Structure and fragmentation mechanisms of isomeric T-rich oligodeoxynucleotides: a comparison of four tandem mass spectrometric methods.

Understanding the product-ion spectra of T-rich tetradeoxynucleotides is a starting point in the development of a mass spectrometric scheme to determine the mutagenicity of individual types of DNA damage. We obtained product-ion spectra for electrospray-produced ions that were activated in the ion source (electrospray ionization-source collision-activated-dissociation) and by high-energy collisions in the MS/MS mode of a four-sector instrument. We also activated singly and doubly charged ions by low-energy collisions in an ion-trap mass spectrometer and investigated post source decompositions of matrix-assisted laser desorbed ions in a time-of-flight mass spectrometer. The various methods of extracting structural information give remarkably consistent results. The difference in the relative abundances of wn and dn ions of the singly charged oligonucleotides and the formation of [a3-B3] ions, where B3 is the base on the third position, are effective for identification and distinction of pairs of isomeric tetranucleotides. A sufficient number of tetramers and pentamers were studied to enable us to propose a charge-remote mechanism for the formation of site-specific [an-Bn] ion.