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Ward S, Childs A, Staley C, Waugh C, Watts JA, Kotowska AM, Bhosale R, Borkar AN. Integrating cryo-OrbiSIMS with computational modelling and metadynamics simulations enhances RNA structure prediction at atomic resolution. Nat Commun 2024; 15:4367. [PMID: 38777820 PMCID: PMC11111741 DOI: 10.1038/s41467-024-48694-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 05/05/2024] [Indexed: 05/25/2024] Open
Abstract
The 3D architecture of RNAs governs their molecular interactions, chemical reactions, and biological functions. However, a large number of RNAs and their protein complexes remain poorly understood due to the limitations of conventional structural biology techniques in deciphering their complex structures and dynamic interactions. To address this limitation, we have benchmarked an integrated approach that combines cryogenic OrbiSIMS, a state-of-the-art solid-state mass spectrometry technique, with computational methods for modelling RNA structures at atomic resolution with enhanced precision. Furthermore, using 7SK RNP as a test case, we have successfully determined the full 3D structure of a native RNA in its apo, native and disease-remodelled states, which offers insights into the structural interactions and plasticity of the 7SK complex within these states. Overall, our study establishes cryo-OrbiSIMS as a valuable tool in the field of RNA structural biology as it enables the study of challenging, native RNA systems.
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Affiliation(s)
- Shannon Ward
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, LE12 5RD, UK
- Wolfson Centre for Global Virus Research, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Alex Childs
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, LE12 5RD, UK
- Wolfson Centre for Global Virus Research, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Ceri Staley
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Christopher Waugh
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, LE12 5RD, UK
- Wolfson Centre for Global Virus Research, University of Nottingham, Nottingham, LE12 5RD, UK
- RHy-X Limited, London, WC2A 2JR, UK
| | - Julie A Watts
- School of Pharmacy, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Anna M Kotowska
- School of Pharmacy, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Rahul Bhosale
- School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Aditi N Borkar
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, LE12 5RD, UK.
- Wolfson Centre for Global Virus Research, University of Nottingham, Nottingham, LE12 5RD, UK.
- RHy-X Limited, London, WC2A 2JR, UK.
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Marinus T, Foster TL, Tych KM. The application of single-molecule optical tweezers to study disease-related structural dynamics in RNA. Biochem Soc Trans 2024; 52:899-909. [PMID: 38533854 PMCID: PMC11088911 DOI: 10.1042/bst20231232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/01/2024] [Accepted: 03/08/2024] [Indexed: 03/28/2024]
Abstract
RNA, a dynamic and flexible molecule with intricate three-dimensional structures, has myriad functions in disease development. Traditional methods, such as X-ray crystallography and nuclear magnetic resonance, face limitations in capturing real-time, single-molecule dynamics crucial for understanding RNA function. This review explores the transformative potential of single-molecule force spectroscopy using optical tweezers, showcasing its capability to directly probe time-dependent structural rearrangements of individual RNA molecules. Optical tweezers offer versatility in exploring diverse conditions, with the potential to provide insights into how environmental changes, ligands and RNA-binding proteins impact RNA behaviour. By enabling real-time observations of large-scale structural dynamics, optical tweezers emerge as an invaluable tool for advancing our comprehension of RNA structure and function. Here, we showcase their application in elucidating the dynamics of RNA elements in virology, such as the pseudoknot governing ribosomal frameshifting in SARS-CoV-2.
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Affiliation(s)
- Tycho Marinus
- Chemical Biology 1, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Toshana L. Foster
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, LE12 5RD Loughborough, U.K
| | - Katarzyna M. Tych
- Chemical Biology 1, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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Listgarten J. The perpetual motion machine of AI-generated data and the distraction of ChatGPT as a 'scientist'. Nat Biotechnol 2024; 42:371-373. [PMID: 38273064 DOI: 10.1038/s41587-023-02103-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Affiliation(s)
- Jennifer Listgarten
- Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, CA, USA.
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.
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