A-Tract Induced DNA Bending is A Local Non-Electrostatic Effect

Abstract

The macroscopic curvature induced in double helical B-DNA by regularly repeated adenine tracts (A-tracts) is a long known, but still unexplained phenomenon. This effect plays a key role in DNA studies because it is unique in the amount and the variety of the available experimental information and, therefore, is likely to serve as a gate to the unknown general mechanisms of recognition and regulation of genome sequences. The dominating idea in the recent years was that, in general, macroscopic bends in DNA are caused by long range electrostatic repulsion between phosphate groups when some of them are neutralized by proximal external charges. In the case of A-tracts this may be specifically bound solvent counterions. Here we report about molecular dynamics simulations where a correct static curvature in a DNA fragment with phased adenine tracts emerges spontaneously in conditions where any role of counterions or long range electrostatic effects can be excluded.