ANALYSIS OF MODIFIED OLIGONUCLEOTIDES BY MATRIX-ASSISTED LASER DESORPTION IONIZATION FOURIER-TRANSFORM MASS-SPECTROMETRY/

Matrix-assisted laser desorption/ionization (MALDI) Fourier transform ion cyclotron resonance mass spectrometry (FTMS) has been applied to t he structural characterization of modified oligodeoxyribonucleotide 4- , 6-, and 11-mers. Each oligonucleotide contained one modified base, e ither an O-6-methyl-substituted guanine, an N-6-(10R)-trans- opened be nzo[a]pyrenediol epoxide adduct of adenine, or an N-2-(R)-styrene oxid e adduct of guanine. 3-Hydroxy-picolinic acid was used as the MALDI ma trix for molecular weight and purity determinations, while either 2,5- dihydroxybenzoic acid (DHBA) or an anthranilic/nicotinic acid (AA/NA) mixture was used to induce fragmentation for the production of structu rally significant fragment ions. For the 4- and 6-mers, the oligonucle otide sequence could be obtained from the direct AA/NA or DHBA spectra . Sequence information was also obtained by inserting a time delay bet ween the laser desorption event and ion detection to permit metastable decomposition. For the 11-mers, high-mass sequence ions were not dete cted. Although similar sequence ions were observed in both the positiv e and the negative ion mass spectra, more fragmentation was generally observed in the positive ion mode. In the positive ion mode, modified base fragment ions were observed when DHBA was used, and these fragmen ts were examined using accurate mass measurements, collisionally induc ed dissociations, and ion-molecule reactions to characterize the modif ied base. MALDI-FTMS signals from one sample application can be used f or the measurement of hundreds of spectra. The direct MALDI-FT mass sp ectra show matrix-dependent, structurally informative fragments, and C ID experiments can be implemented using low-picomole sample quantities .