Characterization of modified and normal deoxyoligonucleotides by MALDI, time-of-flight mass spectrometry

A commercially available, matrix-assisted, laser desorption/ionization (MALDI), time-of-flight mass spectrometer has been used for the successful characterization of picomole quantities of modified deoxyoligonucleotides. The procedure was found to be applicable to the analysis of a variety of modified synthetic structures that included oligos with an intact dimethoxytrityl-blocking group, with omega-aminohexyl- and omega-hexyl-modified bases and with alterations to the normal phosphate backbone: 2'-5' and phosphorothioate linkages. Use of an alpha-cyano-4-hydroxycinnamic acid/ammonium formate based matrix gave sharp peaks, sensitivity to 1 pmol, accuracy to 0.06% on average and avoided the necessity for cryogenic technique and/or specialized equipment. Mixtures of normal and modified oligonucleotides worked well without any special precautions as long as the modified oligonucleotides contained a polyanionic backbone. Modified oligonucleotides that contained an amide linkage in place of the usual phosphate ester link required a sinapinic acid- or esculetin-based matrix with no ammonium formate. Crude oligonucleotides could be rapidly analyzed as a quality-control measure using from 10 to 20 pmol of a typical 0.2-mumol scale synthesis.