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

TitleAnalytical ultracentrifuge: an ideal tool for characterization of non-coding RNAs
Publication TypeJournal Article
Year of Publication2020
AuthorsBadmalia MD, Siddiqui MQ, Mrozowich T, Gemmill DL, Patel TR
JournalEur Biophys J .
Start Page809
Date Published12/2020
KeywordsAggregation, Analytical ultracentrifuge, Flaviviral RNAs, Homogeneity, Long non-coding RNAs, Sedimentation coefficient

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.