Analytical ultracentrifuge: an ideal tool for characterization of non-coding RNAs
- PDF / 868,148 Bytes
- 10 Pages / 595.276 x 790.866 pts Page_size
- 62 Downloads / 131 Views
REVIEW
Analytical ultracentrifuge: an ideal tool for characterization of non‑coding RNAs Maulik D. Badmalia1 · M. Quadir Siddiqui1 · Tyler Mrozowich1 · Darren L. Gemmill1 · Trushar R. Patel1,2,3 Received: 13 June 2020 / Revised: 26 September 2020 / Accepted: 5 October 2020 © European Biophysical Societies’ Association 2020
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. Keywords Aggregation · Analytical ultracentrifuge · Flaviviral RNAs · Homogeneity · Long non-coding RNAs · Sedimentation coefficient
Introduction to analytical ultracentrifuge The development of the analytical ultracentrifuge (AUC) by Svedberg and colleagues in the 1920s revolutionized the characterization of biomolecules in solution (Svedberg and Pedersen 1940). In an AUC experiment, the preparation Special Issue: Analytical Ultracentrifugation 2019. * Trushar R. Patel [email protected] 1
Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Dr. West, Lethbridge, AB T1K 3M4, Canada
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
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
of biomolecules is subjected to high centrifugal force to accelerate their sedimentation governed by hydrodynamic principles, size and shape (Lebowitz et al. 2002; Mitra and Demeler 2020; Patel et al. 2016). The sedimentation of biomolecules is typically monitored by either exploiting the optical absorption of biomolecules at characteristic wavelengths or by Rayleigh interference (refractometric) optical systems (Crepeau et al. 1972; Harding and Rowe 1988). Mo
Data Loading...
