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 succe ssful characterization of picomole quantitites of modified deoxyoligon ucleotides. The procedure was found to be applicable to the analysis o f 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 phosphat e backbone: 2'-5' and phosphorothioate linkages. Use of an alpha-cyano -4-hydroxycinnamic based matrix gave sharp peaks, sensitivity to 1 pmo l, accuracy to 0.06% on average and avoided the necessity for cryogeni c technique and/or specialized equipment. Mixtures of normal and modif ied oligonucleotides worked well without any special precautions as lo ng 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 oligonuclotides could be rapidly analyzed as a quality-control measure using from 10 to 20 pmo l of a typical 0.2-mu mol scale synthesis.