Quantitative MALDI-TOF MS of oligonucleotides and a nuclease assay

DNA oligomers 8 and 12 nucleotides long have been detected quantitatively by MALDI-TOF mass spectrometry using longer oligonucleotides as internal standards. Employing this method, the kinetics of the nuclease degradation of the octamer were analyzed. Reactions performed in the presence of the ssDNA-binding peptide KWK yielded a footprint based on fragments from both the 3′- and the 5′-terminus of the oligonucleotide.