Differentiating Parallel and Antiparallel DNA Duplexes in the Gas Phase Using Trapped Ion Mobility Spectrometry

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• Deoxyribonucleic acids (DNA) exhibit diverse structural motifs beyond the canonical antiparallel duplex.
• Parallel-stranded DNA duplexes, stabilized by reverse Watson-Crick base pairing, represent an alternative structural motif with potential in vivo biological roles.

Purpose of the Study:

• To investigate the structural properties of parallel-stranded DNA duplexes compared to antiparallel-stranded DNA duplexes.
• To analyze the gas-phase behavior of DNA duplexes using advanced mass spectrometry techniques.

Main Methods:

• Native electrospray ionization mass spectrometry (ESI-MS).
• Trapped ion mobility spectrometry coupled with mass spectrometry (TIMS-MS).
• Theoretical calculations for structural analysis.

Main Results:

• Both parallel- and antiparallel-stranded DNA duplexes were formed and transferred to the gas phase.
• A more compact structure was observed for parallel duplexes compared to antiparallel duplexes in the gas phase (ΔΩ ≈ 50 Ų).
• DNA duplex charge significantly influences gas-phase mobility, with more compact forms in negative ion mode.

Conclusions:

• Parallel-stranded DNA duplexes adopt a more compact structure in the gas phase than their antiparallel counterparts.
• The study provides experimental evidence supporting theoretical predictions of DNA structural compaction upon gas-phase transfer.
• These findings enhance our understanding of DNA structural diversity and its behavior under different conditions.