Bending and Base-Stacking Interactions in Double-Stranded DNA

An elastic model for double-stranded polymers is constructed to study the recently observed DNA entropic elasticity, cooperative extensibility, and supercoiling property. With the introduction of a new structural parameter (the folding angle $\varphi$), bending deformations of sugar-phosphate backbones, steric effects of nucleotide base pairs, and base-stacking interactions are considered. The comprehensive agreements between theory and experiments both on torsionally relaxed DNA and on negatively supercoiled DNA strongly indicate that base-stacking interactions, although short-ranged in nature, dominate the elasticity of DNA and, hence, are of vital biological significance.