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Measuring RNA UNCG Tetraloop Refolding Dynamics Using Temperature-Jump/Drop Infrared Spectroscopy
C P Howe1, G M Greetham2, B Procacci1
1Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, U.K.
The Journal of Physical Chemistry Letters
|September 27, 2022
Summary
This study reveals RNA refolding dynamics using a novel temperature-jump/drop infrared spectroscopy method. RNA stem-loop melting is slower than DNA, but refolding occurs rapidly, suggesting complex intermediate pathways.
Area of Science:
- Molecular Biology
- Biophysics
- Spectroscopy
Background:
- Understanding nucleic acid structural dynamics is crucial for cellular function.
- Direct measurement of RNA and DNA strand association and folding is experimentally challenging.
Purpose of the Study:
- To investigate the melting and refolding dynamics of RNA and DNA hairpin sequences.
- To compare the kinetic differences between RNA and DNA hairpin dynamics.
Main Methods:
- Utilized time-resolved temperature-jump/drop infrared spectroscopy.
- Measured melting and refolding kinetics of a 12-nucleotide RNA (UACG tetraloop, GC stem) and an equivalent DNA sequence.
Main Results:
- RNA stem-loop melting was significantly slower (6.0 ± 0.1 μs at 70 °C) than DNA (0.8 ± 0.1 μs).
- Refolding dynamics for both RNA and DNA occurred on similar timescales (approx. 200 μs).
- Both melting and refolding followed Arrhenius temperature dependence, with refolding showing negative activation energy.
Conclusions:
- Refolding kinetics are similar for RNA and DNA hairpins despite differences in melting rates.
- Negative activation energy in refolding suggests a mechanism involving multiple misfolded intermediates before stem zipping.
