Comparative stability determination of oligonucleotide duplexes in gas and solution phase

Area of Science:

• Biochemistry
• Chemical Physics
• Molecular Biology

Background:

• RNA duplex stability is crucial for molecular biology.
• Understanding factors influencing RNA stability is key for RNA-based therapeutics and diagnostics.

Purpose of the Study:

• To compare the relative stability of RNA duplexes in solution and gas phases.
• To investigate the impact of Watson-Crick base pairing versus GA mismatches on RNA duplex stability under different conditions.

Main Methods:

• Solution stability was assessed using spectrophotometric methods.
• Gas phase stability was determined via electrospray ionization mass spectrometry (ESI-MS) with controlled collision energy in an ion trap.

Main Results:

• In solution, Watson-Crick duplexes were more stable than those with one or two GA mismatches.
• In the gas phase, duplexes with two tandem GA mismatches exhibited greater stability than Watson-Crick or single GA mismatch duplexes.
• Stability curves in the gas phase mirrored solution melting curves, but relative stability trends differed.

Conclusions:

• The distinct stability trends in solution versus gas phase are attributed to differing dominant interaction modes: stacking in solution and hydrogen bonding in the gas phase.
• Tandem GA mismatches can form additional hydrogen bonds, explaining their increased stability in the gas phase.
• These findings highlight the environment-dependent nature of RNA duplex stability and the importance of considering interaction modes.