SITE-SPECIFIC PROTONATION DIRECTS LOW-ENERGY DISSOCIATION PATHWAYS OFDINUCLEOTIDES IN THE GAS-PHASE

Fourier transform ion cyclotron resonance mass spectroscopy has been u sed to examine the low-energy collision-induced dissociation (CID) pat hways of protonated dinucleotides. Collisional activation using contin uous off-resonance excitation permits observation of energetically fav orable dissociation pathways. Dissociation products were examined unde r 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 structur es of the protonated dinucleotides and their CID fragments. These calc ulations indicate that the proton is localized exclusively on one of t he nucleic acid bases, with additional stabilization of some systems r esulting from hydrogen bonding interactions between the bases. Protona ted molecular ions dissociate to yield several characteristic products . The major fragmentation pathways are directed by the site of protona tion leading to elimination of a protonated base, generally the 3'-ter minus base. Exceptions are observed only in systems having thymine as the 3'-terminus base, where the major product is the protonated 5'-ter minus base. These observations agree with the known relative proton af finities of the nucleic acid bases, and the existence of stable tautom eric structures of adenine, cytosine, and guanine which make these bas es better leaving groups when protonated. In addition, application of statistical RRKM calculations to model the unimolecular dissociation d ynamics of the reaction leading to the protonated 3'-terminus base pro vides 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 i ons are observed with these quasi-molecular ions. Reaction mechanisms accounting for the observed products are proposed.