Hydrogen-Bonding and π−π Base-Stacking Interactions Are Coupled in DNA, As Suggested by Calculated and Experimental Trans-Hbond Deuterium Isotope Shifts

Abstract

Computational and experimental trans-Hbond deuterium isotope shifts suggest that Hbonding and electronic base-stacking interactions, although largely orthogonal, are coupled in B-form DNA duplexes. For an A:T base pair, the Hbond is shorter and stronger in the RAR:YTY than YAY:RTR context. This difference is due to the greater anharmonicity of the N3−H3 vibrational potential of the thymine in RAR:YTY, which arises from electronic interactions between A:T and adjacent bases. As predicted by the calculations, reduction of the base stacking propensity using ethanol abolishes the experimental sequence dependence of 2hΔ13C2.