Dissociation energies of deoxyribose nucleotide dimer anions measured using blackbody infrared radiative dissociation

Abstract

The dissociation kinetics of deprotonated deoxyribose nucleotide dimers were measured using blackbody infrared radiative dissociation. Experiments were performed with noncovalently bound dimers of phosphate, adenosine (dAMP), cytosine (dCMP), guanosine (dGMP), thymidine (dTMP), and the mixed dimers dAMP · dTMP and dGMP · dCMP. The nucleotide dimers fragment through two parallel pathways, resulting in formation of the individual nucleotide or nucleotide + HPO 3 ion. Master equation modeling of this kinetic data was used to determine threshold dissociation energies. The dissociation energy of (dGMP · dCMP − H) − is much higher than that for the other nucleotide dimers. This indicates that there is a strong interaction between the nucleobases in this dimer, consistent with the existence of Watson–Crick hydrogen bonding between the base pairs. Molecular mechanics simulations indicate that Watson–Crick hydrogen bonding occurs in the lowest energy structures of (dGMP · dCMP − H) −, but not in (dAMP · dTMP − H) −. The trend in gas phase dissociation energies is similar to the trend in binding energies measured in nonaqueous solutions within experimental error. Finally, the acidity ordering of the nucleotides is determined to be dTMP < dGMP < dCMP < dAMP, where dAMP has the highest acidity (largest Δ G acid).