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Proceedings Paper

Fragmentation mechanisms of oligonucleotides in MALDI mass spectrometry
Author(s): Christine M. Nelson; Lin Zhu; Wei Tang; Lloyd M. Smith; Kevin Crellin; Jamal Berry; Jack L. Beauchamp
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Paper Abstract

Early matrix assisted laser desorption/ionization (MALDI) studies of oligonucleotides elucidated many issues inherent to the analysis of nucleic acids. These studies demonstrated that fragmentation is an important issue and is responsible for some of the current limitations associated with the technique. Results in our laboratory and in others confirm that fragmentation is dependent on both oligonucleotide sequence and matrix composition. The proposed fragmentation pathway consists of nucleobase protonation inducing base loss followed by backbone cleavage at the 3' C-O bond on the corresponding deoxyribose. Using theoretical calculations, we explain why the four nucleobases display different fragmentation propensities. Additionally, if nucleobase protonation initiates fragmentation, then differences in fragmentation amounts when different matrices are used must be related to the various matrices' abilities to protonate the nucleobase. Currently, we are investigating the relationship between fragmentation propensity and matrix properties. Proton affinities of five common MALDI matrices have been measured and compared to fragmentation probabilities. By deepening our understanding of the fundamental chemistry of DNA fragmentation, we hope to be able to develop the MALDI technique into a powerful robust and versatile methodology for nucleic acid analysis.

Paper Details

Date Published: 1 April 1996
PDF: 9 pages
Proc. SPIE 2680, Ultrasensitive Biochemical Diagnostics, (1 April 1996); doi: 10.1117/12.237612
Show Author Affiliations
Christine M. Nelson, Univ. of Wisconsin/Madison (United States)
Lin Zhu, Univ. of Wisconsin/Madison (United States)
Wei Tang, Univ. of Wisconsin/Madison (United States)
Lloyd M. Smith, Univ. of Wisconsin/Madison (United States)
Kevin Crellin, California Institute of Technology (United States)
Jamal Berry, California Institute of Technology (United States)
Jack L. Beauchamp, California Institute of Technology (United States)

Published in SPIE Proceedings Vol. 2680:
Ultrasensitive Biochemical Diagnostics
Gerald E. Cohn; Steven A. Soper; C. H. Winston Chen, Editor(s)

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