Analysis of negatively 'charge tagged' DNA by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

An improvement in detectability and stability of DNA analysis by matrix-ass isted laser desorption/ionization time-of-flight mass spectrometry (MALDI-T OFMS) using oligonucleotides modified with a neutralized backbone and a fix ed single, positive charge was recently reported. The attachment of the pos itive charge requires a primary amino group,limiting this approach to accor dingly functionalized DNA, The method described here uses backbone neutrali zed DNA for the same purpose, with a single unmodified phosphate in the DNA backbone carrying the negative charge. Thus, no chemical modification othe r than neutralizing the remaining charges on the phosphorothioates is requi red. This is performed in a single methylation step. The enhancement in sen sitivity is comparable to that for DNA carrying a single positive charge, i nterestingly even when using the same non-protonating matrix. The mechanist ic implications of these findings regarding the MALDI process are discussed , The DNA derivatization methods presented help to make MALDI-MS of DNA app licable and competitive for genome analysis and medical diagnostics. Copyri ght (C) 1999 John Wiley & Sons, Ltd.