Characterization and differentiation of isomeric self-complementary DNA oligomers by electrospray tandem mass spectrometry.

Two series of synthetic self-complementary isomeric DNA hexamers, namely d(CAGCTG), d(CGATCG) and d(CGTACG) (M(r) 1791) and d(CATATG), d(TGATCA) and d(TGTACA) (M(r) 1790) were analysed by negative electrospray mass spectrometry. As expected, these DNA hexamers exhibited identical series of multi-charged deprotonated molecular ions. Low-energy collision-induced dissociation tandem mass spectrometric analysis of the multi-charged oligonucleotide anions [M-3H]3- and [M-4H]4- provided characteristic and distinct finger-print patterns which permitted discrimination amongst the individual isomeric DNA hexamers and allowed complete direct sequence determination.