title: DNA bending by hexamethylene-tethered ammonium ions.
abstract: DNA is bent when complexed with certain proteins. We are exploring the hypothesis that asymmetric neutralization of phosphate charges will cause the DNA double helix to collapse toward the neutralized face. We have previously shown that DNA spontaneously bends toward one face of the double helix when it is partially substituted with neutral methylphosphonate linkages. We have now synthesized DNA duplexes in which cations are tethered by hexamethylene chains near specific phosphates. Electrophoretic phasing experiments demonstrate that tethering six ammonium ions on one helical face causes DNA to bend by approximately 5 degrees toward that face, in qualitative agreement with predictions. Ion pairing between tethered cations and DNA phosphates provides a new model for simulating the electrostatic consequences of phosphate neutralization by proteins.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha 68198, USA.
authors.forename: J K
authors.initials: JK
authors.lastname: Strauss
authors.forename: C
authors.initials: C
authors.lastname: Roberts
authors.forename: M G
authors.initials: MG
authors.lastname: Nelson
authors.forename: C
authors.initials: C
authors.lastname: Switzer
authors.forename: L J
authors.initials: LJ
authors.lastname: Maher
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000187:drug effects*; D004591:Electrophoresis, Polyacrylamide Gel; D008274:Magnesium / Q000378:metabolism; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation / Q000187:drug effects*; D010710:Phosphates / Q000378:metabolism; D000644:Quaternary Ammonium Compounds / Q000494:pharmacology*; D012091:Repetitive Sequences, Nucleic Acid
chemical_list: D010710:Phosphates; D000644:Quaternary Ammonium Compounds; D004247:DNA; D008274:Magnesium