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van den Wildenberg SMJL, Prevo B, Peterman EJG. A Brief Introduction to Single-Molecule Fluorescence Methods. Methods Mol Biol 2024; 2694:111-132. [PMID: 37824002 DOI: 10.1007/978-1-0716-3377-9_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
One of the most popular single-molecule approaches in biological science is single-molecule fluorescence microscopy, which will be the subject of the following section of this volume. Fluorescence methods provide the sensitivity required to study biology on the single-molecule level, but they also allow access to useful measurable parameters on time and length scales relevant for the biomolecular world. Before several detailed experimental approaches will be addressed, we will first give a general overview of single-molecule fluorescence microscopy. We start with discussing the phenomenon of fluorescence in general and the history of single-molecule fluorescence microscopy. Next, we will review fluorescent probes in more detail and the equipment required to visualize them on the single-molecule level. We will end with a description of parameters measurable with such approaches, ranging from protein counting and tracking, single-molecule localization super-resolution microscopy, to distance measurements with Förster resonance energy transfer and orientation measurements with fluorescence polarization.
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Affiliation(s)
- Siet M J L van den Wildenberg
- LaserLaB and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Université Clermont Auvergne, CNRS, IRD, OPGC, Laboratoire Magmas et Volcans, Clermont-Ferrand, France
- Université Clermont Auvergne, CNRS/IN2P3, Laboratoire de Physique de Clermont, Clermont-Ferrand, France
| | - Bram Prevo
- LaserLaB and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Erwin J G Peterman
- LaserLaB and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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2
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Xia H, Yu Z, Zhang L, Liu S, Zhao Y, Huang J, Fu D, Xie Q, Liu H, Zhang Z, Zhao Y, Wu M, Zhang W, Pang D, Chen G. Real-Time Dissection of the Transportation and miRNA-Release Dynamics of Small Extracellular Vesicles. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2205566. [PMID: 36599707 PMCID: PMC9982592 DOI: 10.1002/advs.202205566] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Extracellular vesicles (EVs) are cell-derived membrane-enclosed structures that deliver biomolecules for intercellular communication. Developing visualization methods to elucidate the spatiotemporal dynamics of EVs' behaviors will facilitate their understanding and translation. With a quantum dot (QD) labeling strategy, a single particle tracking (SPT) platform is proposed here for dissecting the dynamic behaviors of EVs. The interplays between tumor cell-derived small EVs (T-sEVs) and endothelial cells (ECs) are specifically investigated based on this platform. It is revealed that, following a clathrin-mediated endocytosis by ECs, T-sEVs are transported to the perinuclear region in a typical three-stage pattern. Importantly, T-sEVs frequently interact with and finally enter lysosomes, followed by quick release of their carried miRNAs. This study, for the first time, reports the entire process and detailed dynamics of T-sEV transportation and cargo-release in ECs, leading to better understanding of their proangiogenic functions. Additionally, the QD-based SPT technique will help uncover more secrets of sEV-mediated cell-cell communication.
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Affiliation(s)
- Hou‐Fu Xia
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei‐MOST) and Key Laboratory of Oral Biomedicine Ministry of EducationSchool and Hospital of StomatologyWuhan UniversityWuhan430079P. R. China
- Department of Oral and Maxillofacial SurgerySchool and Hospital of StomatologyWuhan UniversityWuhan430079P. R. China
| | - Zi‐Li Yu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei‐MOST) and Key Laboratory of Oral Biomedicine Ministry of EducationSchool and Hospital of StomatologyWuhan UniversityWuhan430079P. R. China
- Department of Oral and Maxillofacial SurgerySchool and Hospital of StomatologyWuhan UniversityWuhan430079P. R. China
| | - Li‐Juan Zhang
- College of Chemistry and Molecular SciencesWuhan UniversityWuhan430072P. R. China
| | - Shu‐Lin Liu
- State Key Laboratory of Medicinal Chemical BiologyTianjin Key Laboratory of Biosensing and Molecular RecognitionResearch Center for Analytical Sciencesand College of ChemistryNankai UniversityTianjin300071P. R. China
| | - Yi Zhao
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei‐MOST) and Key Laboratory of Oral Biomedicine Ministry of EducationSchool and Hospital of StomatologyWuhan UniversityWuhan430079P. R. China
- Department of ProsthodonticsSchool and Hospital of StomatologyWuhan UniversityWuhan430079P. R. China
| | - Jue Huang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei‐MOST) and Key Laboratory of Oral Biomedicine Ministry of EducationSchool and Hospital of StomatologyWuhan UniversityWuhan430079P. R. China
| | - Dan‐Dan Fu
- College of Chemistry and Molecular SciencesWuhan UniversityWuhan430072P. R. China
| | - Qi‐Hui Xie
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei‐MOST) and Key Laboratory of Oral Biomedicine Ministry of EducationSchool and Hospital of StomatologyWuhan UniversityWuhan430079P. R. China
| | - Hai‐Ming Liu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei‐MOST) and Key Laboratory of Oral Biomedicine Ministry of EducationSchool and Hospital of StomatologyWuhan UniversityWuhan430079P. R. China
| | - Zhi‐Ling Zhang
- College of Chemistry and Molecular SciencesWuhan UniversityWuhan430072P. R. China
| | - Yi‐Fang Zhao
- Department of Oral and Maxillofacial SurgerySchool and Hospital of StomatologyWuhan UniversityWuhan430079P. R. China
| | - Min Wu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei‐MOST) and Key Laboratory of Oral Biomedicine Ministry of EducationSchool and Hospital of StomatologyWuhan UniversityWuhan430079P. R. China
| | - Wei Zhang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei‐MOST) and Key Laboratory of Oral Biomedicine Ministry of EducationSchool and Hospital of StomatologyWuhan UniversityWuhan430079P. R. China
- Department of Oral and Maxillofacial SurgerySchool and Hospital of StomatologyWuhan UniversityWuhan430079P. R. China
| | - Dai‐Wen Pang
- State Key Laboratory of Medicinal Chemical BiologyTianjin Key Laboratory of Biosensing and Molecular RecognitionResearch Center for Analytical Sciencesand College of ChemistryNankai UniversityTianjin300071P. R. China
| | - Gang Chen
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei‐MOST) and Key Laboratory of Oral Biomedicine Ministry of EducationSchool and Hospital of StomatologyWuhan UniversityWuhan430079P. R. China
- Department of Oral and Maxillofacial SurgerySchool and Hospital of StomatologyWuhan UniversityWuhan430079P. R. China
- TaiKang Center for Life and Medical SciencesWuhan UniversityWuhan430071P. R. China
- Frontier Science Center for Immunology and MetabolismWuhan UniversityWuhan430071P. R. China
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3
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Aaron J, Wait E, DeSantis M, Chew TL. Practical Considerations in Particle and Object Tracking and Analysis. ACTA ACUST UNITED AC 2019; 83:e88. [PMID: 31050869 DOI: 10.1002/cpcb.88] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The rapid advancement of live-cell imaging technologies has enabled biologists to generate high-dimensional data to follow biological movement at the microscopic level. Yet, the "perceived" ease of use of modern microscopes has led to challenges whereby sub-optimal data are commonly generated that cannot support quantitative tracking and analysis as a result of various ill-advised decisions made during image acquisition. Even optimally acquired images often require further optimization through digital processing before they can be analyzed. In writing this article, we presume our target audience to be biologists with a foundational understanding of digital image acquisition and processing, who are seeking to understand the essential steps for particle/object tracking experiments. It is with this targeted readership in mind that we review the basic principles of image-processing techniques as well as analysis strategies commonly used for tracking experiments. We conclude this technical survey with a discussion of how movement behavior can be mathematically modeled and described. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Jesse Aaron
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia
| | - Eric Wait
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia
| | - Michael DeSantis
- Light Microscopy Facility, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia
| | - Teng-Leong Chew
- Advanced Imaging Center, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia.,Light Microscopy Facility, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia
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Pillai SS, Yukawa H, Onoshima D, Biju V, Baba Y. Förster Resonance Energy Transfer Mediated Photoluminescence Quenching in Stoichiometrically Assembled CdSe/ZnS Quantum Dot-Peptide Labeled Black Hole Quencher Conjugates for Matrix Metalloproteinase-2 Sensing. ANAL SCI 2018; 33:137-142. [PMID: 28190830 DOI: 10.2116/analsci.33.137] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The steady state and time-resolved photoluminescence quenching of streptavidin modified CdSe/ZnS quantum dots (QDs) instigated by biotin-peptide-BHQ-1 (biotin-pep-BHQ-1) molecule was investigated. Here, we have achieved an efficient photoluminescence (PL) quenching of QDs with the conjugation of dark quencher (black hole quencher-BHQ) molecules intermediated with the GPLGVRGK peptide. The luminescence of streptavidin-QDs585 was decreased upon titration with a nano molar concentration of the biotin-GPLGVRGK-BHQ-1 molecule. It has been suggested that the decrease of QDs PL occurred through a Förster resonance energy transfer (FRET) mechanism from the analysis of steady state photoluminescence intensity measurements as well as time resolved lifetime measurements of streptavidin-QDs and QDs-(pep-BHQ-1)n conjugates. The sequence of intermediate peptide GPLG↓VRGK can act as a target material for matrix metalloproteinases-2 (MMP-2) produced by cancer cells at its Gly and Val region, shown by the down-headed arrow. Interestingly, here the reported self-assembled QDs-(pep-BHQ-1)n conjugates could detect the presence MMP-2 at a detection limit of 1 ng/mL with a clear luminescence recovery.
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van den Wildenberg SMJL, Prevo B, Peterman EJG. A Brief Introduction to Single-Molecule Fluorescence Methods. Methods Mol Biol 2018; 1665:93-113. [PMID: 28940065 DOI: 10.1007/978-1-4939-7271-5_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
One of the more popular single-molecule approaches in biological science is single-molecule fluorescence microscopy, which will be the subject of the following section of this volume. Fluorescence methods provide the sensitivity required to study biology on the single-molecule level, but they also allow access to useful measurable parameters on time and length scales relevant for the biomolecular world. Before several detailed experimental approaches will be addressed, we will first give a general overview of single-molecule fluorescence microscopy. We start with discussing the phenomenon of fluorescence in general and the history of single-molecule fluorescence microscopy. Next, we will review fluorescent probes in more detail and the equipment required to visualize them on the single-molecule level. We will end with a description of parameters measurable with such approaches, ranging from protein counting and tracking, single-molecule localization super-resolution microscopy, to distance measurements with Förster Resonance Energy Transfer and orientation measurements with fluorescence polarization.
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Affiliation(s)
- Siet M J L van den Wildenberg
- LaserLaB and Department of Physics and Astronomy, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
- Équipe de Volcanologie, Observatoire de Physique de Globe, Clermant-Ferrand, France
| | - Bram Prevo
- LaserLaB and Department of Physics and Astronomy, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Erwin J G Peterman
- LaserLaB and Department of Physics and Astronomy, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands.
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Yukawa H, Watanabe M, Kaji N, Baba Y. Influence of Autofluorescence Derived From Living Body on In Vivo Fluorescence Imaging Using Quantum Dots. CELL MEDICINE 2015; 7:75-82. [PMID: 26858896 PMCID: PMC4733839 DOI: 10.3727/215517914x685169] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Quantum dots (QDs) are thought to be a novel inorganic probe for in vivo fluorescence imaging because of their excellent fluorescence properties. Autofluorescence is generally known to be produced from various living bodies including humans, rats, and mice. However, the influence of the autofluorescence on in vivo fluorescence imaging using QDs remains poorly understood. In this article, we assessed the autofluorescence derived from a mouse body and the influence of the autofluorescence on in vivo fluorescence imaging using QDs. The dorsal and ventral autofluorescence derived from a mouse from which the hair was removed were detected under all kinds of excitation/fluorescence filter settings (blue, green, yellow, red, deep red, and NIR) using the Maestro™ in vivo imaging system. The degree of autofluorescence was found to be extremely high in the red filter condition, but transplanted ASCs labeled with QDs on the back of a mouse could be detected in the red filter condition. Moreover, the ASCs labeled with QDs could be traced for at least 5 days. We suggest that fluorescence imaging using QDs can be useful for the detection of transplanted cells.
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Affiliation(s)
- Hiroshi Yukawa
- *Research Center for Innovative Nanobiodevices, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Masaki Watanabe
- †Department of Applied Chemistry, Nagoya University, Graduate School of Engineering, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Noritada Kaji
- *Research Center for Innovative Nanobiodevices, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
- †Department of Applied Chemistry, Nagoya University, Graduate School of Engineering, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Yoshinobu Baba
- *Research Center for Innovative Nanobiodevices, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
- †Department of Applied Chemistry, Nagoya University, Graduate School of Engineering, Furo-cho, Chikusa-ku, Nagoya, Japan
- ‡Health Technology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Hayashi-cho, Takamatsu, Japan
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Ju L, Zhang G, Zhang C, Sun L, Jiang Y, Yan C, Duerksen-Hughes PJ, Zhang X, Zhu X, Chen FF, Yang J. Quantum dot-related genotoxicity perturbation can be attenuated by PEG encapsulation. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2013; 753:54-64. [DOI: 10.1016/j.mrgentox.2013.01.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 12/30/2012] [Accepted: 01/27/2013] [Indexed: 11/26/2022]
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8
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NMR methods for measuring lateral diffusion in membranes. Chem Phys Lipids 2013; 166:31-44. [DOI: 10.1016/j.chemphyslip.2012.12.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 12/11/2012] [Accepted: 12/12/2012] [Indexed: 02/07/2023]
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Yasui T, Kaji N, Baba Y. Nanobiodevices for biomolecule analysis and imaging. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2013; 6:83-96. [PMID: 23451720 DOI: 10.1146/annurev-anchem-062012-092619] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Nanobiodevices have been developed to analyze biomolecules and cells for biomedical applications. In this review, we discuss several nanobiodevices used for disease-diagnostic devices, molecular imaging devices, regenerative medicine, and drug-delivery systems and describe the numerous advantages of nanobiodevices, especially in biological, medical, and clinical applications. This review also outlines the fabrication technologies for nanostructures and nanomaterials, including top-down nanofabrication and bottom-up molecular self-assembly approaches. We describe nanopillar arrays and nanowall arrays for the ultrafast separation of DNA or protein molecules and nanoball materials for the fast separation of a wide range of DNA molecules, and we present examples of applications of functionalized carbon nanotubes to obtain information about subcellular localization on the basis of mobility differences between free fluorophores and fluorophore-labeled carbon nanotubes. Finally, we discuss applications of newly synthesized quantum dots to the screening of small interfering RNA, highly sensitive detection of disease-related proteins, and development of cancer therapeutics and diagnostics.
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Affiliation(s)
- Takao Yasui
- Department of Applied Chemistry, Graduate School of Engineering, FIRST Research Center for Innovative Nanobiodevices, Nagoya University, Nagoya 464-8603, Japan.
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10
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Lateral diffusion of bilayer lipids measured via 31P CODEX NMR. Chem Phys Lipids 2012; 165:721-30. [DOI: 10.1016/j.chemphyslip.2012.08.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 08/17/2012] [Accepted: 08/18/2012] [Indexed: 11/18/2022]
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Monitoring transplanted adipose tissue-derived stem cells combined with heparin in the liver by fluorescence imaging using quantum dots. Biomaterials 2011; 33:2177-86. [PMID: 22192539 DOI: 10.1016/j.biomaterials.2011.12.009] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Accepted: 12/03/2011] [Indexed: 02/07/2023]
Abstract
Adipose tissue-derived stem cell (ASC) transplantation, when used in combination with heparin, has proven to be an effective treatment for acute liver failure in mice. However, the behavior and organ-specific accumulation of transplanted ASCs alone or in combination with heparin is poorly understood. In this paper, we investigated whether quantum dots (QDs) labeling using octa-arginine peptide (R8) for ASCs could be applied for in vivo fluorescence imaging in mice with acute liver failure, and analyzed the behavior and organ-specific accumulation of ASCs that were transplanted alone or in combination with heparin using an IVIS(®) Spectrum analysis. Almost all of the transplanted ASCs were observed to accumulate in the lungs within 10 min without heparin. However, when heparin was used in combination with the ASCs, the accumulation of the transplanted ASCs was found not only in the lungs but also in the liver. The region of interest (ROI) analysis of ex vivo fluorescence imaging showed that the accumulation rate of transplanted ASCs in the liver increased to about 30%. In the time course analysis, the accumulation rate of ASCs in the liver was about 10% in 1 day and was maintained at that level for at least 2 day. We observed that heparin was effective for increasing the accumulation of transplanted ASCs in the liver using fluorescence imaging technology. We suggest that fluorescence imaging by means of QDs labeling using R8 can be useful for tracing the transplanted cells.
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Huang Y, Zhao S, Shi M, Chen J, Chen ZF, Liang H. Intermolecular and intramolecular quencher based quantum dot nanoprobes for multiplexed detection of endonuclease activity and inhibition. Anal Chem 2011; 83:8913-8. [PMID: 22017679 DOI: 10.1021/ac2013114] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
DNA cleavage by endonucleases plays an important role in many biological events such as DNA replication, recombination, and repair and is used as a powerful tool in medicinal chemistry. However, conventional methods for assaying endonuclease activity and inhibition by gel electrophoresis and chromatography techniques are time-consuming, laborious, not sensitive, or costly. Herein, we combine the high specificity of DNA cleavage reactions with the benefits of quantum dots (QDs) and ultrahigh quenching abilities of inter- and intramolecular quenchers to develop highly sensitive and specific nanoprobes for multiplexed detection of endonucleases. The nanoprobe was prepared by conjugating two sets of DNA substrates carrying quenchers onto the surface of aminated QDs through direct assembly and DNA hybridization. With this new design, the background fluorescence was significantly suppressed by introducing inter- and intramolecular quenchers. When these nanoprobes are exposed to the targeted endonucleases, specific DNA cleavages occur and pieces of DNA fragments are released from the QD surface along with the quenchers, resulting in fluorescence recovery. The endonuclease activity was quantified by monitoring the change in the fluorescence intensity. The detection was accomplished with a single excitation light. Multiplexed detection was demonstrated by simultaneously assaying EcoRI and BamHI (as model analytes) using two different emissions of QDs. The limits of detection were 4.0 × 10(-4) U/mL for EcoRI and 8.0 × 10(-4) U/mL for BamHI, which were at least 100 times more sensitive than traditional gel electrophoresis and chromatography assays. Moreover, the potential application of the proposed method for screening endonuclease inhibitors has also been demonstrated. The assay protocol presented here proved to be simple, sensitive, effective, and easy to carry out.
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Affiliation(s)
- Yong Huang
- Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Ministry of Education of China, College of Chemistry and Chemical Engineering, Guangxi Normal University, Guilin, 541004, China
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13
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Visualizing the endocytic and exocytic processes of wheat germ agglutinin by quantum dot-based single-particle tracking. Biomaterials 2011; 32:7616-24. [DOI: 10.1016/j.biomaterials.2011.06.046] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 06/20/2011] [Indexed: 11/18/2022]
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14
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Baba Y. Nanobiodevices for Genome Analysis, Proteome Analysis, and Biomedical Applications. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2011. [DOI: 10.1246/bcsj.20100341] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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15
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Enzyme digestion of entrapped single-DNA molecules in nanopores. Talanta 2011; 85:2135-41. [PMID: 21872069 DOI: 10.1016/j.talanta.2011.07.058] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Revised: 07/12/2011] [Accepted: 07/15/2011] [Indexed: 12/21/2022]
Abstract
The real-time digestion of entrapped single-DNA molecules by λ-exonuclease in nanoporous alumina membranes was observed using an epifluorescence microscope. The alumina membrane provides pL (∼ 10(-12)L) containers for confining single-DNA molecules without immobilization. When one end of the DNA molecule was inserted into a nanopore, it was possible to monitor the digestion process outside, near and inside the pore, where the individual DNA molecules exhibited different characteristic digestion modes. The digestion rates calculated from the decrease in fluorescence intensity showed different values according to the location of the individual molecules. Entrapment rather than immobilization allows the DNA strand to be fully exposed to the enzyme and the reaction buffer. These results confirm that the enzymatic digestion of DNA molecules is affected by their three-dimensional (3D) environment.
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16
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Ranasinghe RT, Brown T. Ultrasensitive fluorescence-based methods for nucleic acid detection: towards amplification-free genetic analysis. Chem Commun (Camb) 2011; 47:3717-35. [DOI: 10.1039/c0cc04215c] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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17
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van den Wildenberg SMJL, Prevo B, Peterman EJG. A brief introduction to single-molecule fluorescence methods. Methods Mol Biol 2011; 783:81-99. [PMID: 21909884 DOI: 10.1007/978-1-61779-282-3_5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
One of the more popular single-molecule approaches in biological science is single-molecule fluorescence microscopy, which is the subject of the following section of this volume. Fluorescence methods provide the sensitivity required to study biology on the single-molecule level, but they also allow access to useful measurable parameters on time and length scales relevant for the biomolecular world. Before several detailed experimental approaches are addressed, we first give a general overview of single-molecule fluorescence microscopy. We start with discussing the phenomenon of fluorescence in general and the history of single-molecule fluorescence microscopy. Next, we review fluorescent probes in more detail and the equipment required to visualize them on the single-molecule level. We end with a description of parameters measurable with such approaches, ranging from protein counting and tracking, to distance measurements with Förster Resonance Energy Transfer and orientation measurements with fluorescence polarization.
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18
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Zelman-Femiak M, Wang K, Gromova KV, Knaus P, Harms GS. Covalent quantum dot receptor linkage via the acyl carrier protein for single-molecule tracking, internalization, and trafficking studies. Biotechniques 2010; 49:574-9. [DOI: 10.2144/000113466] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Here we describe a labeling technique for the covalent linkage of quantum dots to transmembrane receptors for single-molecule tracking. Our method combines the acyl carrier protein (ACP) technique with coenzyme A (CoA)—functionalized quantum dots to covalently attach quantum dots to ACP fusions of receptor proteins. The advantages of this approach include: (i) the use of a smaller attachment linker than in many other quantum dot—labeling systems; (ii) the ability to achieve a reliable 1:1 fluorophore-to-receptor labeling stoichiometry; (iii) the specificity of the method; and (iv) the covalent nature of the quantum dot linkage. We demonstrate the general suitability of this technique in single-molecule tracking, internalization, and trafficking studies by imaging two different transmembrane receptors in living cells.
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Affiliation(s)
- Monika Zelman-Femiak
- Bio-Imaging Center, Rudolf Virchow Center, University of Würzburg, Würzburg, Germany
| | - Kun Wang
- Bio-Imaging Center, Rudolf Virchow Center, University of Würzburg, Würzburg, Germany
| | - Kira V. Gromova
- Bio-Imaging Center, Rudolf Virchow Center, University of Würzburg, Würzburg, Germany
| | - Petra Knaus
- Institute for Chemistry and Biochemistry, Free University of Berlin, Berlin, Germany
| | - Gregory S. Harms
- Bio-Imaging Center, Rudolf Virchow Center, University of Würzburg, Würzburg, Germany
- Department of Biology and Physics, Wilkes University, Wilkes-Barre, Pennsylvania, USA
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Ruan G, Vieira G, Henighan T, Chen A, Thakur D, Sooryakumar R, Winter JO. Simultaneous magnetic manipulation and fluorescent tracking of multiple individual hybrid nanostructures. NANO LETTERS 2010; 10:2220-2224. [PMID: 20450169 DOI: 10.1021/nl1011855] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Controlled transport of multiple individual nanostructures is crucial for nanoassembly and nanodelivery but is challenging because of small particle size. Although atomic force microscopy and optical and magnetic tweezers can control single particles, it is extremely difficult to scale these technologies for multiple structures. Here, we demonstrate a "nano-conveyer-belt" technology that permits simultaneous transport and tracking of multiple individual nanospecies in a selected direction. The technology consists of two components: nanocontainers, which encapsulate the nanomaterials transported, and nanoconveyer arrays, which use magnetic force to manipulate individual or aggregate nanocontainers. This technology is extremely versatile. For example, nanocontainers encapsulate quantum dots or rods and superparamagnetic iron oxide nanoparticles in <100 nm nanocontainers, the smallest magnetic composites to have been simultaneously moved and optically tracked. Similarly, the nanoconveyers consist of patterned microdisks or zigzag nanowires, whose dimensions can be controlled through micropatterning. The nanoconveyer belt technology could impact multiple fields, including nanoassembly, biomechanics, nanomedicine, and nanofluidics.
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Affiliation(s)
- Gang Ruan
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, USA
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Vial S, Mansuy C, Sagan S, Irinopoulou T, Burlina F, Boudou JP, Chassaing G, Lavielle S. Peptide-Grafted Nanodiamonds: Preparation, Cytotoxicity and Uptake in Cells. Chembiochem 2008; 9:2113-9. [DOI: 10.1002/cbic.200800247] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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