Matrix-assisted laser desorption/ionization time-of-flight analysis of low-concentration oligonucleotides and mini-sequencing products

A new sample preparation procedure has been developed to improve the matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) analysis of low-concentration oligonucleotides. In this method, a few microL of the oligonucleotide solutions are first dispensed and allow drying and shrinking to a small spot on an anchoring target. Thereafter, a small volume (0.1 microL) of the saturated 3-hydroxypicolinic acid (3-HPA) solution is added to the top of the shrunk oligonucleotide spot. It is found that the sample prepared by this procedure is more homogenous and substantially reduces the need to search for 'sweet' spots. Importantly, the increased shot-to-shot and sample-to-sample reproducibility makes it possible to perform high-throughput and quantitative analysis. We demonstrated that this procedure allowed the robust detection of oligonucleotides at a level of 0.01 microM and mini-sequencing products produced using only 50 fmol of the extension primer.