3-Hydroxycoumarin as a new matrix for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of DNA.

3-Hydroxycoumarin (3-HC) was designed, synthesized, and tested as a matrix for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analyses of a variety of synthetic oligodeoxynucleotides ranging long from three to 70 bases. Using the matrix solution of 3-HC dissolved in a mixed solvent of acetone and diammonium hydrogen citrate, DNA segments over the mass range 800 Da to 6900 Da were isotopically resolved with high signal-to-noise (S/N) ratio. The individual isotopic molecular ion peaks of a group of 23-mer mixed-base oligomers differing by one or two bases with mass differences of 9 or 7 Da were recorded. Larger oligodeoxynucleotide segments of 34-mer, 50-mer, and 70-mer have also been analyzed effectively. Less than 250 attomol of a 10-mer DNA segment was clearly detected without any fragmentation. The new matrix can be used for the analysis of DNA segments in both positive- and negative-ion modes, and the quality of all negative-ion mode spectra are as good as that obtained in positive-ion mode shown in this paper. Compared with conventional matrices of 3-hydroxypicolinic acid (3-HPA) and 6-aza-2-thiothymine (ATT), 3-HC had noticeable improvement in resolution, S/N ratio, spot-to-spot-, and sample-to-sample reproducibility for analyzed DNA segments.