DNA bending by a phantom protein

Background: Despite its stiffness, duplex DNA is extensively bent and folded during packiging and gene expression in biological systems. Modulation of the electrostatic repulsion between phosphate 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 bund proteinResults: 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. Thethered ammonium cations, but not neutral acetylated controls, induced 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