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Kiss B, Mudra D, Török G, Mártonfalvi Z, Csík G, Herényi L, Kellermayer M. Single-particle virology. Biophys Rev 2020; 12:1141-1154. [PMID: 32880826 PMCID: PMC7471434 DOI: 10.1007/s12551-020-00747-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 08/18/2020] [Indexed: 01/02/2023] Open
Abstract
The development of advanced experimental methodologies, such as optical tweezers, scanning-probe and super-resolved optical microscopies, has led to the evolution of single-molecule biophysics, a field of science that allows direct access to the mechanistic detail of biomolecular structure and function. The extension of single-molecule methods to the investigation of particles such as viruses permits unprecedented insights into the behavior of supramolecular assemblies. Here we address the scope of viral exploration at the level of individual particles. In an era of increased awareness towards virology, single-particle approaches are expected to facilitate the in-depth understanding, and hence combating, of viral diseases.
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Affiliation(s)
- Bálint Kiss
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Dorottya Mudra
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - György Török
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Zsolt Mártonfalvi
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Gabriella Csík
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Levente Herényi
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Miklós Kellermayer
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary.
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2
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Thamm S, Slesiona N, Dathe A, Csáki A, Fritzsche W. AFM-Based Probing of the Flexibility and Surface Attachment of Immobilized DNA Origami. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:15093-15098. [PMID: 30252490 DOI: 10.1021/acs.langmuir.8b02362] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The flexible and precise immobilization of self-organizing DNA nanostructures represents a key step in the integration of DNA-based material for potential electronic or sensor applications. However, the involved processes have still not been well studied and are not yet fully understood. Thus, we investigated the potential for the mechanical manipulation of DNA origami by atomic force microscopy (AFM) in order to study the interaction between intramolecular flexibility and surface-attachment forces. AFM is particularly suitable for nanoscale manipulation. Previous studies showed the potential for pushing, bending, and cutting double-stranded DNA (dsDNA) with an AFM tip. Understanding the involved parameters may enable control over different processes such as nanointegration, precise cutting, and stretching of preassembled DNA origami. We demonstrate the defined manipulation and flexibility of DNA origami immobilized on mica in the nanometer range: controlled cutting, folding, and stretching as a function of the magnesium concentration.
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Affiliation(s)
- Sophie Thamm
- Leibniz-Institute of Photonic Technology , 07745 Jena , Germany
| | - Nicole Slesiona
- Leibniz-Institute of Photonic Technology , 07745 Jena , Germany
| | - André Dathe
- Leibniz-Institute of Photonic Technology , 07745 Jena , Germany
- Jena University Hospital, Friedrich-Schiller-University , 07745 Jena , Germany
| | - Andrea Csáki
- Leibniz-Institute of Photonic Technology , 07745 Jena , Germany
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3
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Caluori G, Pribyl J, Cmiel V, Pesl M, Potocnak T, Provaznik I, Skladal P, Rotrekl V. Simultaneous study of mechanobiology and calcium dynamics on hESC-derived cardiomyocytes clusters. J Mol Recognit 2018; 32:e2760. [PMID: 30084213 DOI: 10.1002/jmr.2760] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 06/11/2018] [Accepted: 07/07/2018] [Indexed: 12/19/2022]
Abstract
Calcium ions act like ubiquitous second messengers in a wide amount of cellular processes. In cardiac myocytes, Ca2+ handling regulates the mechanical contraction necessary to the heart pump function. The field of intracellular and intercellular Ca2+ handling, employing in vitro models of cardiomyocytes, has become a cornerstone to understand the role and adaptation of calcium signalling in healthy and diseased hearts. Comprehensive in vitro systems and cell-based biosensors are powerful tools to enrich and speed up cardiac phenotypic and drug response evaluation. We have implemented a combined setup to measure contractility and calcium waves in human embryonic stem cells-derived cardiomyocyte 3D clusters, obtained from embryoid body differentiation. A combination of atomic force microscopy to monitor cardiac contractility, and sensitive fast scientific complementary metal-oxide-semiconductor camera for epifluorescence video recording, provided correlated signals in real time. To speed up the integrated data processing, we tested several post-processing algorithms, to improve the automatic detection of relevant functional parameters. The validation of our proposed method was assessed by caffeine stimulation (10mM) and detection/characterization of the induced cardiac response. We successfully report the first simultaneous recording of cardiac contractility and calcium waves on the described cardiac 3D models. The drug stimulation confirmed the automatic detection capabilities of the used algorithms, measuring expected physiological response, such as elongation of contraction time and Ca2+ cytosolic persistence, increased calcium basal fluorescence, and transient peaks. These results contribute to the implementation of novel, integrated, high-information, and reliable experimental systems for cardiac models and drug evaluation.
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Affiliation(s)
- Guido Caluori
- International Clinical Research Centre of Saint Anne Hospital of Brno (FNUSA-ICRC), Interventional Cardiac Electrophysiology Group, Brno, Czech Republic.,Nanobiotechnology Group, Central European Institute of Technology of Masaryk University (CEITEC-MU), Brno, Czech Republic
| | - Jan Pribyl
- Nanobiotechnology Group, Central European Institute of Technology of Masaryk University (CEITEC-MU), Brno, Czech Republic
| | - Vratislav Cmiel
- Department of Biomedical Engineering, Brno University of Technology, Faculty of Electrical Engineering and Communication, Brno, Czech Republic
| | - Martin Pesl
- International Clinical Research Centre of Saint Anne Hospital of Brno (FNUSA-ICRC), Interventional Cardiac Electrophysiology Group, Brno, Czech Republic.,Department of Biology, Masaryk University, Faculty of Medicine, Brno, Czech Republic
| | - Tomas Potocnak
- Department of Biomedical Engineering, Brno University of Technology, Faculty of Electrical Engineering and Communication, Brno, Czech Republic
| | - Ivo Provaznik
- Department of Biomedical Engineering, Brno University of Technology, Faculty of Electrical Engineering and Communication, Brno, Czech Republic
| | - Petr Skladal
- Nanobiotechnology Group, Central European Institute of Technology of Masaryk University (CEITEC-MU), Brno, Czech Republic
| | - Vladimir Rotrekl
- Department of Biology, Masaryk University, Faculty of Medicine, Brno, Czech Republic
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4
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Ikai A, Afrin R, Saito M, Watanabe-Nakayama T. Atomic force microscope as a nano- and micrometer scale biological manipulator: A short review. Semin Cell Dev Biol 2017; 73:132-144. [PMID: 28739341 DOI: 10.1016/j.semcdb.2017.07.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 07/16/2017] [Accepted: 07/19/2017] [Indexed: 11/27/2022]
Abstract
The amazing capacity of atomic force microscope to let us touch the molecular and cellular level samples with a sharp probe stimulated its application to bio-medical field among others. In addition to topographical imaging of the sample surface, a direct mechanical manipulation has attracted innovative minds to develop new methodologies aiming at direct handling of proteins, DNA/RNA, and cells. Measurement of their mechanical properties brought about a vivid picture of their physical nature. Direct handling of individual molecules and cells prompted development of nano-medical applications. This short review summarized recent application of AFM for measurement of mechanical properties of biological samples and attempts to perform direct manipulations of nano-medicine.
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Affiliation(s)
- Atsushi Ikai
- Innovation Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan.
| | - Rehana Afrin
- Innovation Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan.
| | - Masakazu Saito
- Innovation Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan.
| | - Takahiro Watanabe-Nakayama
- Innovation Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan.
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5
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Wan M, Sun D, Wang S, Wu J, Yang Y, Wang K, He Q, Wang G, Bai J. Influence of concentration on distribution properties of stretched-DNA in the MEC studied with fluorescence imaging and drop shape analyzing. Colloids Surf B Biointerfaces 2017; 151:11-18. [PMID: 27939693 DOI: 10.1016/j.colsurfb.2016.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/19/2016] [Accepted: 12/01/2016] [Indexed: 11/28/2022]
Abstract
Stretching and manipulating DNA efficiently is significant for exploring the properties and applications of single DNA molecules. Here, the influence of concentrations of buffer and DNA on properties of stretched DNA molecules in the molecular evaporation combing (MEC) is investigated systematically with the single molecule fluorescence imaging microscopy and the high-precision drop shape analyzing technology. The stretched degree and uniformity of combed DNA molecules decrease as the buffer concentration are increased from 7 to 20mM. When the buffer concentration changes from 12 to 15mM, the stretched DNA molecules are apt to form a ringlike pattern. During the MEC process, there exist two kinds of evaporation modes, i.e., the constant contact angle mode and the constant contact radius mode. The former only takes effect in the lower concentration of buffer and DNA, enabling the uniform stretching. While the latter plays the leading role in the higher concentration, promoting the formation of the ringlike pattern of DNA molecules.
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Affiliation(s)
- Mengjiao Wan
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nanofunctional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, Shaanxi, China; School of Physics, Northwest University, Xi'an 710069, Shaanxi, China
| | - Dan Sun
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nanofunctional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, Shaanxi, China
| | - Shuang Wang
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nanofunctional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, Shaanxi, China
| | - Jianguo Wu
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nanofunctional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, Shaanxi, China
| | - Yuanyuan Yang
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nanofunctional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, Shaanxi, China
| | - Kaige Wang
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nanofunctional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, Shaanxi, China.
| | - Qingli He
- School of Physics, Northwest University, Xi'an 710069, Shaanxi, China
| | - Guiren Wang
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nanofunctional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, Shaanxi, China; Mechanical Engineering Department & Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, USA
| | - Jintao Bai
- State Key Laboratory of Cultivation Base for Photoelectric Technology and Functional Materials, Laboratory of Optoelectronic Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nanofunctional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, Shaanxi, China; School of Physics, Northwest University, Xi'an 710069, Shaanxi, China
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6
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Pires RH, Felix SB, Delcea M. The architecture of neutrophil extracellular traps investigated by atomic force microscopy. NANOSCALE 2016; 8:14193-14202. [PMID: 27387552 DOI: 10.1039/c6nr03416k] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Neutrophils are immune cells that engage in a suicidal pathway leading to the release of partially decondensed chromatin, or neutrophil extracellular traps (NETs). NETs behave as a double edged sword; they can bind to pathogens thereby ensnaring them and limiting their spread during infection; however, they may bind to host circulating materials and trigger thrombotic events, and are associated with autoimmune disorders. Despite the fundamental role of NETs as part of an immune system response, there is currently a very poor understanding of how their nanoscale properties are reflected in their macroscopic impact. In this work, using a combination of fluorescence and atomic force microscopy, we show that NETs appear as a branching filament network that results in a substantially organized porous structure with openings with 0.03 ± 0.04 μm(2) on average and thus in the size range of small pathogens. Topological profiles typically up to 3 ± 1 nm in height are compatible with a "beads on a string" model of nucleosome chromatin. Typical branch lengths of 153 ± 103 nm appearing as rigid rods and height profiles of naked DNA in NETs of 1.2 ± 0.5 nm are indicative of extensive DNA supercoiling throughout NETs. The presence of DNA duplexes could also be inferred from force spectroscopy and the occurrence of force plateaus that ranged from ∼65 pN to 300 pN. Proteolytic digestion of NETs resulted in widespread disassembly of the network structure and considerable loss of mechanical properties. Our results suggest that the underlying structure of NETs is considerably organized and that part of its protein content plays an important role in maintaining its mesh architecture. We anticipate that NETs may work as microscopic mechanical sieves with elastic properties that stem from their DNA-protein composition, which is able to segregate particles also as a result of their size. Such a behavior may explain their participation in capturing pathogens and their association with thrombosis.
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Affiliation(s)
- Ricardo H Pires
- ZIK HIKE - Center for Innovation Competence, Humoral Immune Reactions in Cardiovascular Diseases, University of Greifswald, Germany.
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7
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Jacobs MJ, Blank K. Joining forces: integrating the mechanical and optical single molecule toolkits. Chem Sci 2014. [DOI: 10.1039/c3sc52502c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Combining single molecule force measurements with fluorescence detection opens up exciting new possibilities for the characterization of mechanoresponsive molecules in Biology and Materials Science.
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Affiliation(s)
- Monique J. Jacobs
- Radboud University Nijmegen
- Institute for Molecules and Materials
- Department of Molecular Materials
- 6525 AJ Nijmegen, The Netherlands
| | - Kerstin Blank
- Radboud University Nijmegen
- Institute for Molecules and Materials
- Department of Molecular Materials
- 6525 AJ Nijmegen, The Netherlands
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8
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Frey EW, Gooding AA, Wijeratne S, Kiang CH. Understanding the physics of DNA using nanoscale single-molecule manipulation. FRONTIERS OF PHYSICS 2012; 7:576-581. [PMID: 23467419 PMCID: PMC3586743 DOI: 10.1007/s11467-012-0261-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Processes for decoding the genetic information in cells, including transcription, replication, recombination and repair, involve the deformation of DNA from its equilibrium structures such as bending, stretching, twisting, and unzipping of the double helix. Single-molecule manipulation techniques have made it possible to control DNA conformation and simultaneously detect the induced changes, revealing a rich variety of mechanically-induced conformational changes and thermodynamic states. These single-molecule techniques helped us to reveal the physics of DNA and the processes involved in the passing on of the genetic code.
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9
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Affiliation(s)
- Elias M. Puchner
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158;
| | - Hermann E. Gaub
- Center for Nanoscience and Department of Physics, University of Munich, 80799 Munich, Germany;
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10
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Brenner MD, Zhou R, Ha T. Forcing a connection: impacts of single-molecule force spectroscopy on in vivo tension sensing. Biopolymers 2011; 95:332-44. [PMID: 21267988 PMCID: PMC3097292 DOI: 10.1002/bip.21587] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Revised: 12/21/2010] [Accepted: 12/22/2010] [Indexed: 01/01/2023]
Abstract
Mechanical tension plays a large role in cell development ranging from morphology to gene expression. On the molecular level, the effects of tension can be seen in the dynamic arrangement of membrane proteins as well as the recruitment and activation of intracellular proteins. Forces applied to biopolymers during in vitro force measurements offer greater understanding of the effects of tension on molecules in live cells, and experimental techniques involving test tubes and live cells can often overlap. Indeed, when forces exerted on cellular components can be calibrated ex vivo with force spectroscopy, a powerful tool is available for researchers in probing cellular mechanotransduction on the molecular scale. This review will discuss the techniques used in measuring both cellular traction forces and single-molecule force spectroscopy. Emphasis will be placed on the use of fluorescence reporter systems for the development of in vivo tension sensors that can be used for calibration with single molecule force methods.
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Affiliation(s)
- Michael D Brenner
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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11
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Baclayon M, Roos WH, Wuite GJL. Sampling protein form and function with the atomic force microscope. Mol Cell Proteomics 2010; 9:1678-88. [PMID: 20562411 PMCID: PMC2938060 DOI: 10.1074/mcp.r110.001461] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Indexed: 12/17/2022] Open
Abstract
To study the structure, function, and interactions of proteins, a plethora of techniques is available. Many techniques sample such parameters in non-physiological environments (e.g. in air, ice, or vacuum). Atomic force microscopy (AFM), however, is a powerful biophysical technique that can probe these parameters under physiological buffer conditions. With the atomic force microscope operating under such conditions, it is possible to obtain images of biological structures without requiring labeling and to follow dynamic processes in real time. Furthermore, by operating in force spectroscopy mode, it can probe intramolecular interactions and binding strengths. In structural biology, it has proven its ability to image proteins and protein conformational changes at submolecular resolution, and in proteomics, it is developing as a tool to map surface proteomes and to study protein function by force spectroscopy methods. The power of AFM to combine studies of protein form and protein function enables bridging various research fields to come to a comprehensive, molecular level picture of biological processes. We review the use of AFM imaging and force spectroscopy techniques and discuss the major advances of these experiments in further understanding form and function of proteins at the nanoscale in physiologically relevant environments.
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Affiliation(s)
- Marian Baclayon
- From the Natuur- en Sterrenkunde and Lasercentrum, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Wouter H. Roos
- From the Natuur- en Sterrenkunde and Lasercentrum, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Gijs J. L. Wuite
- From the Natuur- en Sterrenkunde and Lasercentrum, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
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12
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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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13
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Gumpp H, Stahl SW, Strackharn M, Puchner EM, Gaub HE. Ultrastable combined atomic force and total internal reflection fluorescence microscope [corrected]. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2009; 80:063704. [PMID: 19566207 DOI: 10.1063/1.3148224] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Combining atomic force microscope (AFM) with other microscopy techniques has expanded the range of potential applications for single molecule investigations dramatically. Particularly hybrid instruments with total internal reflection fluorescence (TIRF) excitation have opened new routes in life sciences. Here we present a novel design for such a hybrid microscope, which overcomes the limitations of conventional combinations caused by their limited mechanical stability. A thorough analysis of the noise spectra and a comparison of the different designs and the different operation modes are given. With this instrument we demonstrate single molecule manipulation by AFM and simultaneous TIRF imaging.
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Affiliation(s)
- H Gumpp
- Chair for Applied Physics and Center for NanoScience, Ludwig-Maximilians-University Munich, Amalienstr. 54, D-80799 Munich, Germany
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14
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van ’t Hoff M, Reuter M, Dryden DTF, Oheim M. Screening by imaging: scaling up single-DNA-molecule analysis with a novel parabolic VA-TIRF reflector and noise-reduction techniques. Phys Chem Chem Phys 2009; 11:7713-20. [DOI: 10.1039/b823155a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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Asahi T, Sugiyama T, Masuhara H. Laser fabrication and spectroscopy of organic nanoparticles. Acc Chem Res 2008; 41:1790-8. [PMID: 18937507 DOI: 10.1021/ar800125s] [Citation(s) in RCA: 171] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In working with nanoparticles, researchers still face two fundamental challenges: how to fabricate the nanoparticles with controlled size and shape and how to characterize them. In this Account, we describe recent advances in laser technology both for the synthesis of organic nanoparticles and for their analysis by single nanoparticle spectroscopy. Laser ablation of organic microcrystalline powders in a poor solvent has opened new horizons for the synthesis of nanoparticles because the powder sample is converted directly into a stable colloidal solution without additives and chemicals. By tuning laser wavelength, pulse width, laser fluence, and total shot number, we could control the size and phase of the nanoparticles. For example, we describe nanoparticle formation of quinacridone, a well-known red pigment, in water. By modifying the length of time that the sample is excited by the laser, we could control the particle size (30-120 nm) for nanosecond excitation down to 13 nm for femtosecond irradiation. We prepared beta- and gamma-phase nanoparticles from the microcrystal with beta-phase by changing laser wavelength and fluence. We present further results from nanoparticles produced from several dyes, C(60), and an anticancer drug. All the prepared colloidal solutions were transparent and highly dispersive. Such materials could be used for nanoscale device development and for biomedical and environmental applications. We also demonstrated the utility of single nanoparticle spectroscopic analysis in the characterization of organic nanoparticles. The optical properties of these organic nanoparticles depend on their size within the range from a few tens to a few hundred nanometers. We observed perylene nanoscrystals using single-particle spectroscopy coupled with atomic force microscopy. Based on these experiments, we proposed empirical equations explaining their size-dependent fluorescence spectra. We attribute the size effect to the change in elastic properties of the nanocrystal. Based on the results for nanoparticles of polymers and other molecules with flexible conformations, we assert that size-dependent optical properties are common for organic nanoparticles. While "electronic confinement" explains the size-dependent properties of inorganic nanoparticles, we propose "structural confinement" as an analogous paradigm for organic nanoparticles.
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Affiliation(s)
- T. Asahi
- Department of Applied Physics, Osaka University, Suita, Osaka 565-0871, Japan
| | - T. Sugiyama
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - H. Masuhara
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan
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16
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Wang W, Li ADQ. Design and synthesis of efficient fluorescent dyes for incorporation into DNA backbone and biomolecule detection. Bioconjug Chem 2007; 18:1036-52. [PMID: 17508711 PMCID: PMC2546358 DOI: 10.1021/bc060151c] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We report here the design and synthesis of a series of pi-conjugated fluorescent dyes with D-A-D (D, donor; A, acceptor), D-pi-D, A-pi-A, and D-pi-A for applications as the signaling motif in biological-synthetic hybrid foldamers for DNA detection. The Horner-Wadsworth-Emmons (HWE) reaction and Knoevenagel condensation were demonstrated as the optimum ways for construction of long pi-conjugated systems. Such rodlike chromophores have distinct advantages, as their fluorescence properties are not quenched by the presence of DNA. To be incorporated into the backbone of DNA, the chromophores need to be reasonably soluble in organic solvent for solid-phase synthesis, and therefore a strategy of using flexible tetraethylene glycol (TEG) linkers at either end of these rodlike dyes was developed. The presence of TEG facilitates the protection of the chain-growing hydroxyl group with DMTrCl (dimethoxytrityl chloride) as well as the activation of the coupling step with phosphoramidite chemistry on an automated DNA synthesizer. To form fluorescence resonance energy transfer (FRET) pairs, six synthetic chromophores with blue to red fluorescence have been developed, and those with orthogonal fluorescent emission were chosen for incorporation into DNA-chromophore hybrid foldamers.
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Gaiduk A, Kühnemuth R, Felekyan S, Antonik M, Becker W, Kudryavtsev V, Sandhagen C, Seidel CAM. Fluorescence detection with high time resolution: From optical microscopy to simultaneous force and fluorescence spectroscopy. Microsc Res Tech 2007; 70:433-41. [PMID: 17393495 DOI: 10.1002/jemt.20430] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Picosecond time-resolution fluorescence signal detection over many hours is possible using the time-correlated single photon counting (TCSPC) technique. Advanced TCSPC with clock oscillator set by the pulsed laser and data analysis provides a tool to investigate processes in single molecules on time scale from picoseconds to seconds. Optical imaging techniques combined with TCSPC allow one to study the spatial distribution of fluorescence properties in solution and on a surface. Mechanical manipulation of a single macromolecule by means of an atomic-force microscope makes it possible to detect fluorescence signal changes as a function of mechanical conformations of a fluorescent dye attached to a single DNA molecule.
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18
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Laser literature watch. Photomed Laser Surg 2006; 24:537-71. [PMID: 16942439 DOI: 10.1089/pho.2006.24.537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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19
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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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