Metastable decay of negatively charged oligodeoxynucleotides analyzed with ultraviolet matrix-assisted laser desorption/ionization post-source decay and deuterium exchange.

In an effort to understand the initiating step in metastable-ion decay of UV matrix-assisted laser desorption/ionization (MALDI)-produced ions, we conducted experiments in which we exchanged all active protons for deuterons of tetrameric and hexameric oligodeoxynucleotides. We wish to address the controversial proposal that in the negative-ion mode, as in the positive-ion mode, fragmentation is driven by nucleobase protonation. The results show unambiguously that proton transfer, leading to zwitterion formation, charges a nucleobase prior to its elimination. The zwitterion formation directs fragmentation of both positive and negative oligodeoxynucleotide ions. Poly-T-rich oligodeoxynucleotide tetramers show surprising differences in the negative compared to the positive-ion mode, as thymine is preferentially expelled, instead of a nucleobase with higher proton affinity. For the exceptional case of negatively charged poly-T-rich oligodeoxynucleotide tetramers generated by MALDI, we propose that zwitterion formation with positive charging of a nucleobase leads to base stabilization in the negative-ion mode through an interaction of the positive nucleobase with the excess negative charge. Moreover, backbone cleavages (accompanied by H rearrangement) of a phosophodiester bond give first-generation products that can be traced back to this tripolar complex bearing one positive and two negative charges, all of which may be interacting.