Abstract
Matrixβassisted laser desorption/ionization mass spectrometry (MALDIβMS) has the potential for providing a rapid alternative to gel electrophoresis for DNA sequence analysis provided that an intense mass spectrometric response can be obtained from mixtures of DNA fragments containing up to 300 nucleotides. MALDIβMS has not yet proved viable for such analyses because the MS response falls off rapidly for mixedβbase DNA fragments containing more than 20β30 nucleotides. Previous studies have demonstrated that base composition is a critical factor in the MALDIβMS response of oligodeoxyribonucleotides. This paper describes an investigation of the physical roots of the observed influence of base composition on the mass spectrometric response, focusing on homopolymer oligodeoxyribonucleotides (dT~7~, dT~10~, dT~18~, dT~36~, dG~7~, dG~10~, dG~18~, dI~18~ and dU~18~) and dT~5~G~5~. Fortyβeight different matrix compounds were tested for their ability to produce laser desorption masses spectra from such homopolymer oligodeoxyribonucleotides. Considerably stronger mass spectrometric responses were obtained from polydeoxythymidines than from polydeoxyguanosines, polydeoxycytidines and polydeoxyadenosines. Although mass spectral peaks corresponding to dT~18~ were observed from 20 of the matrices studied, no discernible response was observed for dG~18~ from any of these matrices. To elucidate the physical basis for origins of the observed differences in response, a number of factors were investigated including the ionization efficiency, the tendency towards fragmentation and the extent to which the oligodeoxyribonucleotides were incorporated into the matrix crystals. The results of these experiments indicate that low ionization efficiency is not a likely main contributor to the low response to polydeoxyguanosines, fragmentation is a likely main contributor to the low response to polydeoxyguanosines, the overall incorporation of polydeoxyguanosines into matrix crystals is comparable to that for polydeoxythymidines and the exocyclic amino group of guanosine, adenosine and cytidine has a strong inhibitory effect on the mass spectrometric response.