Cleavage reactions of the complex ions derived from self-complementary deoxydinucleotides and alkali-metal ions using positive ion electrospray ionization with tandem mass spectrometry

The dissociation reactions of the adduct ions derived from the four self-complementary deoxydinucleotides, d(ApT), d(TpA), d(CpG), d(GpC), and alkali-metal ions were studied in detail by positive ion electrospray ionization multiple-stage mass spectrometry (ESI-MSn). For the [M + H](+) ions of the four deoxydinucleotides, elimination of 5'-terminus base or loss of both of 5'-terminus base and a deoxyribose were the major dissociation pathway. The ESI-MSn spectra showed that Li+, Na+, and Cs+ bind to deoxydinucleotides mainly by substituting the H. of phosphate group, and these alkali-metal ions preferred to bind to pyrimidine bases rather than purine bases. For a given deoxydinucleotide, the dissociation pathway of [M + K](+) ions differed clearly from that of [M + Li](+), [M + Na](+), and [M + Cs](+) ions. Some interesting and characteristic cleavage reactions were observed in the product-ion spectra of [M + K] ions, including direct elimination of deoxyribose and HPO3 from molecular ions. The fragmentation behavior of the [M - K](+) and [M + W](+) (W = Li, Na, Cs) adduct ions depend upon the sequence of bases, the interaction between alkali-metal ions and nucleobases, and the steric hindrance caused by bases. (C) 2004 American Society for Mass Spectrometry.