DNA bending by asymmetrically tethered cations: influence of tether flexibility.

ABSTRACT

BACKGROUND: We have been studying the proposal that laterally asymmetric charge neutralization along the DNA double helix can induce collapse toward the neutralized surface. Results of previous experiments implied that such a phenomenon can occur, suggesting a role for local interphosphate repulsive forces in DNA shape and rigidity. RESULTS: We now show that, whereas six ammonium ions tethered to one DNA face on flexible propyl chains can induce detectable DNA curvature, tethering of ammonium ions on rigid propynyl tethers does not induce DNA curvature. Molecular modeling indicates differing propensities for phosphate salt bridge formation between propyl- and propynyl-tethered ammonium ions. CONCLUSIONS: Ammonium ion localization is suggested as a key factor in induced bending. Rigidification of the double helix by stacking of propyne groups cannot be excluded.