Degree Name

Doctor of Philosophy


Department of Chemistry


Electrospray ionisation tandem mass spectrometry (ESI-MS/MS) has been used to examine the fragmentation of a range of unmodified oligonucleotides (from tetramers to octamers) and alkylated oligonucleotide adducts on a hybrid sector-time-offlight mass spectrometer. The detailed characterisation of all the product ions observed in the M S / M S spectra of two hexanucleotides 5'-d(CACGTG)-3' and 5'-d(CGTACG)-3' was undertaken using a combination of high resolution M S and M S / M S of product ions generated by in-souree collisional activation of oligonucleotides in both positive and negative ion modes. These experiments provide significant n e w information concerning the identities of the major product ions and their relative propensities for subsequent fragmentation. A comprehensive study of the influence of base composition, base location and precursor ion charge (in both positive and negative ion modes) on the resulting M S / M S spectra of oligonucleotides, showed the major fragmentation pathways i.e. the formation of w and a-B sequence ions, and ions arising from loss of charged and neutral bases, to be strongly influenced by the most probable location of the charges and the location and identity of the bases. The effect of base composition was particular evident in the observed lack of preference for loss of neutral thymine in both modes.

In the second part of this work, the utility of ESI-MS/MS for studying the sequence selectivity of alkylating ligands is demonstrated with three alkylating agents, hedamycin, DC-92B and N-bromohexylphenanathridinium bromide. The M S / MS spectra of the resulting adducts show highly specific fragmentation pathways which allow the facile identification of the site(s) of binding of the ligands on the oligonucleotides. Differences in sequence selectivity exhibited by the three ligands are also demonstrated. Overall this work demonstrates that ESI-MS/MS is a powerful technique for the characterisation of oligonucleotides and oligonucleotide adducts.