Fragmentation reactions of all 64 protonated trimer oligodeoxynucleotides and 16 mixed base tetramer oligodeoxynucleotides via tandem mass spectrometry in an ion trap

Vrkic, AK; O&#39;Hair, RAJ; Foote, S; Reid, GE

Author(s): Vrkic, AK; O'Hair, RAJ; Foote, S; Reid, GE;
Details: Publication Year 2000-01-07,Volume 194,Issue #2-3,Page 145-164
Journal Title: INTERNATIONAL JOURNAL OF MASS SPECTROMETRY
Publication Type: Journal Article
Abstract: The gas phase fragmentation reactions of the [M + H](+) ions derived from all 64 trimer oligodeoxynucleotides and 16 isomeric tetramer oligodeoxynucleotides each containing adenine, thymine, guanine, and cytosine were examined by electrospray ionization using multistage tandem mass spectrometry in a quadrupole ion trap. The MS/MS and MS3 spectra of the [M + 2H](2+) ions of 16 isomeric tetramer oligodeoxynucleotides were also examined. The initial collisionally induced dissociation (CID) reaction mechanism for [M + nH](n+) ions involves neutral base loss. The relative abundance of each of these neutral losses is dependent on the relative proton affinity (where C approximate to G > A >> T), and position within the oligodeoxynucleotide sequence (5' > 3' > internal). These non-sequence [M + H - BnH](+) ions (where B-n denotes the nucleobase in the nth position from the 5' position), provide information on the identity but not the position of the base. MS3 experiments were carried out to demonstrate that these ions can provide further sequence information. It is proposed that intramolecular proton transfer following base loss leads to cleavage of the 3' - C-a phosphodiester bond (relative to the site of base loss) to yield an ion-molecule complex, which then undergoes either proton transfer or direct dissociation to yield complementary w- and (a - B)-type ions. For the trimer oligodeoxynucleotides, loss of the 5' base yields w(2)(+)-type ions, loss of the 3' base yields results in neutral water loss with formation of (a(3) - B-3)(+)-type ions and loss of the internal base yields w(1)(+) and (a(2) - B-2)(+)-type ions. The MS/MS and MS3 spectra of the [M + H](+) and [M + 2H](2+) ions of 16 isomeric tetramers were examined and found to follow the trends observed for the trimers. (Int J Mass Spectrom 194 (2000) 145-164) (C) 2000 Elsevier Science B.V.
Publisher: ELSEVIER SCIENCE BV
Keywords: COLLISION-INDUCED DISSOCIATION; NUCLEIC-ACID BASES; CHARGED OLIGONUCLEOTIDE ANIONS; GAS-PHASE; DINUCLEOTIDES; TAUTOMERISM; AFFINITIES; PATHWAYS; CYTOSINE; THYMINE
Publisher's Version: https://doi.org/10.1016/S1387-3806(99)00150-5
Terms of Use/Rights Notice: Refer to copyright notice on published article.

Creation Date: 2000-01-07 12:00:00