LOW-ENERGY COLLISION-INDUCED DISSOCIATION OF DEPROTONATED DINUCLEOTIDES - DETERMINATION OF THE ENERGETICALLY FAVORED DISSOCIATION PATHWAYS AND THE RELATIVE ACIDITIES OF THE NUCLEIC-ACID BASES

Fourier transform ion cyclotron resonance mass spectroscopy has been u sed to examine the collision-induced dissociation pathways of all 16 o f the possible deprotonated dinucleotides. These quasimolecular ions w ere generated by cesium ion bombardment of a mixture of triethanolamin e, ammonium hydroxide and the dinucleotide. Collisional activation usi ng continuous off-resonance excitation permits observation of energeti cally-favorable dissociation pathways. Dissociation products were exam ined over the range of center of mass energies from 0 to the minimum e nergy required to bring about complete dissociation of the reactant io n which did not exceed 7.7 eV for deprotonated parent ions and 8.8 eV for fragment ions in any of the systems. Semiempirical calculations we re performed using the PM3 method, a variant of the AM1 method, to obt ain gas-phase model structures and energies of the deprotonated dinucl eotides and their collision-induced dissociation fragments. The acidit ies of the nucleic acid bases and dimethyl phosphate were calculated u sing the AM1 method. The deprotonated quasimolecular ions dissociate t o yield several characteristic products. The major products formed in all systems are the deprotonated 5'-terminus base, the ion resulting f rom loss of the neutral 5'-terminus base, or the metaphosphate anion, PO3-. Insight into the relative stabilities of the fragment ions is ga ined by comparing the product distributions observed in each of the sy stems. The relative yields of products involving either the 3'- or 5'- end of the molecule suggest the 3'-terminus base is stabilized through hydrogen bonding interaction with the phosphate group. The relative s trength of this stabilization follows the order guanine > thymine > cy tosine > adenine. Additionally, the relative abundances of the deproto nated nucleic acid fragments suggest that the relative acidities of th e nucleic acid bases follow the order adenine > thymine > guanine > cy tosine. Only minor yields of sequence ions in which one of the phospha te diester linkages is cleaved are observed with these quasimolecular ions. Reaction mechanisms which account for the observed products are proposed.