Site-specific protonation directs low-energy dissociation pathways of dinucleotides in the gas phase

Abstract Fourier transform ion cyclotron resonance mass spectroscopy has been used to examine the low-energy collision-induced dissociation (CID) pathways of protonated dinucleotides. Collisional activation using continuous off-resonance excitation permits observation of energetically favorable dissociation pathways. Dissociation products were examined under multiple collision conditions over a range of average center-of-mass collision energies from 0 to 8.1 eV. Semiempirical calculations were performed using AM1 and PM3 methods to obtain gas-phase model structures of the protonated dinucleotides and their CID fragments. These calculations indicate that the proton is localized exclusively on one of the nucleic acid bases, with additional stabilization of some systems resulting from hydrogen bonding interactions between the bases. Protonated molecular ions dissociate to yield several characteristic products. The major fragmentation pathways are directed by the site of protonation leading to elimination of a protonated base, generally the 3′-terminus base. Exceptions are observed only in systems having thymine as the 3′-terminus base, where the major product is the protonated 5′-terminus base. These observations agree with the known relative proton affinities of the nucleic acid bases, and the existence of stable tautomeric structures of adenine, cytosine, and guanine which make these bases better leaving groups when protonated. In addition, application of statistical RRKM calculations to model the unimolecular dissociation dynamics of the reaction leading to the protonated 3′-terminus base provides an estimate of 1.9 eV for the activation energy associated with this major fragmentation pathway. In some systems, moderate yields of other fragment ions are also observed. Only minor yields of sequence ions are observed with these quasi-molecular ions. Reaction mechanisms accounting for the observed products are proposed.