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Journal of The American Society for Mass Spectrometry

, Volume 17, Issue 9, pp 1229–1238 | Cite as

Thermal decomposition of multiply charged T-rich oligonucleotide anions in the gas phase. Influence of internal solvation on the arrhenius parameters for neutral base loss

  • Rambod Daneshfar
  • John S. Klassen
Articles

Abstract

Arrhenius activation parameters (E a , A) for the loss of neutral nucleobases from a series of T-rich, doubly and triply deprotonated 15-and 20-mer oligodeoxynucleotides (ODN) containing a single reactive base (X = A or C) with the sequence, XT14, XT19 and T19X, have been determined using the blackbody infrared radiative dissociation technique. The A-containing anions are significantly more reactive (≥3000 times) than the C-containing ions over the temperature range investigated. Importantly, the Arrhenius parameters for the loss of AH exhibit a strong dependence on size of the ODN and, to some extent, the charge state; the Arrhenius parameters increase with size and charge (E a = 29–39 kcal mol−1, A=1015–1020 s−1). In contrast, the parameters for the loss of CH are much less sensitive to size (E a =35–39 kcal mol−1, A=1014–1017 s−1). The results are consistent with a greater contribution from the internal solvation of the reactive base to the Arrhenius parameters for the loss of A, compared with C, from the 15-and 20-mers. To further probe differences in internal solvation of A and C, hydrogen/deuterium exchange was carried out on AT 19 −3 , T19A−3, CT 19 −3 and T19C−3 using D2O as the exchange reagent. However, the H/D exchange results did not reveal any differences in internal solvation within the ODN anions. Arrhenius parameters for the dissociation of noncovalent complexes of T 20 −3 and the neutral nucleobase AH or CH have also been determined. Differences in the parameters indicate differences in the nature of the intermolecular interactions. It is proposed that neutral A-T interactions (i.e., base-base), which originate in solution, dominate in the case of (T20+AH)−3, while charge solvation, involving CH and a deprotonated phosphate group, is present for (T20+CH)−3.

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Copyright information

© American Society for Mass Spectrometry 2006

Authors and Affiliations

  1. 1.Department of ChemistryUniversity of AlbertaEdmontonCanada

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