Sequence verification of oligodeoxynucleotides and oligophosphorothioates using electrospray ionization (tandem) mass spectrometry

Abstract

The collision induced dissociations of oligodeoxynucleotides, 5′ and 3′-terminal modified oligodeoxynucleotides and oligophosphorothioates, have been studied by using pneumatically assisted electrospray ionization mass spectrometry on a triple quadrupole instrument. Fragment ions were either produced in the collision gas cell of the triple quadrupole mass spectrometer or by nozzle-skimmer fragmentation. Sequence information was obtained for oligomers up to 21 bases and for 5′- and 3′-terminal modified 15-mers. Main fragments observed for oligodeoxynucleotides resulted from a-B- and w-type cleavages, and were most prominent when the lost base was guanine or cytosine. Positions containing thymine exhibited a low signal intensity for the corresponding a-B- and w-type fragment ions. Internal fragment ions containing from one up to four bases resulted from two subsequent a-b- and w-type cleavages, and were most prominent when both bases lost were guanine and/or cytosine. For oligophosphorothioates fragments resulting from a-B-, w-, b-, c-, x- and y-type cleavages were observed. In contrast to oligodeoxynucleotides none of the fragmentation reactions seems to be favoured, resulting in more sequence specific fragment ions. Compared to oligodeoxynucleotides, internal fragment ions were less prominent for oligophosphorothioates, possibly due to the many low energy fragmentation reactions possible for the intact oligomer and each fragment ion. © 1998 John Wiley & Sons, Ltd.