Improving spot homogeneity by using polymer substrates in matrix-assisted laser desorption/ionization mass spectrometry of oligonucleotides

We describe a method for improving the homogeneity of MALDI samples prepare d for analysis of small, single-stranded oligonucleotides using the widely used DNA matrix system, 3-hydroxypicolinic acid/picolinic acid/ammonium cit rate. This matrix system typically produces large crystals around the rim o f the dried sample and requires tedious searching of this rim with the lase r. However, when a substrate is prepared using both Nafion and a hydrophili c, high-molecular-weight polymer, such as linear polyacrylamide, linear pol y(ethylene oxide), or methyl cellulose, oligonucleotide-doped matrix crysta ls tend to be smaller and more uniformly distributed across the entire spot , thus decreasing the time that is required for locating a usable signal. I n addition to MALDI characterization of the spatial distribution of "sweet spots," fluorescence microscopy allows for imaging dye-labeled DNA in dried MALDI spots. The mechanism of enhanced uniformity may involve increased vi scosity in the MALDI sample droplet due to partial solubilization of the su bstrate by the MALDI sample solvent as well as partitioning of the matrix o r DNA between the solvent and the undissolved portion of the polymer substr ate.