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Analytical ultracentrifuge: an ideal tool for characterization of non-coding RNAs

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Abstract

Analytical ultracentrifugation (AUC) has emerged as a robust and reliable technique for biomolecular characterization with extraordinary sensitivity. AUC is widely used to study purity, conformational changes, biomolecular interactions, and stoichiometry. Furthermore, AUC is used to determine the molecular weight of biomolecules such as proteins, carbohydrates, and DNA and RNA. Due to the multifaceted role(s) of non-coding RNAs from viruses, prokaryotes, and eukaryotes, research aimed at understanding the structure–function relationships of non-coding RNAs is rapidly increasing. However, due to their large size, flexibility, complicated secondary structures, and conformations, structural studies of non-coding RNAs are challenging. In this review, we are summarizing the application of AUC to evaluate the homogeneity, interactions, and conformational changes of non-coding RNAs from adenovirus as well as from Murray Valley, Powassan, and West Nile viruses. We also discuss the application of AUC to characterize eukaryotic long non-coding RNAs, Xist, and HOTAIR. These examples highlight the significant role AUC can play in facilitating the structural determination of non-coding RNAs and their complexes.

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Acknowledgements

MDB is funded by Alberta Innovates Strategic Research Projects to TRP. MQS is funded by the Canada Research Chairs program to TRP. TM is supported by NSERC PGS-D fellowship. DLG is supported by NSERC Discovery grant to TRP. TRP is a Canada Research Chair in RNA and Protein Biophysics.

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Authors and Affiliations

  1. Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Dr. West, Lethbridge, AB, T1K 3M4, Canada

    Maulik D. Badmalia, M. Quadir Siddiqui, Tyler Mrozowich, Darren L. Gemmill & Trushar R. Patel

  2. Department of Microbiology, Immunology and Infectious Diseases, Cumming, School of Medicine, University of Calgary, 2500 University Dr. North West, Calgary, AB, T2N 1N4, Canada

    Trushar R. Patel

  3. Discovery Lab, Faculty of Medicine and Dentistry, Li Ka Shing Institute of Virology, University of Alberta, 6-010 Katz Center for Health Research, Edmonton, AB, T6G 2E1, Canada

    Trushar R. Patel

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  1. Maulik D. Badmalia
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  2. M. Quadir Siddiqui
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Correspondence to Trushar R. Patel.

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Special Issue: Analytical Ultracentrifugation 2019.

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Badmalia, M.D., Siddiqui, M.Q., Mrozowich, T. et al. Analytical ultracentrifuge: an ideal tool for characterization of non-coding RNAs. Eur Biophys J 49, 809–818 (2020). https://doi.org/10.1007/s00249-020-01470-9

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