Detection of double-stranded DNA by IR- and UV-MALDI mass spectrometry

Double-stranded DNA ranging from 9 kDa to over 500 kDa were desorbed and an alyzed by MALDI TOF mass spectrometry. IR-MALDI with glycerol as matrix yie lded excellent results for larger double-stranded DNA by adjustment of the ionic strength through the addition of salts. Very little fragmentation and a routine sensitivity in the subpicomole range were observed in IR-MALDI w hen double-stranded analytes harboring 70 base pairs or more were probed. I n the lower mass range (up to similar to 70 base pairs), UV-MALDI with 6-az a-2-thiothymine as matrix was the ionization method of choice because it al lowed specific double-stranded complexes containing relatively few base pai rs to be desorbed intactly. In this mode, an essentially quantitative detec tion of the double-stranded form was observed for a 70-mer, The UV-MALDI wa s accompanied by a significant fragmentation and a resulting reduced sensit ivity and mass resolution. The methods described open MALDI-MS for the anal ysis of large DNA-DNA and DNA-protein complexes.