Analysis of synthetic oligodeoxynucleotides containing modified components by electrospray ionization mass...

Electrospray ionization mass spectrometry (ESI/MS) has been used to confirm the synthesis of oligodeoxynucleotides containing modified structures and to identify products of unstable oligomer degradation. Negative ion mass spectra of oligomers and dimethoxytrityl-protected oligomers exhibited a distribution of multiply charged molecular ions with few adduct ions present. Molecular masses may be determined from the array of peaks with excellent accuracy and serve to corroborate the synthetic sequence and the inclusion of a modified structure within the sequence. Incorporation of modified deoxynucleotides, stable isotopes, and other novel structures such as a terminal biotin moiety and a phosphorothioate linkage can be rapidly verified by ESI/MS. This technique has also proved useful for the identification of products of unstable oligomers formed during synthesis, deprotection, or purification, including the major products formed under basic conditions from 5'-dimethoxytrityl-protected oligomers containing 8-oxo-2'-deoxyguanosine.