Nucleic Acids Research, 1993, Vol. 21, No. 15 3347-3357
© 1993
METHODS |
Ion stability of nucleic acids in infrared matrix-assisted laser desorption/ionization mass spectrometry
Institute for Medical Physics and Biophysics, University of Münster Robert-Koch-Strasse 31, 4400 Münster, Germany 1Department of Molecular Biology, University of Odense Campusvej 55, 5230 Odense M., Denmark
Received May 28, 1993. Accepted June 21, 1993.
Matrix-assisted laser desorption/lonization mass spectrometry (MALDI-MS) with infrared laser light of a wavelength of 2.94m has been used for the analysis of nucleic acids. Spectra of oligodeoxynucleotides up to 26 nucleotides, oiigothymidylic acids up to 100 nucieotides as well as different synthetic RNA oligomers and RNA transcripts up to 104 nucleotides are presented. A main problem in the analysis of oligodeoxynucieotides was found to be related to the loss of bases. The stability of oligothymldylic 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 MALD1-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.
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