title: DNA bending by a phantom protein.
abstract: BACKGROUND
  Despite its stiffness, duplex DNA is extensively bent and folded during packaging and gene expression in biological systems. Modulation of the electrostatic repulsion between phosphates in the DNA backbone may be important in the bending of DNA by proteins. Here, we analyze the shape of DNA molecules that have been modified chemically to mimic the electrostatic consequences of a bound protein.
  
  
  RESULTS
  We have simulated salt bridges between DNA phosphates and cationic amino acid sidechains of a phantom protein by tethering ammonium cations to one face of the DNA helix. Tethered ammonium cations, but not neutral acetylated controls, induce DNA to bend toward its neutralized surface.
  
  
  CONCLUSIONS
  The shape of DNA molecules bearing a laterally-asymmetric distribution of tethered cations agrees qualitatively with theoretical predictions and with results previously obtained using neutral phosphate analogs. These data suggest principles that might be applied to the design of artificial DNA-bending proteins.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA. maher@mayo.edu
authors.forename: J K
authors.initials: JK
authors.lastname: Strauss
authors.forename: T P
authors.initials: TP
authors.lastname: Prakash
authors.forename: C
authors.initials: C
authors.lastname: Roberts
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 / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides / Q000737:chemistry; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry*; D055672:Static Electricity
chemical_list: D009843:Oligoribonucleotides; D011506:Proteins; D004247:DNA