THE DETECTION OF INTACT DOUBLE-STRANDED DNA BY MALDI

DNA fragments have been analyzed by matrix-assisted laser desorption i onization (MALDI) and electrospray mass spectrometry. In many cases, o nly the single-stranded oligonucleotides have been detected. Recently, spectra of intact double-stranded DNA have been obtained in both elec trospray and massive duster impact ionization. We show here the first MALDI spectra of intact double-stranded DNA (EcoR1 adaptor 12/16) that is clearly not due to nonspecific dimer formation. 6-Aza-2-thiothymin e was used as the matrix in the presence of ammonium citrate. Via the same procedure but with other matrices commonly employed for oligonucl eotide analysis, the intact DNA duplex was not detected. No sign of th e homodimer of either of the single strands is observed. Although the spectrum also shows peaks attributable to each of the single strands, these are demonstrated to arise from the DNA solution and not the samp le preparation or desorption process.