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Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry has been used to measure accurately the molecular masses of synthetic methylphosphonate oligodeoxyribonucleotides, up to 18 nucleotides in length. A simple method has been developed for the complete sequence verification of these compounds, which are intractable by classical means. Sequencing from the 5' end of the molecule is possible because of inefficiencies in the synthetic procedure. Complementary information from the 3' end can be obtained by partial hydrolysis of the methylphosphonate backbone.

The sequences of synthetically prepared methylphosphonate oligodeoxyribonucleotides have been verified using ionspray tandem mass spectrometry with sample introduction via flow injection. The technique involves the use of product-ion scans from multiply protonated (4+ and 5+) precursors. Among the ions detected are several series of fragments of different charge states that indicate the base sequence of the intact molecule. Oligomers as large as 18 bases have been successfully characterized.