Sequence determination of protected oligodeoxyribonucleotides containing phosphotriester linkages by californium-252 plasma desorption mass spectrometry.

A mass spectrometric method for determining the sequence and molecular weight of protected oligodeoxyribonucleotides is described. By using the method of 252Cf plasma desorption mass spectrometry [Macfarlane, R. D. & Torgerson, D. F. (1976) Science 191, 920--925], positive-ion mass spectra were obtained for a series of protected oligonucleotides extending to a decanucleotide; the spectra were dominated by the presence of the oligonucleotide molecular ion. The negative-ion mass spectra were characterized by a nested set of fragment ions extending from the 3'- or 5'-terminal nucleotide to the opposite terminal nucleotide, thereby identifying the sequence. The utility of this method has been demonstrated by the sequence determination of protected tetra-, penta-, and hexanucleotides synthesized by the improved phosphotriester method.