1
|
Weber TM, Özdüzenciler P, Tamgüney G, Pietruszka J. Utilization of a Branched Late-Stage Clickable Biotinylated Chassis on the Example of a Pittsburgh B Analogue. Org Lett 2024; 26:6771-6775. [PMID: 39051841 DOI: 10.1021/acs.orglett.4c02527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Biotinylation is probably the most frequent and practically useful modification of molecules to facilitate selective and highly affine binding to (strept)avidin for immobilization, enrichment, and purification for further (bio)chemical or (bio)physical investigations. We present a protecting-group-free synthesis of a branched biotin bis-azide that enables dual-payload late-stage functionalization with arbitrary alkynes via click chemistry. Utility of the chassis is briefly showcased on the example of a valuable Pittsburgh B analogue, which binds pathological protein aggregates, commonly found in neurodegenerative diseases.
Collapse
Affiliation(s)
- T Moritz Weber
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Bioorganische Chemie, Heinrich-Heine-Universität Düsseldorf im Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Pelin Özdüzenciler
- Institut für Biologische Informationsprozesse 7 (IBI-7: Strukturbiochemie), Forschungszentrum Jülich, 52428 Jülich, Germany
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Gültekin Tamgüney
- Institut für Biologische Informationsprozesse 7 (IBI-7: Strukturbiochemie), Forschungszentrum Jülich, 52428 Jülich, Germany
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Jörg Pietruszka
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Bioorganische Chemie, Heinrich-Heine-Universität Düsseldorf im Forschungszentrum Jülich, 52428 Jülich, Germany
- Institut für Bio- und Geowissenschaften 1 (IBG-1: Biotechnologie), Forschungszentrum Jülich, 52428 Jülich, Germany
| |
Collapse
|
2
|
Chen S, Wang J, Guan D, Tan B, Zhai T, Yang L, Han Y, Liu Y, Liu Q, Zhang Y. Near-Infrared Spontaneously Blinking Fluorophores for Live Cell Super-Resolution Imaging with Minimized Phototoxicity. Anal Chem 2024; 96:10860-10869. [PMID: 38889184 DOI: 10.1021/acs.analchem.4c02445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Single-molecule localization microscopy (SMLM) requires high-intensity laser irradiation, typically exceeding kW/cm2, to yield a sufficient photon count. However, this intense visible light exposure incurs substantial cellular toxicity, hindering its use in living cells. Here, we developed a class of near-infrared (NIR) spontaneously blinking fluorophores for SMLM. These NIR fluorophores are a combination of rhodamine spirolactams and merocyanine derivatives, where the rhodamine spirolactam component converts between a bright and dark state based on pH-dependent spirocyclization and merocyanine derivatives shift the excitation wavelength into the infrared. Single-molecule characterizations demonstrated their potential for SMLM. At a moderate power density of 3.93 kW/cm2, these probes exhibit duty cycle as low as 0.18% and an emission rate as high as 26,700 photons/s. Phototoxicity assessment under single-molecule imaging conditions reveals that NIR illumination (721 nm) minimizes harm to living cells. Employing these NIR fluorophores, we successfully captured time-lapse super-resolution tracking of mitochondria at a Fourier ring correlation (FRC) resolution of 69.4 nm and reconstructed the ultrastructures of endoplasmic reticulum (ER) in living cells.
Collapse
Affiliation(s)
- Song Chen
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
| | - Jing Wang
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
| | - Daoming Guan
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
| | - Baojin Tan
- School of Engineering, China Pharmaceutical University, Nanjing 211198, China
| | - Tianli Zhai
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
| | - Lu Yang
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
| | - Yuheng Han
- School of Engineering, China Pharmaceutical University, Nanjing 211198, China
| | - Yi Liu
- School of Engineering, China Pharmaceutical University, Nanjing 211198, China
| | - Qian Liu
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
| | - Yunxiang Zhang
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai 200438, China
| |
Collapse
|
3
|
Kratochvíl J, Asor R, Helmi S, Struwe WB, Kukura P. Lifting the Concentration Limit of Mass Photometry by PEG Nanopatterning. NANO LETTERS 2024. [PMID: 38950386 DOI: 10.1021/acs.nanolett.4c01667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
Mass photometry (MP) is a rapidly growing optical technique for label-free mass measurement of single biomolecules in solution. The underlying measurement principle provides numerous advantages over ensemble-based methods but has been limited to low analyte concentrations due to the need to uniquely and accurately quantify the binding of individual molecules to the measurement surface, which results in diffraction-limited spots. Here, we combine nanoparticle lithography with surface PEGylation to substantially lower surface binding, resulting in a 2 orders of magnitude improvement in the upper concentration limit associated with mass photometry. We demonstrate the facile tunability of degree of passivation, enabling measurements at increased analyte concentrations. These advances provide access to protein-protein interactions in the high nanomolar to low micromolar range, substantially expanding the application space of mass photometry.
Collapse
Affiliation(s)
- Jiří Kratochvíl
- The Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, U.K
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Roi Asor
- The Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, U.K
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Seham Helmi
- The Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, U.K
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Weston B Struwe
- The Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, U.K
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
| | - Philipp Kukura
- The Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, U.K
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| |
Collapse
|
4
|
Liu J, Zhao B, Zhang X, Guan D, Sun K, Zhang Y, Liu Q. Thiolation for Enhancing Photostability of Fluorophores at the Single-Molecule Level. Angew Chem Int Ed Engl 2024; 63:e202316192. [PMID: 37975636 DOI: 10.1002/anie.202316192] [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: 10/25/2023] [Revised: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 11/19/2023]
Abstract
Fluorescent probes are essential for single-molecule imaging. However, their application in biological systems is often limited by the short photobleaching lifetime. To overcome this, we developed a novel thiolation strategy for squaraine dyes. By introducing thiolation of the central cyclobutene of squaraine (thio-squaraine), we observed a ≈5-fold increase in photobleaching lifetime. Our single-molecule data analysis attributes this improvement to improved photostability resulting from thiolation. Interestingly, bulk measurements show rapid oxidation of thio-squaraine to its oxo-analogue under irradiation, giving the perception of inferior photostability. This discrepancy between bulk and single-molecule environments can be ascribed to the factors in the latter, including larger intermolecular distances and restricted mobility, which reduce the interactions between a fluorophore and reactive oxygen species produced by other fluorophores, ultimately impacting photobleaching and photoconversion rate. We demonstrate the remarkable performance of thio-squaraine probes in various imaging buffers, such as glucose oxidase with catalase (GLOX) and GLOX+trolox. We successfully employed these photostable probes for single-molecule tracking of CD56 membrane protein and monitoring mitochondria movements in live neurons. CD56 tracking revealed distinct motion states and the corresponding protein fractions. This investigation is expected to propel the development of single-molecule imaging probes, particularly in scenarios where bulk measurements show suboptimal performance.
Collapse
Affiliation(s)
- Jinyang Liu
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, 200438, China
| | - Bingjie Zhao
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, 200438, China
| | - Xuebo Zhang
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, 200438, China
| | - Daoming Guan
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, 200438, China
| | - Kuangshi Sun
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, 200438, China
| | - Yunxiang Zhang
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, 200438, China
| | - Qian Liu
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, Shanghai, 200438, China
| |
Collapse
|
5
|
Colson L, Kwon Y, Nam S, Bhandari A, Maya NM, Lu Y, Cho Y. Trends in Single-Molecule Total Internal Reflection Fluorescence Imaging and Their Biological Applications with Lab-on-a-Chip Technology. SENSORS (BASEL, SWITZERLAND) 2023; 23:7691. [PMID: 37765748 PMCID: PMC10537725 DOI: 10.3390/s23187691] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/01/2023] [Accepted: 09/03/2023] [Indexed: 09/29/2023]
Abstract
Single-molecule imaging technologies, especially those based on fluorescence, have been developed to probe both the equilibrium and dynamic properties of biomolecules at the single-molecular and quantitative levels. In this review, we provide an overview of the state-of-the-art advancements in single-molecule fluorescence imaging techniques. We systematically explore the advanced implementations of in vitro single-molecule imaging techniques using total internal reflection fluorescence (TIRF) microscopy, which is widely accessible. This includes discussions on sample preparation, passivation techniques, data collection and analysis, and biological applications. Furthermore, we delve into the compatibility of microfluidic technology for single-molecule fluorescence imaging, highlighting its potential benefits and challenges. Finally, we summarize the current challenges and prospects of fluorescence-based single-molecule imaging techniques, paving the way for further advancements in this rapidly evolving field.
Collapse
Affiliation(s)
- Louis Colson
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; (L.C.); (A.B.); (N.M.M.); (Y.L.)
| | - Youngeun Kwon
- Department of Chemical Engineering, Myongji University, Yongin 17058, Republic of Korea; (Y.K.); (S.N.)
| | - Soobin Nam
- Department of Chemical Engineering, Myongji University, Yongin 17058, Republic of Korea; (Y.K.); (S.N.)
| | - Avinashi Bhandari
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; (L.C.); (A.B.); (N.M.M.); (Y.L.)
| | - Nolberto Martinez Maya
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; (L.C.); (A.B.); (N.M.M.); (Y.L.)
| | - Ying Lu
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; (L.C.); (A.B.); (N.M.M.); (Y.L.)
| | - Yongmin Cho
- Department of Chemical Engineering, Myongji University, Yongin 17058, Republic of Korea; (Y.K.); (S.N.)
| |
Collapse
|
6
|
Bueno-Alejo C, Santana Vega M, Chaplin AK, Farrow C, Axer A, Burley GA, Dominguez C, Kara H, Paschalis V, Tubasum S, Eperon IC, Clark AW, Hudson AJ. Surface Passivation with a Perfluoroalkane Brush Improves the Precision of Single-Molecule Measurements. ACS APPLIED MATERIALS & INTERFACES 2022; 14:49604-49616. [PMID: 36306432 PMCID: PMC9650645 DOI: 10.1021/acsami.2c16647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Single-molecule imaging is invaluable for investigating the heterogeneous behavior and interactions of biological molecules. However, an impediment to precise sampling of single molecules is the irreversible adsorption of components onto the surfaces of cover glasses. This causes continuous changes in the concentrations of different molecules dissolved or suspended in the aqueous phase from the moment a sample is dispensed, which will shift, over time, the position of chemical equilibria between monomeric and multimeric components. Interferometric scattering microscopy (iSCAT) is a technique in the single-molecule toolkit that has the capability to detect unlabeled proteins and protein complexes both as they adsorb onto and desorb from a glass surface. Here, we examine the reversible and irreversible interactions between a number of different proteins and glass via analysis of the adsorption and desorption of protein at the single-molecule level. Furthermore, we present a method for surface passivation that virtually eliminates irreversible adsorption while still ensuring the residence time of molecules on surfaces is sufficient for detection of adsorption by iSCAT. By grafting high-density perfluoroalkane brushes on cover-glass surfaces, we observe approximately equal numbers of adsorption and desorption events for proteins at the measurement surface (±1%). The fluorous-aqueous interface also prevents the kinetic trapping of protein complexes and assists in establishing a thermodynamic equilibrium between monomeric and multimeric components. This surface passivation approach is valuable for in vitro single-molecule experiments using iSCAT microscopy because it allows for continuous monitoring of adsorption and desorption of protein without either a decline in detection events or a change in sample composition due to the irreversible binding of protein to surfaces.
Collapse
Affiliation(s)
- Carlos
J. Bueno-Alejo
- School
of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
- Leicester
Institute of Structural & Chemical Biology, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 7HB, United Kingdom
| | - Marina Santana Vega
- School
of Engineering, Advanced Research Centre, University of Glasgow, 11 Chapel Lane, Glasgow G11 6EW, United Kingdom
| | - Amanda K. Chaplin
- Leicester
Institute of Structural & Chemical Biology, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 7HB, United Kingdom
- Department
of Molecular and Cellular Biology, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 7HB, United Kingdom
| | - Chloe Farrow
- School
of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
- Leicester
Institute of Structural & Chemical Biology, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 7HB, United Kingdom
| | - Alexander Axer
- Strathclyde
Centre for Molecular Bioscience & Department of Pure & Applied
Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Glenn A. Burley
- Strathclyde
Centre for Molecular Bioscience & Department of Pure & Applied
Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Cyril Dominguez
- Leicester
Institute of Structural & Chemical Biology, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 7HB, United Kingdom
- Department
of Molecular and Cellular Biology, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 7HB, United Kingdom
| | - Hesna Kara
- Leicester
Institute of Structural & Chemical Biology, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 7HB, United Kingdom
- Department
of Molecular and Cellular Biology, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 7HB, United Kingdom
| | - Vasileios Paschalis
- Leicester
Institute of Structural & Chemical Biology, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 7HB, United Kingdom
- Department
of Molecular and Cellular Biology, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 7HB, United Kingdom
| | - Sumera Tubasum
- Leicester
Institute of Structural & Chemical Biology, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 7HB, United Kingdom
- Department
of Molecular and Cellular Biology, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 7HB, United Kingdom
| | - Ian C. Eperon
- Leicester
Institute of Structural & Chemical Biology, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 7HB, United Kingdom
- Department
of Molecular and Cellular Biology, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 7HB, United Kingdom
| | - Alasdair W. Clark
- School
of Engineering, Advanced Research Centre, University of Glasgow, 11 Chapel Lane, Glasgow G11 6EW, United Kingdom
| | - Andrew J. Hudson
- School
of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
- Leicester
Institute of Structural & Chemical Biology, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 7HB, United Kingdom
| |
Collapse
|
7
|
Zhao Z, Das S, Zharnikov M. Rational Design of Porous Poly(ethylene glycol) Films as a Matrix for ssDNA Immobilization and Hybridization. Bioengineering (Basel) 2022; 9:bioengineering9090414. [PMID: 36134960 PMCID: PMC9496007 DOI: 10.3390/bioengineering9090414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/24/2022] Open
Abstract
Poly(ethylene glycol) (PEG) films, fabricated by thermally induced crosslinking of amine- and epoxy-terminated four-arm STAR-PEG precursors, were used as porous and bioinert matrix for single-stranded DNA (ssDNA) immobilization and hybridization. The immobilization relied on the reaction between the amine groups in the films and N-hydroxy succinimide (NHS) ester groups of the NHS-ester-decorated ssDNA. Whereas the amount of reactive amine groups in the films with the standard 1:1 composition of the precursors turned out to be too low for efficient immobilization, it could be increased noticeably using an excess (2:1) concentration of the amine-terminated precursor. The respective films retained the bioinertness of the 1:1 prototype and could be successfully decorated with probe ssDNA, resulting in porous, 3D PEG-ssDNA sensing assemblies. These assemblies exhibited high selectivity with respect to the target ssDNA strands, with a hybridization efficiency of 78–89% for the matching sequences and full inertness for non-complementary strands. The respective strategy can be applied to the fabrication of DNA microarrays and DNA sensors. As a suitable transduction technique, requiring no ssDNA labeling and showing high sensitivity in the PEG-ssDNA case, electrochemical impedance spectroscopy is suggested.
Collapse
|
8
|
Chen S, Li J, Vinothkumar KR, Henderson R. Interaction of human erythrocyte catalase with air-water interface in cryoEM. Microscopy (Oxf) 2022; 71:i51-i59. [PMID: 35275189 PMCID: PMC8855524 DOI: 10.1093/jmicro/dfab037] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/13/2021] [Accepted: 09/16/2021] [Indexed: 11/14/2022] Open
Abstract
One of the key goals in single-particle cryo-microscopy is to obtain a uniform distribution of particle orientations, so that the three-dimensional structure has isotropic resolution in Fourier space. A common problem arises from the interaction of protein molecules with the air-water interface that exists on both surfaces of the thin film of liquid that is formed prior to plunge-freezing into liquid ethane. Some proteins and other macromolecular complexes are disrupted by interaction with the air-water interface. Other proteins or macromolecules either become concentrated through their interaction with the interface or are excluded because they bind strongly to some other part of the grid or the filter paper used in blotting. In this paper, the interaction of human erythrocyte catalase with the air-water interface is investigated and minimized by the addition of certain detergents. Detergents can form an amphipathic monolayer at the air-water interface that creates a barrier and leaves the molecules free to adopt a variety of orientations, thus facilitating the 3D structure determination. These results suggest that further characterization and development of detergents for cryo-microscopy plunge-freezing would be useful.
Collapse
Affiliation(s)
- Shaoxia Chen
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jade Li
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Kutti R Vinothkumar
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
- National Centre for Biological Sciences (NCBS), Tata Institute of Fundamental Research, Bellary Road, Bengaluru 560065, India
| | | |
Collapse
|
9
|
Shen S, Naganuma M, Tomari Y, Tadakuma H. Revisiting the Glass Treatment for Single-Molecule Analysis of ncRNA Function. Methods Mol Biol 2022; 2509:209-231. [PMID: 35796966 DOI: 10.1007/978-1-0716-2380-0_13] [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] [Indexed: 06/15/2023]
Abstract
Single-molecule imaging is a powerful method for unveiling precise molecular mechanisms. Particularly, single-molecule analysis with total internal reflection fluorescence (TIRF ) microscopy has been successfully applied to the characterization of molecular mechanisms in ncRNA studies. Tracing interactions at the single-molecule level have elucidated the intermediate states of the reaction, which are hidden by ensemble averaging in combinational biochemical approaches, and clarified the key steps of the interaction. However, applying a single-molecule technique to ncRNA analysis still remains a challenge, requiring laborious trial and error to identify a suitable glass surface passivation method. In this chapter, we revisit the major glass surface passivation methods using polyethylene glycol (PEG) treatment and summarize a detailed protocol for single-molecule analysis of the dicing process of Dcr-2, which may apply piRNA studies in the future.
Collapse
Affiliation(s)
- Shuting Shen
- School of Life Science and Technology & Gene Editing Center, ShanghaiTech University, Shanghai, China
| | - Masahiro Naganuma
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
- RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Yukihide Tomari
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Hisashi Tadakuma
- School of Life Science and Technology & Gene Editing Center, ShanghaiTech University, Shanghai, China.
- Laboratory of RNA Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.
| |
Collapse
|
10
|
Lerner E, Barth A, Hendrix J, Ambrose B, Birkedal V, Blanchard SC, Börner R, Sung Chung H, Cordes T, Craggs TD, Deniz AA, Diao J, Fei J, Gonzalez RL, Gopich IV, Ha T, Hanke CA, Haran G, Hatzakis NS, Hohng S, Hong SC, Hugel T, Ingargiola A, Joo C, Kapanidis AN, Kim HD, Laurence T, Lee NK, Lee TH, Lemke EA, Margeat E, Michaelis J, Michalet X, Myong S, Nettels D, Peulen TO, Ploetz E, Razvag Y, Robb NC, Schuler B, Soleimaninejad H, Tang C, Vafabakhsh R, Lamb DC, Seidel CAM, Weiss S. FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. eLife 2021; 10:e60416. [PMID: 33779550 PMCID: PMC8007216 DOI: 10.7554/elife.60416] [Citation(s) in RCA: 132] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 02/09/2021] [Indexed: 12/18/2022] Open
Abstract
Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever-increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs that employ smFRET approaches have joined forces to inform the smFRET community about streamlining how to perform experiments and analyze results for obtaining quantitative information on biomolecular structure and dynamics. The recent efforts include blind tests to assess the accuracy and the precision of smFRET experiments among different labs using various procedures. These multi-lab studies have led to the development of smFRET procedures and documentation, which are important when submitting entries into the archiving system for integrative structure models, PDB-Dev. This position paper describes the current 'state of the art' from different perspectives, points to unresolved methodological issues for quantitative structural studies, provides a set of 'soft recommendations' about which an emerging consensus exists, and lists openly available resources for newcomers and seasoned practitioners. To make further progress, we strongly encourage 'open science' practices.
Collapse
Affiliation(s)
- Eitan Lerner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, and The Center for Nanoscience and Nanotechnology, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Anders Barth
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Jelle Hendrix
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and Biomedical Research Institute (BIOMED), Hasselt UniversityDiepenbeekBelgium
| | - Benjamin Ambrose
- Department of Chemistry, University of SheffieldSheffieldUnited Kingdom
| | - Victoria Birkedal
- Department of Chemistry and iNANO center, Aarhus UniversityAarhusDenmark
| | - Scott C Blanchard
- Department of Structural Biology, St. Jude Children's Research HospitalMemphisUnited States
| | - Richard Börner
- Laserinstitut HS Mittweida, University of Applied Science MittweidaMittweidaGermany
| | - Hoi Sung Chung
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität MünchenPlanegg-MartinsriedGermany
| | - Timothy D Craggs
- Department of Chemistry, University of SheffieldSheffieldUnited Kingdom
| | - Ashok A Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati School of MedicineCincinnatiUnited States
| | - Jingyi Fei
- Department of Biochemistry and Molecular Biology and The Institute for Biophysical Dynamics, University of ChicagoChicagoUnited States
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia UniversityNew YorkUnited States
| | - Irina V Gopich
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Howard Hughes Medical InstituteBaltimoreUnited States
| | - Christian A Hanke
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of ScienceRehovotIsrael
| | - Nikos S Hatzakis
- Department of Chemistry & Nanoscience Centre, University of CopenhagenCopenhagenDenmark
- Denmark Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagenDenmark
| | - Sungchul Hohng
- Department of Physics and Astronomy, and Institute of Applied Physics, Seoul National UniversitySeoulRepublic of Korea
| | - Seok-Cheol Hong
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science and Department of Physics, Korea UniversitySeoulRepublic of Korea
| | - Thorsten Hugel
- Institute of Physical Chemistry and Signalling Research Centres BIOSS and CIBSS, University of FreiburgFreiburgGermany
| | - Antonino Ingargiola
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
| | - Chirlmin Joo
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of TechnologyDelftNetherlands
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of OxfordOxfordUnited Kingdom
| | - Harold D Kim
- School of Physics, Georgia Institute of TechnologyAtlantaUnited States
| | - Ted Laurence
- Physical and Life Sciences Directorate, Lawrence Livermore National LaboratoryLivermoreUnited States
| | - Nam Ki Lee
- School of Chemistry, Seoul National UniversitySeoulRepublic of Korea
| | - Tae-Hee Lee
- Department of Chemistry, Pennsylvania State UniversityUniversity ParkUnited States
| | - Edward A Lemke
- Departments of Biology and Chemistry, Johannes Gutenberg UniversityMainzGermany
- Institute of Molecular Biology (IMB)MainzGermany
| | - Emmanuel Margeat
- Centre de Biologie Structurale (CBS), CNRS, INSERM, Universitié de MontpellierMontpellierFrance
| | | | - Xavier Michalet
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
| | - Sua Myong
- Department of Biophysics, Johns Hopkins UniversityBaltimoreUnited States
| | - Daniel Nettels
- Department of Biochemistry and Department of Physics, University of ZurichZurichSwitzerland
| | - Thomas-Otavio Peulen
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
| | - Evelyn Ploetz
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-UniversitätMünchenGermany
| | - Yair Razvag
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, and The Center for Nanoscience and Nanotechnology, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalemIsrael
| | - Nicole C Robb
- Warwick Medical School, University of WarwickCoventryUnited Kingdom
| | - Benjamin Schuler
- Department of Biochemistry and Department of Physics, University of ZurichZurichSwitzerland
| | - Hamid Soleimaninejad
- Biological Optical Microscopy Platform (BOMP), University of MelbourneParkvilleAustralia
| | - Chun Tang
- College of Chemistry and Molecular Engineering, PKU-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, Peking UniversityBeijingChina
| | - Reza Vafabakhsh
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Center for Nanoscience (CeNS), Center for Integrated Protein Science Munich (CIPSM) and Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-UniversitätMünchenGermany
| | - Claus AM Seidel
- Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-UniversitätDüsseldorfGermany
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los AngelesLos AngelesUnited States
- Department of Physiology, CaliforniaNanoSystems Institute, University of California, Los AngelesLos AngelesUnited States
| |
Collapse
|
11
|
Vera AM, Tinnefeld P. Single-Molecule Approved Surface Passivation. Structure 2021; 28:1269-1270. [PMID: 33264595 DOI: 10.1016/j.str.2020.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Single-molecule experiments reveal structure function relationships and biomolecular dynamics in physiologically relevant conditions. In this issue of Structure, Park et al. (2020) report an optimized surface passivation strategy with polyethylene glycol in a dense, contracted conformation. Assembly of a functional transcription pre-initiation complex is demonstrated.
Collapse
Affiliation(s)
- Andrés Manuel Vera
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, 80539 München, Germany.
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, 80539 München, Germany.
| |
Collapse
|