Comparison between solution-phase stability and gas-phase kinetic stability of oligodeoxynucleotide duplexes

Area of Science:

• Biophysical Chemistry
• Mass Spectrometry
• Molecular Biophysics

Background:

• Understanding the structural integrity of DNA in the gas phase is crucial for advanced analytical techniques.
• Oligonucleotide duplexes in solution exhibit stability governed by hydrogen bonding and base stacking.
• Electrospray ionization (ESI) is a common method for transferring biomolecules into the gas phase.

Purpose of the Study:

• To investigate the relative kinetic stabilities of 16-mer oligonucleotide duplexes using source collision-induced dissociation (CID).
• To compare gas-phase stability with solution-phase stability determined by thermal denaturation.
• To determine if the electrospray process preserves the DNA double-helix structure.

Main Methods:

• Source collision-induced dissociation (CID) of 16-mer oligonucleotide duplexes in a heated capillary electrospray ion source.
• Thermal denaturation monitored by UV spectrophotometry to assess solution-phase stability.
• Comparison of dissociation pathways and stability metrics between gas and solution phases.

Main Results:

• Gas-phase CID experiments demonstrate that hydrogen bonding and base stacking interactions are maintained in the gas phase.
• The results indicate that the electrospray process preserves the DNA double-helix structure.
• A step-wise opening mechanism for the double helix is proposed for gas-phase dissociation, competing with covalent bond cleavage.

Conclusions:

• Source CID probes the kinetic stability of gas-phase DNA complexes, confirming structural preservation during electrospray.
• Comparisons of kinetic stability are valid only for complexes of the same size.
• This study validates the use of gas-phase techniques like CID for studying DNA structural dynamics.