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Cao X, Wang W, Jiang Y, Feng W, Xu S, Xu W, Zhang W. An atomic force microscopy and total internal reflection fluorescence microscopy correlated system (AFM-TIRF) for fluorescence imaging and spectroscopy of a single particle. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2024; 95:073706. [PMID: 38995931 DOI: 10.1063/5.0210704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 06/25/2024] [Indexed: 07/14/2024]
Abstract
Combining atomic force microscopy (AFM) with other optical microscopic techniques is pivotal in nanoscale investigations, particularly leveraging the surface-sensitive properties of total internal reflection fluorescence microscopy (TIRF). A novel design that integrates AFM with a multi-wavelength TIRF is displayed, providing simultaneous fluorescence imaging and spectral acquisition capabilities. We elaborate on the considerations in the instrument design process and demonstrate the performance and potential applications of the instrument through fluorescence imaging and spectroscopy testing of individual nanoparticles. This AFM and TIRF correlated system (AFM-TIRF) emerges as a promising option for single-molecule fluorescence studies, enabling simultaneous manipulation and detection of fluorescence from individual molecules.
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Affiliation(s)
- Xiumian Cao
- College of Physics, Jilin University, Changchun 130012, People's Republic of China
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, People's Republic of China
| | - Wenquan Wang
- College of Physics, Jilin University, Changchun 130012, People's Republic of China
| | - Yuanfei Jiang
- Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012, People's Republic of China
| | - Wei Feng
- Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012, People's Republic of China
| | - Shuping Xu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, People's Republic of China
- Center for Supramolecular Chemical Biology, College of Chemistry, Jilin University, Changchun 130012, People's Republic of China
| | - Weiqing Xu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, People's Republic of China
| | - Wenke Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, People's Republic of China
- Center for Supramolecular Chemical Biology, College of Chemistry, Jilin University, Changchun 130012, People's Republic of China
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2
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Rahman M, Islam KR, Islam MR, Islam MJ, Kaysir MR, Akter M, Rahman MA, Alam SMM. A Critical Review on the Sensing, Control, and Manipulation of Single Molecules on Optofluidic Devices. MICROMACHINES 2022; 13:968. [PMID: 35744582 PMCID: PMC9229244 DOI: 10.3390/mi13060968] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 02/06/2023]
Abstract
Single-molecule techniques have shifted the paradigm of biological measurements from ensemble measurements to probing individual molecules and propelled a rapid revolution in related fields. Compared to ensemble measurements of biomolecules, single-molecule techniques provide a breadth of information with a high spatial and temporal resolution at the molecular level. Usually, optical and electrical methods are two commonly employed methods for probing single molecules, and some platforms even offer the integration of these two methods such as optofluidics. The recent spark in technological advancement and the tremendous leap in fabrication techniques, microfluidics, and integrated optofluidics are paving the way toward low cost, chip-scale, portable, and point-of-care diagnostic and single-molecule analysis tools. This review provides the fundamentals and overview of commonly employed single-molecule methods including optical methods, electrical methods, force-based methods, combinatorial integrated methods, etc. In most single-molecule experiments, the ability to manipulate and exercise precise control over individual molecules plays a vital role, which sometimes defines the capabilities and limits of the operation. This review discusses different manipulation techniques including sorting and trapping individual particles. An insight into the control of single molecules is provided that mainly discusses the recent development of electrical control over single molecules. Overall, this review is designed to provide the fundamentals and recent advancements in different single-molecule techniques and their applications, with a special focus on the detection, manipulation, and control of single molecules on chip-scale devices.
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Affiliation(s)
- Mahmudur Rahman
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Kazi Rafiqul Islam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Rashedul Islam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Jahirul Islam
- Department of Electrical and Electronic Engineering, Khulna University of Engineering & Technology, Khulna 9203, Bangladesh;
| | - Md. Rejvi Kaysir
- Department of Electrical and Computer Engineering, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada;
- Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada
| | - Masuma Akter
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Arifur Rahman
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - S. M. Mahfuz Alam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
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Cai N, Lai ACK, Liao K, Corridon PR, Graves DJ, Chan V. Recent Advances in Fluorescence Recovery after Photobleaching for Decoupling Transport and Kinetics of Biomacromolecules in Cellular Physiology. Polymers (Basel) 2022; 14:1913. [PMID: 35567083 PMCID: PMC9105003 DOI: 10.3390/polym14091913] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [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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Affiliation(s)
- Ning Cai
- Wuhan Institute of Technology, School of Chemical Engineering and Pharmacy, Wuhan 430073, China;
| | - Alvin Chi-Keung Lai
- Department of Architecture and Civil Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong 999077, China;
| | - Kin Liao
- Department of Aerospace Engineering, Khalifa University of Science and Technology, Abu Dhabi P.O. Box 127788, United Arab Emirates;
| | - Peter R. Corridon
- Department of Physiology and Immunology, Khalifa University of Science and Technology, Abu Dhabi P.O. Box 127788, United Arab Emirates;
- Healthcare Engineering Innovation Center, Khalifa University of Science and Technology, Abu Dhabi P.O. Box 127788, United Arab Emirates
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi P.O. Box 127788, United Arab Emirates
| | - David J. Graves
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA;
| | - Vincent Chan
- Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi P.O. Box 127788, United Arab Emirates
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Ulmefors H, Nissa J, Pace H, Wahlsten O, Gunnarsson A, Simon DT, Berggren M, Höök F. Formation of Supported Lipid Bilayers Derived from Vesicles of Various Compositional Complexity on Conducting Polymer/Silica Substrates. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:5494-5505. [PMID: 33929845 PMCID: PMC8280725 DOI: 10.1021/acs.langmuir.1c00175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 04/26/2021] [Indexed: 05/30/2023]
Abstract
Supported lipid bilayers (SLBs) serve important roles as minimalistic models of cellular membranes in multiple diagnostic and pharmaceutical applications as well as in the strive to gain fundamental insights about their complex biological function. To further expand the utility of SLBs, there is a need to go beyond simple lipid compositions to thereby better mimic the complexity of native cell membranes, while simultaneously retaining their compatibility with a versatile range of analytical platforms. To meet this demand, we have in this work explored SLB formation on PEDOT:PSS/silica nanoparticle composite films and mesoporous silica films, both capable of transporting ions to an underlying conducting PEDOT:PSS film. The SLB formation process was evaluated by using the quartz crystal microbalance with dissipation (QCM-D) monitoring, total internal reflection fluorescence (TIRF) microscopy, and fluorescence recovery after photobleaching (FRAP) for membranes made of pure synthetic lipids with or without the reconstituted membrane protein β-secretase 1 (BACE1) as well as cell-derived native lipid vesicles containing overexpressed BACE1. The mesoporous silica thin film was superior to the PEDOT:PSS/silica nanoparticle composite, providing successful formation of bilayers with high lateral mobility and low defect density even for the most complex native cell membranes.
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Affiliation(s)
- Hanna Ulmefors
- Division
of Nano and Biological Physics, Department of Physics, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Josefin Nissa
- Laboratory
of Organic Electronics, Department of Science and Technology, Linköping University, 601 74 Norrköping, Sweden
| | - Hudson Pace
- Division
of Nano and Biological Physics, Department of Physics, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Olov Wahlsten
- Division
of Nano and Biological Physics, Department of Physics, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Anders Gunnarsson
- Discovery
Sciences, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - Daniel T. Simon
- Laboratory
of Organic Electronics, Department of Science and Technology, Linköping University, 601 74 Norrköping, Sweden
| | - Magnus Berggren
- Laboratory
of Organic Electronics, Department of Science and Technology, Linköping University, 601 74 Norrköping, Sweden
| | - Fredrik Höök
- Division
of Nano and Biological Physics, Department of Physics, Chalmers University of Technology, 412 96 Gothenburg, Sweden
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5
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Luo F, Qin G, Xia T, Fang X. Single-Molecule Imaging of Protein Interactions and Dynamics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2020; 13:337-361. [PMID: 32228033 DOI: 10.1146/annurev-anchem-091619-094308] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Live-cell single-molecule fluorescence imaging has become a powerful analytical tool to investigate cellular processes that are not accessible to conventional biochemical approaches. This has greatly enriched our understanding of the behaviors of single biomolecules in their native environments and their roles in cellular events. Here, we review recent advances in fluorescence-based single-molecule bioimaging of proteins in living cells. We begin with practical considerations of the design of single-molecule fluorescence imaging experiments such as the choice of imaging modalities, fluorescent probes, and labeling methods. We then describe analytical observables from single-molecule data and the associated molecular parameters along with examples of live-cell single-molecule studies. Lastly, we discuss computational algorithms developed for single-molecule data analysis.
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Affiliation(s)
- Fang Luo
- Beijing National Research Center for Molecular Sciences, CAS Key Laboratory of Molecule Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China;
- Department of Chemistry, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Gege Qin
- Beijing National Research Center for Molecular Sciences, CAS Key Laboratory of Molecule Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China;
- Department of Chemistry, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Tie Xia
- School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiaohong Fang
- Beijing National Research Center for Molecular Sciences, CAS Key Laboratory of Molecule Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China;
- Department of Chemistry, University of the Chinese Academy of Sciences, Beijing 100049, China
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6
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Kurniawan J, Ventrici de Souza JF, Dang AT, Liu GY, Kuhl TL. Preparation and Characterization of Solid-Supported Lipid Bilayers Formed by Langmuir-Blodgett Deposition: A Tutorial. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:15622-15639. [PMID: 30465730 DOI: 10.1021/acs.langmuir.8b03504] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The structure, phase behavior, and properties of cellular membranes are derived from their composition, which includes phospholipids, sphingolipids, sterols, and proteins with various levels of glycosylation. Because of the intricate nature of cellular membranes, a plethora of in vitro studies have been carried out with model membrane systems that capture particular properties such as fluidity, permeability, and protein binding but vastly simplify the membrane composition in order to focus in detail on a specialized property or function. Supported lipid bilayers (SLB) are widely used as archetypes for cellular membranes, and this instructional review primarily focuses on the preparation and characterization of SLB systems formed by Langmuir deposition methods. Typical characterization methods, which take advantage of the planar orientation of SLBs, are illustrated, and references that go into more depth are included. This invited instructional review is written so that nonexperts can quickly gain in-depth knowledge regarding the preparation and characterization of SLBs. In addition, this work goes beyond traditional instructional reviews to provide expert readers with new results that cover a wider range of SLB systems than those previously reported in the literature. The quality of an SLB is frequently not well described, and details such as topological defects can influence the results and conclusions of an individual study. This article quantifies and compares the quality of SLBs fabricated from a variety of gel and fluid compositions, in correlation with preparation techniques and parameters, to generate general rules of thumb to guide the construction of designed SLB systems.
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7
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Zhao R, Li N, Xu J, Li W, Fang X. Quantitative single-molecule study of TGF-β/Smad signaling. Acta Biochim Biophys Sin (Shanghai) 2018; 50:51-59. [PMID: 29190315 DOI: 10.1093/abbs/gmx121] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/03/2017] [Indexed: 12/31/2022] Open
Abstract
TGF-β/Smad signaling pathway triggers diverse cellular responses among different cell types and environmental conditions. Quantitative analysis of protein-protein interactions involved in TGF-β/Smad signaling is demanded for understanding the molecular mechanism of this signaling pathway. Live-cell single-molecule microcopy with high spatiotemporal resolution is a new tool to monitor key molecular events in a real-time manner. In this review, we mainly presented the recent work on the quantitative characterization of TGF-β/Smad signaling proteins by single-molecule method, and showed how it enabled us to obtain new insights about this canonical signaling process.
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Affiliation(s)
- Rong Zhao
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nan Li
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiachao Xu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenhui Li
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaohong Fang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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8
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Li N, Zhao R, Sun Y, Ye Z, He K, Fang X. Single-molecule imaging and tracking of molecular dynamics in living cells. Natl Sci Rev 2017. [DOI: 10.1093/nsr/nww055] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Abstract
Unlike the ensemble-averaging measurements, the single-molecule imaging and tracking (SMIT) in living cells provides the real-time quantitative information about the locations, kinetics, dynamics and interactions of individual molecules in their native environments with high spatiotemporal resolution and minimal perturbation. The past decade has witnessed a transforming development in the methods of SMIT with living cells, including fluorescent probes, labeling strategies, fluorescence microscopy, and detection and tracking algorithms. In this review, we will discuss these aspects with a particular focus on their recent advancements. We will then describe representative single-molecule studies to illustrate how the single-molecule approaches can be applied to monitor biomolecular interaction/reaction dynamics, and extract the molecular mechanistic information for different cellular systems.
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Affiliation(s)
- Nan Li
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rong Zhao
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yahong Sun
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zi Ye
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kangmin He
- Department of Cell Biology, Harvard Medical School, and Cellular and Molecular Medicine Program, Boston Children's Hospital, Boston, MA 02115, USA
| | - Xiaohong Fang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Mantil E, Crippin T, Ianoul A, Avis TJ. Experimental Parameters Leading to Optimal Bilayers for Total Internal Reflection Fluorescence Microscopy Visualization. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2017; 23:97-112. [PMID: 28228172 DOI: 10.1017/s1431927617000083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Supported lipid bilayer systems were evaluated following various experimental procedures in an effort to determine their appropriateness for visualization using total internal reflection fluorescence (TIRF) microscopy. The incorporation and distribution of Texas Red® 1,2-dihexadecanoyl-sn-glycero-3-phosphoethanolamine (TR-DHPE) was studied when incorporated into bilayers of variable lipid composition using different forms of mechanical shearing. Results showed that 0.8 mol% TR-DHPE provides the most optimum TIRF images. At this concentration, a sufficient level of photostability can be achieved without an undesirable increase in TR-DHPE aggregates caused by excess probe molecules. Solutions composed of a 3:1 molar ratio of DOPC:DPPC with 0.8 mol% TR-DHPE produce bilayers that consistently display clear, distinct, rounded domains, whereas other lipid compositions did not. This optimum phase separation appears to be influenced by an increase in mechanical shearing during the vesicle formation process, when the lipid solutions were exposed to sonication and extrusion processes. The combination of a sonication and extrusion process also helped with eliminating the presence of TR-DHPE aggregates within the model membranes. It was also shown that bilayers formed on conditioned glass, placed on a slide, produced more highly detailed bilayers in which distinct lipid phase separation could be optimally visualized using TIRF microscopy.
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Affiliation(s)
- Elisabeth Mantil
- 1Department of Chemistry,Carleton University,1125 Colonel By Drive,Ottawa,ON K1S 5B6,Canada
| | - Trinda Crippin
- 2Department of Biology,Carleton University,1125 Colonel By Drive,Ottawa,ON K1S 5B6,Canada
| | - Anatoli Ianoul
- 1Department of Chemistry,Carleton University,1125 Colonel By Drive,Ottawa,ON K1S 5B6,Canada
| | - Tyler J Avis
- 1Department of Chemistry,Carleton University,1125 Colonel By Drive,Ottawa,ON K1S 5B6,Canada
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10
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Probing the dynamics of growth factor receptor by single-molecule fluorescence imaging. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 118:95-102. [DOI: 10.1016/j.pbiomolbio.2015.04.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 04/22/2015] [Accepted: 04/24/2015] [Indexed: 12/14/2022]
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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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12
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Liu P, Wang X, Itano MS, Neumann AK, de Silva AM, Jacobson K, Thompson NL. Low copy numbers of DC-SIGN in cell membrane microdomains: implications for structure and function. Traffic 2013; 15:179-96. [PMID: 24313910 DOI: 10.1111/tra.12138] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 11/07/2013] [Accepted: 11/11/2013] [Indexed: 12/17/2022]
Abstract
Presently, there are few estimates of the number of molecules occupying membrane domains. Using a total internal reflection fluorescence microscopy (TIRFM) imaging approach, based on comparing the intensities of fluorescently labeled microdomains with those of single fluorophores, we measured the occupancy of DC-SIGN, a C-type lectin, in membrane microdomains. DC-SIGN or its mutants were labeled with primary monoclonal antibodies (mAbs) in either dendritic cells (DCs) or NIH3T3 cells, or expressed as GFP fusions in NIH3T3 cells. The number of DC-SIGN molecules per microdomain ranges from only a few to over 20, while microdomain dimensions range from the diffraction limit to > 1 µm. The largest fraction of microdomains, appearing at the diffraction limit, in either immature DCs or 3 T3 cells contains only 4-8 molecules of DC-SIGN, consistent with our preliminary super-resolution Blink microscopy estimates. We further show that these small assemblies are sufficient to bind and efficiently internalize a small (∼ 50 nm) pathogen, dengue virus, leading to infection of host cells.
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Affiliation(s)
- Ping Liu
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-7090, USA
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13
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Affiliation(s)
- Tie Xia
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Key Laboratory of Molecular Nanostructures and Nanotechnology, Chinese Academy of Sciences, Beijing 100190, China;
| | - Nan Li
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Key Laboratory of Molecular Nanostructures and Nanotechnology, Chinese Academy of Sciences, Beijing 100190, China;
| | - Xiaohong Fang
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Key Laboratory of Molecular Nanostructures and Nanotechnology, Chinese Academy of Sciences, Beijing 100190, China;
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14
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Simonsson L, Höök F. Formation and diffusivity characterization of supported lipid bilayers with complex lipid compositions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:10528-10533. [PMID: 22703549 DOI: 10.1021/la301878r] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The moving edge of a hydrodynamically manipulated supported lipid bilayer (SLB) can be used to catalyze SLB formation of adsorbed lipid vesicles that do not undergo spontaneous SLB formation upon adsorption on SiO(2). By removing the lipid reservoir of an initially formed SLB, we show how a hydrodynamically moved SLB patch composed of POPC can be used to form isolated SLBs with compositions that to at least 95% represent that of the adsorbed lipid vesicles. The concept is used to investigate the diffusivity of lissamine rhodamine B 1,2-dihexadecanoyl-sn-glycero-3-phosphoethanolamine (rhodamine-DHPE) in SLBs made from complex lipid compositions, revealing a decrease in diffusivity by a factor of 2 when the cholesterol content was increased from 0% to 50%. We also demonstrate how the concept can be used to induce stationary domains in SLBs containing 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE), and cholesterol (39:21:40 mol %, respectively). Because the method serves as a means to form SLBs with lipid compositions that hamper SLB formation via spontaneous rupture of adsorbed lipid vesicles, it opens up the possibility for new biophysical investigations of SLBs with more nativelike compositions.
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Affiliation(s)
- Lisa Simonsson
- Department of Applied Physics, Chalmers University of Technology, Gothenburg, Sweden
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15
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Simonsson L, Gunnarsson A, Wallin P, Jönsson P, Höök F. Continuous Lipid Bilayers Derived from Cell Membranes for Spatial Molecular Manipulation. J Am Chem Soc 2011; 133:14027-32. [DOI: 10.1021/ja204589a] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lisa Simonsson
- Department of Applied Physics, Chalmers University of Technology, SE 41296 Gothenburg, Sweden
| | - Anders Gunnarsson
- Department of Applied Physics, Chalmers University of Technology, SE 41296 Gothenburg, Sweden
| | - Patric Wallin
- Department of Applied Physics, Chalmers University of Technology, SE 41296 Gothenburg, Sweden
| | - Peter Jönsson
- Department of Applied Physics, Chalmers University of Technology, SE 41296 Gothenburg, Sweden
| | - Fredrik Höök
- Department of Applied Physics, Chalmers University of Technology, SE 41296 Gothenburg, Sweden
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16
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Thompson NL, Navaratnarajah P, Wang X. Measuring surface binding thermodynamics and kinetics by using total internal reflection with fluorescence correlation spectroscopy: practical considerations. J Phys Chem B 2010; 115:120-31. [PMID: 21166379 DOI: 10.1021/jp1069708] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The combination of total internal reflection illumination and fluorescence correlation spectroscopy (TIR-FCS) is an emerging method useful for, among a number of things, measuring the thermodynamic and kinetic parameters describing the reversible association of fluorescently labeled ligands in solution with immobilized, nonfluorescent surface binding sites. However, there are many parameters (both instrumental and intrinsic to the interaction of interest) that determine the nature of the acquired fluorescence fluctuation autocorrelation functions. In this work, we define criteria necessary for successful measurements and then systematically explore the parameter space to define conditions that meet the criteria. The work is intended to serve as a guide for experimental design, in other words, to provide a methodology to identify experimental conditions that will yield reliable values of the thermodynamic and kinetic parameters for a given interaction.
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Affiliation(s)
- Nancy L Thompson
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.
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17
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Macháň R, Hof M. Lipid diffusion in planar membranes investigated by fluorescence correlation spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1798:1377-91. [DOI: 10.1016/j.bbamem.2010.02.014] [Citation(s) in RCA: 197] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Revised: 02/10/2010] [Accepted: 02/10/2010] [Indexed: 11/25/2022]
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18
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Macháň R, Hof M. Recent developments in fluorescence correlation spectroscopy for diffusion measurements in planar lipid membranes. Int J Mol Sci 2010; 11:427-457. [PMID: 20386647 PMCID: PMC2852847 DOI: 10.3390/ijms11020427] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Revised: 01/11/2010] [Accepted: 01/15/2010] [Indexed: 12/11/2022] Open
Abstract
Fluorescence correlation spectroscopy (FCS) is a single molecule technique used mainly for determination of mobility and local concentration of molecules. This review describes the specific problems of FCS in planar systems and reviews the state of the art experimental approaches such as 2-focus, Z-scan or scanning FCS, which overcome most of the artefacts and limitations of standard FCS. We focus on diffusion measurements of lipids and proteins in planar lipid membranes and review the contributions of FCS to elucidating membrane dynamics and the factors influencing it, such as membrane composition, ionic strength, presence of membrane proteins or frictional coupling with solid support.
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Affiliation(s)
- Radek Macháň
- J. Heyrovský Institute of Physical Chemistry of ASCR, v.v.i., Dolejškova 2155/3, 182 23 Prague, Czech Republic; E-Mail:
| | - Martin Hof
- J. Heyrovský Institute of Physical Chemistry of ASCR, v.v.i., Dolejškova 2155/3, 182 23 Prague, Czech Republic; E-Mail:
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19
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Thompson NL, Wang X, Navaratnarajah P. Total internal reflection with fluorescence correlation spectroscopy: Applications to substrate-supported planar membranes. J Struct Biol 2009; 168:95-106. [PMID: 19269331 PMCID: PMC2785550 DOI: 10.1016/j.jsb.2009.02.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2008] [Revised: 02/24/2009] [Accepted: 02/25/2009] [Indexed: 10/21/2022]
Abstract
In this paper, the conceptual basis and experimental design of total internal reflection with fluorescence correlation spectroscopy (TIR-FCS) is described. The few applications to date of TIR-FCS to supported membranes are discussed, in addition to a variety of applications not directly involving supported membranes. Methods related, but not technically equivalent, to TIR-FCS are also summarized. Future directions for TIR-FCS are outlined.
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Affiliation(s)
- Nancy L Thompson
- Department of Chemistry, University of North Carolina at Chapel Hill, 27599-3290, USA.
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20
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Abstract
Imaging membrane dynamics is an important goal, motivated by the abundance of biochemical and biophysical events that are orchestrated at, or by, cellular membranes. The short length scales, fast timescales, and environmental requirements of membrane phenomena present challenges to imaging experiments. Several technical advances offer means to overcome these challenges, and we describe here three powerful techniques applicable to membrane imaging: total internal reflection fluorescence (TIRF) microscopy, fluorescence interference contrast (FLIC) microscopy, and fluorescence correlation spectroscopy (FCS). For each, we discuss the physics underpinning the approach, its practical implementation, and recent examples highlighting its achievements in exploring the membrane environment.
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Affiliation(s)
- Jay T Groves
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.
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21
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Diaz AJ, Albertorio F, Daniel S, Cremer PS. Double cushions preserve transmembrane protein mobility in supported bilayer systems. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:6820-6. [PMID: 18510376 PMCID: PMC3475160 DOI: 10.1021/la800018d] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Supported lipid bilayers (SLBs) have been widely used as model systems to study cell membrane processes because they preserve the same 2D membrane fluidity found in living cells. One of the most significant limitations of this platform, however, is its inability to incorporate mobile transmembrane species. It is often postulated that transmembrane proteins reconstituted in SLBs lose their mobility because of direct interactions between the protein and the underlying substrate. Herein, we demonstrate a highly mobile fraction for a transmembrane protein, annexin V. Our strategy involves supporting the lipid bilayer on a double cushion, where we not only create a large space to accommodate the transmembrane portion of the macromolecule but also passivate the underlying substrate to reduce nonspecific protein-substrate interactions. The thickness of the confined water layer can be tuned by fusing vesicles containing polyethyleneglycol (PEG)-conjugated lipids of various molecular weights to a glass substrate that has first been passivated with a sacrificial layer of bovine serum albumin (BSA). The 2D fluidity of these systems was characterized by fluorescence recovery after photobleaching (FRAP) measurements. Uniform, mobile phospholipid bilayers with lipid diffusion coefficients of around 3 x 10(-8) cm2/s and percent mobile fractions of over 95% were obtained. Moreover, we obtained annexin V diffusion coefficients that were also around 3 x 10(-8) cm2/s with mobile fractions of up to 75%. This represents a significant improvement over bilayer platforms fabricated directly on glass or using single cushion strategies.
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Affiliation(s)
- Arnaldo J. Diaz
- Department of Chemistry, Texas A&M University, College Station, Texas 77843
| | | | - Susan Daniel
- Department of Chemistry, Texas A&M University, College Station, Texas 77843
| | - Paul S. Cremer
- Department of Chemistry, Texas A&M University, College Station, Texas 77843
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22
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Abstract
Total internal reflection fluorescence microscopy (TIRFM), also known as evanescent wave microscopy, is used in a wide range of applications, particularly to view single molecules attached to planar surfaces and to study the position and dynamics of molecules and organelles in living culture cells near the contact regions with the glass coverslip. TIRFM selectively illuminates fluorophores only in a very thin (less than 100 nm deep) layer near the substrate, thereby avoiding excitation of fluorophores outside this subresolution optical section. This chapter reviews the history, current applications in cell biology and biochemistry, basic optical theory, combinations with numerous other optical and spectroscopic approaches, and a range of setup methods, both commercial and custom.
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Affiliation(s)
- Daniel Axelrod
- Departments of Physics and Biophysics, University of Michigan, Ann Arbor, Michigan 48109, USA
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23
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Pero JK, Haas EM, Thompson NL. Size dependence of protein diffusion very close to membrane surfaces: measurement by total internal reflection with fluorescence correlation spectroscopy. J Phys Chem B 2007; 110:10910-8. [PMID: 16771344 DOI: 10.1021/jp056990y] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The diffusion coefficients of nine fluorescently labeled antibodies, antibody fragments, and antibody complexes have been measured in solution very close to supported planar membranes by using total internal reflection with fluorescence correlation spectroscopy (TIR-FCS). The hydrodynamic radii (3-24 nm) of the nine antibody types were determined by comparing literature values with bulk diffusion coefficients measured by spot FCS. The diffusion coefficients very near membranes decreased significantly with molecular size, and the size dependence was greater than that predicted to occur in bulk solution. The observation that membrane surfaces slow the local diffusion coefficient of proteins in a size-dependent manner suggests that the primary effect is hydrodynamic as predicted for simple spheres diffusing close to planar walls. The TIR-FCS data are consistent with predictions derived from hydrodynamic theory. This work illustrates one factor that could contribute to previously observed nonideal ligand-receptor kinetics at model and natural cell membranes.
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Affiliation(s)
- Jamie K Pero
- Department of Chemistry, Campus Box 3290, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, USA
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24
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Koopmans WJA, Brehm A, Logie C, Schmidt T, van Noort J. Single-pair FRET microscopy reveals mononucleosome dynamics. J Fluoresc 2007; 17:785-95. [PMID: 17609864 PMCID: PMC2064943 DOI: 10.1007/s10895-007-0218-9] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Accepted: 06/04/2007] [Indexed: 02/01/2023]
Abstract
We applied spFRET microscopy for direct observation of intranucleosomal DNA dynamics. Mononucleosomes, reconstituted with DNA containing a FRET pair at the dyad axis and exit of the nucleosome core particle, were immobilized through a 30 bp DNA tether on a polyethyleneglycol functionalized slide and visualized using Total Internal Reflection Fluorescence microscopy. FRET efficiency time-traces revealed two types of dynamics: acceptor blinking and intramolecular rearrangements. Both Cy5 and ATTO647N acceptor dyes showed severe blinking in a deoxygenated buffer in the presence of 2% betaME. Replacing the triplet quencher betaME with 1 mM Trolox eliminated most blinking effects. After suppression of blinking three subpopulations were observed: 90% appeared as dissociated complexes; the remaining 10% featured an average FRET efficiency in agreement with intact nucleosomes. In 97% of these intact nucleosomes no significant changes in FRET efficiency were observed in the experimentally accessible time window ranging from 10 ms to 10's of seconds. However, 3% of the intact nucleosomes showed intervals with reduced FRET efficiency, clearly distinct from blinking, with a lifetime of 120 ms. These fluctuations can unambiguously be attributed to DNA breathing. Our findings illustrate not only the merits but also typical caveats encountered in single-molecule FRET studies on complex biological systems.
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Affiliation(s)
- W. J. A. Koopmans
- Physics of Life Processes, Leiden University, Leiden Institute of Physics, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands
| | - A. Brehm
- Institut für Molekularbiologie und Tumorforschung, Philipps-Universtät Marburg, Emil-Mannkopff-Str.2, 35033 Marburg, Germany
| | - C. Logie
- Molecular Biology, Nijmegen Centre for Molecular Life Sciences, Radboud University, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - T. Schmidt
- Physics of Life Processes, Leiden University, Leiden Institute of Physics, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands
| | - J. van Noort
- Physics of Life Processes, Leiden University, Leiden Institute of Physics, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands
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25
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Abstract
Total internal reflection-fluorescence correlation spectroscopy (TIR-FCS) is an emerging technique that is used to measure events at or near an interface, including local fluorophore concentrations, local translational mobilities and the kinetic rate constants that describe the association and dissociation of fluorophores at the interface. TIR-FCS is also an extremely promising method for studying dynamics at or near the basal membranes of living cells. This protocol gives a general overview of the steps necessary to construct and test a TIR-FCS system using either through-prism or through-objective internal reflection geometry adapted for FCS. The expected forms of the autocorrelation function are discussed for the cases in which fluorescent molecules in solution diffuse through the depth of the evanescent field, but do not bind to the surface of interest, and in which reversible binding to the surface also occurs.
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Affiliation(s)
- Nancy L Thompson
- Department of Chemistry, University of North Carolina at Chapel Hill, North Carolina 27599, USA.
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26
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27
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Cannon B, Weaver N, Pu Q, Thiagarajan V, Liu S, Huang J, Vaughn MW, Cheng KH. Cholesterol modulated antibody binding in supported lipid membranes as determined by total internal reflectance microscopy on a microfabricated high-throughput glass chip. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2005; 21:9666-74. [PMID: 16207051 DOI: 10.1021/la0502645] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
A high-throughput microfabricated all-glass microchip, lipid biochip, was created and used to measure fluorescently tagged antibody binding to dinitrophenol (DNP) haptens in planar supported phospholipid/cholesterol lipid bilayers as a function of cholesterol-to-lipid molar ratio (X(CHOL)). Multiple parallel microchannels etched in the lipid biochip allowed simultaneous measurement of antibody binding to hapten-containing and hapten-free lipid bilayers, for a range of aqueous antibody concentrations. Specific and nonspecific antibody binding to the supported lipid bilayers was determined from the internally calibrated intensity of the surface fluorescence using total internal reflectance fluorescence (TIRF) microscopy. The TIRF intensity data of the specific antibody binding were fitted to the Langmuir isotherm and Hill equation models to determine the apparent dissociation constant K(d), the maximum fluorescence parameter F(infinity), and binding cooperativity n. As X(CHOL) increased from 0 to 0.50, K(d) exhibited a minimum of approximately 4 microM and n reached a maximum of approximately 2.2 at X(CHOL) approximately 0.20. However, F(infinity) appeared to be insensitive to the cholesterol content. The nonspecific binding fraction (NS), defined as the ratio of the TIRF intensity for hapten-free bilayers to that with hapten, showed a minimum of approximately 0.08 also at X(CHOL) approximately 0.20. The results suggest that cholesterol regulates the specific binding affinity and cooperativity, as well as suppresses nonspecific binding of aqueous antibody to a planar supported lipid bilayer surface at an optimal cholesterol content of X(CHOL) approximately 0.20. Interestingly, for X(CHOL) approximately 0.40, NS reached a maximum of approximately 0.57, suggesting significant packing defects in the lipid bilayer surface, possibly as a result of lipid domain formation as predicted by the lipid superlattice model. We conclude that cholesterol plays a significant role in regulating both specific and nonspecific antibody/antigen binding events on the lipid bilayer surface and that our lipid biochip represents a new and useful high-resolution microfluidic device for measuring lipid/protein surface binding activities in a parallel and high-throughput fashion.
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Affiliation(s)
- Brian Cannon
- Department of Physics, Texas Tech University, Lubbock, TX 79409, USA
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28
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Liu T, Tucker WC, Bhalla A, Chapman ER, Weisshaar JC. SNARE-driven, 25-millisecond vesicle fusion in vitro. Biophys J 2005; 89:2458-72. [PMID: 16055544 PMCID: PMC1366745 DOI: 10.1529/biophysj.105.062539] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Docking and fusion of single proteoliposomes reconstituted with full-length v-SNAREs (synaptobrevin) into planar lipid bilayers containing binary t-SNAREs (anchored syntaxin associated with SNAP25) was observed in real time by wide-field fluorescence microscopy. This enabled separate measurement of the docking rate k(dock) and the unimolecular fusion rate k(fus). On low t-SNARE-density bilayers at 37 degrees C, docking is efficient: k(dock) = 2.2 x 10(7) M(-1) s(-1), approximately 40% of the estimated diffusion limited rate. Full vesicle fusion is observed as a prompt increase in fluorescence intensity from labeled lipids, immediately followed by outward radial diffusion (D(lipid) = 0.6 microm2 s(-1)); approximately 80% of the docked vesicles fuse promptly as a homogeneous subpopulation with k(fus) = 40 +/- 15 s(-1) (tau(fus) = 25 ms). This is 10(3)-10(4) times faster than previous in vitro fusion assays. Complete lipid mixing occurs in <15 ms. Both the v-SNARE and the t-SNARE are necessary for efficient docking and fast fusion, but Ca2+ is not. Docking and fusion were quantitatively similar on syntaxin-only bilayers lacking SNAP25. At present, in vitro fusion driven by SNARE complexes alone remains approximately 40 times slower than the fastest, submillisecond presynaptic vesicle population response.
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Affiliation(s)
- Tingting Liu
- Departments of Chemistry and Physiology, University of Wisconsin-Madison, Madison, WI 53706, USA
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29
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Gavutis M, Lata S, Lamken P, Müller P, Piehler J. Lateral ligand-receptor interactions on membranes probed by simultaneous fluorescence-interference detection. Biophys J 2005; 88:4289-302. [PMID: 15778442 PMCID: PMC1305658 DOI: 10.1529/biophysj.104.055855] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
We describe an experimental approach for studying ligand-receptor interactions in the plane of the membrane. The extracellular domains of the type I interferon receptor subunits ifnar1-EC and ifnar2-EC were tethered in an oriented fashion onto solid-supported, fluid lipid bilayers, thus mimicking membrane anchoring and lateral diffusion of the receptor. Ligand-induced receptor assembling was investigated by simultaneous total internal reflection fluorescence spectroscopy and reflectance interferometry (RIf). Based on a rigorous characterization of the interactions of fluorescence-labeled IFNalpha2 with each of the receptor subunits, the dynamics of the ternary complex formation on the fluid lipid bilayer was addressed in further detail making use of the features of the simultaneous detection. All these measurements supported the formation of a ternary complex in two steps, i.e., association of the ligand to ifnar2-EC and subsequent recruitment of ifnar1-EC on the surface of the membrane. Based on the ability to control and quantify the receptor surface concentrations, equilibrium, and rate constants of the interaction in the plane of the membrane were determined by monitoring ligand dissociation at different receptor surface concentrations. Using mutants of IFNalpha2 binding to ifnar2-EC with different association rate constants, the key role of the association rate constants for the assembling mechanism was demonstrated.
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Affiliation(s)
- Martynas Gavutis
- Institute of Biochemistry, Biocenter N210 Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
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30
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Lieto AM, Cush RC, Thompson NL. Ligand-receptor kinetics measured by total internal reflection with fluorescence correlation spectroscopy. Biophys J 2004; 85:3294-302. [PMID: 14581230 PMCID: PMC1303606 DOI: 10.1016/s0006-3495(03)74748-1] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Total internal reflection excitation used in combination with fluorescence correlation spectroscopy (TIR-FCS) is a method for characterizing the dynamic behavior and absolute concentrations of fluorescent molecules near or at the interface of a planar substrate and a solution. In this work, we demonstrate for the first time the use of TIR-FCS for examining the interaction kinetics of fluorescent ligands in solution which specifically and reversibly associate with receptors in substrate-supported planar membranes. Fluorescence fluctuation autocorrelation functions were obtained for a fluorescently labeled IgG reversibly associating with the mouse receptor FcgammaRII, which was purified and reconstituted into substrate-supported planar membranes. Data were obtained as a function of the IgG solution concentration, the Fc receptor surface density, the observation area size, and the incident intensity. Best fits of the autocorrelation functions to appropriate theoretical forms gave measures of the average surface density of bound IgG, the local solution concentration of IgG, the kinetic rate constant for surface dissociation, and the rate of diffusion through the depth of the evanescent field. The average number of observed fluorescent molecules, both in solution and bound to the surface, scaled with the solution concentration of IgG, observation area size, and Fc receptor surface density as expected. The dissociation rate constant and rate of diffusion through the evanescent field agree with previous results, and all measured parameters were independent of the incident intensity.
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Affiliation(s)
- Alena M Lieto
- Department of Physics and Astronomy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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31
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Schapper F, Gonçalves JT, Oheim M. Fluorescence imaging with two-photon evanescent wave excitation. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2003; 32:635-43. [PMID: 12955359 DOI: 10.1007/s00249-003-0326-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2002] [Accepted: 05/02/2003] [Indexed: 10/26/2022]
Abstract
We demonstrate broad-field, non-scanning, two-photon excitation fluorescence (2PEF) close to a glass/cell interface by total internal reflection of a femtosecond-pulsed infrared laser beam. We exploit the quadratic intensity dependence of 2PEF to provide non-linear evanescent wave (EW) excitation in a well-defined sample volume and to eliminate scattered background excitation. A simple model is shown to describe the resulting 2PEF intensity and to predict the effective excitation volume in terms of easily measurable beam, objective and interface properties. We demonstrate non-linear evanescent wave excitation at 860 nm of acridine orange-labelled secretory granules in live chromaffin cells, and excitation at 900 nm of TRITC-phalloidin-actin/GPI-GFP double-labelled fibroblasts. The confined excitation volume and the possibility of simultaneous multi-colour excitation of several fluorophores make EW 2PEF particularly advantageous for quantitative microscopy, imaging biochemistry inside live cells, or biosensing and screening applications in miniature high-density multi-well plates.
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Affiliation(s)
- Florian Schapper
- Neurophysiology and New Microscopies, Ecole Supérieure de Physique et Chimie Industrielles (ESPCI), 10 rue Vauquelin, 75005 Paris, France
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32
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Affiliation(s)
- Daniel Axelrod
- Department of Physics and Biophysics Research Division, University of Michigan, Ann Arbor, Michigan 48109, USA
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33
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Wang L, Schönhoff M, Möhwald H. Lipids Coupled to Polyelectrolyte Multilayers: Ultraslow Diffusion and the Dynamics of Electrostatic Interactions. J Phys Chem B 2002. [DOI: 10.1021/jp0256600] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Liying Wang
- Max-Planck Institute of Colloids and Interfaces, D-14424 Potsdam/Golm, Germany
| | - Monika Schönhoff
- Max-Planck Institute of Colloids and Interfaces, D-14424 Potsdam/Golm, Germany
| | - Helmuth Möhwald
- Max-Planck Institute of Colloids and Interfaces, D-14424 Potsdam/Golm, Germany
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34
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Starr TE, Thompson NL. Local Diffusion and Concentration of IgG near Planar Membranes: Measurement by Total Internal Reflection with Fluorescence Correlation Spectroscopy. J Phys Chem B 2002. [DOI: 10.1021/jp012689f] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tammy E. Starr
- Department of Chemistry, Campus Box 3290, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290
| | - Nancy L. Thompson
- Department of Chemistry, Campus Box 3290, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290
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35
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Abstract
Key events in cellular trafficking occur at the cell surface, and it is desirable to visualize these events without interference from other regions deeper within. This review describes a microscopy technique based on total internal reflection fluorescence which is well suited for optical sectioning at cell-substrate regions with an unusually thin region of fluorescence excitation. The technique has many other applications as well, most notably for studying biochemical kinetics and single biomolecule dynamics at surfaces. A brief summary of these applications is provided, followed by presentations of the physical basis for the technique and the various ways to implement total internal reflection fluorescence in a standard fluorescence microscope.
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Affiliation(s)
- D Axelrod
- Department of Physics & Biophysics Research Division, University of Michigan, Ann Arbor, MI 48109, USA.
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36
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Gu Y, LaBell R, O'Brien DF, Saavedra SS. Quantitative Studies of Binding between Synthetic Galactosyl Ceramide Analogues and HIV-1 Gp120 at Planar Membrane Surfaces. Angew Chem Int Ed Engl 2001. [DOI: 10.1002/1521-3757(20010618)113:12<2382::aid-ange2382>3.0.co;2-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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37
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Starr TE, Thompson NL. Total internal reflection with fluorescence correlation spectroscopy: combined surface reaction and solution diffusion. Biophys J 2001; 80:1575-84. [PMID: 11222318 PMCID: PMC1301349 DOI: 10.1016/s0006-3495(01)76130-9] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Total internal reflection with fluorescence correlation spectroscopy (TIR-FCS) is a method for measuring the surface association/dissociation rates and absolute densities of fluorescent molecules at the interface of solution and a planar substrate. This method can also report the apparent diffusion coefficient and absolute concentration of fluorescent molecules very close to the surface. An expression for the fluorescence fluctuation autocorrelation function in the absence of contributions from diffusion through the evanescent wave, in solution, has been published previously (N. L. Thompson, T. P. Burghardt, and D. Axelrod. 1981, Biophys. J. 33:435-454). This work describes the nature of the TIR-FCS autocorrelation function when both surface association/dissociation kinetics and diffusion through the evanescent wave contribute to the fluorescence fluctuations. The fluorescence fluctuation autocorrelation function depends in general on the kinetic association and dissociation rate constants, the surface site density, the concentration of fluorescent molecules in solution, the solution diffusion coefficient, and the depth of the evanescent field. Both general and approximate expressions are presented.
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Affiliation(s)
- T E Starr
- Department of Chemistry, University of North Carolina, Chapel Hill 27599-3290, USA
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38
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Wagner ML, Tamm LK. Tethered polymer-supported planar lipid bilayers for reconstitution of integral membrane proteins: silane-polyethyleneglycol-lipid as a cushion and covalent linker. Biophys J 2000; 79:1400-14. [PMID: 10969002 PMCID: PMC1301034 DOI: 10.1016/s0006-3495(00)76392-2] [Citation(s) in RCA: 365] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
There is increasing interest in supported membranes as models of biological membranes and as a physiological matrix for studying the structure and function of membrane proteins and receptors. A common problem of protein-lipid bilayers that are directly supported on a hydrophilic substrate is nonphysiological interactions of integral membrane proteins with the solid support to the extent that they will not diffuse in the plane of the membrane. To alleviate some of these problems we have developed a new tethered polymer-supported planar lipid bilayer system, which permitted us to reconstitute integral membrane proteins in a laterally mobile form. We have supported lipid bilayers on a newly designed polyethyleneglycol cushion, which provided a soft support and, for increased stability, covalent linkage of the membranes to the supporting quartz or glass substrates. The formation and morphology of the bilayers were followed by total internal reflection and epifluorescence microscopy, and the lateral diffusion of the lipids and proteins in the bilayer was monitored by fluorescence recovery after photobleaching. Uniform bilayers with high lateral lipid diffusion coefficients (0.8-1.2 x 10(-8) cm(2)/s) were observed when the polymer concentration was kept slightly below the mushroom-to-brush transition. Cytochrome b(5) and annexin V were used as first test proteins in this system. When reconstituted in supported bilayers that were directly supported on quartz, both proteins were largely immobile with mobile fractions < 25%. However, two populations of laterally mobile proteins were observed in the polymer-supported bilayers. Approximately 25% of cytochrome b(5) diffused with a diffusion coefficient of approximately 1 x 10(-8) cm(2)/s, and 50-60% diffused with a diffusion coefficient of approximately 2 x 10(-10) cm(2)/s. Similarly, one-third of annexin V diffused with a diffusion coefficient of approximately 3 x 10(-9) cm(2)/s, and two-thirds diffused with a diffusion coefficient of approximately 4 x 10(-10) cm(2)/s. A model for the interaction of these proteins with the underlying polymer is discussed.
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Affiliation(s)
- M L Wagner
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908-0736 USA
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39
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Abstract
We present the results of three-dimensional lattice Monte Carlo simulations of protein diffusion on the liquid-solid interface in a wide temperature range including the most interesting temperatures (from slightly below T(f) and up to T(c), where T(f) and T(c) are the folding and collapse temperatures). For the model under consideration (27 monomers of two types), the temperature dependence of the diffusion coefficient is found to obey the Arrhenius law with the normal value (approximately 10(-2)-10(-3) cm(2)/s) of the preexponential factor. Proteins 2000;39:76-81.
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Affiliation(s)
- V P Zhdanov
- Department of Applied Physics, Chalmers University of Technology, Göteborg, Sweden.
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40
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Effect of Hydrophobicity and Electrostatics on Adsorption and Surface Diffusion of DNA Oligonucleotides at Liquid/Solid Interfaces. J Colloid Interface Sci 1998. [DOI: 10.1006/jcis.1998.5495] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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41
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Liley M, Bouvier J, Vogel H. Incorporation and Antibody Recognition of a Lipid-Anchored Membrane Protein in Supported Lipid Layers. J Colloid Interface Sci 1997; 194:53-8. [PMID: 9367584 DOI: 10.1006/jcis.1997.5111] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The formation of supported lipid layers incorporating promastigote surface protease (PSP), a glycosylphosphatidylinositol-anchored protein, is investigated using surface plasmon resonance. Both hydrophilic and hydrophobic substrates are used for the formation of lipid layers, and results are consistent with the formation of lipid bilayers and monolayers, respectively. Specific antibody binding to layers containing PSP is observed, whereas nonspecific binding of the antibody to the surface is effectively suppressed by the phosphatidylcholine lipid layer. Phosphatidylinositol-specific phospholipase C is used to remove the lipid moieties from the membrane-incorporated PSP, releasing it into solution in a hydrophilic form and demonstrating that a large fraction of the protein is anchored in the lipid layer via the lipid moieties. Copyright 1997 Academic Press. Copyright 1997Academic Press
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Affiliation(s)
- M Liley
- Laboratoire de Chimie Physique de Polymeres et de Membranes, Ecole Polytechnique Federale de Lausanne, Lausanne, CH-1015, Switzerland
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42
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Mc Kiernan AE, MacDonald RI, MacDonald RC, Axelrod D. Cytoskeletal protein binding kinetics at planar phospholipid membranes. Biophys J 1997; 73:1987-98. [PMID: 9336194 PMCID: PMC1181099 DOI: 10.1016/s0006-3495(97)78229-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
It has been hypothesized that nonspecific reversible binding of cytoskeletal proteins to lipids in cells may guide their binding to integral membrane anchor proteins. In a model system, we measured desorption rates k(off) (off-rates) of the erythrocyte cytoskeletal proteins spectrin and protein 4.1 labeled with carboxyfluorescein (CF), at two different compositions of planar phospholipid membranes (supported on glass), using the total internal reflection/fluorescence recovery after photobleaching (TIR/FRAP) technique. The lipid membranes consisted of either pure phosphatidylcholine (PC) or a 3:1 mixture of PC with phosphatidylserine (PS). In general, the off-rates were not single exponentials and were fit to a combination of fast, slow, and irreversible fractions, reported both separately and as a weighted average. By a variation of TIR/FRAP, we also measured equilibrium affinities (the ratio of surface-bound to bulk protein concentration) and thereby calculated on-rates, k(on). The average off-rate of CF-4.1 from PC/PS (approximately 0.008/s) is much slower than that from pure PC (approximately 1.7/s). Despite the consequent increase in equilibrium affinity at PC/PS, the on-rate at PC/PS is also substantially decreased (by a factor of 40) relative to that at pure PC. The simultaneous presence of (unlabeled) spectrin tends to substantially decrease the on-rate (and the affinity) of CF-4.1 at both membrane types. Similar experiments for CF-spectrin alone showed much less sensitivity to membrane type and generally faster off-rates than those exhibited by CF-4.1. However, when mixed with (unlabeled) 4.1, both the on-rate and off-rate of CF-spectrin decreased drastically at PC/PS (but not PC), leading to a somewhat increased affinity. Clearly, changes in affinity often involve countervailing changes in both on-rates and off-rates. In many of these studies, the effect of varying ionic strength and bulk concentrations was examined; it appears that the binding is an electrostatic attraction and is far from saturation at the concentrations employed. These results and the techniques implemented carry general implications for understanding the functional role of nonspecific protein binding to cellular lipid membranes.
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Affiliation(s)
- A E Mc Kiernan
- Biophysics Research Division, University of Michigan, Ann Arbor 48109, USA
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43
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Berk DA, Yuan F, Leunig M, Jain RK. Direct in vivo measurement of targeted binding in a human tumor xenograft. Proc Natl Acad Sci U S A 1997; 94:1785-90. [PMID: 9050856 PMCID: PMC19994 DOI: 10.1073/pnas.94.5.1785] [Citation(s) in RCA: 110] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Binding is crucial to the function of most biologically active molecules, but difficult to quantify directly in living tissue. To this end, fluorescence recovery after photobleaching was used to detect the immobilization of fluorescently labeled ligand caused by binding to receptors in vivo. Measurements of mAb affinity to target antigen within human tumor xenografts revealed a saturable binding isotherm, from which an in vivo carcinoembryonic antigen density of 0.56 nmol/g (5.0 x 10(5)/cell) and an association constant of Ka < or = 4 x 10(7) M(-1) were estimated. The present method can be adapted for in vivo studies of cell signaling, targeted drugs, gene therapy, and other processes involving receptor-ligand binding.
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Affiliation(s)
- D A Berk
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston 02114, USA
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44
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Gesty-Palmer D, Thompson NL. Binding of the soluble, truncated form of an Fc receptor (mouse Fc gamma RII) to membrane-bound IgG as measured by total internal reflection fluorescence microscopy. J Mol Recognit 1997; 10:63-72. [PMID: 9376129 DOI: 10.1002/(sici)1099-1352(199703/04)10:2<63::aid-jmr342>3.0.co;2-h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Total internal reflection fluorescence microscopy has been used to investigate the binding of the soluble extracellular domain of mouse Fc gamma RII (sFc gamma RII) to an anti-trinitrophenyl monoclonal mouse IgG2b (GK14.1) specifically bound to substrate-supported planar membranes composed of dipalmitoylphosphatidylcholine (DPPC) and trinitrophenylaminocaproyldipalmitoylphosphatidylethanolamine (TNP-cap-DPPE). The equilibrium dissociation constants for sFc gamma RII at GK14.1-coated TNP-cap-DPPE/DPPC planar membranes containing 0.5-25 mol% TNP-cap-DPPE were approximately 1 microM. Total internal reflection with fluorescence photobleaching recovery was used to examine the dissociation kinetics. The fluorescence recovery curves were better described as a sum of two exponentials rather than by one exponential; the rates and fractional recoveries were approximately 1 s-1 (65%) and approximately 0.1 s-1 (35%). The similarity between the values of these equilibrium and kinetic parameters to those previously measured for the binding of IgG in solution to intact mouse Fc gamma RII reconstituted into planar membranes suggests that conformational changes which may occur when IgG is constrained to a membrane surface do not significantly affect the equilibrium or kinetics of IgG-mouse Fc gamma RII binding. The stoichiometry of sFc gamma RII-GK14.1 binding was 1:4, indicating that a significant fraction of the membrane-bound antibodies were not accessible for receptor binding. Possible mechanisms that might underlay the observed heterogeneity in sFc gamma RII-IgG binding kinetics are discussed.
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Affiliation(s)
- D Gesty-Palmer
- Department of Chemistry, University of North Carolina, Chapel Hill 27599-3290, USA
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45
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Thompson NL, Lagerholm BC. Total internal reflection fluorescence: applications in cellular biophysics. Curr Opin Biotechnol 1997; 8:58-64. [PMID: 9013655 DOI: 10.1016/s0958-1669(97)80158-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Molecular interactions occurring on or near cell membrane surfaces are expected to have different properties from those occurring in bulk solutions. One particularly useful technique for studying surface-associated processes at the molecular level is total internal reflection fluorescence. In this method, the evanescent field from an internally reflected excitation source selectively excites fluorescent molecules on or near a surface. Evanescent excitation has been used recently with a variety of techniques in fluorescence microscopy and spectroscopy to probe the fundamental physicochemical properties of biochemical reactions at natural or model biological surfaces. These studies are providing enhanced understanding of cellular function. Several recent developments in total internal reflection fluorescence methodology from other fields are likely to find future application in cellular biophysics.
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Affiliation(s)
- N L Thompson
- Department of Chemistry, Campus Box 3290, University of North Carolina, Chapel Hill, NC 27599-3290, USA.
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46
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Thompson NL, Drake AW, Chen L, Vanden Broek W. Equilibrium, kinetics, diffusion and self-association of proteins at membrane surfaces: measurement by total internal reflection fluorescence microscopy. Photochem Photobiol 1997; 65:39-46. [PMID: 9066286 DOI: 10.1111/j.1751-1097.1997.tb01875.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The equilibrium, kinetics, diffusion and self-association of proteins at membrane/solution interfaces may deviate substantially from these processes in bulk solution. A set of methods for examining these phenomena combines substrate-supported planar model membranes and the use of evanescent illumination with laser-based, quantitative fluorescence microscopy. Measurement of the steady-state, surface-associated fluorescence can be used to examine the thermodynamic properties of proteins at membranes. When combined with fluorescence photobleaching recovery, this technique provides information about membrane-binding kinetics; and when combined with fluorescence pattern photobleaching recovery, measurement of the translational diffusion coefficients of proteins weakly bound to membranes is possible. The use of polarized evanescent illumination can provide information about the orientation distributions of adsorbed fluorophores. Fluorescence correlation spectroscopy provides information about the self-association (e.g. dimerization) of membrane-associated proteins.
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Affiliation(s)
- N L Thompson
- Department of Chemistry, University of North Carolina, Chapel Hill 27599-3290, USA.
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47
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Chan V, Graves DJ, McKenzie SE. The biophysics of DNA hybridization with immobilized oligonucleotide probes. Biophys J 1995; 69:2243-55. [PMID: 8599632 PMCID: PMC1236463 DOI: 10.1016/s0006-3495(95)80095-0] [Citation(s) in RCA: 179] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
A mathematical model based on receptor-ligand interactions at a cell surface has been modified and further developed to represent heterogeneous DNA-DNA hybridization on a solid surface. The immobilized DNA molecules with known sequences are called probes, and the DNA molecules in solution with unknown sequences are called targets in this model. Capture of the perfectly complementary target is modeled as a combined reaction-diffusion limited irreversible reaction. In the model, there are two different mechanisms by which targets can hybridize with the complementary probes: direct hybridization from the solution and hybridization by molecules that adsorb nonspecifically and then surface diffuse to the probe. The results indicate that nonspecific adsorption of single-stranded DNA on the surface and subsequent two-dimensional diffusion can significantly enhance the overall reaction rate. Heterogeneous hybridization depends strongly on the rate constants for DNA adsorption/desorption in the non-probe-covered regions of the surface, the two-dimensional (2D) diffusion coefficient, and the size of probes and targets. The model shows that the overall kinetics of DNA hybridization to DNA on a solid support may be an extremely efficient process for physically realistic 2D diffusion coefficients, target concentrations, and surface probe densities. The implication for design and operation of a DNA hybridization surface is that there is an optimal surface probe density when 2D diffusion occurs; values above that optimum do not increase the capture rate. Our model predicts capture rates in agreement with those from recent experimental literature. The results of our analysis predict that several things can be done to improve heterogeneous hybridization: 1) the solution phase target molecules should be about 100 bases or less in size to speed solution-phase and surface diffusion; 2) conditions should be created such that reversible adsorption and two-dimensional diffusion occur in the surface regions between DNA probe molecules; 3) provided that 2) is satisfied, one can achieve results with a sparse probe coverage that are equal to or better than those obtained with a surface totally covered with DNA probes.
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Affiliation(s)
- V Chan
- Department of Chemical Engineering, University of Pennsylvania, Philadelphia, USA
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48
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Ramsden JJ, Bachmanova GI, Archakov AI. Kinetic evidence for protein clustering at a surface. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1994; 50:5072-5076. [PMID: 9962592 DOI: 10.1103/physreve.50.5072] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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49
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Huang Z, Pearce KH, Thompson NL. Translational diffusion of bovine prothrombin fragment 1 weakly bound to supported planar membranes: measurement by total internal reflection with fluorescence pattern photobleaching recovery. Biophys J 1994; 67:1754-66. [PMID: 7819508 PMCID: PMC1225538 DOI: 10.1016/s0006-3495(94)80650-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Previous work has shown that bovine prothrombin fragment 1 binds to substrate-supported planar membranes composed of phosphatidylcholine (PC) and phosphatidylserine (PS) in a Ca(2+)-specific manner. The apparent equilibrium dissociation constant is 1-15 microM, and the average membrane residency time is approximately 0.25 s-1. In the present work, fluorescence pattern photobleaching recovery with evanescent interference patterns (TIR-FPPR) has been used to measure the translational diffusion coefficients of the weakly bound fragment 1. The results show that the translational diffusion coefficients on fluid-like PS/PC planar membranes are on the order of 10(-9) cm2/s and are reduced when the fragment 1 surface density is increased. Control measurements were carried out for fragment 1 on solid-like PS/PC planar membranes. The dissociation kinetics were similar to those on fluid-like membranes, but protein translational mobility was not detected. TIR-FPPR was also used to measure the diffusion coefficient of the fluorescent lipid NBD-PC in fluid-like PS/PC planar membranes. In these measurements, the diffusion coefficient was approximately 10(-8) cm2/s, which is consistent with that measured by conventional fluorescence pattern photobleaching recovery. This work represents the first measurement of a translational diffusion coefficient for a protein weakly bound to a membrane surface.
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Affiliation(s)
- Z Huang
- Department of Chemistry, University of North Carolina at Chapel Hill 27599-3290
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