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Chua GNL, Liu S. When Force Met Fluorescence: Single-Molecule Manipulation and Visualization of Protein-DNA Interactions. Annu Rev Biophys 2024; 53:169-191. [PMID: 38237015 DOI: 10.1146/annurev-biophys-030822-032904] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Myriad DNA-binding proteins undergo dynamic assembly, translocation, and conformational changes while on DNA or alter the physical configuration of the DNA substrate to control its metabolism. It is now possible to directly observe these activities-often central to the protein function-thanks to the advent of single-molecule fluorescence- and force-based techniques. In particular, the integration of fluorescence detection and force manipulation has unlocked multidimensional measurements of protein-DNA interactions and yielded unprecedented mechanistic insights into the biomolecular processes that orchestrate cellular life. In this review, we first introduce the different experimental geometries developed for single-molecule correlative force and fluorescence microscopy, with a focus on optical tweezers as the manipulation technique. We then describe the utility of these integrative platforms for imaging protein dynamics on DNA and chromatin, as well as their unique capabilities in generating complex DNA configurations and uncovering force-dependent protein behaviors. Finally, we give a perspective on the future directions of this emerging research field.
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Affiliation(s)
- Gabriella N L Chua
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, New York, USA;
- Tri-Institutional PhD Program in Chemical Biology, New York, New York, USA
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, New York, USA;
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2
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Ray S, Widom JR, Walter NG. Life under the Microscope: Single-Molecule Fluorescence Highlights the RNA World. Chem Rev 2018; 118:4120-4155. [PMID: 29363314 PMCID: PMC5918467 DOI: 10.1021/acs.chemrev.7b00519] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The emergence of single-molecule (SM) fluorescence techniques has opened up a vast new toolbox for exploring the molecular basis of life. The ability to monitor individual biomolecules in real time enables complex, dynamic folding pathways to be interrogated without the averaging effect of ensemble measurements. In parallel, modern biology has been revolutionized by our emerging understanding of the many functions of RNA. In this comprehensive review, we survey SM fluorescence approaches and discuss how the application of these tools to RNA and RNA-containing macromolecular complexes in vitro has yielded significant insights into the underlying biology. Topics covered include the three-dimensional folding landscapes of a plethora of isolated RNA molecules, their assembly and interactions in RNA-protein complexes, and the relation of these properties to their biological functions. In all of these examples, the use of SM fluorescence methods has revealed critical information beyond the reach of ensemble averages.
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Affiliation(s)
| | | | - Nils G. Walter
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109, USA
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3
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Duman M, Pfleger M, Zhu R, Rankl C, Chtcheglova LA, Neundlinger I, Bozna BL, Mayer B, Salio M, Shepherd D, Polzella P, Moertelmaier M, Kada G, Ebner A, Dieudonne M, Schütz GJ, Cerundolo V, Kienberger F, Hinterdorfer P. Improved localization of cellular membrane receptors using combined fluorescence microscopy and simultaneous topography and recognition imaging. NANOTECHNOLOGY 2010; 21:115504. [PMID: 20173232 DOI: 10.1088/0957-4484/21/11/115504] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The combination of fluorescence microscopy and atomic force microscopy has a great potential in single-molecule-detection applications, overcoming many of the limitations coming from each individual technique. Here we present a new platform of combined fluorescence and simultaneous topography and recognition imaging (TREC) for improved localization of cellular receptors. Green fluorescent protein (GFP) labeled human sodium-glucose cotransporter (hSGLT1) expressed Chinese Hamster Ovary (CHO) cells and endothelial cells (MyEnd) from mouse myocardium stained with phalloidin-rhodamine were used as cell systems to study AFM topography and fluorescence microscopy on the same surface area. Topographical AFM images revealed membrane features such as lamellipodia, cytoskeleton fibers, F-actin filaments and small globular structures with heights ranging from 20 to 30 nm. Combined fluorescence and TREC imaging was applied to detect density, distribution and localization of YFP-labeled CD1d molecules on alpha-galactosylceramide (alphaGalCer)-loaded THP1 cells. While the expression level, distribution and localization of CD1d molecules on THP1 cells were detected with fluorescence microscopy, the nanoscale distribution of binding sites was investigated with molecular recognition imaging by using a chemically modified AFM tip. Using TREC on the inverted light microscope, the recognition sites of cell receptors were detected in recognition images with domain sizes ranging from approximately 25 to approximately 160 nm, with the smaller domains corresponding to a single CD1d molecule.
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Affiliation(s)
- M Duman
- Institute for Biophysics, University of Linz, Linz, Austria
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4
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Trache A, Meininger GA. Total internal reflection fluorescence (TIRF) microscopy. ACTA ACUST UNITED AC 2008; Chapter 2:Unit 2A.2.1-2A.2.22. [PMID: 18729056 DOI: 10.1002/9780471729259.mc02a02s10] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Total internal reflection fluorescence (TIRF) microscopy represents a method of exciting and visualizing fluorophores present in the near-membrane region of live or fixed cells grown on coverslips. TIRF microscopy is based on the total internal reflection phenomenon that occurs when light passes from a high-refractive medium (e.g., glass) into a low-refractive medium (e.g., cell, water). The evanescent field produced by total internally reflected light excites the fluorescent molecules at the cell-substrate interface and is accompanied by minimal exposure of the remaining cell volume. This technique provides high-contrast fluorescence images, with very low background and virtually no out-of-focus light, ideal for visualization and spectroscopy of single-molecule fluorescence near a surface. This unit presents, in a concise manner, the principle of operation, instrument diversity, and TIRF microscopy applications for the study of biological samples.
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Affiliation(s)
- Andreea Trache
- Department of Systems Biology and Translational Medicine, College of Medicine, Texas A&M Health Science Center, College Station, Texas, USA
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Affiliation(s)
- Jeffrey R. Moffitt
- Department of Physics, University of California, Berkeley, California 94720
| | - Yann R. Chemla
- Department of Physics, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801
| | - Steven B. Smith
- Department of Physics, University of California, Berkeley, California 94720
| | - Carlos Bustamante
- Department of Physics, University of California, Berkeley, California 94720
- Departments of Chemistry, and Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, California 94720;
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6
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Ando T, Uchihashi T, Kodera N, Yamamoto D, Miyagi A, Taniguchi M, Yamashita H. High-speed AFM and nano-visualization of biomolecular processes. Pflugers Arch 2007; 456:211-25. [DOI: 10.1007/s00424-007-0406-0] [Citation(s) in RCA: 201] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2007] [Accepted: 11/15/2007] [Indexed: 11/28/2022]
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7
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Abstract
A recent study has analysed the action of bacterial DNA gyrase on a single substrate DNA molecule, discriminating the initial DNA wrapping and subsequent supercoiling steps in the reaction cycle.
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Affiliation(s)
- Andrew D Bates
- School of Biological Sciences, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK.
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Madl J, Rhode S, Stangl H, Stockinger H, Hinterdorfer P, Schütz GJ, Kada G. A combined optical and atomic force microscope for live cell investigations. Ultramicroscopy 2006; 106:645-51. [PMID: 16677764 DOI: 10.1016/j.ultramic.2005.12.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2005] [Accepted: 12/01/2005] [Indexed: 10/24/2022]
Abstract
We present an easy-to-use combination of an atomic force microscope (AFM) and an epi-fluorescence microscope, which allows live cell imaging under physiological conditions. High-resolution AFM images were acquired while simultaneously monitoring either the fluorescence image of labeled membrane components, or a high-contrast optical image (DIC, differential interference contrast). By applying two complementary techniques at the same time, additional information and correlations between structure and function of living organisms were obtained. The synergy effects between fluorescence imaging and AFM were further demonstrated by probing fluorescence-labeled receptor clusters in the cell membrane via force spectroscopy using antibody-functionalized tips. The binding probability on receptor-containing areas identified with fluorescence microscopy ("receptor-positive sites") was significantly higher than that on sites lacking receptors.
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Affiliation(s)
- Josef Madl
- Institute for Biophysics, Johannes Kepler University Linz, Altenbergerstr. 69, 4040 Linz, Austria
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9
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Pedersen UR, Leidy C, Westh P, Peters GH. The effect of calcium on the properties of charged phospholipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2006; 1758:573-82. [PMID: 16730642 DOI: 10.1016/j.bbamem.2006.03.035] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2005] [Revised: 03/08/2006] [Accepted: 03/14/2006] [Indexed: 11/28/2022]
Abstract
We have performed molecular dynamics simulations to investigate the structure and dynamics of charged bilayers as well as the distribution of counterions at the bilayer interface. For this, we have considered the negatively charged di-myristoyl-phosphatidyl-glycerol (DMPG) and di-myristoyl-phosphatidyl-serine (DMPS) bilayers as well as a protonated di-myristoyl-phosphatidyl-serine (DMPSH) bilayer. We were particularly interested in calcium ions due to their important role in biological systems. Simulations performed in the presence of calcium ions (DMPG, DMPS) or sodium ions (DMPS) were run for 45-60 ns. Simulation results for DMPG are compared with fluorescence measurements. The average areas per molecule were 47.4+/-0.5 A2 (DMPG with calcium), 47.3+/-0.5 A2 (DMPS with calcium), 51.3+/-1.0 A2 (DMPS with sodium) and 45.3+/-0.5 A2 (DMPSH). The structure of the negatively charged lipids is significantly affected by the counterions, where calcium ions have a more pronounced effect than sodium ions. Calcium ions were found to be tightly bound to the anionic groups of the lipid molecules and as such appear to constitute an integral part of the membrane interface on nanoseconds time scales. In contrast to sodium ions, calcium ions are localised in a narrow (approximately 10 A) band around the phosphate group. The interaction of calcium with the lipid molecules enhances the molecular packing of the PG and PS lipids. This observation is in good agreement with emission spectra of the membrane partitioning probe Laurdan in DMPG multilamellar vesicles that indicate an increase in the ordering of the DMPG bilayer due to the presence of calcium. Our results indicate that calcium ions, which often function as a second messengers in living cells have a pronounced effect on membrane structures, which may have implications during signal transduction events.
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Affiliation(s)
- Ulf R Pedersen
- Department of Life Science and Chemistry, Roskilde University, MEMPHYS-Center for Biomembrane Physics, 1 Universitetsvej, DK-4000 Roskilde, Denmark
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Brau RR, Tarsa PB, Ferrer JM, Lee P, Lang MJ. Interlaced optical force-fluorescence measurements for single molecule biophysics. Biophys J 2006; 91:1069-77. [PMID: 16648165 PMCID: PMC1563781 DOI: 10.1529/biophysj.106.082602] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Combining optical tweezers with single molecule fluorescence offers a powerful technique to study the biophysical properties of single proteins and molecules. However, such integration into a combined, coincident arrangement has been severely limited by the dramatic reduction in fluorescence longevity of common dyes under simultaneous exposure to trapping and fluorescence excitation beams. We present a novel approach to overcome this problem by alternately modulating the optical trap and excitation beams to prevent simultaneous exposure of the fluorescent dye. We demonstrate the dramatic reduction of trap-induced photobleaching effects on the common single molecule fluorescence dye Cy3, which is highly susceptible to this destructive pathway. The extension in characteristic fluorophore longevity, a 20-fold improvement when compared to simultaneous exposure to both beams, prolongs the fluorescence emission to several tens of seconds in a combined, coincident arrangement. Furthermore, we show that this scheme, interlaced optical force-fluorescence, does not compromise the trap stiffness or single molecule fluorescence sensitivity at sufficiently high modulation frequencies. Such improvement permits the simultaneous measurement of the mechanical state of a system with optical tweezers and the localization of molecular changes with single molecule fluorescence, as demonstrated by mechanically unzipping a 15-basepair DNA segment labeled with Cy3.
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Affiliation(s)
- Ricardo R Brau
- Department of Mechanical Engineering, Biological Engineering Division, Massachusetts Institute of Technology, Cambridge, 02139, USA
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11
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Gaiduk A, Kühnemuth R, Antonik M, Seidel CAM. Optical Characteristics of Atomic Force Microscopy Tips for Single-Molecule Fluorescence Applications. Chemphyschem 2005; 6:976-83. [PMID: 15884085 DOI: 10.1002/cphc.200400485] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Knowledge of the optical properties of atomic force microscopy (AFM) tips is relevant for the combination of optical and force spectroscopy. The luminescence properties of five commercial AFM tips were characterized using a combination of multiparameter fluorescence detection (MFD) and scanning confocal techniques. These include three Si3N4 tips, one silicon tip, and one high-density carbon (HDC) tip grown on top of a silicon tip. Time-decay histograms of the signal were analyzed to determine the strength of scatter, constant background, and fluorescence in the observed signal. Intensity and anisotropy images with optical resolution down to the diffraction limit were generated. The optical signal recorded from the apex of the Si3N4 tips ranged from 0.7 to 1.9 times the count rates from single Rhodamine 110 molecules under similar illumination conditions. The signal is predominantly composed of scatter and background (>85%), plus a small fluorescence component with lifetimes between 1 and 3 ns. The intensity of the recorded signal fell with increasing distance from the apex, and by 300 nm the signals fell below single-molecule levels for all Si3N4 cantilevers. Silicon cantilevers demonstrated very low count rates relative to single-molecule measurements under all conditions, and virtually no fluorescence. The high-density carbon tips also demonstrated low count rates, but the signal contained a short lifetime fluorescence component (0.7 ns). The intensity of the signals from each of the tips was geometry dependent, demonstrating the highest intensities at the edges and corners. Likewise, the anisotropy of all tip signals was observed to be geometry dependent, with the dependence varying on a case-by-case basis. The implications for using confocal illumination instead of total internal reflection are discussed.
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Affiliation(s)
- Alexander Gaiduk
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, Universitätsstrasse 1, Geb 26.32, 40225 Düsseldorf, Germany
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12
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Kassies R, van der Werf KO, Lenferink A, Hunter CN, Olsen JD, Subramaniam V, Otto C. Combined AFM and confocal fluorescence microscope for applications in bio-nanotechnology. J Microsc 2005; 217:109-16. [PMID: 15655068 DOI: 10.1111/j.0022-2720.2005.01428.x] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a custom-designed atomic force fluorescence microscope (AFFM), which can perform simultaneous optical and topographic measurements with single molecule sensitivity throughout the whole visible to near-infrared spectral region. Integration of atomic force microscopy (AFM) and confocal fluorescence microscopy combines the high-resolution topographical imaging of AFM with the reliable (bio)-chemical identification capability of optical methods. The AFFM is equipped with a spectrograph enabling combined topographic and fluorescence spectral imaging, which significantly enhances discrimination of spectroscopically distinct objects. The modular design allows easy switching between different modes of operation such as tip-scanning, sample-scanning or mechanical manipulation, all of which are combined with synchronous optical detection. We demonstrate that coupling the AFM with the fluorescence microscope does not compromise its ability to image with a high spatial resolution. Examples of several modes of operation of the AFFM are shown using two-dimensional crystals and membranes containing light-harvesting complexes from the photosynthetic bacterium Rhodobacter sphaeroides.
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Affiliation(s)
- R Kassies
- BMTI Institute for Biomedical Technology, University of Twente, PO Box 217, 7500 AE Enschede, The Netherlands
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Santos NC, Castanho MARB. An overview of the biophysical applications of atomic force microscopy. Biophys Chem 2004; 107:133-49. [PMID: 14962595 DOI: 10.1016/j.bpc.2003.09.001] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2002] [Revised: 07/30/2003] [Accepted: 09/04/2003] [Indexed: 11/27/2022]
Abstract
The potentialities of the atomic force microscopy (AFM) make it a tool of undeniable value for the study of biologically relevant samples. AFM is progressively becoming a usual benchtop technique. In average, more than one paper is published every day on AFM biological applications. This figure overcomes materials science applications, showing that 17 years after its invention, AFM has completely crossed the limits of its traditional areas of application. Its potential to image the structure of biomolecules or bio-surfaces with molecular or even sub-molecular resolution, study samples under physiological conditions (which allows to follow in situ the real time dynamics of some biological events), measure local chemical, physical and mechanical properties of a sample and manipulate single molecules should be emphasized.
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Affiliation(s)
- Nuno C Santos
- Instituto de Bioquímica/Instituto de Medicina Molecular, Faculdade de Medicina de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal.
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