Structural Characterization of Normal and Modified Oligonucleotides by Matrix-assisted Laser Desorption Fourier Transform Mass Spectrometry.

Matrix-assisted UV laser desorption Fourier transform mass spectrometry (266 nm, nicotinic acid matrix) can be used for the detailed structural characterization of normal and modified oligonucleotides. The negative ion spectra for these compounds revealed abundant (M - H) (-) ions as well as fragment ions that provided the information necessary to determine oligomer sequence and to differentiate isomers. The nicotinic acid matrix was required for the production of (M - H) (-) ions for the oligonucleotide dimers, trimers, tetramers, and hexamers examined in this study. Elimination of the nicotinic acid matrix resulted in complete loss of the (M -H) (-) ions as well as most of the larger fragment ions for the oligomers. The primary fragmentation pathway was observed to be phosphate ester bond cleavage with the resulting charge retained on the 3' end of the oligomer and enabled isomeric differentiation of compounds such as d(S'-CGCG-3') and d(S'-CCGG-3'). Collisioninduced dissociation experiments of the (M - H) (-) ions for these compounds confirmed the preferential loss of nucleotides from the 5' end of the oligomers. The presence and location of modifications such as methyl and ethyl alkyl groups to the oligonucleotides could also be identified.