Location of the Na+ cation in negative ions of DNA evidenced by using MS2 experiments in ion trap mass spectrometry

Collision-induced dissociation (CID) spectra of deprotonated molecules prep ared from a variety of monocationized homonucleotides and heteronucleotides , using an external nanoelectrospray source with an ion trap mass spectrome ter, are described. Under such conditions, the achieved sensitivity in the negative ion mode is sufficient to obtain useful CID mass spectra of deprot onated oligonucleotides from doubly or triply charged negative ions. Result s from the analysis of the daughter ions show that the negative charges are located on 5'- or 3'-terminal sites whereas the salt group is at a central position. The cation appears to remain stationary during the CID process. Moreover, evidence exists that the central cation site is neither influence d by the size of the oligonucleotide nor by the nature of the 5'- or 3'-ter minus base, which indicates particular stability for the doubly or triply c harged quasimolecular anion. (Int J Mass Spectrom 190/191 (1999) 303-312) ( C) 1999 Elsevier Science B.V.