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Updated: May 25, 2026

Determination of the Gas-phase Acidities of Oligopeptides
11:00

Determination of the Gas-phase Acidities of Oligopeptides

Published on: June 24, 2013

Mass spectrometric study on sodium ion induced central nucleotide deletion in the gas phase

Helga Dögg Flosadóttir1, Kristmann Gíslason, Snorri Thor Sigurdsson

  • 1Science Institute and University of Iceland, Department of Chemistry, Dunhagi 3, 107 Reykjavík, Iceland.

Journal of the American Society for Mass Spectrometry
|February 1, 2012
PubMed

Insights

Sodium ions induce central nucleotide deletion in protonated oligonucleotides (ONTs), causing terminal nucleotide recombination. This study systematically investigates the mechanism of this gas-phase fragmentation channel.

Area of Science:

  • Mass Spectrometry
  • Chemical Dynamics
  • Molecular Ion Chemistry

Background:

  • Oligonucleotides (ONTs) are crucial biomolecules.
  • Gas-phase fragmentation of ONTs is vital for structural analysis.
  • Sodium ion interactions with ONTs can induce unique fragmentation pathways.

Purpose of the Study:

  • To investigate the mechanism of sodium ion-induced central nucleotide deletion in protonated ONTs.
  • To explore the concurrent recombination of terminal nucleotides during this fragmentation process.
  • To systematically study this fragmentation channel using various oligonucleotide lengths and sodium ion substitutions.

Main Methods:

  • Mass spectrometric analysis of protonated oligonucleotides.
  • Study of metastable decay of hexameric and octameric ONTs.
  • Controlled substitution of exchangeable protons with sodium ions (0-6 and 0-8).
  • Analysis of subsequent fragmentation of parent ions after initial base loss.

Main Results:

  • Observed central nucleotide deletion and terminal nucleotide recombination in sodium ion-treated ONTs.
  • Proposed a reaction mechanism involving sequential elimination of high proton affinity (PA) bases.
  • Demonstrated this is the first systematic study of this specific gas-phase fragmentation mechanism.

Conclusions:

  • The study elucidates a novel gas-phase fragmentation pathway for oligonucleotides.
  • Findings support a mechanism involving sequential high PA base elimination and terminal nucleotide recombination.
  • This research provides a foundation for understanding complex ion-molecule reactions in mass spectrometry.

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