Oligodeoxynucleotide Fragmentation in MALDI/TOF Mass Spectrometry Using 355-nm Radiation

The fragmentation of small oligodeoxynucleotides using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry with 355-nm radiation from the matrix 2, 5-dihydroxybenzoic acid is studied. Negative ion mass spectra of the homopolymer oligodeoxynucleotides d(A)n d(C)n, and d(G)n(n = 4, 6, 8, and 10) show substantial cleavage at N-glycosidic and phosphodiester bonds, in contrast to d(T)n which shows little fragmentation. The number and intensity of the fragment peaks increases significantly with the length of the parent molecules. A series of asymmetric oligodeoxynucleotides were synthesized to study this fragmentation in greater detail. In dT4GT10, dT4G4T7, and dT7G4T4, the primary fragmentation pathway is loss of a base followed by backbone cleavage at the 3' C-O bond of the corresponding deoxyribose. Similar fragmentation patterns were observed with dT4N4T7 samples where N = C or A. A statistical cleavage model described the observed patterns of fragmentation well; the model yields fractions of backbone cleavage at A, C, and G of 0.13, 0.26, and 0.27, respectively. In contrast to the fragmentation observed using 2, 5-dihydroxybenzoic acid as a matrix, little or no fragmentation is observed with the matrix 3-hydroxypicolinic acid. Fragmentation of oligodeoxynucleotides in UV/MALDI is thus both nucleobase and matrix dependent. © 1995, American Chemical Society. All rights reserved.

Duke Scholars

Author Michael C. Fitzgerald Chemistry