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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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2
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Kotowska AM, Zhang J, Carabelli A, Watts J, Aylott JW, Gilmore IS, Williams P, Scurr DJ, Alexander MR. Toward Comprehensive Analysis of the 3D Chemistry of Pseudomonas aeruginosa Biofilms. Anal Chem 2023; 95:18287-18294. [PMID: 38044628 PMCID: PMC10719885 DOI: 10.1021/acs.analchem.3c04443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/05/2023]
Abstract
Bacterial biofilms are structured communities consisting of cells enmeshed in a self-generated extracellular matrix usually attached to a surface. They contain diverse classes of molecules including polysaccharides, lipids, proteins, nucleic acids, and diverse small organic molecules (primary and secondary metabolites) which are organized to optimize survival and facilitate dispersal to new colonization sites. In situ characterization of the chemical composition and structure of bacterial biofilms is necessary to fully understand their development on surfaces relevant to biofouling in health, industry, and the environment. Biofilm development has been extensively studied using confocal microscopy using targeted fluorescent labels providing important insights into the architecture of biofilms. Recently, cryopreparation has been used to undertake targeted in situ chemical characterization using Orbitrap secondary ion mass spectrometry (OrbiSIMS), providing a label-free method for imaging biofilms in their native state. Although the high mass resolution of OrbiSIMS enables more confident peak assignments, it is still very challenging to assign most of the peaks in the spectra due to complexity of SIMS spectra and lack of automatic peak assignment methods. Here, we analyze the same OrbiSIMS depth profile data generated from the frozen-hydrated biofilm, but employ a new untargeted chemical filtering process utilizing mass spectral databases to assign secondary ions to decipher the large number of fragments present in the SIMS spectra. To move towards comprehensive analysis of different chemistries in the sample, we apply a molecular formula prediction approach which putatively assigns 81% of peaks in the 3D OrbiSIMS depth profile analysis. This enables us to catalog over 1000 lipids and their fragments, 3500 protein fragments, 71 quorum sensing-related molecules (2-alkyl-4-quinolones and N-acylhomoserine lactones), 150 polysaccharide fragments, and glycolipids simultaneously from one data set and map these separated molecular classes spatially through a Pseudomonas aeruginosa biofilm. Assignment of different chemistries in this sample facilitates identification of differences between biofilms grown on biofilm-promoting and biofilm-resistant polymers.
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Affiliation(s)
- Anna M. Kotowska
- School
of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K.
| | - Junting Zhang
- National
Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, U.K.
| | | | - Julie Watts
- School
of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K.
| | | | - Ian S. Gilmore
- National
Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, U.K.
| | - Paul Williams
- National
Biofilms Innovation Centre, Biodiscovery Institute and School of Life
Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K.
| | - David J. Scurr
- School
of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K.
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3
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Trindade GF, Sul S, Kim J, Havelund R, Eyres A, Park S, Shin Y, Bae HJ, Sung YM, Matjacic L, Jung Y, Won J, Jeon WS, Choi H, Lee HS, Lee JC, Kim JH, Gilmore IS. Direct identification of interfacial degradation in blue OLEDs using nanoscale chemical depth profiling. Nat Commun 2023; 14:8066. [PMID: 38052834 DOI: 10.1038/s41467-023-43840-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 11/21/2023] [Indexed: 12/07/2023] Open
Abstract
Understanding the degradation mechanism of organic light-emitting diodes (OLED) is essential to improve device performance and stability. OLED failure, if not process-related, arises mostly from chemical instability. However, the challenges of sampling from nanoscale organic layers and interfaces with enough analytical information has hampered identification of degradation products and mechanisms. Here, we present a high-resolution diagnostic method of OLED degradation using an Orbitrap mass spectrometer equipped with a gas cluster ion beam to gently desorb nanometre levels of materials, providing unambiguous molecular information with 7-nm depth resolution. We chemically depth profile and analyse blue phosphorescent and thermally-activated delayed fluorescent (TADF) OLED devices at different degradation levels. For OLED devices with short operational lifetimes, dominant chemical degradation mainly relate to oxygen loss of molecules that occur at the interface between emission and electron transport layers (EML/ETL) where exciton distribution is maximised, confirmed by emission zone measurements. We also show approximately one order of magnitude increase in lifetime of devices with slightly modified host materials, which present minimal EML/ETL interfacial degradation and show the method can provide insight for future material and device architecture development.
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Affiliation(s)
| | - Soohwan Sul
- Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., 130 Samsung-ro, Suwon, 16678, Republic of Korea
| | - Joonghyuk Kim
- Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., 130 Samsung-ro, Suwon, 16678, Republic of Korea
| | - Rasmus Havelund
- National Physical Laboratory, NiCE-MSI, Teddington, TW11 0LW, UK
| | - Anya Eyres
- National Physical Laboratory, NiCE-MSI, Teddington, TW11 0LW, UK
| | - Sungjun Park
- Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., 130 Samsung-ro, Suwon, 16678, Republic of Korea
| | - Youngsik Shin
- Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., 130 Samsung-ro, Suwon, 16678, Republic of Korea
| | - Hye Jin Bae
- Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., 130 Samsung-ro, Suwon, 16678, Republic of Korea
| | - Young Mo Sung
- Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., 130 Samsung-ro, Suwon, 16678, Republic of Korea
| | - Lidija Matjacic
- National Physical Laboratory, NiCE-MSI, Teddington, TW11 0LW, UK
| | - Yongsik Jung
- Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., 130 Samsung-ro, Suwon, 16678, Republic of Korea
| | - Jungyeon Won
- Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., 130 Samsung-ro, Suwon, 16678, Republic of Korea
| | - Woo Sung Jeon
- Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., 130 Samsung-ro, Suwon, 16678, Republic of Korea
| | - Hyeonho Choi
- Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., 130 Samsung-ro, Suwon, 16678, Republic of Korea
| | - Hyo Sug Lee
- Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., 130 Samsung-ro, Suwon, 16678, Republic of Korea
| | - Jae-Cheol Lee
- Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., 130 Samsung-ro, Suwon, 16678, Republic of Korea
- Korea Research Institute of Material Property Analysis (KRIMPA), 712, Nongseo-dong 455, Yongin, 17111, Republic of Korea
| | - Jung-Hwa Kim
- Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., 130 Samsung-ro, Suwon, 16678, Republic of Korea.
| | - Ian S Gilmore
- National Physical Laboratory, NiCE-MSI, Teddington, TW11 0LW, UK.
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4
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Aoyagi S, Cant DJH, Dürr M, Eyres A, Fearn S, Gilmore IS, Iida SI, Ikeda R, Ishikawa K, Lagator M, Lockyer N, Keller P, Matsuda K, Murayama Y, Okamoto M, Reed BP, Shard AG, Takano A, Trindade GF, Vorng JL. Quantitative and Qualitative Analyses of Mass Spectra of OEL Materials by Artificial Neural Network and Interface Evaluation: Results from a VAMAS Interlaboratory Study. Anal Chem 2023; 95:15078-15085. [PMID: 37715701 PMCID: PMC10569169 DOI: 10.1021/acs.analchem.3c03173] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/05/2023] [Indexed: 09/18/2023]
Abstract
Quantitative analysis of binary mixtures of tris(2-phenylpyridinato)iridium(III) (Ir(ppy)3) and tris(8-hydroxyquinolinato)aluminum (Alq3) by using an artificial neural network (ANN) system to mass spectra was attempted based on the results of a VAMAS (Versailles Project on Advanced Materials and Standards) interlaboratory study (TW2 A31) to evaluate matrix-effect correction and to investigate interface determination. Monolayers of binary mixtures having different Ir(ppy)3 ratios (0, 0.25, 0.50, 0.75, and 1.00), and the multilayers containing these mixtures and pure samples were measured using time-of-flight secondary ion mass spectrometry (ToF-SIMS) with different primary ion beams, OrbiSIMS (SIMS with both Orbitrap and ToF mass spectrometers), laser desorption ionization (LDI), desorption/ionization induced by neutral clusters (DINeC), and X-ray photoelectron spectroscopy (XPS). The mass spectra were analyzed using a simple ANN with one hidden layer. The Ir(ppy)3 ratios of the unknown samples and the interfaces of the multilayers were predicted using the simple ANN system, even though the mass spectra of binary mixtures exhibited matrix effects. The Ir(ppy)3 ratios at the interfaces indicated by the simple ANN were consistent with the XPS results and the ToF-SIMS depth profiles. The simple ANN system not only provided quantitative information on unknown samples, but also indicated important mass peaks related to each molecule in the samples without a priori information. The important mass peaks indicated by the simple ANN depended on the ionization process. The simple ANN results of the spectra sets obtained by a softer ionization method, such as LDI and DINeC, suggested large ions such as trimers. From the first step of the investigation to build an ANN model for evaluating mixture samples influenced by matrix effects, it was indicated that the simple ANN method is useful for obtaining candidate mass peaks for identification and for assuming mixture conditions that are helpful for further analysis.
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Affiliation(s)
- Satoka Aoyagi
- Faculty
of Science and Technology, Seikei University, Musashino, Tokyo 180-8633, Japan
| | - David J. H. Cant
- National
Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, United Kingdom
| | - Michael Dürr
- Institute
of Applied Physics and Center for Materials Research, Justus Liebig University Giessen, 35394 Giessen, Germany
| | - Anya Eyres
- National
Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, United Kingdom
| | - Sarah Fearn
- Department
of Materials, Imperial College London, London SW7 2AZ, United Kingdom
| | - Ian S. Gilmore
- National
Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, United Kingdom
| | - Shin-ichi Iida
- ULVAC-PHI,
Inc., 2500 Hagisono, Chigasaki, Kanagawa 253-8522, Japan
| | - Reiko Ikeda
- Analytical
Science Research Laboratory, Kao Corp., Minato 1334, Wakayama-shi, Wakayama 640-8580, Japan
| | - Kazutaka Ishikawa
- Analytical
Science Research Laboratory, Kao Corp., Minato 1334, Wakayama-shi, Wakayama 640-8580, Japan
| | - Matija Lagator
- Photon
Science Institute, Department of Chemistry, University of Manchester, Manchester M13 9PL, United
Kingdom
| | - Nicholas Lockyer
- Photon
Science Institute, Department of Chemistry, University of Manchester, Manchester M13 9PL, United
Kingdom
| | - Philip Keller
- Institute
of Applied Physics and Center for Materials Research, Justus Liebig University Giessen, 35394 Giessen, Germany
| | - Kazuhiro Matsuda
- Surface
Science Laboratories, Toray Research Center, Inc., 3-3-7, Sonoyama, Otsu, Shiga 520-8567, Japan
| | - Yohei Murayama
- Specialty
Chemicals Development Center, Peripheral Products Operations, Canon Inc., 4202, Fukara, Susono, Shizuoka 410-1196, Japan
| | - Masayuki Okamoto
- Analytical
Science Research Laboratory, Kao Corp., Minato 1334, Wakayama-shi, Wakayama 640-8580, Japan
| | - Benjamen P. Reed
- National
Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, United Kingdom
| | - Alexander G. Shard
- National
Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, United Kingdom
| | - Akio Takano
- Toyama Co., Ltd., 3816-1 Kishi, Yamakita-machi, Ashigarakami-gun Kanagawa 258-0112, Japan
| | - Gustavo F. Trindade
- National
Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, United Kingdom
| | - Jean-Luc Vorng
- National
Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, United Kingdom
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5
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Edney MK, He W, Smith EF, Wilmot E, Reid J, Barker J, Griffiths RL, Alexander MR, Snape CE, Scurr DJ. Time resolved growth of (N)-polycyclic aromatic hydrocarbons in engine deposits uncovered with OrbiSIMS depth profiling. Analyst 2022; 147:3854-3866. [DOI: 10.1039/d2an00798c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Insoluble carbonaceous deposits were grown in internal combustion engine components and interrogated by OrbiSIMS depth profiling, and we uncovered the composition and proposed time resolved growth mechanisms of these materials.
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Affiliation(s)
- Max K. Edney
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, University Park, Nottingham, NG7 7RD, UK
| | - Wenshi He
- School of Pharmacy, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Emily F. Smith
- Department of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Edward Wilmot
- Innospec Ltd., Oil Sites Road, Ellesmere Port, Cheshire, CH65 4EY, UK
| | - Jacqueline Reid
- Innospec Ltd., Oil Sites Road, Ellesmere Port, Cheshire, CH65 4EY, UK
| | - Jim Barker
- Innospec Ltd., Oil Sites Road, Ellesmere Port, Cheshire, CH65 4EY, UK
| | - Rian L. Griffiths
- School of Pharmacy, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Morgan R. Alexander
- School of Pharmacy, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Colin E. Snape
- Department of Chemical and Environmental Engineering, Faculty of Engineering, University of Nottingham, University Park, Nottingham, NG7 7RD, UK
| | - David J. Scurr
- School of Pharmacy, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
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