Compaction of Duplex Nucleic Acids upon Native Electrospray Mass Spectrometry

Area of Science:

• Structural biology
• Biophysical chemistry
• Mass spectrometry

Background:

• Native mass spectrometry coupled to ion mobility spectrometry is increasingly used in structural biology.
• Conformation survival of biomolecules in the gas phase is often assumed.
• Previous studies successfully analyzed protein conformations in the gas phase.

Purpose of the Study:

• To investigate the gas-phase conformation of nucleic acid duplexes.
• To determine if nucleic acid structures survive native electrospray conditions.
• To understand the forces driving gas-phase conformations.

Main Methods:

• Native mass spectrometry
• Ion mobility spectrometry
• Molecular modeling (density functional calculations, semiempirical calculations, molecular dynamics)

Main Results:

• DNA and RNA duplexes adopt significantly more compact gas-phase structures than canonical solution structures.
• Compaction increases with duplex size, observed for both DNA and RNA.
• Molecular modeling indicates compaction is due to phosphate group self-solvation overcoming Coulomb repulsion.

Conclusions:

• Nucleic acid duplexes undergo significant structural rearrangements during desolvation in electrospray ionization.
• Gas-phase compaction is driven by novel phosphate-phosphate hydrogen bonds formed late in the process.
• Standard molecular dynamics simulations may not accurately capture these desolvation-induced structural changes.