Bead-Ejection Scenario in Electrospray Ionization of Multidomain Nucleic Acids

Area of Science:

• Biochemistry
• Analytical Chemistry
• Structural Biology

Background:

• Understanding biomolecule ionization is key for native mass spectrometry (MS).
• Electrospray ionization (ESI) charging and conformation retention are critical for interpreting native MS data.
• Nucleic acids present unique ionization challenges due to their complex structures.

Purpose of the Study:

• To investigate the charging and gas-phase conformation of nucleic acid constructs with folded G-quadruplex "beads" linked by polythymine regions.
• To elucidate the mechanisms of ion production and structural preservation during electrospray ionization.
• To expand the conceptual framework for nucleic acid ionization in native MS.

Main Methods:

• Native mass spectrometry (native MS) analysis of nucleic acid constructs.
• Examination of charge-state and collision cross-section distributions.
• Comparison of experimental data with proposed ionization mechanisms (e.g., bead-ejection, charge residue, chain ejection).

Main Results:

• Oligonucleotides with folded G-quadruplexes showed multimodal charge-state and collision cross-section distributions, indicating multiple conformational ensembles.
• Ion production mechanisms varied with charge state, including bead-ejection, charge residue, and chain ejection scenarios.
• Local structures were preserved in ions charged above the Rayleigh limit, suggesting the presence of folded subunits.

Conclusions:

• The folding of G-quadruplex subunits significantly impacts nucleic acid ionization and gas-phase conformation.
• Ionic strength and G-quadruplex position influence charging and structural retention.
• Findings provide a broader understanding of nucleic acid ionization mechanisms in native MS.