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Energy-Dependent Changes in Ion Mobility Peak Width Reveal Stability Shifts in Ribonucleic Acid Stem Loops
Anna G Anders1, Jacqueline Anthenien1, Ingrid R Kilde2
1Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States.
Summary
Native ion mobility-mass spectrometry (IM-MS) can track RNA stem-loop structural changes. IM peak width (fwhm) shows promise for evaluating RNA stability, especially for small molecules.
Area of Science:
- Biochemistry
- Structural Biology
- Biophysics
Background:
- Ribonucleic acids (RNAs) are crucial in cellular biology and biotherapeutics.
- RNA structural characterization is challenging due to their dynamic and polydisperse nature.
- RNA stem-loops (hairpins) are common secondary structures with significant biological roles.
Purpose of the Study:
- To investigate RNA stem-loop structures using native ion mobility-mass spectrometry (IM-MS) and collision-induced unfolding (CIU).
- To assess the utility of IM-MS and CIU for studying disease-relevant mitochondrial tRNA stem-loop mutants.
- To explore the potential of IM peak full-width half-maximum (fwhm) for characterizing RNA stem-loop stability.
Main Methods:
- Native ion mobility-mass spectrometry (IM-MS) was employed to analyze RNA stem-loops.
- Collision-induced unfolding (CIU) was used to probe RNA stability.
- Analysis of IM peak full-width half-maximum (fwhm) values was performed to assess stability.
Main Results:
- Native IM-MS successfully tracked structural changes in stem-loops upon cofactor binding and mutation.
- Standard CIU workflows faced challenges in evaluating the stability of small RNAs.
- RNA stem-loop IM fwhm values decreased upon activation and showed lesser changes when bound to Mg2+.
Conclusions:
- Native IM-MS is effective for monitoring RNA stem-loop structural dynamics.
- IM fwhm analysis offers a promising approach for characterizing RNA stem-loop stability.
- Further development of IM fwhm analysis could enhance RNA CIU assay capabilities.
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