Aptamer-ligand recognition studied by native ion mobility-mass spectrometry

Area of Science:

• Biochemistry
• Analytical Chemistry
• Molecular Biology

Background:

• Aptamers are oligonucleotide-based receptors with expanding applications.
• Understanding aptamer-ligand recognition mechanisms is crucial for rational aptamer design.
• Current understanding of aptamer higher-order structure and binding lags behind application development.

Purpose of the Study:

• To demonstrate the capabilities and limitations of native ion mobility-mass spectrometry (IM-MS) for analyzing aptamer higher-order structure and non-covalent interactions.
• To investigate the conformational behavior and ligand binding of cocaine-binding aptamers using IM-MS.
• To correlate IM-MS data with aptamer binding affinities and conformational changes.

Main Methods:

• Utilized native ion mobility-mass spectrometry (IM-MS) with positive and negative electrospray ionization.
• Employed a set of cocaine-binding aptamers with varying folding properties and affinities.
• Used quinine as a surrogate ligand for cocaine to probe aptamer-ligand interactions under controlled conditions.

Main Results:

• Apparent quinine-binding affinities were ranked by analyzing ratios of bound and unbound aptamers in mass spectra, qualitatively matching published data.
• Arrival time differences between free aptamers and aptamer-quinine complexes indicated small ligand-induced conformational changes.
• These arrival time differences showed an inverse correlation with binding affinity.

Conclusions:

• Native IM-MS is a fast and convenient method for studying the molecular basis of aptamer-ligand recognition.
• The technique provides insights into aptamer higher-order structure and non-covalent interactions.
• IM-MS data can inform the rational design and optimization of aptamers for various applications.