Application of multiphoton ionization mass spectrometry: protected dideoxyribonucleotides

Abstract

This work demonstrates how IR-laser desorption of neutral molecules followed by resonantly enhanced multiphoton ionization can be employed to determine the molecular weight, base sequence of synthetic protected dinucleotides. All sixteen possible combinations of isomeric deoxyribodinucleotides which contain the phosphotriester linkage used in oligonucleotide synthesis have been investigated. The positively charged molecular ion was detected for each dinucleotide at low laser powers at an ionizing wavelength of 242.5 nm. In addition, fragment ions reflecting the primary structure were observed in the soft ionization mode. In the hard ionization mode intensive low mass fragment ions are formed by multiphoton absorption of the molecular ion. In this way the nucleic base composition of the dideoxyribonucleotide can be determined. Fragments containing the 5′ end are preferentially detected indicating the high UV absorptivity of the aromatic protective function located at the 5′ end. Beside absorption cross-sections, the stability of the N-glycosidic bond between the ribose, the nucleic base affects the intensity of both parent and daughter ions. By assigning the fragment ions generated by multiphoton absorption it is possible to distinguish isomeric sequences of these deoxyribodinucleotides. The influence of the type of the nucleobase and the position of the nucleoside with respect to the phosphate linkage on the relative intensities of the fragment ions are discussed.