Analysis of trityl-on oligos by MALDI and ESI/LC/MS
Summary
- Labile trityl protecting groups can dissociate in the acidic MALDI matrix or during desorption/ionization
- ESI/LC/MS allows direct detection of trityl-on oligos
- Mass accuracy for ESI/LC/MS is shown to be better than 0.01%
Dimethoxytrityl (DMT) protecting groups are commonly used in oligonucleotide synthesis. Since incomplete deprotection can lead to problems in the performance of oligos in certain assays, it is important to choose an analytical method that accurately reflects whether a DMT is present. The oligo 5'-DMT-TAATACGACTCACTATAGGGTAATACGACTCACTATAGGG-3' was analyzed by MALDI-ToF and by Novatia's ESI/LC/MS methods. The theoretical mass of the DMT-on oligo is 12614.4 Da. The ESI result is within 0.009% of this expected value. Note that the MALDI result is consistent with loss of the DMT (MW 12312 Da). MALDI is not the method of choice for determining the presence of terminal protecting groups, since the labile moeities may be lost during the desorption/ionization process.
MALDI data and oligo synthesis courtesy of Scott Olsen, St. Jude Children's Research Hospital
 
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