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Temperature-Dependent Conformational Evolution of SARS CoV-2 RNA Genome Using Network Analysis.
Omkar Singh1, Pushyaraga P Venugopal1, Apoorva Mathur1
1Biophysical and Computational Chemistry Laboratory, Department of Chemistry, National Institute of Technology Karnataka, Mangalore, Karnataka 575025, India.
The Journal of Physical Chemistry. B
|September 15, 2021
Summary
Network analysis reveals how SARS-CoV-2 RNA structure changes with temperature. High temperatures destroy RNA structure, with stability at higher temperatures linked to non-native base pairs.
Area of Science:
- Computational biology
- Virology
- Biophysics
Background:
- Understanding SARS-CoV-2 RNA dynamics is crucial for combating COVID-19.
- Computational analysis of large RNA datasets presents significant challenges.
Purpose of the Study:
- To investigate the conformational evolution and dominant structures of the SARS-CoV-2 RNA genome at varying temperatures.
- To apply network analysis as a tool for studying RNA structural dynamics.
Main Methods:
- Network analysis was employed to examine RNA genome structures at six different temperatures.
- Structural variations and communities within the RNA were identified.
- Thermal denaturation free energy (ΔΔG) was calculated for specific RNA structures.
Main Results:
- Network analysis effectively distinguished RNA communities with structural variations.
- At temperatures of 348 K and above, approximately 80% of the RNA structure was found to be destroyed.
- Calculated thermal denaturation free energy values align with experimental data for SARS-CoV-NP.
- RNA conformation stability at higher temperatures is attributed to non-native base pairs.
Conclusions:
- Network analysis is a valuable tool for understanding RNA conformational changes.
- Higher temperatures significantly destabilize the SARS-CoV-2 RNA genome.
- The presence of non-native base pairs contributes to RNA stability under specific high-temperature conditions.
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