Ion stability of nucleic acids in infrared matrix-assisted laser desorption/ionization mass spectrometry

E. Nordhoff, R. Cramer, M. Karas, F. Hillenkamp, F. Kirpekar, K. Kristiansen, P. Roepstorff
1993 Nucleic Acids Research  
Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) with infrared laser light of a wavelength of 2.94 zm has been used for the analysis of nucleic acids. Spectra of oligodeoxynucleotides up to 26 nucleotides, oligothymidylic acids up to 100 nucleotides as well as different synthetic RNA oligomers and RNA transcripts up to 104 nucleotides are presented. A main problem in the analysis of oligodeoxynucleotides was found to be related to the loss of bases. The stability of
more » ... thymidylic acids as opposed to oligodeoxynucleotides containing all four bases indicates that the loss of bases is correlated with A, C and G protonation which decreases the stability of the N-glycosidic bond. Experiments indicate that the breakage of the N-glycosidic bond probably occurs during the desorption process due to proton transfer from the phosphodiester groups to the ionizable bases. RNA displayed a significantly higher stability in MALDI-MS due to the presence of a 2'-OH group. Consequently, signals of RNA transcripts with a length of up to 142 nucleotides could be detected by MALDI-MS. Technical details of the method, including the distribution of positive counterions on the phosphodiester backbone, the upper mass limit and mass accuracy are discussed along with a number of potential analytical applications.
doi:10.1093/nar/21.15.3347 pmid:7688451 pmcid:PMC331430 fatcat:exbemggbknh7bdh3dhhtw67ofu