can instigate additional ligand-DNA contacts that would not be possible in simple linear DNA sequences.
authors.affiliation: Department of Physics, Biological Physical Sciences Institute, University of York, York, United Kingdom.
authors.forename: Agnes
authors.initials: A
authors.lastname: Noy
authors.affiliation: Department of Biological Chemistry, John Innes Centre Norwich Research Park, Norwich, United Kingdom.
authors.forename: Anthony
authors.initials: A
authors.lastname: Maxwell
authors.affiliation: School of Physics and Astronomy, University of Leeds, Leeds, United Kingdom; Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom. Electronic address: s.a.harris@leeds.ac.uk.
authors.forename: Sarah A
authors.initials: SA
authors.lastname: Harris
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D004278:DNA, Superhelical / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D008024:Ligands; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D011485:Protein Binding
chemical_list: D004278:DNA, Superhelical; D008024:Ligands; C051802:triplex DNA; D004247:DNA