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Charge state-dependent fragmentation of oligonucleotide/metal complexes
Karin M Keller1, Jennifer S Brodbelt
1Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712, USA.
Journal of the American Society for Mass Spectrometry
|January 18, 2005
Summary
Collision-activated dissociation (CAD) reveals how metal ions influence oligodeoxynucleotide (ODN) fragmentation. Metal complexation alters base loss and promotes unique metallated fragment ions, especially with barium.
Area of Science:
- Mass Spectrometry
- Oligonucleotide Chemistry
- Coordination Chemistry
Background:
- Collision-activated dissociation (CAD) is a key technique for analyzing gas-phase biomolecule fragmentation.
- Understanding how metal ions interact with and modify oligonucleotide structures is crucial for their characterization.
- Previous studies on deprotonated oligonucleotides show specific fragmentation patterns under CAD.
Purpose of the Study:
- To investigate the gas-phase fragmentation behavior of oligodeoxynucleotide (ODN):metal complexes using CAD.
- To determine how various metal ions (alkali, alkaline earth, transition) affect ODN fragmentation at different charge states.
- To explore the formation of novel metallated fragment ions in ODN:metal complexes.
Main Methods:
- Utilized collision-activated dissociation (CAD) mass spectrometry.
- Examined 1:1 complexes of ten-residue oligodeoxynucleotides (ODNs) with a range of metal ions.
- Analyzed fragmentation patterns across low, intermediate, and high charge states.
Main Results:
- Metal complexation, particularly with Ca(+2), Sr(+2), and Ba(+2), altered relative intensities of M-B species, favoring cytosine loss over guanine loss.
- Sequence ion intensities remained largely unaffected, but metal complexation influenced fragmentation in isomeric sequences with terminal complementary residues.
- In high charge states, ODN:Ba(+2) complexes yielded abundant metallated a(n)(-m) fragment ions, especially with thymine at Position 6.
Conclusions:
- Metal ion complexation can significantly alter the gas-phase fragmentation pathways of oligodeoxynucleotides (ODNs).
- The observed changes in fragmentation, including preferential base loss and formation of metallated ions, suggest metal-induced conformational or dynamic changes.
- The formation of metallated a(n)(-m) ions is likely directed by the proximity of the metal ion to neutral phosphate groups and specific nucleobases like thymine.