1
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Pati AK, Kilic Z, Martin MI, Terry DS, Borgia A, Bar S, Jockusch S, Kiselev R, Altman RB, Blanchard SC. Recovering true FRET efficiencies from smFRET investigations requires triplet state mitigation. Nat Methods 2024:10.1038/s41592-024-02293-8. [PMID: 38877317 DOI: 10.1038/s41592-024-02293-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 04/25/2024] [Indexed: 06/16/2024]
Abstract
Single-molecule fluorescence resonance energy transfer (smFRET) methods employed to quantify time-dependent compositional and conformational changes within biomolecules require elevated illumination intensities to recover robust photon emission streams from individual fluorophores. Here we show that outside the weak-excitation limit, and in regimes where fluorophores must undergo many rapid cycles of excitation and relaxation, non-fluorescing, excitation-induced triplet states with lifetimes orders of magnitude longer lived than photon-emitting singlet states degrade photon emission streams from both donor and acceptor fluorophores resulting in illumination-intensity-dependent changes in FRET efficiency. These changes are not commonly taken into consideration; therefore, robust strategies to suppress excited state accumulations are required to recover accurate and precise FRET efficiency, and thus distance, estimates. We propose both robust triplet state suppression and data correction strategies that enable the recovery of FRET efficiencies more closely approximating true values, thereby extending the spatial and temporal resolution of smFRET.
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Affiliation(s)
- Avik K Pati
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Chemistry, Birla Institute of Technology and Science, Pilani, Rajasthan, India
| | - Zeliha Kilic
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Maxwell I Martin
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Daniel S Terry
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Alessandro Borgia
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sukanta Bar
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Steffen Jockusch
- Center for Photochemical Sciences and Department of Chemistry, Bowling Green State University, Bowling Green, OH, USA
| | - Roman Kiselev
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Roger B Altman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Scott C Blanchard
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA.
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2
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Liu T, Khanal S, Hertslet GD, Lamichhane R. Single-molecule analysis reveals that a glucagon-bound extracellular domain of the glucagon receptor is dynamic. J Biol Chem 2023; 299:105160. [PMID: 37586587 PMCID: PMC10514447 DOI: 10.1016/j.jbc.2023.105160] [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: 02/13/2023] [Revised: 08/07/2023] [Accepted: 08/10/2023] [Indexed: 08/18/2023] Open
Abstract
Dynamic information is vital to understanding the activation mechanism of G protein-coupled receptors (GPCRs). Despite the availability of high-resolution structures of different conformational states, the dynamics of those states at the molecular level are poorly understood. Here, we used total internal reflection fluorescence microscopy to study the extracellular domain (ECD) of the glucagon receptor (GCGR), a class B family GPCR that controls glucose homeostasis. Single-molecule fluorescence resonance energy transfer was used to observe the ECD dynamics of GCGR molecules expressed and purified from mammalian cells. We observed that for apo-GCGR, the ECD is dynamic and spent time predominantly in a closed conformation. In the presence of glucagon, the ECD is wide open and also shows more dynamic behavior than apo-GCGR, a finding that was not previously reported. These results suggest that both apo-GCGR and glucagon-bound GCGRs show reversible opening and closing of the ECD with respect to the seven-transmembrane (7TM) domain. This work demonstrates a molecular approach to visualizing the dynamics of the GCGR ECD and provides a foundation for understanding the conformational changes underlying GPCR activation, which is critical in the development of new therapeutics.
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Affiliation(s)
- Ting Liu
- Department of Biochemistry & Cellular and Molecular Biology, College of Arts & Sciences, University of Tennessee, Knoxville, Tennessee, USA
| | - Susmita Khanal
- Department of Biochemistry & Cellular and Molecular Biology, College of Arts & Sciences, University of Tennessee, Knoxville, Tennessee, USA
| | - Gillian D Hertslet
- Department of Biochemistry & Cellular and Molecular Biology, College of Arts & Sciences, University of Tennessee, Knoxville, Tennessee, USA
| | - Rajan Lamichhane
- Department of Biochemistry & Cellular and Molecular Biology, College of Arts & Sciences, University of Tennessee, Knoxville, Tennessee, USA.
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3
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Svirelis J, Adali Z, Emilsson G, Medin J, Andersson J, Vattikunta R, Hulander M, Järlebark J, Kolman K, Olsson O, Sakiyama Y, Lim RYH, Dahlin A. Stable trapping of multiple proteins at physiological conditions using nanoscale chambers with macromolecular gates. Nat Commun 2023; 14:5131. [PMID: 37612271 PMCID: PMC10447545 DOI: 10.1038/s41467-023-40889-4] [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: 02/07/2023] [Accepted: 08/11/2023] [Indexed: 08/25/2023] Open
Abstract
The possibility to detect and analyze single or few biological molecules is very important for understanding interactions and reaction mechanisms. Ideally, the molecules should be confined to a nanoscale volume so that the observation time by optical methods can be extended. However, it has proven difficult to develop reliable, non-invasive trapping techniques for biomolecules under physiological conditions. Here we present a platform for long-term tether-free (solution phase) trapping of proteins without exposing them to any field gradient forces. We show that a responsive polymer brush can make solid state nanopores switch between a fully open and a fully closed state with respect to proteins, while always allowing the passage of solvent, ions and small molecules. This makes it possible to trap a very high number of proteins (500-1000) inside nanoscale chambers as small as one attoliter, reaching concentrations up to 60 gL-1. Our method is fully compatible with parallelization by imaging arrays of nanochambers. Additionally, we show that enzymatic cascade reactions can be performed with multiple native enzymes under full nanoscale confinement and steady supply of reactants. This platform will greatly extend the possibilities to optically analyze interactions involving multiple proteins, such as the dynamics of oligomerization events.
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Affiliation(s)
- Justas Svirelis
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Zeynep Adali
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Gustav Emilsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Jesper Medin
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - John Andersson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Radhika Vattikunta
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Mats Hulander
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Julia Järlebark
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Krzysztof Kolman
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Oliver Olsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Yusuke Sakiyama
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, 4056, Basel, Switzerland
| | - Roderick Y H Lim
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, 4056, Basel, Switzerland
| | - Andreas Dahlin
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden.
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4
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Guan R, Yu Q, Li J. Aggregation enhanced fluorescence and Raman signals for highly sensitive cancer detection. Methods 2023; 216:11-20. [PMID: 37295579 DOI: 10.1016/j.ymeth.2023.06.001] [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: 04/17/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/12/2023] Open
Abstract
The implementation of early cancer detection benefits the treatment outcomes with remarkably improved survival rate through the detection of rare circulating biomarkers in body fluids. Spectroscopic technologies play a crucial role in sensitive biomarker measurements by outputting extremely strong signals. In particular, the aggregation enhanced fluorescence and Raman technologies feature the detection of targets down to single-molecule level, thereby demonstrating the great promise of early cancer detection. In this review, we focus on the aggregation-induced emission (AIE) and aggregation-related surface-enhanced Raman scattering (SERS) spectroscopic strategies for detecting cancer biomarkers. We discuss the AIE and SERS based biomarker detection using target-driven aggregation as well as the aggregated nanoprobes. Furthermore, we deliberate on the progress of developing AIE and SERS integrated platforms. Ultimately, we put forth the potential challenges and perspectives on the way to use these two spectroscopic technologies in clinical settings. It is expected this review can inspire the design of AIE and SERS integrated platform for highly sensitive and accurate cancer detection.
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Affiliation(s)
- Rui Guan
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan 430072, PR China
| | - Qi Yu
- Key Laboratory of Fermentation Engineering (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics, School of Food and Biological Engineering, Hubei University of Technology, Wuhan 430068, PR China.
| | - Junrong Li
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan 430072, PR China.
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5
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Zhang Y, Yang C, Peng S, Ling J, Chen P, Ma Y, Wang W, Chen Z, Chen C. General Strategy To Improve the Photon Budget of Thiol-Conjugated Cyanine Dyes. J Am Chem Soc 2023; 145:4187-4198. [PMID: 36756850 DOI: 10.1021/jacs.2c12635] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Maleimide-cysteine chemistry has been a routine practice for the site-specific labeling of fluorophores to proteins since the 1950s. This approach, however, cannot bring out the best photon budget of fluorophores. Here, we systematically measured the Cyanine3/5 dye conjugates via maleimide-thiol and amide linkages by counting the total emitted photons at the single-molecule level. While brightness and signal-to-noise ratios do not change significantly, dyes with thioether linkages exhibit more severe photobleaching than amide linkers. We then screened modern arylation-type bioconjugation strategies to alleviate this damage. Labeling thiols with phenyloxadiazole (POD) methyl sulfone, p-chloronitrobenzene, and fluorobenzene probes gave rise to electron-deficient aryl thioethers, effectively increasing the total emitted photons by 1.5-3 fold. Among the linkers, POD maintains labeling efficiency and specificity that are comparable to maleimide. Such an increase has proved to be universal among bulk and single-molecule assays, with or without triplet-state quenchers and oxygen scavengers, and on conformationally unrestricted or restricted cyanines. We demonstrated that cyanine-POD conjugates are general and superior fluorophores for thiol labeling in single-molecule FRET measurements of biomolecular conformational dynamics and in two-color STED nanoscopy using site-selectively labeled nanobodies. This work sheds light on the photobleaching mechanism of cyanines under single-molecule imaging while highlighting the interplay between the protein microenvironment, bioconjugation chemistry, and fluorophore photochemistry.
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Affiliation(s)
- Yuan Zhang
- Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
| | - Chen Yang
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
| | - Sijia Peng
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
| | - Jing Ling
- Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Peng Chen
- PKU-Nanjing Institute of Translational Medicine, Nanjing 211800, China
| | - Yumiao Ma
- BSJ Institute, Beijing 100084, China
- Hangzhou Yanqu Information Technology Co., Ltd., Xihu District, Hangzhou City, Zhejiang Province 310003, China
| | - Wenjuan Wang
- School of Life Sciences, Technology Center for Protein Sciences, Tsinghua University, Beijing 100084, China
| | - Zhixing Chen
- Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- PKU-Nanjing Institute of Translational Medicine, Nanjing 211800, China
| | - Chunlai Chen
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
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6
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Searles EK, Gomez E, Lee S, Ostovar B, Link S, Landes CF. Single-Particle Photoluminescence and Dark-Field Scattering during Charge Density Tuning. J Phys Chem Lett 2023; 14:318-325. [PMID: 36603176 DOI: 10.1021/acs.jpclett.2c03566] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Single-particle spectroelectrochemistry provides optical insight into understanding physical and chemical changes occurring on the nanoscale. While changes in dark-field scattering during electrochemical charging are well understood, changes to the photoluminescence of plasmonic nanoparticles under similar conditions are less studied. Here, we use correlated single-particle photoluminescence and dark-field scattering to compare their plasmon modulation at applied potentials. We find that changes in the emission of a single gold nanorod during charge density tuning of intraband photoluminescence can be attributed to changes in the Purcell factor and absorption cross section. Finally, modulation of interband photoluminescence provides an additional constructive observable, giving promise for establishing dual channel sensing in spectroelectrochemical measurements.
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Affiliation(s)
- Emily K Searles
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas77005, United States
| | - Eric Gomez
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas77005, United States
| | - Stephen Lee
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas77005, United States
| | - Behnaz Ostovar
- Department of Electrical and Computer Engineering, Rice University, 6100 Main Street, Houston, Texas77005, United States
| | - Stephan Link
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas77005, United States
- Department of Electrical and Computer Engineering, Rice University, 6100 Main Street, Houston, Texas77005, United States
- Smalley-Curl Institute, Rice University, 6100 Main Street, Houston, Texas77005, United States
| | - Christy F Landes
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas77005, United States
- Department of Electrical and Computer Engineering, Rice University, 6100 Main Street, Houston, Texas77005, United States
- Smalley-Curl Institute, Rice University, 6100 Main Street, Houston, Texas77005, United States
- Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main Street, Houston, Texas77005, United States
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7
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Schmidt K, Hageneder S, Lechner B, Zbiral B, Fossati S, Ahmadi Y, Minunni M, Toca-Herrera JL, Reimhult E, Barisic I, Dostalek J. Rolling Circle Amplification Tailored for Plasmonic Biosensors: From Ensemble to Single-Molecule Detection. ACS APPLIED MATERIALS & INTERFACES 2022; 14:55017-55027. [PMID: 36446038 PMCID: PMC9756284 DOI: 10.1021/acsami.2c14500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
We report on the tailoring of rolling circle amplification (RCA) for affinity biosensors relying on the optical probing of their surface with confined surface plasmon field. Affinity capture of the target analyte at the metallic sensor surface (e.g., by using immunoassays) is followed by the RCA step for subsequent readout based on increased refractive index (surface plasmon resonance, SPR) or RCA-incorporated high number of fluorophores (in surface plasmon-enhanced fluorescence, PEF). By combining SPR and PEF methods, this work investigates the impact of the conformation of long RCA-generated single-stranded DNA (ssDNA) chains to the plasmonic sensor response enhancement. In order to confine the RCA reaction within the evanescent surface plasmon field and hence maximize the sensor response, an interface carrying analyte-capturing molecules and additional guiding ssDNA strands (complementary to the repeating segments of RCA-generated chains) is developed. When using the circular padlock probe as a model target analyte, the PEF readout shows that the reported RCA implementation improves the limit of detection (LOD) from 13 pM to high femtomolar concentration when compared to direct labeling. The respective enhancement factor is of about 2 orders of magnitude, which agrees with the maximum number of fluorophore emitters attached to the RCA chain that is folded in the evanescent surface plasmon field by the developed biointerface. Moreover, the RCA allows facile visualizing of individual binding events by fluorescence microscopy, which enables direct counting of captured molecules. This approach offers a versatile route toward a fast digital readout format of single-molecule detection with further reduced LOD.
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Affiliation(s)
- Katharina Schmidt
- Biosensor
Technologies, AIT-Austrian Institute of
Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
- CEST
Competence Center for Electrochemical Surface Technologies, 3430 Tulln an der
Donau, Austria
| | - Simone Hageneder
- Biosensor
Technologies, AIT-Austrian Institute of
Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
| | - Bernadette Lechner
- Biosensor
Technologies, AIT-Austrian Institute of
Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
- CEST
Competence Center for Electrochemical Surface Technologies, 3430 Tulln an der
Donau, Austria
| | - Barbara Zbiral
- Department
of Nanobiotechnology, University of Natural
Resources and Life Sciences Vienna (BOKU), 1190 Vienna, Austria
| | - Stefan Fossati
- Biosensor
Technologies, AIT-Austrian Institute of
Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
| | - Yasaman Ahmadi
- Molecular
Diagnostics, Health & Environment, AIT
Austrian Institute of Technology GmbH, 1210 Vienna, Austria
| | - Maria Minunni
- Department
of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 3-13, Sesto Fiorentino, 50019 Firenze, Italy
| | - Jose Luis Toca-Herrera
- Department
of Nanobiotechnology, University of Natural
Resources and Life Sciences Vienna (BOKU), 1190 Vienna, Austria
| | - Erik Reimhult
- Department
of Nanobiotechnology, University of Natural
Resources and Life Sciences Vienna (BOKU), 1190 Vienna, Austria
| | - Ivan Barisic
- Molecular
Diagnostics, Health & Environment, AIT
Austrian Institute of Technology GmbH, 1210 Vienna, Austria
| | - Jakub Dostalek
- Biosensor
Technologies, AIT-Austrian Institute of
Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
- FZU-Institute
of Physics, Czech Academy of Sciences, Na Slovance 2, 182 21 Prague, Czech Republic
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8
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Spatiotemporally controlled generation of NTPs for single-molecule studies. Nat Chem Biol 2022; 18:1144-1151. [PMID: 36131148 PMCID: PMC9512701 DOI: 10.1038/s41589-022-01100-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 06/29/2022] [Indexed: 12/22/2022]
Abstract
Many essential processes in the cell depend on proteins that use nucleoside triphosphates (NTPs). Methods that directly monitor the often-complex dynamics of these proteins at the single-molecule level have helped to uncover their mechanisms of action. However, the measurement throughput is typically limited for NTP-utilizing reactions, and the quantitative dissection of complex dynamics over multiple sequential turnovers remains challenging. Here we present a method for controlling NTP-driven reactions in single-molecule experiments via the local generation of NTPs (LAGOON) that markedly increases the measurement throughput and enables single-turnover observations. We demonstrate the effectiveness of LAGOON in single-molecule fluorescence and force spectroscopy assays by monitoring DNA unwinding, nucleosome sliding and RNA polymerase elongation. LAGOON can be readily integrated with many single-molecule techniques, and we anticipate that it will facilitate studies of a wide range of crucial NTP-driven processes. ![]()
A new method for controlling NTP-driven reactions in single-molecule experiments via the local generation of NTPs (LAGOON) markedly increases the measurement throughput and enables single-turnover observations.
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9
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Milstein JN, Nino DF, Zhou X, Gradinaru CC. Single-molecule counting applied to the study of GPCR oligomerization. Biophys J 2022; 121:3175-3187. [PMID: 35927960 PMCID: PMC9463696 DOI: 10.1016/j.bpj.2022.07.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/29/2022] [Accepted: 07/28/2022] [Indexed: 11/24/2022] Open
Abstract
Single-molecule counting techniques enable a precise determination of the intracellular abundance and stoichiometry of proteins and macromolecular complexes. These details are often challenging to quantitatively assess yet are essential for our understanding of cellular function. Consider G-protein-coupled receptors-an expansive class of transmembrane signaling proteins that participate in many vital physiological functions making them a popular target for drug development. While early evidence for the role of oligomerization in receptor signaling came from ensemble biochemical and biophysical assays, innovations in single-molecule measurements are now driving a paradigm shift in our understanding of its relevance. Here, we review recent developments in single-molecule counting with a focus on photobleaching step counting and the emerging technique of quantitative single-molecule localization microscopy-with a particular emphasis on the potential for these techniques to advance our understanding of the role of oligomerization in G-protein-coupled receptor signaling.
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Affiliation(s)
- Joshua N Milstein
- Department of Physics, University of Toronto, Toronto, Ontario, Canada; Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada.
| | - Daniel F Nino
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Xiaohan Zhou
- Department of Physics, University of Toronto, Toronto, Ontario, Canada; Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Claudiu C Gradinaru
- Department of Physics, University of Toronto, Toronto, Ontario, Canada; Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada.
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10
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Del Alamo D, Meiler J, Mchaourab HS. Principles of Alternating Access in LeuT-fold Transporters: Commonalities and Divergences. J Mol Biol 2022; 434:167746. [PMID: 35843285 DOI: 10.1016/j.jmb.2022.167746] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/08/2022] [Accepted: 07/09/2022] [Indexed: 11/15/2022]
Abstract
Found in all domains of life, transporters belonging to the LeuT-fold class mediate the import and exchange of hydrophilic and charged compounds such as amino acids, metals, and sugar molecules. Nearly two decades of investigations on the eponymous bacterial transporter LeuT have yielded a library of high-resolution snapshots of its conformational cycle linked by solution-state experimental data obtained from multiple techniques. In parallel, its topology has been observed in symporters and antiporters characterized by a spectrum of substrate specificities and coupled to gradients of distinct ions. Here we review and compare mechanistic models of transport for LeuT, its well-studied homologs, as well as functionally distant members of the fold, emphasizing the commonalities and divergences in alternating access and the corresponding energy landscapes. Our integrated summary illustrates how fold conservation, a hallmark of the LeuT fold, coincides with divergent choreographies of alternating access that nevertheless capitalize on recurrent structural motifs. In addition, it highlights the knowledge gap that hinders the leveraging of the current body of research into detailed mechanisms of transport for this important class of membrane proteins.
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Affiliation(s)
- Diego Del Alamo
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA; Department of Chemistry, Vanderbilt University, Nashville, TN, USA. https://twitter.com/DdelAlamo
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA; Institute for Drug Discovery, Leipzig University, Leipzig, DE, USA. https://twitter.com/MeilerLab
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA.
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11
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Park C, Jung S, Park H. Single vesicle tracking for studying synaptic vesicle dynamics in small central synapses. Curr Opin Neurobiol 2022; 76:102596. [PMID: 35803103 DOI: 10.1016/j.conb.2022.102596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/20/2022] [Accepted: 05/27/2022] [Indexed: 11/26/2022]
Abstract
Sustained neurotransmission is driven by a continuous supply of synaptic vesicles to the release sites and modulated by synaptic vesicle dynamics. However, synaptic vesicle dynamics in synapses remain elusive because of technical limitations. Recent advances in fluorescence imaging techniques have enabled the tracking of single synaptic vesicles in small central synapses in living neurons. Single vesicle tracking has uncovered a wealth of new information about synaptic vesicle dynamics both within and outside presynaptic terminals, showing that single vesicle tracking is an effective tool for studying synaptic vesicle dynamics. Particularly, single vesicle tracking with high spatiotemporal resolution has revealed the dependence of synaptic vesicle dynamics on the location, stages of recycling, and neuronal activity. This review summarizes the recent findings from single synaptic vesicle tracking in small central synapses and their implications in synaptic transmission and pathogenic mechanisms of neurodegenerative diseases.
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Affiliation(s)
- Chungwon Park
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, 999077, Hong Kong
| | - Sangyong Jung
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A∗STAR), 11 Biopolis Way, 138667, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 119077, Singapore
| | - Hyokeun Park
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, 999077, Hong Kong; Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, 999077, Hong Kong; State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, 999077, Hong Kong.
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12
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Asher WB, Terry DS, Gregorio GGA, Kahsai AW, Borgia A, Xie B, Modak A, Zhu Y, Jang W, Govindaraju A, Huang LY, Inoue A, Lambert NA, Gurevich VV, Shi L, Lefkowitz RJ, Blanchard SC, Javitch JA. GPCR-mediated β-arrestin activation deconvoluted with single-molecule precision. Cell 2022; 185:1661-1675.e16. [PMID: 35483373 PMCID: PMC9191627 DOI: 10.1016/j.cell.2022.03.042] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 02/11/2022] [Accepted: 03/29/2022] [Indexed: 01/14/2023]
Abstract
β-arrestins bind G protein-coupled receptors to terminate G protein signaling and to facilitate other downstream signaling pathways. Using single-molecule fluorescence resonance energy transfer imaging, we show that β-arrestin is strongly autoinhibited in its basal state. Its engagement with a phosphopeptide mimicking phosphorylated receptor tail efficiently releases the β-arrestin tail from its N domain to assume distinct conformations. Unexpectedly, we find that β-arrestin binding to phosphorylated receptor, with a phosphorylation barcode identical to the isolated phosphopeptide, is highly inefficient and that agonist-promoted receptor activation is required for β-arrestin activation, consistent with the release of a sequestered receptor C tail. These findings, together with focused cellular investigations, reveal that agonism and receptor C-tail release are specific determinants of the rate and efficiency of β-arrestin activation by phosphorylated receptor. We infer that receptor phosphorylation patterns, in combination with receptor agonism, synergistically establish the strength and specificity with which diverse, downstream β-arrestin-mediated events are directed.
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Affiliation(s)
- Wesley B Asher
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
| | - Daniel S Terry
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - G Glenn A Gregorio
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
| | - Alem W Kahsai
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Alessandro Borgia
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Bing Xie
- Computational Chemistry and Molecular Biophysics Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Arnab Modak
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ying Zhu
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
| | - Wonjo Jang
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Alekhya Govindaraju
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
| | - Li-Yin Huang
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Nevin A Lambert
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | | | - Lei Shi
- Computational Chemistry and Molecular Biophysics Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Robert J Lefkowitz
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA; Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Scott C Blanchard
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Jonathan A Javitch
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA; Department of Molecular Pharmacology and Therapeutics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
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13
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Boruah A, Saikia BK. Synthesis, Characterization, Properties, and Novel Applications of Fluorescent Nanodiamonds. J Fluoresc 2022; 32:863-885. [PMID: 35230567 DOI: 10.1007/s10895-022-02898-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 02/01/2022] [Indexed: 11/26/2022]
Abstract
In the last few years, fluorescent nanodiamonds (FNDs) have been developed significantly as a new member in the nanocarbon family. The surface of FNDs is embedded with some crystallographic defects containing color centres which surmount the properties of other fluorochromes including up conversion and down conversion nanoparticles, quantum dots, nano tubes, fullerenes, organic dyes, silica etc. Some of the intriguing properties like inevitable photostability, inherent bio-compatibility, outstanding optical and robust mechanical properties, excellent magnetic field, and electric field sensing potentiality make FNDs appealing to some benevolent applications in numerous fields like bio-imaging, delivering drugs, fighting cancer, spin electronics, imaging of magnetic structure at nanoscale and as promising nanometric temperature sensor. The structure of FNDs has certain point defects on the surface among which negatively charged nitrogen vacancy centre (NV-) is the most investigated color centre. The production of NV- fluorescence nanodiamonds is the most challenging task as substitution of carbon atoms is required to create vacancies by causing irradiation from an electron beam which is followed by high temperature annealing. Thus, this review points out the relative advantages of FNDs containing negatively charged nitrogen vacancy centres produced from HPHT method or CVD method with those nanodiamonds produced through detonation process or pulsed laser ablation (PLA) method. The steps involved in the fabrication of FNDs are described along with the major challenges and struggles underwent during the process in this review. This review also summarizes the recent developments made in the functionalization and applications predominantly made in the field of biological science and it is understood that depending on the defect color centres they can exhibit different emitted wavelengths ranging from UV-visible to near infrared with broad or narrow bandwidths. This review also highlights some of the fluorescent NDs that emit stable and strong red or green photoluminescence from the defect centers of NV- which are implanted in the crystal lattice. This critical and extensive review will be useful for the further progress in this futuristic field of FNDs.
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Affiliation(s)
- Anusuya Boruah
- Coal & Energy Group, Materials Science and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat-785006, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Binoy K Saikia
- Coal & Energy Group, Materials Science and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat-785006, Assam, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India.
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14
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Engineered lanthanide-doped upconversion nanoparticles for biosensing and bioimaging application. Mikrochim Acta 2022; 189:109. [PMID: 35175435 DOI: 10.1007/s00604-022-05180-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/07/2022] [Indexed: 01/26/2023]
Abstract
Various fluctuations of intracellular ions, biomolecules, and other conditions in the physiological environment play crucial roles in fundamental biological processes. These factors are of great importance for analysis in biomedical detection. Nevertheless, developments of the simple, rapid, and accurate proof for specific detection still encounter major challenges. Upconversion nanoparticles (UCNPs), which could absorb multiple low-energy near-infrared light (NIR) photon excitation and emits high-energy photons caused by anti-Stokes shift, show unique upconversion luminescence (UCL) properties, for example, sharp emission band, high physicochemical stability like near-zero photobleaching, photo blinking in biological tissues, and long luminescence lifetime. Furthermore, the NIR used for the light source to excite UCNPs enable lower photo-damage effect and deeper penetration of tissue, and in the meantime, it can avoid the auto-fluorescence and light scattering from biological tissue interference. Thus, the lanthanide-doped UCNP-based functional platform with controlled structure, crystalline phase, size, and multicolor emission has become an appropriate nanomaterial for bioapplications such as biosensing, bioimaging, drug release, and therapies. In this review, the recent progress about synthesis and biomedical applications of UCNPs related to sensing and bioimaging is summarized. Firstly, the different luminescence mechanisms of the upconversion process are presented. Secondly, four of the most common methods for synthesizing UCNPs are compared as well as the advantages and disadvantages of these synthetic routes. Meanwhile, the surface modification of lanthanide-doped UCNPs was introduced to pave the way for their biochemistry applications. Next, this review detailed the biological applications of lanthanide-doped UCNPs, particularly in bioimaging, including UCL and multi-modal imaging and biosensing (monitoring intracellular ions and biomolecules). Finally, the challenges and future perspectives in materials science and biomedical fields of UCNPs are concluded: the low quantum yield of the upconversion process should be considered when they are executed as imaging contrast agents. And the biosafety of lanthanide-doped UCNPs needs to be evaluated.
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15
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Iizuka R, Yamazaki H, Uemura S. Zero-mode waveguides and nanopore-based sequencing technologies accelerate single-molecule studies. Biophys Physicobiol 2022; 19:e190032. [DOI: 10.2142/biophysico.bppb-v19.0032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/26/2022] [Indexed: 12/01/2022] Open
Affiliation(s)
- Ryo Iizuka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
| | - Hirohito Yamazaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
| | - Sotaro Uemura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
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16
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Rusková R, Račko D. Channels with Helical Modulation Display Stereospecific Sensitivity for Chiral Superstructures. Polymers (Basel) 2021; 13:3726. [PMID: 34771282 PMCID: PMC8588256 DOI: 10.3390/polym13213726] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/23/2021] [Accepted: 10/23/2021] [Indexed: 01/03/2023] Open
Abstract
By means of coarse-grained molecular dynamics simulations, we explore chiral sensitivity of confining spaces modelled as helical channels to chiral superstructures represented by polymer knots. The simulations show that helical channels exhibit stereosensitivity to chiral knots localized on linear chains by effect of external pulling force and also to knots embedded on circular chains. The magnitude of the stereoselective effect is stronger for torus knots, the effect is weaker in the case of twist knots, and amphichiral knots do exhibit no chiral effects. The magnitude of the effect can be tuned by the so-far investigated radius of the helix, the pitch of the helix and the strength of the pulling force. The model is aimed to simulate and address a range of practical situations that may occur in experimental settings such as designing of nanotechnological devices for the detection of topological state of molecules, preparation of new gels with tailor made stereoselective properties, or diffusion of knotted DNA in biological conditions.
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Affiliation(s)
- Renáta Rusková
- Polymer Institute, Slovak Academy of Sciences, Dúbravská Cesta 3, 84541 Bratislava, Slovakia;
- Department of Plastics, Rubber and Fibres (IPM FCFT), Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 81237 Bratislava, Slovakia
| | - Dušan Račko
- Polymer Institute, Slovak Academy of Sciences, Dúbravská Cesta 3, 84541 Bratislava, Slovakia;
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17
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Bartels K, Lasitza‐Male T, Hofmann H, Löw C. Single-Molecule FRET of Membrane Transport Proteins. Chembiochem 2021; 22:2657-2671. [PMID: 33945656 PMCID: PMC8453700 DOI: 10.1002/cbic.202100106] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/03/2021] [Indexed: 12/31/2022]
Abstract
Uncovering the structure and function of biomolecules is a fundamental goal in structural biology. Membrane-embedded transport proteins are ubiquitous in all kingdoms of life. Despite structural flexibility, their mechanisms are typically studied by ensemble biochemical methods or by static high-resolution structures, which complicate a detailed understanding of their dynamics. Here, we review the recent progress of single molecule Förster Resonance Energy Transfer (smFRET) in determining mechanisms and timescales of substrate transport across membranes. These studies do not only demonstrate the versatility and suitability of state-of-the-art smFRET tools for studying membrane transport proteins but they also highlight the importance of membrane mimicking environments in preserving the function of these proteins. The current achievements advance our understanding of transport mechanisms and have the potential to facilitate future progress in drug design.
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Affiliation(s)
- Kim Bartels
- Centre for Structural Systems Biology (CSSB)DESY and European Molecular Biology Laboratory HamburgNotkestrasse 8522607HamburgGermany
| | - Tanya Lasitza‐Male
- Department of Structural BiologyWeizmann Institute of ScienceHerzl St. 2347610001RehovotIsrael
| | - Hagen Hofmann
- Department of Structural BiologyWeizmann Institute of ScienceHerzl St. 2347610001RehovotIsrael
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB)DESY and European Molecular Biology Laboratory HamburgNotkestrasse 8522607HamburgGermany
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18
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Song J, Li J, Chan HS. Small-Angle X-ray Scattering Signatures of Conformational Heterogeneity and Homogeneity of Disordered Protein Ensembles. J Phys Chem B 2021; 125:6451-6478. [PMID: 34115515 DOI: 10.1021/acs.jpcb.1c02453] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
An accurate account of disordered protein conformations is of central importance to deciphering the physicochemical basis of biological functions of intrinsically disordered proteins and the folding-unfolding energetics of globular proteins. Physically, disordered ensembles of nonhomopolymeric polypeptides are expected to be heterogeneous, i.e., they should differ from those homogeneous ensembles of homopolymers that harbor an essentially unique relationship between average values of end-to-end distance REE and radius of gyration Rg. It was posited recently, however, that small-angle X-ray scattering (SAXS) data on conformational dimensions of disordered proteins can be rationalized almost exclusively by homopolymer ensembles. Assessing this perspective, chain-model simulations are used to evaluate the discriminatory power of SAXS-determined molecular form factors (MFFs) with regard to homogeneous versus heterogeneous ensembles. The general approach adopted here is not bound by any assumption about ensemble encodability, in that the postulated heterogeneous ensembles we evaluated are not restricted to those entailed by simple interaction schemes. Our analysis of MFFs for certain heterogeneous ensembles with more narrowly distributed REE and Rg indicates that while they deviate from MFFs of homogeneous ensembles, the differences can be rather small. Remarkably, some heterogeneous ensembles with asphericity and REE drastically different from those of homogeneous ensembles can nonetheless exhibit practically identical MFFs, demonstrating that SAXS MFFs do not afford unique characterizations of basic properties of conformational ensembles in general. In other words, the ensemble to MFF mapping is practically many-to-one and likely nonsmooth. Heteropolymeric variations of the REE-Rg relationship were further showcased using an analytical perturbation theory developed here for flexible heteropolymers. Ramifications of our findings for interpretation of experimental data are discussed.
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Affiliation(s)
- Jianhui Song
- School of Polymer Science and Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 266042, China
| | - Jichen Li
- School of Polymer Science and Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao 266042, China
| | - Hue Sun Chan
- Department of Biochemistry, University of Toronto Faculty of Medicine, Toronto, Ontario M5S 1A8, Canada
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19
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Wu F, Wang Y, Chen Y, Li Z, Ding CF. Alkali metal ion-induced conformation changes of methionine- and leucine enkephalin investigated by gas-phase hydrogen/deuterium exchange combined with theoretical calculations. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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20
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Hang X, He S, Dong Z, Minnick G, Rosenbohm J, Chen Z, Yang R, Chang L. Nanosensors for single cell mechanical interrogation. Biosens Bioelectron 2021; 179:113086. [DOI: 10.1016/j.bios.2021.113086] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 02/08/2023]
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21
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Loeff L, Kerssemakers JWJ, Joo C, Dekker C. AutoStepfinder: A fast and automated step detection method for single-molecule analysis. PATTERNS 2021; 2:100256. [PMID: 34036291 PMCID: PMC8134948 DOI: 10.1016/j.patter.2021.100256] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/12/2020] [Accepted: 04/08/2021] [Indexed: 01/05/2023]
Abstract
Single-molecule techniques allow the visualization of the molecular dynamics of nucleic acids and proteins with high spatiotemporal resolution. Valuable kinetic information of biomolecules can be obtained when the discrete states within single-molecule time trajectories are determined. Here, we present a fast, automated, and bias-free step detection method, AutoStepfinder, that determines steps in large datasets without requiring prior knowledge on the noise contributions and location of steps. The analysis is based on a series of partition events that minimize the difference between the data and the fit. A dual-pass strategy determines the optimal fit and allows AutoStepfinder to detect steps of a wide variety of sizes. We demonstrate step detection for a broad variety of experimental traces. The user-friendly interface and the automated detection of AutoStepfinder provides a robust analysis procedure that enables anyone without programming knowledge to generate step fits and informative plots in less than an hour. Fast, automated, and bias-free detection of steps within single-molecule trajectories Robust step detection without any prior knowledge on the data A dual-pass strategy for the detection of steps over a wide variety of scales A user-friendly interface for a simplified step fitting procedure
Single-molecule techniques have made it possible to track individual protein complexes in real time with a nanometer spatial resolution and a millisecond timescale. Accurate determination of the dynamic states within single-molecule time traces provides valuable kinetic information that underlie the function of biological macromolecules. Here, we present a new automated step detection method called AutoStepfinder, a versatile, robust, and easy-to-use algorithm that allows researchers to determine the kinetic states within single-molecule time trajectories without any bias.
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Affiliation(s)
- Luuk Loeff
- Kavli Institute of Nanoscience and Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Jacob W J Kerssemakers
- Kavli Institute of Nanoscience and Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Chirlmin Joo
- Kavli Institute of Nanoscience and Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Cees Dekker
- Kavli Institute of Nanoscience and Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
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22
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Speranza G. Carbon Nanomaterials: Synthesis, Functionalization and Sensing Applications. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:967. [PMID: 33918769 PMCID: PMC8069879 DOI: 10.3390/nano11040967] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 02/07/2023]
Abstract
Recent advances in nanomaterial design and synthesis has resulted in robust sensing systems that display superior analytical performance. The use of nanomaterials within sensors has accelerated new routes and opportunities for the detection of analytes or target molecules. Among others, carbon-based sensors have reported biocompatibility, better sensitivity, better selectivity and lower limits of detection to reveal a wide range of organic and inorganic molecules. Carbon nanomaterials are among the most extensively studied materials because of their unique properties spanning from the high specific surface area, high carrier mobility, high electrical conductivity, flexibility, and optical transparency fostering their use in sensing applications. In this paper, a comprehensive review has been made to cover recent developments in the field of carbon-based nanomaterials for sensing applications. The review describes nanomaterials like fullerenes, carbon onions, carbon quantum dots, nanodiamonds, carbon nanotubes, and graphene. Synthesis of these nanostructures has been discussed along with their functionalization methods. The recent application of all these nanomaterials in sensing applications has been highlighted for the principal applicative field and the future prospects and possibilities have been outlined.
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Affiliation(s)
- Giorgio Speranza
- CMM—FBK, v. Sommarive 18, 38123 Trento, Italy;
- IFN—CNR, CSMFO Lab., via alla Cascata 56/C Povo, 38123 Trento, Italy
- Department of Industrial Engineering, University of Trento, v. Sommarive 9, 38123 Trento, Italy
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23
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Shoup D, Roth A, Thapa R, Puchalla J, Rye HS. Development and application of multicolor burst analysis spectroscopy. Biophys J 2021; 120:2192-2204. [PMID: 33831389 DOI: 10.1016/j.bpj.2021.03.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 02/24/2021] [Accepted: 03/24/2021] [Indexed: 10/21/2022] Open
Abstract
The formation and disassembly of macromolecular particles is a ubiquitous and essential feature of virtually all living organisms. Additionally, diseases are often associated with the accumulation and propagation of biologically active nanoparticles, like the formation of toxic protein aggregates in protein misfolding diseases and the growth of infectious viral particles. The heterogeneous and dynamic nature of biologically active particles can make them exceedingly challenging to study. The single-particle fluorescence technique known as burst analysis spectroscopy (BAS) was developed to facilitate real-time measurement of macromolecular particle distributions in the submicron range in a minimally perturbing, free-solution environment. Here, we develop a multicolor version of BAS and employ it to examine two problems in macromolecular assembly: 1) the extent of DNA packing heterogeneity in bacteriophage viral particles and 2) growth models of non-native protein aggregates. We show that multicolor BAS provides a powerful and flexible approach to studying hidden properties of important biological particles like viruses and protein aggregates.
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Affiliation(s)
- Daniel Shoup
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Andrew Roth
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Rajan Thapa
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Jason Puchalla
- Department of Physics, Princeton University, Princeton, New Jersey.
| | - Hays S Rye
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas.
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24
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Single-molecule FRET imaging of GPCR dimers in living cells. Nat Methods 2021; 18:397-405. [PMID: 33686301 PMCID: PMC8232828 DOI: 10.1038/s41592-021-01081-y] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 01/29/2021] [Indexed: 12/18/2022]
Abstract
Class C G protein-coupled receptors (GPCRs) are known to form stable homodimers or heterodimers critical for function, but the oligomeric status of class A and B receptors, which constitute >90% of all GPCRs, remains hotly debated. Single-molecule fluorescence resonance energy transfer (smFRET) is a powerful approach with the potential to reveal valuable insights into GPCR organization but has rarely been used in living cells to study protein systems. Here, we report generally applicable methods for using smFRET to detect and track transmembrane proteins diffusing within the plasma membrane of mammalian cells. We leverage this in-cell smFRET approach to show agonist-induced structural dynamics within individual metabotropic glutamate receptor dimers. We apply these methods to representative class A, B and C receptors, finding evidence for receptor monomers, density-dependent dimers and constitutive dimers, respectively.
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25
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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: 125] [Impact Index Per Article: 41.7] [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.
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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
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26
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Abstract
A series of free base meso-tetraarylporphyrins functionalized with substituents containing one, two, and four cyclooctatetraene (COT) moieties have been obtained and characterized by spectral and photophysical studies. Three COT-free porphyrins served as reference compounds. COT is a triplet quencher, well-known to enhance the photostability of several, but not all, fluorophores. In the case of porphyrins, substitution with COT improves photostability in zinc derivatives, but for free bases, the effect is the opposite. We show that placing the COT moiety further from the free base porphyrin core enhances the photostability when the COT group lies in the direct vicinity of the macrocycle. The quantum yields of photobleaching inversely correlate with porphyrin oxidation potentials. An improvement in photostability in both COT-containing and COT-free porphyrins can be achieved by screening the porphyrin core from oxygen by switching from tolyl to mesityl substituents. This leads to a decrease in the photobleaching quantum yield, even though triplet lifetimes are longer. The results confirm the involvement of oxygen in the photodegradation of porphyrins.
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27
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Abstract
X-ray crystallography enables detailed structural studies of proteins to understand and modulate their function. Conducting crystallographic experiments at cryogenic temperatures has practical benefits but potentially limits the identification of functionally important alternative protein conformations that can be revealed only at room temperature (RT). This review discusses practical aspects of preparing, acquiring, and analyzing X-ray crystallography data at RT to demystify preconceived impracticalities that freeze progress of routine RT data collection at synchrotron sources. Examples are presented as conceptual and experimental templates to enable the design of RT-inspired studies; they illustrate the diversity and utility of gaining novel insights into protein conformational landscapes. An integrative view of protein conformational dynamics enables opportunities to advance basic and biomedical research.
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28
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Yang Z, Tang D, Hu J, Tang M, Zhang M, Cui HL, Wang L, Chang C, Fan C, Li J, Wang H. Near-Field Nanoscopic Terahertz Imaging of Single Proteins. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2005814. [PMID: 33306275 DOI: 10.1002/smll.202005814] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/22/2020] [Indexed: 05/26/2023]
Abstract
Terahertz (THz) biological imaging has attracted intense attention due to its capability of acquiring physicochemical information in a label-free, noninvasive, and nonionizing manner. However, extending THz imaging to the single-molecule level remains a challenge, partly due to the weak THz reflectivity of biomolecules with low dielectric constants. Here, the development of graphene-mediated THz scattering-type scanning near-field optical microscope for direct imaging of single proteins is reported. Importantly, it is found that a graphene substrate with high THz reflectivity and atomic flatness can provide high THz contrast against the protein molecules. In addition, a platinum probe with an optimized shaft length is found enabling the enhancement of the amplitude of the scattered THz near-field signals. By coupling these effects, the topographical and THz scattering images of individual immunoglobulin G (IgG) and ferritin molecules with the size of a few nanometers are obtained, simultaneously. The demonstrated strategy thus opens new routes to imaging single biomolecules with THz.
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Affiliation(s)
- Zhongbo Yang
- Research Center of Applied Physics, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- Chongqing Engineering Research Center of High-Resolution and Three-Dimensional Dynamic Imaging Technology, Chongqing, 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Dongyun Tang
- Research Center of Applied Physics, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- Chongqing Engineering Research Center of High-Resolution and Three-Dimensional Dynamic Imaging Technology, Chongqing, 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Jiao Hu
- Research Center of Applied Physics, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- Chongqing Engineering Research Center of High-Resolution and Three-Dimensional Dynamic Imaging Technology, Chongqing, 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Mingjie Tang
- Research Center of Applied Physics, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- Chongqing Engineering Research Center of High-Resolution and Three-Dimensional Dynamic Imaging Technology, Chongqing, 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Mingkun Zhang
- Research Center of Applied Physics, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- Chongqing Engineering Research Center of High-Resolution and Three-Dimensional Dynamic Imaging Technology, Chongqing, 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Hong-Liang Cui
- Research Center of Applied Physics, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- Chongqing Engineering Research Center of High-Resolution and Three-Dimensional Dynamic Imaging Technology, Chongqing, 400714, China
| | - Lihua Wang
- Bioimaging Center, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China
| | - Chao Chang
- Department of Engineering Physics, Tsinghua University, Beijing, 100084, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiang Li
- Bioimaging Center, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China
| | - Huabin Wang
- Research Center of Applied Physics, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- Chongqing Engineering Research Center of High-Resolution and Three-Dimensional Dynamic Imaging Technology, Chongqing, 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
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29
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Samaan GN, Wyllie MK, Cizmic JM, Needham LM, Nobis D, Ngo K, Andersen S, Magennis SW, Lee SF, Purse BW. Single-molecule fluorescence detection of a tricyclic nucleoside analogue. Chem Sci 2020; 12:2623-2628. [PMID: 34164030 PMCID: PMC8179283 DOI: 10.1039/d0sc03903a] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Fluorescent nucleobase surrogates capable of Watson–Crick hydrogen bonding are essential probes of nucleic acid structure and dynamics, but their limited brightness and short absorption and emission wavelengths have rendered them unsuitable for single-molecule detection. Aiming to improve on these properties, we designed a new tricyclic pyrimidine nucleoside analogue with a push–pull conjugated system and synthesized it in seven sequential steps. The resulting C-linked 8-(diethylamino)benzo[b][1,8]naphthyridin-2(1H)-one nucleoside, which we name ABN, exhibits ε442 = 20 000 M−1 cm−1 and Φem,540 = 0.39 in water, increasing to Φem = 0.50–0.53 when base paired with adenine in duplex DNA oligonucleotides. Single-molecule fluorescence measurements of ABN using both one-photon and two-photon excitation demonstrate its excellent photostability and indicate that the nucleoside is present to > 95% in a bright state with count rates of at least 15 kHz per molecule. This new fluorescent nucleobase analogue, which, in duplex DNA, is the brightest and most red-shifted known, is the first to offer robust and accessible single-molecule fluorescence detection capabilities. Fluorescent nucleoside analogue ABN is readily detected at the single-molecule level and retains a quantum yield >50% in duplex DNA oligonucleotides.![]()
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Affiliation(s)
- George N Samaan
- Department of Chemistry and Biochemistry and the Viral Information Institute, San Diego State University San Diego CA 92182 USA
| | - Mckenzie K Wyllie
- Department of Chemistry and Biochemistry and the Viral Information Institute, San Diego State University San Diego CA 92182 USA
| | - Julian M Cizmic
- Department of Chemistry and Biochemistry and the Viral Information Institute, San Diego State University San Diego CA 92182 USA
| | - Lisa-Maria Needham
- University of Cambridge, Chemistry Department Lensfield Road Cambridge CB2 1EW UK
| | - David Nobis
- School of Chemistry, University of Glasgow University Avenue Glasgow G12 8QQ UK
| | - Katrina Ngo
- Department of Chemistry and Biochemistry and the Viral Information Institute, San Diego State University San Diego CA 92182 USA
| | - Susan Andersen
- Department of Chemistry and Biochemistry and the Viral Information Institute, San Diego State University San Diego CA 92182 USA
| | - Steven W Magennis
- School of Chemistry, University of Glasgow University Avenue Glasgow G12 8QQ UK
| | - Steven F Lee
- University of Cambridge, Chemistry Department Lensfield Road Cambridge CB2 1EW UK
| | - Byron W Purse
- Department of Chemistry and Biochemistry and the Viral Information Institute, San Diego State University San Diego CA 92182 USA
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30
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Abstract
Labeling of nucleic acids is required for many studies aiming to elucidate their functions and dynamics in vitro and in cells. Out of the numerous labeling concepts that have been devised, covalent labeling provides the most stable linkage, an unrivaled choice of small and highly fluorescent labels and - thanks to recent advances in click chemistry - an incredible versatility. Depending on the approach, site-, sequence- and cell-specificity can be achieved. DNA and RNA labeling are rapidly developing fields that bring together multiple areas of research: on the one hand, synthetic and biophysical chemists develop new fluorescent labels and isomorphic nucleobases as well as faster and more selective bioorthogonal reactions. On the other hand, the number of enzymes that can be harnessed for post-synthetic and site-specific labeling of nucleic acids has increased significantly. Together with protein engineering and genetic manipulation of cells, intracellular and cell-specific labeling has become possible. In this review, we provide a structured overview of covalent labeling approaches for nucleic acids and highlight notable developments, in particular recent examples. The majority of this review will focus on fluorescent labeling; however, the principles can often be readily applied to other labels. We will start with entirely chemical approaches, followed by chemo-enzymatic strategies and ribozymes, and finish with metabolic labeling of nucleic acids. Each section is subdivided into direct (or one-step) and two-step labeling approaches and will start with DNA before treating RNA.
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Affiliation(s)
- Nils Klöcker
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, D-48149 Münster, Germany.
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31
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Che Y, Feng S, Guo J, Hou J, Zhu X, Chen L, Yang H, Chen M, Li Y, Chen S, Cheng Z, Luo Z, Chen J. In vivo live imaging of bone using shortwave infrared fluorescent quantum dots. NANOSCALE 2020; 12:22022-22029. [PMID: 33141143 DOI: 10.1039/d0nr06261h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Bone plays an increasingly critical role in human health and disease. More noninvasive multi-scale imaging techniques are urgently required for investigations on the substructures and biological functions of bones. Our results firstly revealed that SWIR QDs prepared by us acted as a bone-specific imaging contrast to achieve real-time observation of bone structures both in vivo and ex vivo. The major bone structures of both Balb/C nude mice and Balb/C mice including their skull, spine, pelvis, limbs, and sternum could be rapidly and gradually identified via blood circulation after QD injection in vivo. More importantly, the binding capability of our QDs mainly depended on the biological activities of bone tissues, suggesting that our technique is suitable for in vivo live imaging. In addition, the cell imaging results suggested that the potential mechanism of our bone imaging could be ascribed to the highly specific interaction between QDs and MC3T3-E1 cells. In a word, the skeletal structures and biological activities of bones are anticipated to be observed and monitored with this QD-guided SWIR imaging strategy, respectively. This radiation-free QD-guided SWIR live imaging of bone can add new insights into a comprehensive study of bones in vivo and provide a basis for early diagnosis of bone diseases.
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Affiliation(s)
- Yanjun Che
- Department of Orthopaedics, The First Affiliated Hospital of SooChow University, Suzhou, Jiangsu, China. and Department of Orthopedics, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi, China
| | - Sijia Feng
- Institute of Sports Medicine of Fudan University, Department of Orthopaedic Sports Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China.
| | - Jiangbo Guo
- Department of Orthopaedics, The First Affiliated Hospital of SooChow University, Suzhou, Jiangsu, China.
| | - Junjun Hou
- Department of Geriatrics, Xinghu Hospital, Suzhou industrial park, Suzhou, Jiangsu, China
| | - Xuesong Zhu
- Department of Orthopaedics, The First Affiliated Hospital of SooChow University, Suzhou, Jiangsu, China.
| | - Liang Chen
- Department of Orthopaedics, The First Affiliated Hospital of SooChow University, Suzhou, Jiangsu, China.
| | - Huilin Yang
- Department of Orthopaedics, The First Affiliated Hospital of SooChow University, Suzhou, Jiangsu, China.
| | - Mo Chen
- Institute of Sports Medicine of Fudan University, Department of Orthopaedic Sports Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China.
| | - Yunxia Li
- Institute of Sports Medicine of Fudan University, Department of Orthopaedic Sports Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China.
| | - Shiyi Chen
- Institute of Sports Medicine of Fudan University, Department of Orthopaedic Sports Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China.
| | - Zhen Cheng
- Molecular Imaging Program at Stanford (MIPS), Bio-X Program, and Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University, Stanford, California 94305-5344, USA.
| | - Zongping Luo
- Department of Orthopaedics, The First Affiliated Hospital of SooChow University, Suzhou, Jiangsu, China.
| | - Jun Chen
- Institute of Sports Medicine of Fudan University, Department of Orthopaedic Sports Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China.
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32
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Micura R, Höbartner C. Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes. Chem Soc Rev 2020; 49:7331-7353. [PMID: 32944725 DOI: 10.1039/d0cs00617c] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review aims at juxtaposing common versus distinct structural and functional strategies that are applied by aptamers, riboswitches, and ribozymes/DNAzymes. Focusing on recently discovered systems, we begin our analysis with small-molecule binding aptamers, with emphasis on in vitro-selected fluorogenic RNA aptamers and their different modes of ligand binding and fluorescence activation. Fundamental insights are much needed to advance RNA imaging probes for detection of exo- and endogenous RNA and for RNA process tracking. Secondly, we discuss the latest gene expression-regulating mRNA riboswitches that respond to the alarmone ppGpp, to PRPP, to NAD+, to adenosine and cytidine diphosphates, and to precursors of thiamine biosynthesis (HMP-PP), and we outline new subclasses of SAM and tetrahydrofolate-binding RNA regulators. Many riboswitches bind protein enzyme cofactors that, in principle, can catalyse a chemical reaction. For RNA, however, only one system (glmS ribozyme) has been identified in Nature thus far that utilizes a small molecule - glucosamine-6-phosphate - to participate directly in reaction catalysis (phosphodiester cleavage). We wonder why that is the case and what is to be done to reveal such likely existing cellular activities that could be more diverse than currently imagined. Thirdly, this brings us to the four latest small nucleolytic ribozymes termed twister, twister-sister, pistol, and hatchet as well as to in vitro selected DNA and RNA enzymes that promote new chemistry, mainly by exploiting their ability for RNA labelling and nucleoside modification recognition. Enormous progress in understanding the strategies of nucleic acids catalysts has been made by providing thorough structural fundaments (e.g. first structure of a DNAzyme, structures of ribozyme transition state mimics) in combination with functional assays and atomic mutagenesis.
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Affiliation(s)
- Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck CMBI, Leopold-Franzens University Innsbruck, Innsbruck, Austria.
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33
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Tuning the Baird aromatic triplet-state energy of cyclooctatetraene to maximize the self-healing mechanism in organic fluorophores. Proc Natl Acad Sci U S A 2020; 117:24305-24315. [PMID: 32913060 PMCID: PMC7533661 DOI: 10.1073/pnas.2006517117] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Bright, photostable, and nontoxic fluorescent contrast agents are critical for biological imaging. "Self-healing" dyes, in which triplet states are intramolecularly quenched, enable fluorescence imaging by increasing fluorophore brightness and longevity, while simultaneously reducing the generation of reactive oxygen species that promote phototoxicity. Here, we systematically examine the self-healing mechanism in cyanine-class organic fluorophores spanning the visible spectrum. We show that the Baird aromatic triplet-state energy of cyclooctatetraene can be physically altered to achieve order of magnitude enhancements in fluorophore brightness and signal-to-noise ratio in both the presence and absence of oxygen. We leverage these advances to achieve direct measurements of large-scale conformational dynamics within single molecules at submillisecond resolution using wide-field illumination and camera-based detection methods. These findings demonstrate the capacity to image functionally relevant conformational processes in biological systems in the kilohertz regime at physiological oxygen concentrations and shed important light on the multivariate parameters critical to self-healing organic fluorophore design.
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34
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Isselstein M, Zhang L, Glembockyte V, Brix O, Cosa G, Tinnefeld P, Cordes T. Self-Healing Dyes-Keeping the Promise? J Phys Chem Lett 2020; 11:4462-4480. [PMID: 32401520 DOI: 10.1021/acs.jpclett.9b03833] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Self-healing dyes have emerged as a new promising class of fluorescent labels. They consist of two units, a fluorescent dye and a photostabilizer. The latter heals whenever the fluorescent dye is in danger of taking a reaction pathway toward photobleaching. We describe the underlying concepts and summarize the developmental history and state-of-the-art, including latest applications in high-resolution microscopy, live-cell, and single-molecule imaging. We further discuss remaining limitations, which are (i) lower photostabilization of most self-healing dyes when compared to solution additives, (ii) limited mechanistic understanding on the influence of the biochemical environment and molecular oxygen on self-healing, and (iii) the lack of cheap and facile bioconjugation strategies. Finally, we provide ideas on how to further advance self-healing dyes, show new data on redox blinking caused by double-stranded DNA, and highlight forthcoming work on intramolecular photostabilization of fluorescent proteins.
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Affiliation(s)
- Michael Isselstein
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany
| | - Lei Zhang
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany
| | - Viktorija Glembockyte
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, Haus E 81377 München, Germany
- Department of Chemistry and Quebec Centre for Applied Materials (QCAM), McGill University, 801 Sherbrooke Street W., H3A 0B8 Montreal, Quebec, Canada
| | - Oliver Brix
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany
| | - Gonzalo Cosa
- Department of Chemistry and Quebec Centre for Applied Materials (QCAM), McGill University, 801 Sherbrooke Street W., H3A 0B8 Montreal, Quebec, Canada
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, Haus E 81377 München, Germany
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany
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35
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Abstract
Single-molecule techniques have been used successfully to visualize real-time enzymatic activities, revealing transient complex properties and heterogeneity of various biological events. Especially, conventional force spectroscopy including optical tweezers and magnetic tweezers has been widely used to monitor change in DNA length by enzymes with high spatiotemporal resolutions of ~ nanometers and ~ milliseconds. However, DNA metabolism results from coordination of a number of components during the processes, requiring efficient monitoring of a complex of proteins catalyzing DNA substrates. In this min-review, we will introduce a simple and multiplexed single-molecule assay to detect DNA substrates catalyzed by enzymes with high-throughput data collection. We conclude with a perspective of possible directions that enhance capability of the assay to reveal complex biological events with higher resolution.
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Affiliation(s)
- Ryanggeun Lee
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Keunsang Yang
- School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang 37673, Korea
| | - Jong-Bong Lee
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
- School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang 37673, Korea
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36
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DNA probes that store mechanical information reveal transient piconewton forces applied by T cells. Proc Natl Acad Sci U S A 2019; 116:16949-16954. [PMID: 31391300 DOI: 10.1073/pnas.1904034116] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The advent of molecular tension probes for real-time mapping of piconewton forces in living systems has had a major impact on mechanobiology. For example, DNA-based tension probes have revealed roles for mechanics in platelet, B cell, T cell, and fibroblast function. Nonetheless, imaging short-lived forces transmitted by low-abundance receptors remains a challenge. This is a particular problem for mechanoimmunology where ligand-receptor bindings are short lived, and a few antigens are sufficient for cell triggering. Herein, we present a mechanoselection strategy that uses locking oligonucleotides to preferentially and irreversibly bind DNA probes that are mechanically strained over probes at rest. Thus, infrequent and short-lived mechanical events are tagged. This strategy allows for integration and storage of mechanical information into a map of molecular tension history. Upon addition of unlocking oligonucleotides that drive toehold-mediated strand displacement, the probes reset to the real-time state, thereby erasing stored mechanical information. As a proof of concept, we applied this strategy to study OT-1 T cells, revealing that the T cell receptor (TCR) mechanically samples antigens carrying single amino acid mutations. Such events are not detectable using conventional tension probes. Each mutant peptide ligand displayed a different level of mechanical sampling and spatial scanning by the TCR that strongly correlated with its functional potency. Finally, we show evidence that T cells transmit pN forces through the programmed cell death receptor-1 (PD1), a major target in cancer immunotherapy. We anticipate that mechanical information storage will be broadly useful in studying the mechanobiology of the immune system.
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37
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LeVine MV, Terry DS, Khelashvili G, Siegel ZS, Quick M, Javitch JA, Blanchard SC, Weinstein H. The allosteric mechanism of substrate-specific transport in SLC6 is mediated by a volumetric sensor. Proc Natl Acad Sci U S A 2019; 116:15947-15956. [PMID: 31324743 PMCID: PMC6689989 DOI: 10.1073/pnas.1903020116] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Neurotransmitter:sodium symporters (NSSs) in the SLC6 family terminate neurotransmission by coupling the thermodynamically favorable transport of ions to the thermodynamically unfavorable transport of neurotransmitter back into presynaptic neurons. Results from many structural, functional, and computational studies on LeuT, a bacterial NSS homolog, have provided critical insight into the mechanism of sodium-coupled transport, but the mechanism underlying substrate-specific transport rates is still not understood. We present a combination of molecular dynamics simulations, single-molecule fluorescence resonance energy transfer (smFRET) imaging, and measurements of Na+ binding and substrate transport that reveals an allosteric substrate specificity mechanism. In this mechanism, residues F259 and I359 in the substrate binding pocket couple the binding of substrate to Na+ release from the Na2 site by allosterically modulating the stability of a partially open, inward-facing state. We propose a model for transport selectivity in which residues F259 and I359 act as a volumetric sensor that inhibits the transport of bulky amino acids.
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Affiliation(s)
- Michael V LeVine
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065;
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021
| | - Daniel S Terry
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021
| | - Zarek S Siegel
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021
| | - Matthias Quick
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032
| | - Jonathan A Javitch
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032
- Department of Pharmacology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Scott C Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065
| | - Harel Weinstein
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065;
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021
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38
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Fareh M, van Lopik J, Katechis I, Bronkhorst AW, Haagsma AC, van Rij RP, Joo C. Viral suppressors of RNAi employ a rapid screening mode to discriminate viral RNA from cellular small RNA. Nucleic Acids Res 2019; 46:3187-3197. [PMID: 29325071 PMCID: PMC5888754 DOI: 10.1093/nar/gkx1316] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 01/03/2018] [Indexed: 11/14/2022] Open
Abstract
RNA interference (RNAi) is an indispensable mechanism for antiviral defense in insects, including mosquitoes that transmit human diseases. To escape this antiviral defense system, viruses encode suppressors of RNAi that prevent elimination of viral RNAs, and thus ensure efficient virus accumulation. Although the first animal Viral Suppressor of RNAi (VSR) was identified more than a decade ago, the molecular basis of RNAi suppression by these viral proteins remains unclear. Here, we developed a single-molecule fluorescence assay to investigate how VSRs inhibit the recognition of viral RNAs by Dcr-2, a key endoribonuclease enzyme in the RNAi pathway. Using VSRs from three insect RNA viruses (Culex Y virus, Drosophila X virus and Drosophila C virus), we reveal bimodal physical interactions between RNA molecules and VSRs. During initial interactions, these VSRs rapidly discriminate short RNA substrates from long dsRNA. VSRs engage nearly irreversible binding with long dsRNAs, thereby shielding it from recognition by Dcr-2. We propose that the length-dependent switch from rapid screening to irreversible binding reflects the main mechanism by which VSRs distinguish viral dsRNA from cellular RNA species such as microRNAs.
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Affiliation(s)
- Mohamed Fareh
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, Delft 2629 HZ, The Netherlands
| | - Jasper van Lopik
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, Delft 2629 HZ, The Netherlands
| | - Iason Katechis
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, Delft 2629 HZ, The Netherlands
| | - Alfred W Bronkhorst
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen 6525 GA, The Netherlands
| | - Anna C Haagsma
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, Delft 2629 HZ, The Netherlands
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen 6525 GA, The Netherlands
| | - Chirlmin Joo
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, Delft 2629 HZ, The Netherlands
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39
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Sirbu D, Diharce J, Martinić I, Chopin N, Eliseeva SV, Guillaumet G, Petoud S, Bonnet P, Suzenet F. An original class of small sized molecules as versatile fluorescent probes for cellular imaging. Chem Commun (Camb) 2019; 55:7776-7779. [PMID: 31210218 DOI: 10.1039/c9cc03765a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
An unusual class, compact in size, of fluorescent probes based on pyridazino-1,3a,6a-triazapentalene scaffolds exhibits promising fluorescent properties (quantum yield values up to 73%, large Stokes shifts, emission wavelengths located in the green-yellow range, excellent solubility) with good photostability suitable for optical imaging applications.
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Affiliation(s)
- Doina Sirbu
- Institut de Chimie Organique et Analytique - ICOA UMR7311, rue de Chartres, 45100 Orléans, France.
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40
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Juliusson HY, Segler ALJ, Sigurdsson ST. Benzoyl-Protected Hydroxylamines for Improved Chemical Synthesis of Oligonucleotides Containing Nitroxide Spin Labels. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900553] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Haraldur Y. Juliusson
- Department of Chemistry; Science Institute; University of Iceland; Dunhaga 3 107 Reykjavik Iceland
| | - Anna-Lena J. Segler
- Department of Chemistry; Science Institute; University of Iceland; Dunhaga 3 107 Reykjavik Iceland
| | - Snorri Th. Sigurdsson
- Department of Chemistry; Science Institute; University of Iceland; Dunhaga 3 107 Reykjavik Iceland
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41
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Choi J, Grosely R, Puglisi EV, Puglisi JD. Expanding single-molecule fluorescence spectroscopy to capture complexity in biology. Curr Opin Struct Biol 2019; 58:233-240. [PMID: 31213390 DOI: 10.1016/j.sbi.2019.05.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 05/03/2019] [Accepted: 05/08/2019] [Indexed: 11/16/2022]
Abstract
Fundamental biological processes are driven by diverse molecular machineries. In recent years, single-molecule fluorescence spectroscopy has matured as a unique tool in biology to study how structural dynamics of molecular complexes drive various biochemical reactions. In this review, we highlight underlying developments in single-molecule fluorescence methods that enable deep biological investigations. Recent progress in these methods points toward increasing complexity of measurements to capture biological processes in a living cell, where multiple processes often occur simultaneously and are mechanistically coupled.
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Affiliation(s)
- Junhong Choi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305-4090, USA
| | - Rosslyn Grosely
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
| | - Elisabetta V Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.
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42
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Extreme mechanical diversity of human telomeric DNA revealed by fluorescence-force spectroscopy. Proc Natl Acad Sci U S A 2019; 116:8350-8359. [PMID: 30944218 DOI: 10.1073/pnas.1815162116] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
G-quadruplexes (GQs) can adopt diverse structures and are functionally implicated in transcription, replication, translation, and maintenance of telomere. Their conformational diversity under physiological levels of mechanical stress, however, is poorly understood. We used single-molecule fluorescence-force spectroscopy that combines fluorescence resonance energy transfer with optical tweezers to measure human telomeric sequences under tension. Abrupt GQ unfolding with K+ in solution occurred at as many as four discrete levels of force. Added to an ultrastable state and a gradually unfolding state, there were six mechanically distinct structures. Extreme mechanical diversity was also observed with Na+, although GQs were mechanically weaker. Our ability to detect small conformational changes at low forces enabled the determination of refolding forces of about 2 pN. Refolding was rapid and stochastically redistributed molecules to mechanically distinct states. A single guanine-to-thymine substitution mutant required much higher ion concentrations to display GQ-like unfolding and refolded via intermediates, contrary to the wild type. Contradicting an earlier proposal, truncation to three hexanucleotide repeats resulted in a single-stranded DNA-like mechanical behavior under all conditions, indicating that at least four repeats are required to form mechanically stable structures.
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43
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Jalihal AP, Lund PE, Walter NG. Coming Together: RNAs and Proteins Assemble under the Single-Molecule Fluorescence Microscope. Cold Spring Harb Perspect Biol 2019; 11:11/4/a032441. [PMID: 30936188 DOI: 10.1101/cshperspect.a032441] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
RNAs, across their numerous classes, often work in concert with proteins in RNA-protein complexes (RNPs) to execute critical cellular functions. Ensemble-averaging methods have been instrumental in revealing many important aspects of these RNA-protein interactions, yet are insufficiently sensitive to much of the dynamics at the heart of RNP function. Single-molecule fluorescence microscopy (SMFM) offers complementary, versatile tools to probe RNP conformational and compositional changes in detail. In this review, we first outline the basic principles of SMFM as applied to RNPs, describing key considerations for labeling, imaging, and quantitative analysis. We then sample applications of in vitro and in vivo single-molecule visualization using the case studies of pre-messenger RNA (mRNA) splicing and RNA silencing, respectively. After discussing specific insights single-molecule fluorescence methods have yielded, we briefly review recent developments in the field and highlight areas of anticipated growth.
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Affiliation(s)
- Ameya P Jalihal
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, Michigan 48109.,Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Paul E Lund
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109.,Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan 48109
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44
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Abstract
Time series obtained from time-dependent experiments contain rich information on kinetics and dynamics of the system under investigation. This work describes an unsupervised learning framework, along with the derivation of the necessary analytical expressions, for the analysis of Gaussian-distributed time series that exhibit discrete states. After the time series has been partitioned into segments in a model-free manner using the previously developed change-point (CP) method, this protocol starts with an agglomerative hierarchical clustering algorithm to classify the detected segments into possible states. The initial state clustering is further refined using an expectation-maximization (EM) procedure, and the number of states is determined by a Bayesian information criterion (BIC). Also introduced here is an achievement scalarization function, usually seen in artificial intelligence literature, for quantitatively assessing the performance of state determination. The statistical learning framework, which is comprised of three stages, detection of signal change, clustering, and number-of-state determination, was thoroughly characterized using simulated trajectories with random intensity segments that have no underlying kinetics, and its performance was critically evaluated. The application to experimental data is also demonstrated. The results suggested that this general framework, the implementation of which is based on firm theoretical foundations and does not require the imposition of any kinetics model, is powerful in determining the number of states, the parameters contained in each state, as well as the associated statistical significance.
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Affiliation(s)
- Hao Li
- Department of Chemistry , Princeton University , Princeton , New Jersey 08544 , United States
| | - Haw Yang
- Department of Chemistry , Princeton University , Princeton , New Jersey 08544 , United States
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45
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Xue L, Cadinu P, Paulose Nadappuram B, Kang M, Ma Y, Korchev Y, Ivanov AP, Edel JB. Gated Single-Molecule Transport in Double-Barreled Nanopores. ACS APPLIED MATERIALS & INTERFACES 2018; 10:38621-38629. [PMID: 30360085 PMCID: PMC6243394 DOI: 10.1021/acsami.8b13721] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Single-molecule methods have been rapidly developing with the appealing prospect of transforming conventional ensemble-averaged analytical techniques. However, challenges remain especially in improving detection sensitivity and controlling molecular transport. In this article, we present a direct method for the fabrication of analytical sensors that combine the advantages of nanopores and field-effect transistors for simultaneous label-free single-molecule detection and manipulation. We show that these hybrid sensors have perfectly aligned nanopores and field-effect transistor components making it possible to detect molecular events with up to near 100% synchronization. Furthermore, we show that the transport across the nanopore can be voltage-gated to switch on/off translocations in real time. Finally, surface functionalization of the gate electrode can also be used to fine tune transport properties enabling more active control over the translocation velocity and capture rates.
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Affiliation(s)
- Liang Xue
- Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ, U.K.
| | - Paolo Cadinu
- Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ, U.K.
| | | | - Minkyung Kang
- Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ, U.K.
| | - Ye Ma
- Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ, U.K.
| | - Yuri Korchev
- Department
of Medicine, Imperial College London, London W12 0NN, U.K.
| | - Aleksandar P. Ivanov
- Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ, U.K.
- E-mail: (A.P.I)
| | - Joshua B. Edel
- Department of Chemistry, Imperial College London, Exhibition Road, London SW7 2AZ, U.K.
- E-mail: (J.B.E.)
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46
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Razgoniaeva N, Rogers S, Moroz P, Cassidy J, Zamkov M. Improving the spectral resolution in fluorescence microscopy through shaped-excitation imaging. Methods Appl Fluoresc 2018; 6:045006. [PMID: 30078787 DOI: 10.1088/2050-6120/aad81c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The visualization of distinct molecular species represents an important challenge of bio-imaging research. In past decades, the development of multicolor fluorescent (FL) labels has greatly improved our ability to track biological analytes, paving the way for important advances in understanding the cell dynamics. It remains challenging, however, to visualize a large number of different fluorephores simultaneously. Owing to a spectrally broad absorption of fluorescent dyes, only up to five color categories can be resolved at once. Here, we demonstrate a general strategy for distinguishing between multiple fluorescent targets in acquired microscopy images with improved accuracy. The present strategy is enabled through spectral shaping of the excitation light with an optical filter that uniquely attenuates the light absorption of each fluorophore in the investigated sample. The resulting emission changes, induced by such excitation modulation, are therefore target-specific and can be used for identifying various fluorescent species. The technique is demonstrated through an accurate identification of 8 different CdSe dyes with absorption maxima spanning the 520-620 spectral range. It is subsequently applied for accurate measurements of the pH balance in buffers emulating a metabolism of tumor cells.
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Affiliation(s)
- N Razgoniaeva
- The Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, United States of America. Department of Physics, Bowling Green State University, Bowling Green, Ohio 43403, United States of America
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47
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Glembockyte V, Wieneke R, Gatterdam K, Gidi Y, Tampé R, Cosa G. Tris-N-Nitrilotriacetic Acid Fluorophore as a Self-Healing Dye for Single-Molecule Fluorescence Imaging. J Am Chem Soc 2018; 140:11006-11012. [DOI: 10.1021/jacs.8b04681] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Viktorija Glembockyte
- Department of Chemistry and Quebec Centre for Applied Materials (QCAM), McGill University, 801 Sherbrooke Street W., H3A 0B8 Montreal, Quebec, Canada
| | - Ralph Wieneke
- Institute of Biochemistry, Biocenter, and Cluster of Excellence − Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
| | - Karl Gatterdam
- Institute of Biochemistry, Biocenter, and Cluster of Excellence − Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
| | - Yasser Gidi
- Department of Chemistry and Quebec Centre for Applied Materials (QCAM), McGill University, 801 Sherbrooke Street W., H3A 0B8 Montreal, Quebec, Canada
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, and Cluster of Excellence − Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
| | - Gonzalo Cosa
- Department of Chemistry and Quebec Centre for Applied Materials (QCAM), McGill University, 801 Sherbrooke Street W., H3A 0B8 Montreal, Quebec, Canada
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48
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Baibakov M, Wenger J. Laser-induced fluorescence quenching of red fluorescent dyes with green excitation: Avoiding artifacts in PIE-FRET and FCCS analysis. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.06.057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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49
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Visser EWA, Yan J, van IJzendoorn LJ, Prins MWJ. Continuous biomarker monitoring by particle mobility sensing with single molecule resolution. Nat Commun 2018; 9:2541. [PMID: 29959314 PMCID: PMC6026194 DOI: 10.1038/s41467-018-04802-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 05/16/2018] [Indexed: 12/21/2022] Open
Abstract
Healthcare is in demand of technologies for real-time sensing in order to continuously guard the state of patients. Here we present biomarker-monitoring based on the sensing of particle mobility, a concept wherein particles are coupled to a substrate via a flexible molecular tether, with both the particles and substrate provided with affinity molecules for effectuating specific and reversible interactions. Single-molecular binding and unbinding events modulate the Brownian particle motion and the state changes are recorded using optical scattering microscopy. The technology is demonstrated with DNA and protein as model biomarkers, in buffer and in blood plasma, showing sensitivity to picomolar and nanomolar concentrations. The sensing principle is direct and self-contained, without consuming or producing any reactants. With its basis in reversible interactions and single-molecule resolution, we envisage that the presented technology will enable biosensors for continuous biomarker monitoring with high sensitivity, specificity, and accuracy.
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Affiliation(s)
- Emiel W A Visser
- Department of Applied Physics, Eindhoven University of Technology, 5600 MB, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB, Eindhoven, Netherlands
| | - Junhong Yan
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB, Eindhoven, Netherlands
- Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB, Eindhoven, Netherlands
| | - Leo J van IJzendoorn
- Department of Applied Physics, Eindhoven University of Technology, 5600 MB, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB, Eindhoven, Netherlands
| | - Menno W J Prins
- Department of Applied Physics, Eindhoven University of Technology, 5600 MB, Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB, Eindhoven, Netherlands.
- Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB, Eindhoven, Netherlands.
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50
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Sun L, Wei R, Feng J, Zhang H. Tailored lanthanide-doped upconversion nanoparticles and their promising bioapplication prospects. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2018.03.007] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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