1
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Sundara Rajan S, Ebegboni VJ, Pichling P, Ludwig KR, Jones TL, Chari R, Tran A, Kruhlak MJ, Loncarek J, Caplen NJ. Endogenous EWSR1 Exists in Two Visual Modalities That Reflect Its Associations with Nucleic Acids and Concentration at Sites of Active Transcription. Mol Cell Biol 2024; 44:103-122. [PMID: 38506112 PMCID: PMC10986767 DOI: 10.1080/10985549.2024.2315425] [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: 01/10/2024] [Accepted: 02/02/2024] [Indexed: 03/21/2024] Open
Abstract
EWSR1 is a member of the FET family of nucleic acid binding proteins that includes FUS and TAF15. Here, we report the systematic analysis of endogenous EWSR1's cellular organization in human cells. We demonstrate that EWSR1, which contains low complexity and nucleic acid binding domains, is present in cells in faster and slower-recovering fractions, indicative of a protein undergoing both rapid exchange and longer-term interactions. The employment of complementary high-resolution imaging approaches shows EWSR1 exists in two visual modalities, a distributed state which is present throughout the nucleoplasm, and a concentrated state consistent with the formation of foci. Both EWSR1 visual modalities localize with nascent RNA. EWSR1 foci concentrate in regions of euchromatin, adjacent to protein markers of transcriptional activation, and significantly colocalize with phosphorylated RNA polymerase II. Our results contribute to bridging the gap between our understanding of the biophysical and biochemical properties of FET proteins, including EWSR1, their functions as transcriptional regulators, and the participation of these proteins in tumorigenesis and neurodegenerative disease.
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Affiliation(s)
- Soumya Sundara Rajan
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Vernon J. Ebegboni
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Patricio Pichling
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Katelyn R. Ludwig
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Tamara L. Jones
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Raj Chari
- Genome Modification Core, Laboratory Animal Sciences Program, Frederick National Lab for Cancer Research, Frederick, Maryland, USA
| | - Andy Tran
- CCR Confocal Microscopy Core Facility, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael J. Kruhlak
- CCR Confocal Microscopy Core Facility, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jadranka Loncarek
- Centrosome Biology Section, Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Natasha J. Caplen
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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2
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Zhang Z, Faez S. Iontronic microscopy of a tungsten microelectrode: "seeing" ionic currents under an optical microscope. Faraday Discuss 2023; 246:426-440. [PMID: 37404127 PMCID: PMC10568260 DOI: 10.1039/d3fd00040k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 03/27/2023] [Indexed: 07/06/2023]
Abstract
Optical methods for monitoring electrochemical reactions at an interface are advantageous because of their table-top setup and ease of integration into reactors. Here we apply EDL-modulation microscopy to one of the main components of amperometric measurement devices: a microelectrode. We present experimental measurements of the EDL-modulation contrast from the tip of a tungsten microelectrode at various electrochemical potentials inside a ferrocene-dimethanol Fe(MeOH)2 solution. Using the combination of the dark-field scattering microscope and the lock-in detection technique, we measure the phase and amplitude of local ion-concentration oscillations in response to an AC potential as the electrode potential is scanned through the redox-activity window of the dissolved species. We present the amplitude and phase map of this response, as such this method can be used to study the spatial and temporal variations of the ion-flux due to an electrochemical reaction close to metallic and semiconducting objects of general geometry. We discuss the advantages and possible extensions of using this microscopy method for wide-field imaging of ionic currents.
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Affiliation(s)
- Zhu Zhang
- Nanophotonics, Debye Institute for Nanomaterials Science, Utrecht University, 3584CC Utrecht, The Netherlands.
| | - Sanli Faez
- Nanophotonics, Debye Institute for Nanomaterials Science, Utrecht University, 3584CC Utrecht, The Netherlands.
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3
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Rajan SS, Ebegboni VJ, Pichling P, Ludwig KR, Jones TL, Chari R, Tran A, Kruhlak MJ, Loncarek J, Caplen NJ. EWSR1's visual modalities are defined by its association with nucleic acids and RNA polymerase II. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.16.553246. [PMID: 37645932 PMCID: PMC10462028 DOI: 10.1101/2023.08.16.553246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
We report systematic analysis of endogenous EWSR1's cellular organization. We demonstrate that EWSR1, which contains low complexity and nucleic acid binding domains, is present in cells in faster and slower-recovering fractions, indicative of a protein undergoing both rapid exchange and longer-term interactions. The employment of complementary high-resolution imaging approaches shows EWSR1 exists in in two visual modalities, a distributed state which is present throughout the nucleoplasm, and a concentrated state consistent with the formation of foci. Both EWSR1 visual modalities localize with nascent RNA. EWSR1 foci concentrate in regions of euchromatin, adjacent to protein markers of transcriptional activation, and significantly colocalize with phosphorylated RNA polymerase II. Interestingly, EWSR1 and FUS, another FET protein, exhibit distinct spatial organizations. Our results contribute to bridging the gap between our understanding of the biophysical and biochemical properties of FET proteins, including EWSR1, their functions as transcriptional regulators, and the participation of these proteins in tumorigenesis and neurodegenerative disease.
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Affiliation(s)
- Soumya Sundara Rajan
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health MD 20892, USA
| | - Vernon J. Ebegboni
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health MD 20892, USA
| | - Patricio Pichling
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health MD 20892, USA
| | - Katelyn R. Ludwig
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health MD 20892, USA
| | - Tamara L. Jones
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health MD 20892, USA
| | - Raj Chari
- Genome Modification Core, Laboratory Animal Sciences Program at the Frederick National Lab for Cancer Research, Frederick, MD 21702, USA
| | - Andy Tran
- CCR Confocal Microscopy Core Facility, Laboratory of Cancer Biology and Genetics, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Michael J. Kruhlak
- CCR Confocal Microscopy Core Facility, Laboratory of Cancer Biology and Genetics, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jadranka Loncarek
- Centrosome Biology Section, Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702 USA
| | - Natasha J. Caplen
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health MD 20892, USA
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4
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Recent Advances in Fluorescence Recovery after Photobleaching for Decoupling Transport and Kinetics of Biomacromolecules in Cellular Physiology. Polymers (Basel) 2022; 14:polym14091913. [PMID: 35567083 PMCID: PMC9105003 DOI: 10.3390/polym14091913] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/27/2022] [Accepted: 04/29/2022] [Indexed: 12/16/2022] Open
Abstract
Among the new molecular tools available to scientists and engineers, some of the most useful include fluorescently tagged biomolecules. Tools, such as green fluorescence protein (GFP), have been applied to perform semi-quantitative studies on biological signal transduction and cellular structural dynamics involved in the physiology of healthy and disease states. Such studies focus on drug pharmacokinetics, receptor-mediated endocytosis, nuclear mechanobiology, viral infections, and cancer metastasis. In 1976, fluorescence recovery after photobleaching (FRAP), which involves the monitoring of fluorescence emission recovery within a photobleached spot, was developed. FRAP allowed investigators to probe two-dimensional (2D) diffusion of fluorescently-labelled biomolecules. Since then, FRAP has been refined through the advancements of optics, charged-coupled-device (CCD) cameras, confocal microscopes, and molecular probes. FRAP is now a highly quantitative tool used for transport and kinetic studies in the cytosol, organelles, and membrane of a cell. In this work, the authors intend to provide a review of recent advances in FRAP. The authors include epifluorescence spot FRAP, total internal reflection (TIR)/FRAP, and confocal microscope-based FRAP. The underlying mathematical models are also described. Finally, our understanding of coupled transport and kinetics as determined by FRAP will be discussed and the potential for future advances suggested.
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5
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Li Y, Hu J, Cao D, Wang S, Dasgupta P, Liu H. Optical-Waveguide Based Tactile Sensing for Surgical Instruments of Minimally Invasive Surgery. Front Robot AI 2022; 8:773166. [PMID: 35127835 PMCID: PMC8808597 DOI: 10.3389/frobt.2021.773166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 12/22/2021] [Indexed: 11/26/2022] Open
Abstract
In recent years, with the rapid development of minimally invasive surgery (MIS), the lack of force sensing associated with the surgical instrument used in MIS has been increasingly a desirable technology amongst clinicians. However, it is still an open technical challenge to date since most existing tactile sensing principles are not suitable to small 3-dimensional (3D) curved surfaces often seen in surgical instruments, and as a result multi-point force detection cannot be realized. In this paper, a novel optical waveguide-based sensor was proposed to deal with the above research gap. A sensor prototype for curved surfaces resembling the surface of dissection forceps was developed and experimentally evaluated. The static parameters and dynamic response characteristics of the sensor were measured. Results show that the static hysteresis error is less than 3%, the resolution is 0.026 N, and the repeatability is less than 1.5%. Under a frequency of 12.5 Hz, the sensor could quickly measure the variation of the force signal. We demonstrated that this small and high-precision sensitive sensor design is promising to be used for creating multiple-point tactile sensing for minimally invasive surgical instruments with 3D surfaces.
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Affiliation(s)
- Yue Li
- School of Biomedical Engineering & Imaging Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Jian Hu
- School of Biomedical Engineering & Imaging Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Danqian Cao
- School of Biomedical Engineering & Imaging Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Stephen Wang
- Huawei Technologies R&D UK Ltd., Cambridge, United Kingdom
| | - Prokar Dasgupta
- Guy’s Hospital, Faculty of Life Sciences and Medicine, King’s College London, King’s Health Partners, London, United Kingdom
| | - Hongbin Liu
- School of Biomedical Engineering & Imaging Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
- *Correspondence: Hongbin Liu,
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6
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Abbineni PS, Briguglio JS, Chapman ER, Holz RW, Axelrod D. VAMP2 and synaptotagmin mobility in chromaffin granule membranes: implications for regulated exocytosis. Mol Biol Cell 2021; 33:ar53. [PMID: 34851717 PMCID: PMC9265163 DOI: 10.1091/mbc.e21-10-0494] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Granule-plasma membrane docking and fusion can only occur when proteins that enable these reactions are present at the granule-plasma membrane contact. Thus, the mobility of granule membrane proteins may influence docking, and membrane fusion. We measured the mobility of vesicle associated membrane protein 2 (VAMP2), synaptotagmin 1 (Syt1), and synaptotagmin 7 (Syt7) in chromaffin granule membranes in living chromaffin cells. We used a method that is not limited by standard optical resolution. A bright flash of strongly decaying evanescent field produced by total internal reflection (TIR) was used to photobleach GFP-labeled proteins in the granule membrane. Fluorescence recovery occurs as unbleached protein in the granule membrane distal from the glass interface diffuses into the more bleached proximal regions, enabling the measurement of diffusion coefficients. We found that VAMP2-EGFP and Syt7-EGFP are mobile with a diffusion coefficient of approximately 3 × 10-10 cm2/s. Syt1-EGFP mobility was below the detection limit. Utilizing these diffusion parameters, we estimated the time required for these proteins to arrive at docking and nascent fusion sites to be many tens of milliseconds. Our analyses raise the possibility that the diffusion characteristics of VAMP2 and Syt proteins could be a factor that influences the rate of exocytosis.
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Affiliation(s)
- Prabhodh S Abbineni
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan.,Department of Pharmacology, University of Michigan, Ann Arbor, Michigan
| | - Joseph S Briguglio
- Howard Hughes Medical Institute, Department of Neuroscience, University of Wisconsin, Madison, WI
| | - Edwin R Chapman
- Howard Hughes Medical Institute, Department of Neuroscience, University of Wisconsin, Madison, WI
| | - Ronald W Holz
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan
| | - Daniel Axelrod
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan.,Department of Physics, University of Michigan, Ann Arbor, Michigan
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7
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Oasa S, Krmpot AJ, Nikolić SN, Clayton AHA, Tsigelny IF, Changeux JP, Terenius L, Rigler R, Vukojević V. Dynamic Cellular Cartography: Mapping the Local Determinants of Oligodendrocyte Transcription Factor 2 (OLIG2) Function in Live Cells Using Massively Parallel Fluorescence Correlation Spectroscopy Integrated with Fluorescence Lifetime Imaging Microscopy (mpFCS/FLIM). Anal Chem 2021; 93:12011-12021. [PMID: 34428029 PMCID: PMC8427561 DOI: 10.1021/acs.analchem.1c02144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
Compartmentalization
and integration of molecular
processes through diffusion are basic mechanisms through which cells
perform biological functions. To characterize these mechanisms in
live cells, quantitative and ultrasensitive analytical methods with
high spatial and temporal resolution are needed. Here, we present
quantitative scanning-free confocal microscopy with single-molecule
sensitivity, high temporal resolution (∼10 μs/frame),
and fluorescence lifetime imaging capacity, developed by integrating
massively parallel fluorescence correlation spectroscopy with fluorescence
lifetime imaging microscopy (mpFCS/FLIM); we validate the method,
use it to map in live cell location-specific variations in the concentration,
diffusion, homodimerization, DNA binding, and local environment of
the oligodendrocyte transcription factor 2 fused with the enhanced
Green Fluorescent Protein (OLIG2-eGFP), and characterize the effects
of an allosteric inhibitor of OLIG2 dimerization on these determinants
of OLIG2 function. In particular, we show that cytoplasmic OLIG2-eGFP
is largely monomeric and freely diffusing, with the fraction of freely
diffusing OLIG2-eGFP molecules being fD,freecyt = (0.75
± 0.10) and the diffusion time τD,freecyt = (0.5 ± 0.3) ms. In contrast,
OLIG2-eGFP homodimers are abundant in the cell nucleus, constituting
∼25% of the nuclear pool, some fD,boundnuc = (0.65
± 0.10) of nuclear OLIG2-eGFP is bound to chromatin DNA, whereas
freely moving OLIG2-eGFP molecules diffuse at the same rate as those
in the cytoplasm, as evident from the lateral diffusion times τD,freenuc = τD,freecyt = (0.5
± 0.3) ms. OLIG2-eGFP interactions with chromatin DNA, revealed
through their influence on the apparent diffusion behavior of OLIG2-eGFP,
τD,boundnuc (850 ± 500) ms, are characterized by an apparent dissociation
constant Kd,appOLIG2-DNA = (45 ± 30) nM. The apparent
dissociation constant of OLIG2-eGFP homodimers was estimated to be Kd,app(OLIG2-eGFP)2 ≈ 560 nM. The allosteric inhibitor of OLIG2 dimerization,
compound NSC 50467, neither affects OLIG2-eGFP properties in the cytoplasm
nor does it alter the overall cytoplasmic environment. In contrast,
it significantly impedes OLIG2-eGFP homodimerization in the cell nucleus,
increasing five-fold the apparent dissociation constant, Kd,app,NSC50467(OLIG2-eGFP)2 ≈ 3 μM, thus reducing homodimer levels to below 7%
and effectively abolishing OLIG2-eGFP specific binding to chromatin
DNA. The mpFCS/FLIM methodology has a myriad of applications in biomedical
research and pharmaceutical industry. For example, it is indispensable
for understanding how biological functions emerge through the dynamic
integration of location-specific molecular processes and invaluable
for drug development, as it allows us to quantitatively characterize
the interactions of drugs with drug targets in live cells.
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Affiliation(s)
- Sho Oasa
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institutet, 17176 Stockholm, Sweden
| | - Aleksandar J Krmpot
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institutet, 17176 Stockholm, Sweden.,Institute of Physics Belgrade, University of Belgrade, 11080 Belgrade, Serbia
| | - Stanko N Nikolić
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institutet, 17176 Stockholm, Sweden.,Institute of Physics Belgrade, University of Belgrade, 11080 Belgrade, Serbia
| | - Andrew H A Clayton
- Optical Sciences Centre, Department of Physics and Astronomy, School of Science, Swinburne University of Technology, Melbourne, Victoria 3122, Australia
| | - Igor F Tsigelny
- Department of Neurosciences, University of California San Diego, La Jolla, California 92093-0819, United States
| | - Jean-Pierre Changeux
- Department of Neuroscience, Unité Neurobiologie Intégrative des Systèmes Cholinergiques, Institut Pasteur, F-75724 Paris 15, France
| | - Lars Terenius
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institutet, 17176 Stockholm, Sweden
| | - Rudolf Rigler
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institutet, 17176 Stockholm, Sweden.,Department of Medical Biochemistry and Biophysics (MBB), Karolinska Institutet, 17177 Stockholm, Sweden
| | - Vladana Vukojević
- Department of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institutet, 17176 Stockholm, Sweden
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8
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Hedge O, Höök F, Joyce P, Bergström CAS. Investigation of Self-Emulsifying Drug-Delivery System Interaction with a Biomimetic Membrane under Conditions Relevant to the Small Intestine. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:10200-10213. [PMID: 34379976 PMCID: PMC8388123 DOI: 10.1021/acs.langmuir.1c01689] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/31/2021] [Indexed: 06/13/2023]
Abstract
Self-emulsifying drug-delivery systems (SEDDS) have been extensively shown to increase oral absorption of solvation-limited compounds. However, there has been little clinical and commercial use of these formulations, in large part because the demonstrated advantages of SEDDS have been outweighed by our inability to precisely predict drug absorption from SEDDS using current in vitro assays. To overcome this limitation and increase the biological relevancy of in vitro assays, an absorption function can be incorporated using biomimetic membranes. However, the effects that SEDDS have on the integrity of a biomimetic membrane are not known. In this study, a quartz crystal microbalance with dissipation monitoring and total internal reflection fluorescence microscopy were employed as complementary methods to in vitro lipolysis-permeation assays to characterize the interaction of various actively digested SEDDS with a liquescent artificial membrane comprising lecithin in dodecane (LiDo). Observations from surface analysis showed that interactions between the digesting SEDDS and LiDo membrane coincided with inflection points in the digestion profiles. Importantly, no indications of membrane damage could be observed, which was supported by flux profiles of the lipophilic model drug felodipine (FEL) and impermeable marker Lucifer yellow on the basal side of the membrane. There was a correlation between the digestion kinetics of the SEDDS and the flux of FEL, but no clear correlation between solubilization and absorption profiles. Membrane interactions were dependent on the composition of lipids within each SEDDS, with the more digestible lipids leading to more pronounced interactions, but in all cases, the integrity of the membrane was maintained. These insights demonstrate that LiDo membranes are compatible with in vitro lipolysis assays for improving predictions of drug absorption from lipid-based formulations.
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Affiliation(s)
- Oliver
J. Hedge
- Department
of Pharmacy, Uppsala University, 751 23 Uppsala, Sweden
| | - Fredrik Höök
- Division
of Nano and Biophysics, Department of Physics, Chalmers Technical University, 412 96 Gothenburg, Sweden
| | - Paul Joyce
- Division
of Nano and Biophysics, Department of Physics, Chalmers Technical University, 412 96 Gothenburg, Sweden
- UniSA
Clinical & Health Sciences, University
of South Australia, 5090 Adelaide, Australia
- ARC
Centre of Excellence in Convergent Bio-Nano Science and Technology, University of South Australia, 5090 Adelaide, Australia
| | - Christel A. S. Bergström
- Department
of Pharmacy, Uppsala University, 751 23 Uppsala, Sweden
- The
Swedish Drug Delivery Center, Department of Pharmacy, Uppsala University, 751
23 Uppsala, Sweden
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9
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Axelrod JJ, Axelrod D. Light scattering in TIRF microscopy: A theoretical study of the limits to surface selectivity. Biophys J 2021; 120:2952-2968. [PMID: 34214540 PMCID: PMC8391032 DOI: 10.1016/j.bpj.2021.06.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/29/2021] [Accepted: 06/17/2021] [Indexed: 10/21/2022] Open
Abstract
In TIRF microscopy, the sample resides near a surface in an evanescent optical field that, ideally, decreases in intensity with distance from the surface in a pure exponential fashion. In practice, multiple surfaces and imperfections in the optical system and refractive index (RI) inhomogeneities in the sample (often living cells) produce propagating scattered light that degrades the exponential purity. RI inhomogeneities cannot easily be avoided. How severe is the consequent optical degradation? Starting from Maxwell's equations, we derive a first-order perturbative approximation of the electric field strength of light scattered by sample RI inhomogeneities of several types under coherent evanescent field illumination. The approximation provides an expression for the scattering field of any arbitrary RI inhomogeneity pattern. The scattering is not all propagating; some is evanescent and remains near the scattering centers. The results presented here are only a first-order approximation, and they ignore multiple scattering and reflections off the total internal reflection (TIR) surface. For simplicity, we assume that the RI variations in the z direction are insignificant within the depth of the evanescent field and consider only scattering of excitation light, not fluorescence emission light. The general conclusion of most significance from this study is that TIR scattering from a sample with RI variations typical of those on a cell culture alters the effective thickness of the illumination to only ∼50% greater than it would be without scattering. The qualitative surface selectivity of TIR fluorescence is largely retained even in the presence of scattering. Quantitatively, however, scattering will cause a deviation from the incident exponential decay at shorter distances, adding a slower decaying background. Calculations that assume a pure exponential decay will be approximations, and scattering should be taken into account. TIR scattering is only slightly dependent on polarization but is strongly reduced for the highest accessible incidence angles.
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Affiliation(s)
- Jeremy J Axelrod
- Department of Physics, University of California, Berkeley, California
| | - Daniel Axelrod
- Department of Physics and LSA Biophysics, University of Michigan, Ann Arbor, Michigan.
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10
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Tracking single particles for hours via continuous DNA-mediated fluorophore exchange. Nat Commun 2021; 12:4432. [PMID: 34290254 PMCID: PMC8295357 DOI: 10.1038/s41467-021-24223-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 06/07/2021] [Indexed: 01/13/2023] Open
Abstract
Monitoring biomolecules in single-particle tracking experiments is typically achieved by employing fixed organic dyes or fluorescent fusion proteins linked to a target of interest. However, photobleaching typically limits observation times to merely a few seconds, restricting downstream statistical analysis and observation of rare biological events. Here, we overcome this inherent limitation via continuous fluorophore exchange using DNA-PAINT, where fluorescently-labeled oligonucleotides reversibly bind to a single-stranded DNA handle attached to the target molecule. Such versatile and facile labeling allows uninterrupted monitoring of single molecules for extended durations. We demonstrate the power of our approach by observing DNA origami on membranes for tens of minutes, providing perspectives for investigating cellular processes on physiologically relevant timescales. The length of single-particle tracking experiments are limited due to photobleaching. Here the authors achieve long-term single-particle tracking with continuous fluorophore exchange in DNA-PAINT and use this to observe DNA origami on lipid bilayers for tens of minutes.
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11
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Wu X, Deng J, Guo G, Zheng Y, Xiong Q, Zheng T, Zhao X, Yu Z. Spatiotemporal Resolved Live Cell Membrane Tracking through Photo-click Reactions Enriched in Lipid Phase. Chemistry 2021; 27:11957-11965. [PMID: 34057766 DOI: 10.1002/chem.202101653] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Indexed: 01/04/2023]
Abstract
A set of photo-switchable monopeptides derived from cis-β-dibenzodiazocine-l-alanine (cis-DBDAA) have been designed and synthesized, which are capable of photo-click reacting with diaryltetrazoles or diarylsydnones in a hydrophobic phospholipid bilayer environment. The DBDAA monopeptides include both a hydrophobic tail on C-terminal, providing high affinity toward lipid membrane, and a modularized functional moiety on N-terminal, enabling rapid optimization of the self-assembly strength to form multifunctional supramolecules. With the cis-DBDAA monopeptides photo-switched into trans-configuration, we were able to disrupt the supramolecular assembly through an efficient photo-click reaction across the lipid bilayer of liposomes. We reveal that the performance of the photo-click reactions between the monopeptides and photo-generated nitrile imine intermediates is significantly enhanced by enrichment of both reactants in the hydrophobic membrane lamel of liposomes. Enrichment of the DBDAA monopeptide in lipid phase serves as a convenient method to introduce bioorthogonal chemical handles on live cell membranes, which enables fluorescence labelling of single cell's membrane with high spatiotemporal resolution to facilitate the studies on cell membrane dynamics.
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Affiliation(s)
- Xueting Wu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, 610064, P. R. China
| | - Jiajie Deng
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, 610064, P. R. China
| | - Guiling Guo
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, 610064, P. R. China
| | - Yuanqin Zheng
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, 610064, P. R. China
| | - Qin Xiong
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, 610064, P. R. China
| | - Tingting Zheng
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, 610064, P. R. China
| | - Xiaohu Zhao
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, 610064, P. R. China
| | - Zhipeng Yu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, 610064, P. R. China
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12
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Chandler JM, Xu H. Nanowaveguide-illuminated fluorescence correlation spectroscopy for single molecule studies. AIP ADVANCES 2021; 11:065112. [PMID: 34104537 PMCID: PMC8179723 DOI: 10.1063/5.0051679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/22/2021] [Indexed: 06/12/2023]
Abstract
Fluorescence Correlation Spectroscopy (FCS) is a method of investigating concentration fluctuations of fluorescent particles typically in the nM range as a result of its femtoliter-sized sample volume. However, biological processes on cell membranes that involve molecules in the μM concentration range require sample volumes well below the conventional FCS limit as well as nanoscale confinement in the longitudinal direction. In this study, we show that an effective measurement volume down to the zeptoliter range can be achieved via the introduction of a nanowire waveguide, resulting in an illumination spot of about 50 nm in lateral dimensions and a longitudinal confinement of around 20 nm just above the waveguide exit surface. Using illumination profiles obtained from finite element method simulations of dielectric nanowaveguides, we perform Monte Carlo simulations of fluorescence fluctuations for two scenarios of fluorophore movement: fluorophores freely diffusing in the three-dimensional (3D) space above the nanowaveguide and fluorophores moving in a two-dimensional (2D) membrane situated directly above the nanowaveguide exit surface. We have developed analytical functions to fit the simulation results and found that an effective illumination size of about 150 zl and 4 × 10-3 µm2 can be obtained for the 3D and 2D scenarios, respectively. Given the flat surface geometry and the deep-subwavelength confinement of its illumination spot, this nanowaveguide-illuminated fluorescence correlation spectroscopy technique may be well suited for studying the concentration and dynamics of densely distributed protein molecules on cell membranes.
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Affiliation(s)
- Joseph M. Chandler
- Department of Physics and Astronomy, San Francisco State University, 1600 Holloway Avenue, San Francisco, California 94132, USA
| | - Huizhong Xu
- Department of Physics and Astronomy, San Francisco State University, 1600 Holloway Avenue, San Francisco, California 94132, USA
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13
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Joyce P, Jõemetsa S, Isaksson S, Hossain S, Larsson P, Bergström C, Höök F. TIRF Microscopy-Based Monitoring of Drug Permeation Across a Lipid Membrane Supported on Mesoporous Silica. Angew Chem Int Ed Engl 2021; 60:2069-2073. [PMID: 32926534 PMCID: PMC7894553 DOI: 10.1002/anie.202011931] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Indexed: 11/12/2022]
Abstract
There is an urgent demand for analytic approaches that enable precise and representative quantification of the transport of biologically active compounds across cellular membranes. In this study, we established a new means to monitor membrane permeation kinetics, using total internal reflection fluorescence microscopy confined to a ≈500 nm thick mesoporous silica substrate, positioned underneath a planar supported cell membrane mimic. This way, we demonstrate spatiotemporally resolved membrane permeation kinetics of a small-molecule model drug, felodipine, while simultaneously controlling the integrity of, and monitoring the drug binding to, the cell membrane mimic. By contrasting the permeation behaviour of pure felodipine with felodipine coupled to the permeability enhancer caprylate (C8), we provide evidence for C8-facilitated transport across lipid membranes, thus validating the potential for this approach to successfully quantify carrier system-induced changes to cellular membrane permeation.
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Affiliation(s)
- Paul Joyce
- Department of PhysicsChalmers University of TechnologyGothenburgSE-412 96Sweden
| | - Silver Jõemetsa
- Department of PhysicsChalmers University of TechnologyGothenburgSE-412 96Sweden
| | - Simon Isaksson
- Department of PhysicsChalmers University of TechnologyGothenburgSE-412 96Sweden
| | - Shakhawath Hossain
- Department of PharmacyUppsala UniversityUppsalaSE-751 23Sweden
- The Swedish Drug Delivery ForumDepartment of PharmacyUppsala UniversityUppsalaSE-751 23Sweden
| | - Per Larsson
- Department of PharmacyUppsala UniversityUppsalaSE-751 23Sweden
- The Swedish Drug Delivery ForumDepartment of PharmacyUppsala UniversityUppsalaSE-751 23Sweden
| | - Christel Bergström
- Department of PharmacyUppsala UniversityUppsalaSE-751 23Sweden
- The Swedish Drug Delivery ForumDepartment of PharmacyUppsala UniversityUppsalaSE-751 23Sweden
| | - Fredrik Höök
- Department of PhysicsChalmers University of TechnologyGothenburgSE-412 96Sweden
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14
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Joyce P, Jõemetsa S, Isaksson S, Hossain S, Larsson P, Bergström C, Höök F. TIRF Microscopy‐Based Monitoring of Drug Permeation Across a Lipid Membrane Supported on Mesoporous Silica. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202011931] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Paul Joyce
- Department of Physics Chalmers University of Technology Gothenburg SE-412 96 Sweden
| | - Silver Jõemetsa
- Department of Physics Chalmers University of Technology Gothenburg SE-412 96 Sweden
| | - Simon Isaksson
- Department of Physics Chalmers University of Technology Gothenburg SE-412 96 Sweden
| | - Shakhawath Hossain
- Department of Pharmacy Uppsala University Uppsala SE-751 23 Sweden
- The Swedish Drug Delivery Forum Department of Pharmacy Uppsala University Uppsala SE-751 23 Sweden
| | - Per Larsson
- Department of Pharmacy Uppsala University Uppsala SE-751 23 Sweden
- The Swedish Drug Delivery Forum Department of Pharmacy Uppsala University Uppsala SE-751 23 Sweden
| | - Christel Bergström
- Department of Pharmacy Uppsala University Uppsala SE-751 23 Sweden
- The Swedish Drug Delivery Forum Department of Pharmacy Uppsala University Uppsala SE-751 23 Sweden
| | - Fredrik Höök
- Department of Physics Chalmers University of Technology Gothenburg SE-412 96 Sweden
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15
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Sankaran J, Wohland T. Fluorescence strategies for mapping cell membrane dynamics and structures. APL Bioeng 2020; 4:020901. [PMID: 32478279 PMCID: PMC7228782 DOI: 10.1063/1.5143945] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 04/17/2020] [Indexed: 12/20/2022] Open
Abstract
Fluorescence spectroscopy has been a cornerstone of research in membrane dynamics and organization. Technological advances in fluorescence spectroscopy went hand in hand with discovery of various physicochemical properties of membranes at nanometric spatial and microsecond timescales. In this perspective, we discuss the various challenges associated with quantification of physicochemical properties of membranes and how various modes of fluorescence spectroscopy have overcome these challenges to shed light on the structure and organization of membranes. Finally, we discuss newer measurement strategies and data analysis tools to investigate the structure, dynamics, and organization of membranes.
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16
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Joyce P, Ulmefors H, Maghrebi S, Subramaniam S, Wignall A, Jõemetsa S, Höök F, Prestidge CA. Enhancing the Cellular Uptake and Antibacterial Activity of Rifampicin through Encapsulation in Mesoporous Silica Nanoparticles. NANOMATERIALS 2020; 10:nano10040815. [PMID: 32344619 PMCID: PMC7221943 DOI: 10.3390/nano10040815] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/18/2020] [Accepted: 04/20/2020] [Indexed: 12/23/2022]
Abstract
An urgent demand exists for the development of novel delivery systems that efficiently transport antibacterial agents across cellular membranes for the eradication of intracellular pathogens. In this study, the clinically relevant poorly water-soluble antibiotic, rifampicin, was confined within mesoporous silica nanoparticles (MSN) to investigate their ability to serve as an efficacious nanocarrier system against small colony variants of Staphylococcus aureus (SCV S. aureus) hosted within Caco-2 cells. The surface chemistry and particle size of MSN were varied through modifications during synthesis, where 40 nm particles with high silanol group densities promoted enhanced cellular uptake. Extensive biophysical analysis was performed, using quartz crystal microbalance with dissipation (QCM-D) and total internal reflection fluorescence (TIRF) microscopy, to elucidate the mechanism of MSN adsorption onto semi-native supported lipid bilayers (snSLB) and, thus, uncover potential cellular uptake mechanisms of MSN into Caco-2 cells. Such studies revealed that MSN with reduced silanol group densities were prone to greater particle aggregation on snSLB, which was expected to restrict endocytosis. MSN adsorption and uptake into Caco-2 cells correlated well with antibacterial efficacy against SCV S. aureus, with 40 nm hydrophilic particles triggering a ~2.5-log greater reduction in colony forming units, compared to the pure rifampicin. Thus, this study provides evidence for the potential to design silica nanocarrier systems with controlled surface chemistries that can be used to re-sensitise intracellular bacteria to antibiotics by delivering them to the site of infection.
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Affiliation(s)
- Paul Joyce
- Department of Physics, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden; (P.J.); (S.J.); (F.H.)
| | - Hanna Ulmefors
- School of Pharmacy & Medical Sciences, University of South Australia, Adelaide, South Australia 5090, Australia; (H.U.); (S.M.); (S.S.); (A.W.)
- ARC Centre of Excellence in Bio-Nano Science and Technology, University of South Australia, Adelaide, South Australia 5090, Australia
| | - Sajedeh Maghrebi
- School of Pharmacy & Medical Sciences, University of South Australia, Adelaide, South Australia 5090, Australia; (H.U.); (S.M.); (S.S.); (A.W.)
- ARC Centre of Excellence in Bio-Nano Science and Technology, University of South Australia, Adelaide, South Australia 5090, Australia
| | - Santhni Subramaniam
- School of Pharmacy & Medical Sciences, University of South Australia, Adelaide, South Australia 5090, Australia; (H.U.); (S.M.); (S.S.); (A.W.)
- ARC Centre of Excellence in Bio-Nano Science and Technology, University of South Australia, Adelaide, South Australia 5090, Australia
| | - Anthony Wignall
- School of Pharmacy & Medical Sciences, University of South Australia, Adelaide, South Australia 5090, Australia; (H.U.); (S.M.); (S.S.); (A.W.)
- ARC Centre of Excellence in Bio-Nano Science and Technology, University of South Australia, Adelaide, South Australia 5090, Australia
| | - Silver Jõemetsa
- Department of Physics, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden; (P.J.); (S.J.); (F.H.)
| | - Fredrik Höök
- Department of Physics, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden; (P.J.); (S.J.); (F.H.)
| | - Clive A. Prestidge
- School of Pharmacy & Medical Sciences, University of South Australia, Adelaide, South Australia 5090, Australia; (H.U.); (S.M.); (S.S.); (A.W.)
- ARC Centre of Excellence in Bio-Nano Science and Technology, University of South Australia, Adelaide, South Australia 5090, Australia
- Correspondence:
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17
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Ali H, Ni H, Xu X. Near-UV luminescence tomography with an aperture-free meta super oscillatory lens for single molecule detection. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2020; 37:621-628. [PMID: 32400541 DOI: 10.1364/josaa.383854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/22/2020] [Indexed: 06/11/2023]
Abstract
Medical physics offers super oscillatory lenses (SOL) to attain subwavelength focusing for efficient image resolution in the detection of a single molecule. In this paper, we propose a negative-indexed permeability-controlled meta SOL, which restores the light concentration via exciting surface plasmon resonance and enhances luminescence at our region of interest, i.e., fluid sample (${S_L}$SL). The meta SOL is aperture-free in comparison with other techniques (zero-mode waveguides and nano antennas) and hence avoids the constraints, which are posed by nano apertures, to insert a small volume of $ S_L $SL into these nano apertures for detection purposes. The meta SOL is a unique combination of gold split rings mounted on silicon dioxide (${{\rm SiO}_2}$SiO2) substrate and operational in the near-ultraviolet (UV) region. We utilized the phenomena of negative index of refraction, and our simulated trails exploit the magnetic (${\mu _r}$μr) response of the meta SOL by analyzing its transmission spectra in the frequency range from 3.53 to 3.57 Peta Hz. We observe the methodical response of the meta SOL with its ample potential to surpass the resolution at a working wavelength of $\lambda ={84.173}\;{\rm nm}$λ=84.173nm, which enhances luminescence by restoring the evanescent UV magnetic field (${B_{\rm UV}}$BUV) at ${S_L}$SL. This technique will offer a new and easy approach to uplift the efficiency of super oscillatory lenses in the near-UV regime to benefit single molecule detection techniques and thus the novelty.
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18
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Kubota R, Nakamura K, Torigoe S, Hamachi I. The Power of Confocal Laser Scanning Microscopy in Supramolecular Chemistry: In situ Real-time Imaging of Stimuli-Responsive Multicomponent Supramolecular Hydrogels. ChemistryOpen 2020; 9:67-79. [PMID: 31988842 PMCID: PMC6967000 DOI: 10.1002/open.201900328] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/15/2019] [Indexed: 12/20/2022] Open
Abstract
Multicomponent supramolecular hydrogels are promising scaffolds for applications in biosensors and controlled drug release due to their designer stimulus responsiveness. To achieve rational construction of multicomponent supramolecular hydrogel systems, their in-depth structural analysis is essential but still challenging. Confocal laser scanning microscopy (CLSM) has emerged as a powerful tool for structural analysis of multicomponent supramolecular hydrogels. CLSM imaging enables real-time observation of the hydrogels without the need of drying and/or freezing to elucidate their static and dynamic properties. Through multiple, selective fluorescent staining of materials of interest, multiple domains formed in supramolecular hydrogels (e. g. inorganic materials and self-sorting nanofibers) can also be visualized. CLSM and the related microscopic techniques will be indispensable to investigate complex life-inspired supramolecular chemical systems.
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Affiliation(s)
- Ryou Kubota
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of EngineeringKyoto University, Nishikyo-ku, KatsuraKyoto615-8510Japan
| | - Keisuke Nakamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of EngineeringKyoto University, Nishikyo-ku, KatsuraKyoto615-8510Japan
| | - Shogo Torigoe
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of EngineeringKyoto University, Nishikyo-ku, KatsuraKyoto615-8510Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of EngineeringKyoto University, Nishikyo-ku, KatsuraKyoto615-8510Japan
- JST-ERATO, Hamachi Innovative Molecular Technology for NeuroscienceKyoto University, Nishikyo-kuKyoto615-8530Japan
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19
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Stein J, Stehr F, Schueler P, Blumhardt P, Schueder F, Mücksch J, Jungmann R, Schwille P. Toward Absolute Molecular Numbers in DNA-PAINT. NANO LETTERS 2019; 19:8182-8190. [PMID: 31535868 PMCID: PMC6856960 DOI: 10.1021/acs.nanolett.9b03546] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 09/16/2019] [Indexed: 05/17/2023]
Abstract
Single-molecule localization microscopy (SMLM) has revolutionized optical microscopy, extending resolution down to the level of individual molecules. However, the actual counting of molecules relies on preliminary knowledge of the blinking behavior of individual targets or on a calibration to a reference. In particular for biological applications, great care has to be taken because a plethora of factors influence the quality and applicability of calibration-dependent approaches to count targets in localization clusters particularly in SMLM data obtained from heterogeneous samples. Here, we present localization-based fluorescence correlation spectroscopy (lbFCS) as the first absolute molecular counting approach for DNA-points accumulation for imaging in nanoscale topography (PAINT) microscopy and, to our knowledge, for SMLM in general. We demonstrate that lbFCS overcomes the limitation of previous DNA-PAINT counting and allows the quantification of target molecules independent of the localization cluster density. In accordance with the promising results of our systematic proof-of-principle study on DNA origami structures as idealized targets, lbFCS could potentially also provide quantitative access to more challenging biological targets featuring heterogeneous cluster sizes in the future.
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Affiliation(s)
- Johannes Stein
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Florian Stehr
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Patrick Schueler
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | | | - Florian Schueder
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
- Faculty
of Physics, Ludwig Maximilian University, 80539 Munich, Germany
| | - Jonas Mücksch
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Ralf Jungmann
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
- Faculty
of Physics, Ludwig Maximilian University, 80539 Munich, Germany
| | - Petra Schwille
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
- E-mail:
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20
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Su D, Hou Y, Dong C, Ren J. Fluctuation correlation spectroscopy and its applications in homogeneous analysis. Anal Bioanal Chem 2019; 411:4523-4540. [DOI: 10.1007/s00216-019-01884-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 04/12/2019] [Accepted: 04/29/2019] [Indexed: 12/11/2022]
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21
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Tanaka W, Shigemitsu H, Fujisaku T, Kubota R, Minami S, Urayama K, Hamachi I. Post-assembly Fabrication of a Functional Multicomponent Supramolecular Hydrogel Based on a Self-Sorting Double Network. J Am Chem Soc 2019; 141:4997-5004. [PMID: 30835456 DOI: 10.1021/jacs.9b00715] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Living cells exhibit sophisticated functions because they contain numerous endogenous stimuli-responsive molecular systems that independently and cooperatively act in response to an external circumstance. On the other hand, artificial soft materials containing multiple stimuli-responsive molecular systems are still rare. Herein, we demonstrate a unique multicomponent hydrogel composed of a self-sorting double network prepared through a post-assembly fabrication (PAF) protocol. The PAF protocol allowed the construction of a well-ordered hydrogel with a dual-biomolecule response to two important biomolecules (adenosine triphosphate (ATP) and sarcosine). Such a hydrogel could not be prepared through a one-step mixing protocol. The resultant multicomponent hydrogel responded to ATP and sarcosine through gel-sol transition behavior programmed in an AND logic gate fashion. Finally, we applied the multicomponent hydrogel to the controlled release of an antibody.
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Affiliation(s)
- Wataru Tanaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering , Kyoto University , Katsura , Kyoto 615-8510 , Japan
| | - Hajime Shigemitsu
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering , Kyoto University , Katsura , Kyoto 615-8510 , Japan
| | - Takahiro Fujisaku
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering , Kyoto University , Katsura , Kyoto 615-8510 , Japan
| | - Ryou Kubota
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering , Kyoto University , Katsura , Kyoto 615-8510 , Japan
| | - Saori Minami
- Department of Macromolecular Science and Engineering , Kyoto Institute of Technology , Matsugasaki , Kyoto 606-8585 , Japan
| | - Kenji Urayama
- Department of Macromolecular Science and Engineering , Kyoto Institute of Technology , Matsugasaki , Kyoto 606-8585 , Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering , Kyoto University , Katsura , Kyoto 615-8510 , Japan.,Core Research for Evolutional Science and Technology (CREST) , Japan Science and Technology Agency (JST) , 5 Sanbancho , Chiyoda-ku , Tokyo 102-0075 , Japan
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22
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Gomes de Castro MA, Wildhagen H, Sograte-Idrissi S, Hitzing C, Binder M, Trepel M, Engels N, Opazo F. Differential organization of tonic and chronic B cell antigen receptors in the plasma membrane. Nat Commun 2019; 10:820. [PMID: 30778055 PMCID: PMC6379438 DOI: 10.1038/s41467-019-08677-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 01/24/2019] [Indexed: 11/09/2022] Open
Abstract
Stimulation of the B cell antigen receptor (BCR) triggers signaling pathways that promote the differentiation of B cells into plasma cells. Despite the pivotal function of BCR in B cell activation, the organization of the BCR on the surface of resting and antigen-activated B cells remains unclear. Here we show, using STED super-resolution microscopy, that IgM-containing BCRs exist predominantly as monomers and dimers in the plasma membrane of resting B cells, but form higher oligomeric clusters upon stimulation. By contrast, a chronic lymphocytic leukemia-derived BCR forms dimers and oligomers in the absence of a stimulus, but a single amino acid exchange reverts its organization to monomers in unstimulated B cells. Our super-resolution microscopy approach for quantitatively analyzing cell surface proteins may thus help reveal the nanoscale organization of immunoreceptors in various cell types.
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Affiliation(s)
- Maria Angela Gomes de Castro
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Hanna Wildhagen
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Shama Sograte-Idrissi
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany.,Center for Biostructural Imaging of Neurodegeneration (BIN), University of Göttingen Medical Center, von-Siebold-Straße 3a, 37075, Göttingen, Germany
| | - Christoffer Hitzing
- Institute of Cellular and Molecular Immunology, University Medical Center Göttingen, Humboldtallee 34, 37073, Göttingen, Germany
| | - Mascha Binder
- Department of Oncology and Hematology, BMT with section Pneumology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - Martin Trepel
- Department of Oncology and Hematology, BMT with section Pneumology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany.,Department of Hematology and Oncology, Augsburg Medical Center, Stenglinstr. 2, 86156, Augsburg, Germany
| | - Niklas Engels
- Institute of Cellular and Molecular Immunology, University Medical Center Göttingen, Humboldtallee 34, 37073, Göttingen, Germany.
| | - Felipe Opazo
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany. .,Center for Biostructural Imaging of Neurodegeneration (BIN), University of Göttingen Medical Center, von-Siebold-Straße 3a, 37075, Göttingen, Germany.
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23
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Niederauer C, Blumhardt P, Mücksch J, Heymann M, Lambacher A, Schwille P. Direct characterization of the evanescent field in objective-type total internal reflection fluorescence microscopy. OPTICS EXPRESS 2018; 26:20492-20506. [PMID: 30119359 DOI: 10.1364/oe.26.020492] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 07/08/2018] [Indexed: 05/22/2023]
Abstract
Total internal reflection fluorescence (TIRF) microscopy is a commonly used method for studying fluorescently labeled molecules in close proximity to a surface. Usually, the TIRF axial excitation profile is assumed to be single-exponential with a characteristic penetration depth, governed by the incident angle of the excitation laser beam towards the optical axis. However, in practice, the excitation profile does not only comprise the theoretically predicted single-exponential evanescent field, but also an additional non-evanescent contribution, supposedly caused by scattering within the optical path or optical aberrations. We developed a calibration slide to directly characterize the TIRF excitation field. Our slide features ten height steps ranging from 25 to 550 nanometers, fabricated from a polymer with a refractive index matching that of water. Fluorophores in aqueous solution above the polymer step layers sample the excitation profile at different heights. The obtained excitation profiles confirm the theoretically predicted exponential decay over increasing step heights as well as the presence of a non-evanescent contribution.
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24
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Mücksch J, Blumhardt P, Strauss MT, Petrov EP, Jungmann R, Schwille P. Quantifying Reversible Surface Binding via Surface-Integrated Fluorescence Correlation Spectroscopy. NANO LETTERS 2018; 18:3185-3192. [PMID: 29658275 PMCID: PMC5946168 DOI: 10.1021/acs.nanolett.8b00875] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/13/2018] [Indexed: 05/03/2023]
Abstract
We present a simple and versatile single-molecule-based method for the accurate determination of binding rates to surfaces or surface bound receptors. To quantify the reversible surface attachment of fluorescently labeled molecules, we have modified previous schemes for fluorescence correlation spectroscopy with total internal reflection illumination (TIR-FCS) and camera-based detection. In contrast to most modern applications of TIR-FCS, we completely disregard spatial information in the lateral direction. Instead, we perform correlation analysis on a spatially integrated signal, effectively converting the illuminated surface area into the measurement volume. In addition to providing a high surface selectivity, our new approach resolves association and dissociation rates in equilibrium over a wide range of time scales. We chose the transient hybridization of fluorescently labeled single-stranded DNA to the complementary handles of surface-immobilized DNA origami structures as a reliable and well-characterized test system. We varied the number of base pairs in the duplex, yielding different binding times in the range of hundreds of milliseconds to tens of seconds, allowing us to quantify the respective surface affinities and binding rates.
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Affiliation(s)
- Jonas Mücksch
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | | | - Maximilian T. Strauss
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
- Ludwig
Maximilian University, 80539 Munich, Germany
| | - Eugene P. Petrov
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
- Ludwig
Maximilian University, 80539 Munich, Germany
| | - Ralf Jungmann
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
- Ludwig
Maximilian University, 80539 Munich, Germany
| | - Petra Schwille
- Max
Planck Institute of Biochemistry, 82152 Martinsried, Germany
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25
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James Shirley F, Neutens P, Vos R, Mahmud-Ul-Hasan M, Lagae L, Verellen N, Van Dorpe P. Supercritical Angle Fluorescence Characterization Using Spatially Resolved Fourier Plane Spectroscopy. Anal Chem 2018. [PMID: 29528622 DOI: 10.1021/acs.analchem.7b04822] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Most fluorescent immunoassays require a wash step prior to read-out due to the otherwise overwhelming signal of the large number of unbound (bulk) fluorescent molecules that dominate over the signal from the molecules of interest, usually bound to a substrate. Supercritical angle fluorescence (SAF) sensing is one of the most promising alternatives to total internal reflection fluorescence for fluorescence imaging and sensing. However, detailed experimental investigation of the influence of collection angle on the SAF surface sensitivity, i.e., signal to background ratio (SBR), is still lacking. In this Letter, we present a novel technique that allows to discriminate the emission patterns of free and bound fluorophores simultaneously by collecting both angular and spectral information. The spectrum was probed at multiple positions in the back focal plane using a multimode fiber connected to a spectrometer and the difference in intensity between two fluorophores was used to calculate the SBR. Our study clearly reveals that increasing the angle of SAF collection enhances the surface sensitivity, albeit at the cost of decreased signal intensity. Furthermore, our findings are fully supported by full-field 3D simulations.
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Affiliation(s)
- Finub James Shirley
- KU Leuven , Laboratory of Solid-State Physics and Magnetism , Celestijnenlaan 200D , B-3001 Leuven , Belgium.,imec , Kapeldreef 75 , 3001 Heverlee , Belgium
| | | | - Rita Vos
- imec , Kapeldreef 75 , 3001 Heverlee , Belgium
| | - Md Mahmud-Ul-Hasan
- KU Leuven , Laboratory of Solid-State Physics and Magnetism , Celestijnenlaan 200D , B-3001 Leuven , Belgium.,imec , Kapeldreef 75 , 3001 Heverlee , Belgium
| | - Liesbet Lagae
- KU Leuven , Laboratory of Solid-State Physics and Magnetism , Celestijnenlaan 200D , B-3001 Leuven , Belgium.,imec , Kapeldreef 75 , 3001 Heverlee , Belgium
| | - Niels Verellen
- KU Leuven , Laboratory of Solid-State Physics and Magnetism , Celestijnenlaan 200D , B-3001 Leuven , Belgium.,imec , Kapeldreef 75 , 3001 Heverlee , Belgium
| | - Pol Van Dorpe
- KU Leuven , Laboratory of Solid-State Physics and Magnetism , Celestijnenlaan 200D , B-3001 Leuven , Belgium.,imec , Kapeldreef 75 , 3001 Heverlee , Belgium
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26
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Li H, Yang H. A versatile optical microscope for time-dependent single-molecule and single-particle spectroscopy. J Chem Phys 2018; 148:123316. [DOI: 10.1063/1.5009134] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- Hao Li
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Haw Yang
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
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27
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Shigemitsu H, Fujisaku T, Tanaka W, Kubota R, Minami S, Urayama K, Hamachi I. An adaptive supramolecular hydrogel comprising self-sorting double nanofibre networks. NATURE NANOTECHNOLOGY 2018; 13:165-172. [PMID: 29311611 DOI: 10.1038/s41565-017-0026-6] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 11/05/2017] [Indexed: 06/07/2023]
Abstract
Novel soft materials should comprise multiple supramolecular nanostructures whose responses (for example, assembly and disassembly) to external stimuli can be controlled independently. Such multicomponent systems are present in living cells and control the formation and break-up of a variety of supramolecular assemblies made of proteins, lipids, DNA and RNA in response to external stimuli; however, artificial counterparts are challenging to make. Here, we present a hybrid hydrogel consisting of a self-sorting double network of nanofibres in which each network responds to an applied external stimulus independent of the other. The hydrogel can be made to change its mechanical properties and rates of release of encapsulated proteins by adding Na2S2O4 or bacterial alkaline phosphatase. Notably, the properties of the gel depend on the order in which the external stimuli are applied. Multicomponent hydrogels comprising orthogonal stimulus-responsive supramolecular assemblies would be suitable for designing novel adaptive materials.
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Affiliation(s)
- Hajime Shigemitsu
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Takahiro Fujisaku
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Wataru Tanaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Ryou Kubota
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Saori Minami
- Department of Macromolecular Science and Engineering, Kyoto Institute of Technology, Kyoto, Japan
| | - Kenji Urayama
- Department of Macromolecular Science and Engineering, Kyoto Institute of Technology, Kyoto, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan.
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo, Japan.
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28
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Elson EL. Introduction to fluorescence correlation Spectroscopy-Brief and simple. Methods 2017; 140-141:3-9. [PMID: 29155128 DOI: 10.1016/j.ymeth.2017.11.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 11/13/2017] [Indexed: 02/04/2023] Open
Affiliation(s)
- Elliot L Elson
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA.
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29
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Weger L, Hoffmann-Jacobsen K. A total internal reflection-fluorescence correlation spectroscopy setup with pulsed diode laser excitation. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2017; 88:093102. [PMID: 28964231 DOI: 10.1063/1.4986235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 08/22/2017] [Indexed: 06/07/2023]
Abstract
Fluorescence correlation spectroscopy (FCS) measures fluctuations in a (sub-)femtoliter volume to analyze the diffusive behavior of fluorescent particles. This highly sensitive method has proven to be useful for the analysis of dynamic biological systems as well as in chemistry, physics, and material sciences. It is routinely performed with commercial fluorescence microscopes, which provide a confined observation volume by the confocal technique. The evanescent wave of total internal reflectance (TIR) is used in home-built systems to permit a surface sensitive FCS analysis. We present a combined confocal and TIR-FCS setup which uses economic low-power pulsed diode lasers for excitation. Excitation and detection are coupled to time-correlated photon counting hardware. This allows simultaneous fluorescence lifetime and FCS measurements in a surface-sensitive mode. Moreover, the setup supports fluorescence lifetime correlation spectroscopy at surfaces. The excitation can be easily switched between TIR and epi-illumination to compare the surface properties with those in liquid bulk. The capabilities of the presented setup are demonstrated by measuring the diffusion coefficients of a free dye molecule, a labeled polyethylene glycol, and a fluorescent nanoparticle in confocal as well as in TIR-FCS.
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Affiliation(s)
- Lukas Weger
- Department of Chemistry, Niederrhein University of Applied Sciences, Adlerstr. 32, 47798 Krefeld, Germany
| | - Kerstin Hoffmann-Jacobsen
- Department of Chemistry, Niederrhein University of Applied Sciences, Adlerstr. 32, 47798 Krefeld, Germany
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30
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Sly KL, Conboy JC. Second Harmonic Correlation Spectroscopy: Theory and Principles for Determining Surface Binding Kinetics. APPLIED SPECTROSCOPY 2017; 71:1368-1379. [PMID: 28534678 DOI: 10.1177/0003702816681797] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A novel application of second harmonic correlation spectroscopy (SHCS) for the direct determination of molecular adsorption and desorption kinetics to a surface is discussed in detail. The surface-specific nature of second harmonic generation (SHG) provides an efficient means to determine the kinetic rates of adsorption and desorption of molecular species to an interface without interference from bulk diffusion, which is a significant limitation of fluorescence correlation spectroscopy (FCS). The underlying principles of SHCS for the determination of surface binding kinetics are presented, including the role of optical coherence and optical heterodyne mixing. These properties of SHCS are extremely advantageous and lead to an increase in the signal-to-noise (S/N) of the correlation data, increasing the sensitivity of the technique. The influence of experimental parameters, including the uniformity of the TEM00 laser beam, the overall photon flux, and collection time are also discussed, and are shown to significantly affect the S/N of the correlation data. Second harmonic correlation spectroscopy is a powerful, surface-specific, and label-free alternative to other correlation spectroscopic methods for examining surface binding kinetics.
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Affiliation(s)
- Krystal L Sly
- Department of Chemistry, University of Utah, Utah, USA
| | - John C Conboy
- Department of Chemistry, University of Utah, Utah, USA
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31
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Li J, Dong C, Ren J. Strategies to reduce detection volume of fluorescence correlation spectroscopy (FCS) to realize physiological concentration measurements. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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32
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Wulf V, Knoch F, Speck T, Sönnichsen C. Gold Nanorods as Plasmonic Sensors for Particle Diffusion. J Phys Chem Lett 2016; 7:4951-4955. [PMID: 27934054 DOI: 10.1021/acs.jpclett.6b02165] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Plasmonic gold nanoparticles are normally used as sensor to detect analytes permanently bound to their surface. If the interaction between the analyte and the nanosensor surface is negligible, it only diffuses through the sensor's sensing volume, causing a small temporal shift of the plasmon resonance position. By using a very sensitive and fast detection scheme, we are able to detect these small fluctuations in the plasmon resonance. With the help of a theoretical model consistent with our detection geometry, we determine the analyte's diffusion coefficient. The method is verified by observing the trends upon changing diffusor size and medium viscosity, and the diffusion coefficients obtained were found to reflect reduced diffusion close to a solid interface. Our method, which we refer to as NanoPCS (for nanoscale plasmon correlation spectroscopy), is of practical importance for any application involving the diffusion of analytes close to nanoparticles.
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Affiliation(s)
- Verena Wulf
- Institute of Physical Chemistry and ‡Institute of Physics, University of Mainz , D-55128 Mainz, Germany
| | - Fabian Knoch
- Institute of Physical Chemistry and ‡Institute of Physics, University of Mainz , D-55128 Mainz, Germany
| | - Thomas Speck
- Institute of Physical Chemistry and ‡Institute of Physics, University of Mainz , D-55128 Mainz, Germany
| | - Carsten Sönnichsen
- Institute of Physical Chemistry and ‡Institute of Physics, University of Mainz , D-55128 Mainz, Germany
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33
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Borejdo J, Talent J, Akopova I. Measuring Rotations of a Few Cross-Bridges in Skeletal Muscle. Exp Biol Med (Maywood) 2016; 231:28-38. [PMID: 16380642 DOI: 10.1177/153537020623100104] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The ability to measure properties of a single cross-bridge in working muscle is important because it avoids averaging the signal from a large number of molecules and because it probes cross-bridges in their native crowded environment. Because the concentration of myosin in muscle is large, observing the kinetics of a single myosin molecule requires that the signal be collected from small volumes. The introduction of small observational volumes defined by diffraction-limited laser beams and confocal detection has made it possible to limit the observational volume to a femtoliter (10 15 liter). By restraining labeling to 1 fluorophore per 100 myosin molecules, we were able to follow the kinetics of approximately 400 cross-bridges. To reduce this number further, we used two-photon (2P) microscopy. The focal plane in which the laser power density was high enough to produce 2P absorption was thinner than in confocal microscopy. Using 2P microscopy, we were able to observe approximately 200 cross-bridges during contraction. The novel method of confocal total internal reflection (CTIR) provides a method to reduce the observational volume even further, to approximately 1 attoliter (10 18 liter), and to measure fluorescence with a high signal-to-noise (S/N) ratio. In this method, the observational volume is made shallow by illuminating the sample with an evanescent field produced by total internal reflection (TIR) of the incident laser beam. To guarantee the small lateral dimensions of the observational volume, a confocal aperture is inserted in the conjugate-image plane of the objective. With a 3.5-μm confocal aperture, we achieved a volume of 1.5 attoliter. Association-dissociation of the myosin head was probed with rhodamine attached at cys707 of the heavy chain of myosin. Signal was contributed by one to five fluorescent myosin molecules. Fluorescence decayed in a series of discrete steps, corresponding to bleaching of individual molecules of rhodamine. The S/N ratio was sufficiently large to make statistically significant comparisons from rigor and contracting myofibrils.
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Affiliation(s)
- Julian Borejdo
- Department of Molecular Biology and Immunology, University of North Texas, Fort Worth, TX 76107, USA.
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34
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In situ real-time imaging of self-sorted supramolecular nanofibres. Nat Chem 2016; 8:743-52. [PMID: 27442279 DOI: 10.1038/nchem.2526] [Citation(s) in RCA: 160] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 04/13/2016] [Indexed: 12/22/2022]
Abstract
Self-sorted supramolecular nanofibres-a multicomponent system that consists of several types of fibre, each composed of distinct building units-play a crucial role in complex, well-organized systems with sophisticated functions, such as living cells. Designing and controlling self-sorting events in synthetic materials and understanding their structures and dynamics in detail are important elements in developing functional artificial systems. Here, we describe the in situ real-time imaging of self-sorted supramolecular nanofibre hydrogels consisting of a peptide gelator and an amphiphilic phosphate. The use of appropriate fluorescent probes enabled the visualization of self-sorted fibres entangled in two and three dimensions through confocal laser scanning microscopy and super-resolution imaging, with 80 nm resolution. In situ time-lapse imaging showed that the two types of fibre have different formation rates and that their respective physicochemical properties remain intact in the gel. Moreover, we directly visualized stochastic non-synchronous fibre formation and observed a cooperative mechanism.
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35
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Alam MS, Karim F, Zhao C. Single-molecule detection at high concentrations with optical aperture nanoantennas. NANOSCALE 2016; 8:9480-9487. [PMID: 27120086 DOI: 10.1039/c6nr01645f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Single-molecule detection has become an indispensable technology in life science, and medical research. In order to get meaningful information on many biological processes, single-molecule analysis is required in micro-molar concentrations. At such high concentrations, it is very challenging to isolate a single molecule with conventional diffraction-limited optics. Recently, optical aperture nanoantennas (OANs) have emerged as a powerful tool to enhance the single-molecule detection under a physiological environment. The OANs, which consist of nano-scale apertures on a metallic film, have the following unique properties: (1) nanoscale light confinement; (2) enhanced fluorescence emission; (3) tunable radiation pattern; (4) reduced background noise; and (5) massive parallel detection. This review presents the fundamentals, recent developments and future perspectives in this emerging field.
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Affiliation(s)
- Md Shah Alam
- Electro-Optics Program, University of Dayton, 300 College Park, Dayton, Ohio 45469-2314, USA.
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36
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Superresolution microscopy with transient binding. Curr Opin Biotechnol 2016; 39:8-16. [PMID: 26773299 DOI: 10.1016/j.copbio.2015.12.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/12/2015] [Accepted: 12/16/2015] [Indexed: 01/05/2023]
Abstract
For single-molecule localization based superresolution, the concentration of fluorescent labels has to be thinned out. This is commonly achieved by photophysically or photochemically deactivating subsets of molecules. Alternatively, apparent switching of molecules can be achieved by transient binding of fluorescent labels. Here, a diffusing dye yields bright fluorescent spots when binding to the structure of interest. As the binding interaction is weak, the labeling is reversible and the dye ligand construct diffuses back into solution. This approach of achieving superresolution by transient binding (STB) is reviewed in this manuscript. Different realizations of STB are discussed and compared to other localization-based superresolution modalities. We propose the development of labeling strategies that will make STB a highly versatile tool for superresolution microscopy at highest resolution.
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37
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Cherney LT, Petrov AP, Krylov SN. One-Dimensional Approach to Study Kinetics of Reversible Binding of Protein on Capillary Walls. Anal Chem 2015; 87:1219-25. [DOI: 10.1021/ac503880j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Leonid T. Cherney
- Department of Chemistry and Centre for Research on Biomolecular
Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Alexander P. Petrov
- Department of Chemistry and Centre for Research on Biomolecular
Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Sergey N. Krylov
- Department of Chemistry and Centre for Research on Biomolecular
Interactions, York University, Toronto, Ontario M3J 1P3, Canada
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38
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Cherney LT, Krylov SN. Slow-equilibration approximation in studying kinetics of protein adsorption on capillary walls. Analyst 2015; 140:2797-803. [DOI: 10.1039/c4an02380c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A slow-equilibration approximation and a new parameter-based approach to studying protein adsorption in capillary electrophoresis are developed.
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Affiliation(s)
- Leonid T. Cherney
- Department of Chemistry and Centre for Research on Biomolecular Interactions
- York University
- Toronto
- Canada M3J 1P3
| | - Sergey N. Krylov
- Department of Chemistry and Centre for Research on Biomolecular Interactions
- York University
- Toronto
- Canada M3J 1P3
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39
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Knight AE. Single-molecule fluorescence imaging by total internal reflection fluorescence microscopy (IUPAC Technical Report). PURE APPL CHEM 2014. [DOI: 10.1515/pac-2012-0605] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractTotal internal reflection fluorescence (TIRF) is a popular illumination technique in microscopy, with many applications in cell and molecular biology and biophysics. The chief advantage of the technique is the high contrast that can be achieved by restricting fluorescent excitation to a thin layer. We summarise the optical theory needed to understand the technique and various aspects required for a practical implementation of it, including the merits of different TIRF geometries. Finally, we discuss a variety of applications including super-resolution microscopy and high-throughput DNA sequencing technologies.
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Affiliation(s)
- Alex E. Knight
- 1Analytical Science Division, National Physical Laboratory, Hampton Road, Teddington, Middlesex, TW11 0LW, UK
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40
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Cooper JT, Harris JM. Imaging Fluorescence-Correlation Spectroscopy for Measuring Fast Surface Diffusion at Liquid/Solid Interfaces. Anal Chem 2014; 86:7618-26. [DOI: 10.1021/ac5014354] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Justin T. Cooper
- Department
of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0805, United States
| | - Joel M. Harris
- Department
of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0805, United States
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41
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Weiss AN, Bittner MA, Holz RW, Axelrod D. Protein mobility within secretory granules. Biophys J 2014; 107:16-25. [PMID: 24988337 PMCID: PMC4478961 DOI: 10.1016/j.bpj.2014.04.063] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 02/14/2014] [Accepted: 04/11/2014] [Indexed: 10/25/2022] Open
Abstract
We investigated the basis for previous observations that fluorescent-labeled neuropeptide Y (NPY) is usually released within 200 ms after fusion, whereas labeled tissue plasminogen activator (tPA) is often discharged over many seconds. We found that tPA and NPY are endogenously expressed in small and different subpopulations of bovine chromaffin cells in culture. We measured the mobility of these proteins (tagged with fluorophore) within the lumen of individual secretory granules in living chromaffin cells, and related their mobilities to postfusion release kinetics. A method was developed that is not limited by standard optical resolution, in which a bright flash of strongly decaying evanescent field (∼64 nm exponential decay constant) produced by total internal reflection (TIR) selectively bleaches cerulean-labeled protein proximal to the glass coverslip within individual granules. Fluorescence recovery occurred as unbleached protein from distal regions within the 300 nm granule diffused into the bleached proximal regions. The fractional bleaching of tPA-cerulean (tPA-cer) was greater when subsequently probed with TIR excitation than with epifluorescence, indicating that tPA-cer mobility was low. The almost equal NPY-cer bleaching when probed with TIR and epifluorescence indicated that NPY-cer equilibrated within the 300 ms bleach pulse, and therefore had a greater mobility than tPA-cer. TIR-fluorescence recovery after photobleaching revealed a significant recovery of tPA-cer (but not NPY-cer) fluorescence within several hundred milliseconds after bleaching. Numerical simulations, which take into account bleach duration, granule diameter, and the limited number of fluorophores in a granule, are consistent with tPA-cer being 100% mobile, with a diffusion coefficient of 2 × 10(-10) cm(2)/s (∼1/3000 of that for a protein of similar size in aqueous solution). However, the low diffusive mobility of tPA cannot alone explain its slow postfusion release. In the accompanying study, we suggest that, additionally, tPA itself stabilizes the fusion pore with dimensions that restrict its own exit.
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Affiliation(s)
| | - Mary A Bittner
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan
| | - Ronald W Holz
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan.
| | - Daniel Axelrod
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan; Department of Physics and LSA Biophysics, University of Michigan, Ann Arbor, Michigan
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42
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Turunen P, Rowan AE, Blank K. Single-enzyme kinetics with fluorogenic substrates: lessons learnt and future directions. FEBS Lett 2014; 588:3553-63. [DOI: 10.1016/j.febslet.2014.06.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 06/04/2014] [Accepted: 06/05/2014] [Indexed: 01/05/2023]
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43
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Sahl SJ, Leutenegger M, Hell SW, Eggeling C. High-resolution tracking of single-molecule diffusion in membranes by confocalized and spatially differentiated fluorescence photon stream recording. Chemphyschem 2014; 15:771-83. [PMID: 24596277 DOI: 10.1002/cphc.201301090] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Indexed: 01/26/2023]
Abstract
The performance of a method is assessed which allows for the spatiotemporal tracking of single dye-labeled molecules during two-dimensional (2D) diffusional transits through the focal area of a modified confocal microscope. In addition to facilitating the observation of molecular diffusion paths at the shot-noise limit of bright organic emitters with spatial and temporal precisions of ∼10-20 nm and <0.5 ms, respectively, the direct access to the complete stream of detected photons is beneficial for characterizing nanoscale details such as transient pausing (binding). We discuss technical aspects of this approach, along with results from its application to measuring lipid membrane dynamics in live mammalian cells. Presented topics include a discussion of the advantages of the single-photon collection mode and instrument as well as computational considerations for the localization process. A proof-of-principle experiment shows that optical nanoscopy by stochastic single-molecule switching and position readout could be implementable in parallel with such fast molecular tracking. This would allow direct access to contextual imaging data of local cytoskeletal structural elements or localized longer-lived protein assemblies.
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Affiliation(s)
- Steffen J Sahl
- Department of Chemistry, Stanford University, Stanford, CA 94305 (USA)
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44
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Traylor SJ, Bowes BD, Ammirati AP, Timmick SM, Lenhoff AM. Fluorescence recovery after photobleaching investigation of protein transport and exchange in chromatographic media. J Chromatogr A 2014; 1340:33-49. [PMID: 24685162 DOI: 10.1016/j.chroma.2014.02.072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 02/21/2014] [Accepted: 02/25/2014] [Indexed: 11/29/2022]
Abstract
A fully-mechanistic understanding of protein transport and sorption in chromatographic materials has remained elusive despite the application of modern continuum and molecular observation techniques. While measuring overall uptake rates in proteins in chromatographic media is relatively straightforward, quantifying mechanistic contributions is much more challenging. Further, at equilibrium in fully-loaded particles, measuring rates of kinetic exchange and diffusion can be very challenging. As models of multicomponent separations rely on accurate depictions of protein displacement and elution, a straightforward method is desired to measure the mobility of bound protein in chromatographic media. We have adapted fluorescence recovery after photobleaching (FRAP) methods to study transport and exchange of protein at equilibrium in a single particle. Further, we have developed a mathematical model to capture diffusion and desorption rates governing fluorescence recovery and investigate how these rates vary as a function of protein size, binding strength and media type. An emphasis is placed on explaining differences between polymer-modified and traditional media, which in the former case is characterized by rapid uptake, slow displacement and large elution pools, differences that have been postulated to result from steric and kinetic limitations. Finally, good qualitative agreement is achieved predicting flow confocal displacement profiles in polymer-modified materials, based solely on estimates of kinetic and diffusion parameters from FRAP observations.
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Affiliation(s)
- Steven J Traylor
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
| | - Brian D Bowes
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
| | - Anthony P Ammirati
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
| | - Steven M Timmick
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
| | - Abraham M Lenhoff
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA.
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45
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Brandão HB, Sangji H, Pandžić E, Bechstedt S, Brouhard GJ, Wiseman PW. Measuring ligand–receptor binding kinetics and dynamics using k-space image correlation spectroscopy. Methods 2014; 66:273-82. [DOI: 10.1016/j.ymeth.2013.07.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Revised: 07/25/2013] [Accepted: 07/27/2013] [Indexed: 10/26/2022] Open
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46
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Woods DA, Bain CD. Total internal reflection spectroscopy for studying soft matter. SOFT MATTER 2014; 10:1071-1096. [PMID: 24651911 DOI: 10.1039/c3sm52817k] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Total internal reflection (TIR) spectroscopy is a widely used technique to study soft matter at interfaces. This tutorial review aims to provide researchers with an overview of the principles, experimental design and applications of TIR spectroscopy to enable them to understand how this class of techniques might be used in their research. It also highlights limitations and pitfalls of TIR techniques, which will assist readers in critically analysing the literature. Techniques covered include attenuated total reflection infrared spectroscopy (ATR-IR), TIR fluorescence, TIR Raman scattering and cavity-enhanced techniques. Other related techniques are briefly described.
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Affiliation(s)
- David A Woods
- Department of Chemistry, Durham University, South Road, Durham, UKDH1 3LE.
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47
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Punj D, Ghenuche P, Moparthi SB, de Torres J, Grigoriev V, Rigneault H, Wenger J. Plasmonic antennas and zero-mode waveguides to enhance single molecule fluorescence detection and fluorescence correlation spectroscopy toward physiological concentrations. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2014; 6:268-82. [DOI: 10.1002/wnan.1261] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Deep Punj
- CNRS, Aix Marseille Université, Centrale Marseille, Institut Fresnel; UMR 7249; 13013 Marseille France
| | - Petru Ghenuche
- CNRS, Aix Marseille Université, Centrale Marseille, Institut Fresnel; UMR 7249; 13013 Marseille France
| | - Satish Babu Moparthi
- CNRS, Aix Marseille Université, Centrale Marseille, Institut Fresnel; UMR 7249; 13013 Marseille France
| | - Juan de Torres
- CNRS, Aix Marseille Université, Centrale Marseille, Institut Fresnel; UMR 7249; 13013 Marseille France
| | - Victor Grigoriev
- CNRS, Aix Marseille Université, Centrale Marseille, Institut Fresnel; UMR 7249; 13013 Marseille France
| | - Hervé Rigneault
- CNRS, Aix Marseille Université, Centrale Marseille, Institut Fresnel; UMR 7249; 13013 Marseille France
| | - Jérôme Wenger
- CNRS, Aix Marseille Université, Centrale Marseille, Institut Fresnel; UMR 7249; 13013 Marseille France
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48
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Liu H, Dong C, Ren J. Tempo-Spatially Resolved Scattering Correlation Spectroscopy under Dark-Field Illumination and Its Application to Investigate Dynamic Behaviors of Gold Nanoparticles in Live Cells. J Am Chem Soc 2014; 136:2775-85. [DOI: 10.1021/ja410284j] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Heng Liu
- College of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiaotong University, Shanghai 200240, People’s Republic of China
| | - Chaoqing Dong
- College of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiaotong University, Shanghai 200240, People’s Republic of China
| | - Jicun Ren
- College of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiaotong University, Shanghai 200240, People’s Republic of China
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49
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50
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Otero C, Linke M, Sanchez P, González A, Schaap IAT. Propranolol restricts the mobility of single EGF-receptors on the cell surface before their internalization. PLoS One 2013; 8:e83086. [PMID: 24349439 PMCID: PMC3857351 DOI: 10.1371/journal.pone.0083086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 10/30/2013] [Indexed: 12/02/2022] Open
Abstract
The epidermal growth factor receptor is involved in morphogenesis, proliferation and cell migration. Its up-regulation during tumorigenesis makes this receptor an interesting therapeutic target. In the absence of the ligand, the inhibition of phosphatidic acid phosphohydrolase activity by propranolol treatment leads to internalization of empty/inactive receptors. The molecular events involved in this endocytosis remain unknown. Here, we quantified the effects of propranolol on the mobility of single quantum-dot labelled receptors before the actual internalization took place. The single receptors showed a clear stop-and-go motion; their diffusive tracks were continuously interrupted by sub-second stalling events, presumably caused by transient clustering. In the presence of propranolol we found that: i) the diffusion rate reduced by 22 %, which indicates an increase in drag of the receptor. Atomic force microscopy measurements did not show an increase of the effective membrane tension, such that clustering of the receptor remains the likely mechanism for its reduced mobility. ii) The receptor got frequently stalled for longer periods of multiple seconds, which may signal the first step of the internalization process.
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Affiliation(s)
- Carolina Otero
- Center for Integrative Medicine and Innovative Science (CIMIS), Universidad Andres Bello, Santiago, Chile ; Centro para el Desarrollo de la Nanociencia y Nanotecnologia, Santiago, Chile
| | - Max Linke
- III. Physikalisches Institut, Faculty of Physics, Georg-August Universität, Göttingen, Germany
| | - Paula Sanchez
- III. Physikalisches Institut, Faculty of Physics, Georg-August Universität, Göttingen, Germany ; Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany
| | - Alfonso González
- Departamento de Inmunología Clínica y Reumatología, Facultad de Medicina and Centro de Envejecimiento y Regeneración, Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Iwan A T Schaap
- III. Physikalisches Institut, Faculty of Physics, Georg-August Universität, Göttingen, Germany ; Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany
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