51
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Ma G, Hu C, Li S, Gao X, Li H, Hu X. Simultaneous, hybrid single-molecule method by optical tweezers and fluorescence. NANOTECHNOLOGY AND PRECISION ENGINEERING 2019. [DOI: 10.1016/j.npe.2019.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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52
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Abstract
Single-molecule techniques have been used successfully to visualize real-time enzymatic activities, revealing transient complex properties and heterogeneity of various biological events. Especially, conventional force spectroscopy including optical tweezers and magnetic tweezers has been widely used to monitor change in DNA length by enzymes with high spatiotemporal resolutions of ~ nanometers and ~ milliseconds. However, DNA metabolism results from coordination of a number of components during the processes, requiring efficient monitoring of a complex of proteins catalyzing DNA substrates. In this min-review, we will introduce a simple and multiplexed single-molecule assay to detect DNA substrates catalyzed by enzymes with high-throughput data collection. We conclude with a perspective of possible directions that enhance capability of the assay to reveal complex biological events with higher resolution.
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Affiliation(s)
- Ryanggeun Lee
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Keunsang Yang
- School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang 37673, Korea
| | - Jong-Bong Lee
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
- School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang 37673, Korea
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53
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Mohapatra S, Lin CT, Feng XA, Basu A, Ha T. Single-Molecule Analysis and Engineering of DNA Motors. Chem Rev 2019; 120:36-78. [DOI: 10.1021/acs.chemrev.9b00361] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
| | | | | | | | - Taekjip Ha
- Howard Hughes Medical Institute, Baltimore, Maryland 21205, United States
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54
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Miyamoto K, Sano K, Miyakawa T, Niinomi H, Toyoda K, Vallés A, Omatsu T. Generation of high-quality terahertz OAM mode based on soft-aperture difference frequency generation. OPTICS EXPRESS 2019; 27:31840-31849. [PMID: 31684408 DOI: 10.1364/oe.27.031840] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 10/08/2019] [Indexed: 06/10/2023]
Abstract
We demonstrate the generation of high-quality tunable terahertz (THz) vortices in an eigenmode by employing soft-aperture difference frequency generation of vortex and Gaussian modes. The generated THz vortex output exhibits a high-quality orbital angular momentum (OAM) mode with a topological charge of ℓTHz = ±1 in a frequency range of 2-6 THz. The maximum average power of the THz vortex output obtained was ∼3.3 µW at 4 THz.
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55
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Chuang CY, Zammit M, Whitmore ML, Comstock MJ. Combined High-Resolution Optical Tweezers and Multicolor Single-Molecule Fluorescence with an Automated Single-Molecule Assembly Line. J Phys Chem A 2019; 123:9612-9620. [PMID: 31621318 DOI: 10.1021/acs.jpca.9b08282] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present an instrument that combines high-resolution optical tweezers and multicolor confocal fluorescence spectroscopy along with automated single-molecule assembly. The multicolor allows the simultaneous observation of multiple molecules or multiple degrees of freedom, which allows, for example, the observation of multiple proteins simultaneously within a complex. The instrument incorporates three fluorescence excitation lasers, with a reliable alignment scheme, which will allow three independent fluorescent probe or FRET measurements and also increases flexibility in the choice of fluorescent molecules. We demonstrate the ability to simultaneously measure angstrom-scale changes in tether extension and fluorescence signals. Simultaneous tweezers and fluorescence measurement are particularly challenging because of fluorophore photobleaching, even more so if multiple fluorophores are to be measured. Therefore, (1) fluorescence excitation and detection is interlaced with time-shared dual optical traps. (2) We investigated the photostability of common fluorophores. The mean number of photons emitted before bleaching was unaffected by the trap laser and decreased only slightly with increasing excitation laser intensity. Surprisingly, we found that Cy5 outperforms other commonly used fluorophores by more than fivefold. (3) We devised computer-controlled automation, which conserves fluorophore lifetime by quickly detecting fluorophore-labeled molecule binding, turning off lasers, and moving to add the next fluorophore-labeled component. The single-molecule assembly line enables the precise assembly of multimolecule complexes while preserving fluorophores.
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Affiliation(s)
- Cho-Ying Chuang
- Department of Physics and Astronomy , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Matthew Zammit
- Department of Physics and Astronomy , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Miles L Whitmore
- Department of Physics and Astronomy , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Matthew J Comstock
- Department of Physics and Astronomy , Michigan State University , East Lansing , Michigan 48824 , United States
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56
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Marchetti M, Kamsma D, Cazares Vargas E, Hernandez García A, van der Schoot P, de Vries R, Wuite GJL, Roos WH. Real-Time Assembly of Viruslike Nucleocapsids Elucidated at the Single-Particle Level. NANO LETTERS 2019; 19:5746-5753. [PMID: 31368710 PMCID: PMC6696885 DOI: 10.1021/acs.nanolett.9b02376] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/24/2019] [Indexed: 05/20/2023]
Abstract
While the structure of a multitude of viral particles has been resolved to atomistic detail, their assembly pathways remain largely elusive. Key unresolved issues are particle nucleation, particle growth, and the mode of genome compaction. These issues are difficult to address in bulk approaches and are effectively only accessible by the real-time tracking of assembly dynamics of individual particles. This we do here by studying the assembly into rod-shaped viruslike particles (VLPs) of artificial capsid polypeptides. Using fluorescence optical tweezers, we establish that small oligomers perform one-dimensional diffusion along the DNA. Larger oligomers are immobile and nucleate VLP growth. A multiplexed acoustic force spectroscopy approach reveals that DNA is compacted in regular steps, suggesting packaging via helical wrapping into a nucleocapsid. By reporting how real-time assembly tracking elucidates viral nucleation and growth principles, our work opens the door to a fundamental understanding of the complex assembly pathways of both VLPs and naturally evolved viruses.
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Affiliation(s)
- Margherita Marchetti
- Department
of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
- Moleculaire
Biofysica, Zernike Instituut, Rijksuniversiteit
Groningen, 9712 CP Groningen, The Netherlands
| | - Douwe Kamsma
- Department
of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Ernesto Cazares Vargas
- Institute
of Chemistry, Department of Chemistry of Biomacromolecules, National Autonomous University of Mexico, 04510 Mexico City, Mexico
| | - Armando Hernandez García
- Institute
of Chemistry, Department of Chemistry of Biomacromolecules, National Autonomous University of Mexico, 04510 Mexico City, Mexico
| | - Paul van der Schoot
- Institute
for Theoretical Physics, Utrecht University, 3512 JE Utrecht, The Netherlands
- Department
of Applied Physics, Eindhoven University
of Technology, 5612 AZ Eindhoven, The Netherlands
| | - Renko de Vries
- Laboratory
of Physical Chemistry and Colloid Science, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Gijs J. L. Wuite
- Department
of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
- E-mail:
| | - Wouter H. Roos
- Moleculaire
Biofysica, Zernike Instituut, Rijksuniversiteit
Groningen, 9712 CP Groningen, The Netherlands
- E-mail:
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57
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Abstract
STimulated emission depletion (STED) nanoscopy has been proposed to extend greatly our capability of using light to study a variety of biological problems with nanometer-scale resolution. However, in practice the unwanted background noise degrades the STED image quality and precludes quantitative analysis. Here, we discuss the underlying sources of the background noise in STED images, and review current approaches to alleviate this problem, such as time-gating, anti-Stokes excitation removal, and off-focus incomplete depletion suppression. Progress in correcting uncorrelated background photons in fluorescence correlation spectroscopy combined with STED (STED-FCS) will also be discussed.
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Affiliation(s)
- Ye Ma
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States of America
| | - Taekjip Ha
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States of America.,Departments of Biophysics and Biophysical Chemistry, Biophysics, Johns Hopkins University, Baltimore, MD, United States of America.,Howard Hughes Medical Institute, Baltimore, MD, United States of America.,Author to whom any correspondence should be addressed
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58
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Label-free Imaging and Bending Analysis of Microtubules by ROCS Microscopy and Optical Trapping. Biophys J 2019; 114:168-177. [PMID: 29320684 DOI: 10.1016/j.bpj.2017.10.036] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 10/10/2017] [Accepted: 10/23/2017] [Indexed: 11/24/2022] Open
Abstract
Mechanical manipulation of single cytoskeleton filaments and their monitoring over long times is difficult because of fluorescence bleaching or phototoxic protein degradation. The integration of label-free microscopy techniques, capable of imaging freely diffusing, weak scatterers such as microtubules (MTs) in real-time, and independent of their orientation, with optical trapping and tracking systems, would allow many new applications. Here, we show that rotating-coherent-scattering microscopy (ROCS) in dark-field mode can also provide strong contrast for structures far from the coverslip such as arrangements of isolated MTs and networks. We could acquire thousands of images over up to 30 min without loss in image contrast or visible photodamage. We further demonstrate the combination of ROCS imaging with fast and nanometer-precise 3D interferometric back-focal-plane tracking of multiple beads in time-shared optical traps using acoustooptic deflectors to specifically construct and microrheologically probe small microtubule networks with well-defined geometries. Thereby, we explore the frequency-dependent elastic response of single microtubule filaments between 0.5 Hz and 5 kHz, which allows for investigating their viscoelastic response up to the fourth-order bending mode. Our spectral analysis reveals constant filament stiffness at low frequencies and frequency-dependent stiffening following a power law ∼ωp with a length-dependent exponent p(L). We find further evidence for the dependence of the MT persistence length on the contour length L, which is still controversially debated. We could also demonstrate slower stiffening at high frequencies for longer filaments, which we believe is determined by the molecular architecture of the MT. Our results shed new light on the nanomechanics of this essential, multifunctional cytoskeletal element and pose new questions about the adaptability of the cytoskeleton.
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59
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Single-Molecule Nanoscopy Elucidates RNA Polymerase II Transcription at Single Genes in Live Cells. Cell 2019; 178:491-506.e28. [PMID: 31155237 DOI: 10.1016/j.cell.2019.05.029] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 12/23/2018] [Accepted: 05/14/2019] [Indexed: 01/10/2023]
Abstract
Transforming the vast knowledge from genetics, biochemistry, and structural biology into detailed molecular descriptions of biological processes inside cells remains a major challenge-one in sore need of better imaging technologies. For example, transcription involves the complex interplay between RNA polymerase II (Pol II), regulatory factors (RFs), and chromatin, but visualizing these dynamic molecular transactions in their native intracellular milieu remains elusive. Here, we zoom into single tagged genes using nanoscopy techniques, including an active target-locking, ultra-sensitive system that enables single-molecule detection in addressable sub-diffraction volumes, within crowded intracellular environments. We image, track, and quantify Pol II with single-molecule resolution, unveiling its dynamics during the transcription cycle. Further probing multiple functionally linked events-RF-chromatin interactions, Pol II dynamics, and nascent transcription kinetics-reveals detailed operational parameters of gene-regulatory mechanisms hitherto-unseen in vivo. Our approach sets the stage for single-molecule studies of complex molecular processes in live cells.
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60
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Yokota H. Fluorescence microscopy for visualizing single-molecule protein dynamics. Biochim Biophys Acta Gen Subj 2019; 1864:129362. [PMID: 31078674 DOI: 10.1016/j.bbagen.2019.05.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 04/26/2019] [Accepted: 05/07/2019] [Indexed: 01/06/2023]
Abstract
BACKGROUND Single-molecule fluorescence imaging (smFI) has evolved into a valuable method used in biophysical and biochemical studies as it can observe the real-time behavior of individual protein molecules, enabling understanding of their detailed dynamic features. smFI is also closely related to other state-of-the-art microscopic methods, optics, and nanomaterials in that smFI and these technologies have developed synergistically. SCOPE OF REVIEW This paper provides an overview of the recently developed single-molecule fluorescence microscopy methods, focusing on critical techniques employed in higher-precision measurements in vitro and fluorescent nanodiamond, an emerging promising fluorophore that will improve single-molecule fluorescence microscopy. MAJOR CONCLUSIONS smFI will continue to improve regarding the photostability of fluorophores and will develop via combination with other techniques based on nanofabrication, single-molecule manipulation, and so on. GENERAL SIGNIFICANCE Quantitative, high-resolution single-molecule studies will help establish an understanding of protein dynamics and complex biomolecular systems.
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Affiliation(s)
- Hiroaki Yokota
- Biophotonics Laboratory, Graduate School for the Creation of New Photonics Industries, Kurematsu-cho, Nishi-ku, Hamamatsu, Shizuoka 431-1202, Japan.
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61
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Liang Y, Yan S, He M, Li M, Cai Y, Wang Z, Lei M, Yao B. Generation of a double-ring perfect optical vortex by the Fourier transform of azimuthally polarized Bessel beams. OPTICS LETTERS 2019; 44:1504-1507. [PMID: 30874687 DOI: 10.1364/ol.44.001504] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 02/17/2019] [Indexed: 06/09/2023]
Abstract
The perfect optical vortex (POV), the ring size being independent of its topological charge, has found potential applications in optical tweezers and optical communications. In this Letter, we report a new kind of POV, termed as double-ring POV (DR-POV), whose diameters of the two rings are independent of topological charge. We theoretically demonstrate that such a vortex is the Fourier transform of an azimuthally polarized Bessel beam. Experimental results agree well with theoretical prediction. We further investigate the vortex nature of the DR-POV through an interferometric method, showing that the two rings of the vortex have the same topological charge value (magnitude and sign). The specular properties of the DR-POV may find application in optical tweezers, such as trapping and rotating of low-refractive-index particles in the dark region between the two rings.
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62
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Newton MD, Taylor BJ, Driessen RPC, Roos L, Cvetesic N, Allyjaun S, Lenhard B, Cuomo ME, Rueda DS. DNA stretching induces Cas9 off-target activity. Nat Struct Mol Biol 2019; 26:185-192. [PMID: 30804513 PMCID: PMC7613072 DOI: 10.1038/s41594-019-0188-z] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/18/2019] [Indexed: 12/24/2022]
Abstract
CRISPR/Cas9 is a powerful genome-editing tool, but spurious off-target edits present a barrier to therapeutic applications. To understand how CRISPR/Cas9 discriminates between on-targets and off-targets, we have developed a single-molecule assay combining optical tweezers with fluorescence to monitor binding to λ-DNA. At low forces, the Streptococcus pyogenes Cas9 complex binds and cleaves DNA specifically. At higher forces, numerous off-target binding events appear repeatedly at the same off-target sites in a guide-RNA-sequence-dependent manner, driven by the mechanical distortion of the DNA. Using single-molecule Förster resonance energy transfer (smFRET) and cleavage assays, we show that DNA bubbles induce off-target binding and cleavage at these sites, even with ten mismatches, as well as at previously identified in vivo off-targets. We propose that duplex DNA destabilization during cellular processes (for example, transcription, replication, etc.) can expose these cryptic off-target sites to Cas9 activity, highlighting the need for improved off-target prediction algorithms.
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Affiliation(s)
- Matthew D Newton
- Molecular Virology, Department of Medicine, Imperial College London, London, UK
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, UK
| | | | | | - Leonie Roos
- Computational Regulatory Genomics, MRC-London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Nevena Cvetesic
- Computational Regulatory Genomics, MRC-London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Shenaz Allyjaun
- Molecular Virology, Department of Medicine, Imperial College London, London, UK
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, UK
| | - Boris Lenhard
- Computational Regulatory Genomics, MRC-London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | | | - David S Rueda
- Molecular Virology, Department of Medicine, Imperial College London, London, UK.
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, UK.
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63
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Kotnala A, Zheng Y, Fu J, Cheng W. Back-focal-plane interferometric detection of nanoparticles in spatially confined microfluidic channels. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2019; 90:023107. [PMID: 30831709 PMCID: PMC6382495 DOI: 10.1063/1.5074194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 02/01/2019] [Indexed: 05/08/2023]
Abstract
Nanoparticles are important in several areas of modern biomedical research. However, detection and characterization of nanoparticles is challenging due to their small size. Back-focal-plane interferometry (BFPI) is a highly sensitive technique that has been used in laser tweezers for quantitative measurement of force and displacement. The utility of BFPI for detection and characterization of nanoparticles, however, has not yet been achieved. Here we show that BFPI can be used for rapid probing of a suspension of nanoparticles in a spatially confined microfluidic channel. We show that the Gaussian Root-mean-squared noise of the BFPI signal is highly sensitive to the nanoparticle size and can be used as a parameter for rapid detection of nanoparticles at a single-particle level and characterization of particle heterogeneities in a suspension. By precisely aligning the optical trap relative to the channel boundaries, individual polystyrene particles with a diameter as small as 63 nm can be detected using BFPI with a high signal-to-noise ratio.
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Affiliation(s)
- Abhay Kotnala
- Department of Pharmaceutical Sciences, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, USA
| | - Yi Zheng
- Department of Mechanical Engineering, University of Michigan, 2350 Hayward Street, Ann Arbor, Michigan 48109, USA
| | - Jianping Fu
- Department of Mechanical Engineering, University of Michigan, 2350 Hayward Street, Ann Arbor, Michigan 48109, USA
| | - Wei Cheng
- Department of Pharmaceutical Sciences, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, USA
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64
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Du Y, Pan J, Choi JH. A review on optical imaging of DNA nanostructures and dynamic processes. Methods Appl Fluoresc 2019; 7:012002. [PMID: 30523978 DOI: 10.1088/2050-6120/aaed11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA self-assembly offers a powerful means to construct complex nanostructures and program dynamic molecular processes such as strand displacement. DNA nanosystems pack high structural complexity in a small scale (typically, <100 nm) and span dynamic features over long periods of time, which bring new challenges for characterizations. The spatial and temporal features of DNA nanosystems require novel experimental methods capable of high resolution imaging over long time periods. This article reviews recent advances in optical imaging methods for characterizing self-assembled DNA nanosystems, with particular emphasis on super-resolved fluorescence microscopy. Several advanced strategies are developed to obtain accurate and detailed images of intricate DNA nanogeometries and to perform precise tracking of molecular motions in dynamic processes. We present state-of-the-art instruments and imaging strategies including localization microscopy and spectral imaging. We discuss how they are used in biological studies and biomedical applications, and also provide current challenges and future outlook. Overall, this review serves as a practical guide in optical microscopy for the field of DNA nanotechnology.
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Affiliation(s)
- Yancheng Du
- School of Mechanical Engineering, Purdue University, West Lafayette, IN 47907
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65
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Gong W, Das P, Samanta S, Xiong J, Pan W, Gu Z, Zhang J, Qu J, Yang Z. Redefining the photo-stability of common fluorophores with triplet state quenchers: mechanistic insights and recent updates. Chem Commun (Camb) 2019; 55:8695-8704. [PMID: 31073568 DOI: 10.1039/c9cc02616a] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Light microscopy can offer certain advantages over electron microscopy in terms of acquiring detailed insights into the biological/intra-cellular milieu. In recent years, with the development of new fluorescence imaging technologies, it has become extremely important to assess the role of designing appropriate fluorophores in acquiring desired biological information without encountering any untoward hitches. Over the years, external fluorophores have been prevalently used in fluorescence microscopy and single-molecule fluorescence microscopy-based studies. Photostable fluorogenic probes with high extinction coefficients and quantum yields, exhibiting minimum autofluorescence and photobleaching properties, are preferred in single-molecule microscopy as they can tolerate long-term laser exposure. Therefore, the development of triplet state quenchers and/or any other suitable new strategy to ensure the photo-stability of the fluorophores during long-term live cell imaging exercises is highly anticipated. In this feature article, various strategies for stabilizing fluorophores, including the mechanisms of TSQ-induced stabilization, have been thoroughly reviewed considering contemporary literature reports and applications.
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Affiliation(s)
- Wanjun Gong
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
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66
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Nan F, Yan Z. Creating Multifunctional Optofluidic Potential Wells for Nanoparticle Manipulation. NANO LETTERS 2018; 18:7400-7406. [PMID: 30351963 DOI: 10.1021/acs.nanolett.8b03844] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Optical forces have enabled various nanomanipulation in microfluidics such as optical trapping, sorting, and transporting of nanoparticles (NPs), but the manipulation is usually specific with a certain optical field. Tightly focused Gaussian beams can trap NPs but not sort them; moderately focused Gaussian beams allow sorting microparticles in a flow but not NPs; quasi-Bessel beams can sort NPs in a flow but cannot control their positions due to low trapping stiffness. All these methods rely on the axial variation of laser intensity. Here we show that multifunctional and tunable optofluidic potential wells can be created for nanomanipulation by synchronizing optical phase gradient force with fluid drag force. We demonstrate controlled trapping and transporting of 150 nm Ag NPs over 10 μm and sorting of 80 and 100 nm Au NPs using optical line traps with tunable phase gradients in experiments. Our simulations further predict that simultaneous sorting and trapping of sub-50 nm Au NPs can be achieved with a sorting resolution of 1 nm using optimized optical fields. Our method provides great freedom and flexibility for nanomanipulation in optofluidics with potential applications in nanophotonics and biomedicine.
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Affiliation(s)
- Fan Nan
- Department of Chemical and Biomolecular Engineering , Clarkson University , Potsdam , New York 13699 , United States
| | - Zijie Yan
- Department of Chemical and Biomolecular Engineering , Clarkson University , Potsdam , New York 13699 , United States
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67
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Su QP, Ju LA. Biophysical nanotools for single-molecule dynamics. Biophys Rev 2018; 10:1349-1357. [PMID: 30121743 PMCID: PMC6233351 DOI: 10.1007/s12551-018-0447-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/06/2018] [Indexed: 12/11/2022] Open
Abstract
The focus of the cell biology field is now shifting from characterizing cellular activities to organelle and molecular behaviors. This process accompanies the development of new biophysical visualization techniques that offer high spatial and temporal resolutions with ultra-sensitivity and low cell toxicity. They allow the biology research community to observe dynamic behaviors from scales of single molecules, organelles, cells to organoids, and even live animal tissues. In this review, we summarize these biophysical techniques into two major classes: the mechanical nanotools like dynamic force spectroscopy (DFS) and the optical nanotools like single-molecule and super-resolution microscopy. We also discuss their applications in elucidating molecular dynamics and functionally mapping of interactions between inter-cellular networks and intra-cellular components, which is key to understanding cellular processes such as adhesion, trafficking, inheritance, and division.
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Affiliation(s)
- Qian Peter Su
- Institute for Biomedical Materials & Devices (IBMD), Faculty of Science, University of Technology Sydney, Ultimo, New South Wales, 2007, Australia.
| | - Lining Arnold Ju
- Charles Perkins Centre and Heart Research Institute, University of Sydney, Camperdown, New South Wales, 2006, Australia.
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68
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Chen Q, Jin C, Shao X, Guan R, Tian Z, Wang C, Liu F, Ling P, Guan JL, Ji L, Wang F, Chao H, Diao J. Super-Resolution Tracking of Mitochondrial Dynamics with An Iridium(III) Luminophore. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1802166. [PMID: 30350549 DOI: 10.1002/smll.201802166] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/09/2018] [Indexed: 06/08/2023]
Abstract
Combining luminescent transition metal complex with super-resolution microscopy is an excellent strategy for the long-term visualization of the dynamics of subcellular structures in living cells. However, it remains unclear whether iridium(III) complexes are applicable for a particular type of super-resolution technique, structured illumination microscopy (SIM), to image subcellular structures. Herein, an iridium(III) dye, to track mitochondrial dynamics in living cells under SIM is described. The dye demonstrates excellent specificity and photostability and satisfactory cell permeability. While using SIM to image mitochondria, an ≈80 nm resolution is achieved that allows the clear observation of the structure of mitochondrial cristae. The dye is used to monitor and quantify mitochondrial dynamics relative to lysosomes, including fusion involved in mitophagy, and newly discovered mitochondria-lysosome contact (MLC) under different conditions. The MLC remains intact and fusion vanishes when five receptors, p62, NDP52, OPTN, NBR1, and TAX1BP1, are knocked out, suggesting that these two processes are independent.
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Affiliation(s)
- Qixin Chen
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
- School of Pharmaceutical Sciences, Shandong University, Jinan, 250101, China
- Shandong Academy of Pharmaceutical Science, Key Laboratory of Biopharmaceuticals, Engineering Laboratory of Polysaccharide Drugs, National-Local Joint Engineering Laboratory of Polysaccharide Drugs, Jinan, 250101, China
| | - Chengzhi Jin
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Xintian Shao
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
- School of Pharmaceutical Sciences, Shandong University, Jinan, 250101, China
- Shandong Academy of Pharmaceutical Science, Key Laboratory of Biopharmaceuticals, Engineering Laboratory of Polysaccharide Drugs, National-Local Joint Engineering Laboratory of Polysaccharide Drugs, Jinan, 250101, China
| | - Ruilin Guan
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Zhiqi Tian
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Chenran Wang
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Fei Liu
- School of Pharmaceutical Sciences, Shandong University, Jinan, 250101, China
- Shandong Academy of Pharmaceutical Science, Key Laboratory of Biopharmaceuticals, Engineering Laboratory of Polysaccharide Drugs, National-Local Joint Engineering Laboratory of Polysaccharide Drugs, Jinan, 250101, China
| | - Peixue Ling
- School of Pharmaceutical Sciences, Shandong University, Jinan, 250101, China
- Shandong Academy of Pharmaceutical Science, Key Laboratory of Biopharmaceuticals, Engineering Laboratory of Polysaccharide Drugs, National-Local Joint Engineering Laboratory of Polysaccharide Drugs, Jinan, 250101, China
| | - Jun-Lin Guan
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Liangnian Ji
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Fengshan Wang
- School of Pharmaceutical Sciences, Shandong University, Jinan, 250101, China
| | - Hui Chao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
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69
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Simmert S, Abdosamadi MK, Hermsdorf G, Schäffer E. LED-based interference-reflection microscopy combined with optical tweezers for quantitative three-dimensional microtubule imaging. OPTICS EXPRESS 2018; 26:14499-14513. [PMID: 29877486 DOI: 10.1364/oe.26.014499] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 04/28/2018] [Indexed: 06/08/2023]
Abstract
Optical tweezers combined with various microscopy techniques are a versatile tool for single-molecule force spectroscopy. However, some combinations may compromise measurements. Here, we combined optical tweezers with total-internal-reflection-fluorescence (TIRF) and interference-reflection microscopy (IRM). Using a light-emitting diode (LED) for IRM illumination, we show that single microtubules can be imaged with high contrast. Furthermore, we converted the IRM interference pattern of an upward bent microtubule to its three-dimensional (3D) profile calibrated against the optical tweezers and evanescent TIRF field. In general, LED-based IRM is a powerful method for high-contrast 3D microscopy.
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70
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Lee SH. Optimal integration of wide field illumination and holographic optical tweezers for multimodal microscopy with ultimate flexibility and versatility. OPTICS EXPRESS 2018; 26:8049-8058. [PMID: 29715778 DOI: 10.1364/oe.26.008049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 03/04/2018] [Indexed: 05/29/2023]
Abstract
We introduce one-of-a-kind optical microscope that we have developed through optimized integration of wide-field and focused-light microscopies. This new instrument has accomplished operation of the same laser for both wide field illumination and holographic focused beam illumination interchangeably or simultaneously in a way scalable to multiple lasers. We have demonstrated its powerful capability by simultaneously carrying out Epi-fluorescence, total internal reflection fluorescence microscopy, selective plane illumination microscopy, and holographic optical tweezers with five lasers. Our instrument and the optical design will provide researchers across diverse fields, cell-biology and biophysics in particular, with a practical guidance to build an all-around multimodal microscope that will further inspire the development of novel hybrid microscopy experiments.
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71
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Madariaga-Marcos J, Hormeño S, Pastrana CL, Fisher GLM, Dillingham MS, Moreno-Herrero F. Force determination in lateral magnetic tweezers combined with TIRF microscopy. NANOSCALE 2018; 10:4579-4590. [PMID: 29461549 PMCID: PMC5831119 DOI: 10.1039/c7nr07344e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 12/07/2017] [Indexed: 06/08/2023]
Abstract
Combining single-molecule techniques with fluorescence microscopy has attracted much interest because it allows the correlation of mechanical measurements with directly visualized DNA : protein interactions. In particular, its combination with total internal reflection fluorescence microscopy (TIRF) is advantageous because of the high signal-to-noise ratio this technique achieves. This, however, requires stretching long DNA molecules across the surface of a flow cell to maximize polymer exposure to the excitation light. In this work, we develop a module to laterally stretch DNA molecules at a constant force, which can be easily implemented in regular or combined magnetic tweezers (MT)-TIRF setups. The pulling module is further characterized in standard flow cells of different thicknesses and glass capillaries, using two types of micrometer size superparamagnetic beads, long DNA molecules, and a home-built device to rotate capillaries with mrad precision. The force range achieved by the magnetic pulling module was between 0.1 and 30 pN. A formalism for estimating forces in flow-stretched tethered beads is also proposed, and the results compared with those of lateral MT, demonstrating that lateral MT achieve higher forces with lower dispersion. Finally, we show the compatibility with TIRF microscopy and the parallelization of measurements by characterizing DNA binding by the centromere-binding protein ParB from Bacillus subtilis. Simultaneous MT pulling and fluorescence imaging demonstrate the non-specific binding of BsParB on DNA under conditions restrictive to condensation.
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Affiliation(s)
- J. Madariaga-Marcos
- Department of Macromolecular Structures , Centro Nacional de Biotecnología , Consejo Superior de Investigaciones Científicas , 28049 Cantoblanco , Madrid , Spain .
| | - S. Hormeño
- Department of Macromolecular Structures , Centro Nacional de Biotecnología , Consejo Superior de Investigaciones Científicas , 28049 Cantoblanco , Madrid , Spain .
| | - C. L. Pastrana
- Department of Macromolecular Structures , Centro Nacional de Biotecnología , Consejo Superior de Investigaciones Científicas , 28049 Cantoblanco , Madrid , Spain .
| | - G. L. M. Fisher
- DNA:Protein Interactions Unit , School of Biochemistry , Biomedical Sciences Building , University of Bristol , Bristol , BS8 1TD , UK
| | - M. S. Dillingham
- DNA:Protein Interactions Unit , School of Biochemistry , Biomedical Sciences Building , University of Bristol , Bristol , BS8 1TD , UK
| | - F. Moreno-Herrero
- Department of Macromolecular Structures , Centro Nacional de Biotecnología , Consejo Superior de Investigaciones Científicas , 28049 Cantoblanco , Madrid , Spain .
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72
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Shi YZ, Xiong S, Zhang Y, Chin LK, Chen YY, Zhang JB, Zhang TH, Ser W, Larrson A, Lim SH, Wu JH, Chen TN, Yang ZC, Hao YL, Liedberg B, Yap PH, Wang K, Tsai DP, Qiu CW, Liu AQ. Sculpting nanoparticle dynamics for single-bacteria-level screening and direct binding-efficiency measurement. Nat Commun 2018; 9:815. [PMID: 29483548 PMCID: PMC5827716 DOI: 10.1038/s41467-018-03156-5] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 01/24/2018] [Indexed: 01/21/2023] Open
Abstract
Particle trapping and binding in optical potential wells provide a versatile platform for various biomedical applications. However, implementation systems to study multi-particle contact interactions in an optical lattice remain rare. By configuring an optofluidic lattice, we demonstrate the precise control of particle interactions and functions such as controlling aggregation and multi-hopping. The mean residence time of a single particle is found considerably reduced from 7 s, as predicted by Kramer’s theory, to 0.6 s, owing to the mechanical interactions among aggregated particles. The optofluidic lattice also enables single-bacteria-level screening of biological binding agents such as antibodies through particle-enabled bacteria hopping. The binding efficiency of antibodies could be determined directly, selectively, quantitatively and efficiently. This work enriches the fundamental mechanisms of particle kinetics and offers new possibilities for probing and utilising unprecedented biomolecule interactions at single-bacteria level. Optical trapping is a versatile tool for biomedical applications. Here, the authors use an optofluidic lattice to achieve controllable multi-particle hopping and demonstrate single-bacteria-level screening and measurement of binding efficiency of biological binding agents through particle-enabled bacteria hopping.
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Affiliation(s)
- Y Z Shi
- School of Mechanical Engineering, Xi'an Jiaotong University, Xi'an, 710049, China.,School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - S Xiong
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore, 639798, Singapore.
| | - Y Zhang
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - L K Chin
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Y -Y Chen
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - J B Zhang
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - T H Zhang
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore, 117583, Singapore
| | - W Ser
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - A Larrson
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | - S H Lim
- School of Biological Sciences, Nanyang Technological University, Singapore, 639798, Singapore
| | - J H Wu
- School of Mechanical Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - T N Chen
- School of Mechanical Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Z C Yang
- National Key Laboratory of Science and Technology on Micro/Nano Fabrication, Institute of Microelectronics, Peking University, Beijing, 100871, China
| | - Y L Hao
- National Key Laboratory of Science and Technology on Micro/Nano Fabrication, Institute of Microelectronics, Peking University, Beijing, 100871, China
| | - B Liedberg
- Centre for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - P H Yap
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - K Wang
- College of Biomedical Engineering, Taipei Medical University, Taipei, 11031, Taiwan.,Nanyang Environment & Water Research Institute, Nanyang Technological University, Singapore, 637141, Singapore
| | - D P Tsai
- Department of Physics, National Taiwan University, Taipei, 10617, Taiwan
| | - C-W Qiu
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore, 117583, Singapore. .,SZU-NUS Collaborative Innovation Center for Optoelectronic Science and Technology, Shenzhen University, Shenzhen, 518060, China.
| | - A Q Liu
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore, 639798, Singapore. .,National Key Laboratory of Science and Technology on Micro/Nano Fabrication, Institute of Microelectronics, Peking University, Beijing, 100871, China.
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73
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Araki S, Ando K, Miyamoto K, Omatsu T. Ultra-widely tunable mid-infrared (6-18 μm) optical vortex source. APPLIED OPTICS 2018; 57:620-624. [PMID: 29400727 DOI: 10.1364/ao.57.000620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 12/27/2017] [Indexed: 06/07/2023]
Abstract
We demonstrate the generation of an ultra-widely tunable mid-infrared (6-18 μm) optical vortex output with a moderate pulse energy from a AgGaSe2 difference frequency generator pumped by an optical vortex parametric oscillator. The handedness of the vortex output can be controlled/selected by swapping the lasing frequencies of the signal and idler outputs and rotating the AgGaSe2 crystal by 90 deg.
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74
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van Mameren J, Wuite GJL, Heller I. Introduction to Optical Tweezers: Background, System Designs, and Commercial Solutions. Methods Mol Biol 2018; 1665:3-23. [PMID: 28940061 DOI: 10.1007/978-1-4939-7271-5_1] [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
Optical tweezers are a means to manipulate objects with light. With the technique, microscopically small objects can be held and steered, while forces on the trapped objects can be accurately measured and exerted. Optical tweezers can typically obtain a nanometer spatial resolution, a picoNewton force resolution, and a millisecond time resolution, which makes them excellently suited to study biological processes from the single-cell down to the single-molecule level. In this chapter, we will provide an introduction on the use of optical tweezers in single-molecule approaches. We will introduce the basic principles and methodology involved in optical trapping, force calibration, and force measurements. Next we describe the components of an optical tweezers setup and their experimental relevance in single-molecule approaches. Finally, we provide a concise overview of commercial optical tweezers systems. Commercial systems are becoming increasingly available and provide access to single-molecule optical tweezers experiments without the need for a thorough background in physics.
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Affiliation(s)
- Joost van Mameren
- Institute of Physics, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Gijs J L Wuite
- LaserLaB and Department of Physics and Astronomy, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands.
| | - Iddo Heller
- LaserLaB and Department of Physics and Astronomy, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
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75
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Shi Y, Xiong S, Chin LK, Zhang J, Ser W, Wu J, Chen T, Yang Z, Hao Y, Liedberg B, Yap PH, Tsai DP, Qiu CW, Liu AQ. Nanometer-precision linear sorting with synchronized optofluidic dual barriers. SCIENCE ADVANCES 2018; 4:eaao0773. [PMID: 29326979 PMCID: PMC5756665 DOI: 10.1126/sciadv.aao0773] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 11/30/2017] [Indexed: 05/18/2023]
Abstract
The past two decades have witnessed the revolutionary development of optical trapping of nanoparticles, most of which deal with trapping stiffness larger than 10-8 N/m. In this conventional regime, however, it remains a formidable challenge to sort out sub-50-nm nanoparticles with single-nanometer precision, isolating us from a rich flatland with advanced applications of micromanipulation. With an insightfully established roadmap of damping, the synchronization between optical force and flow drag force can be coordinated to attempt the loosely overdamped realm (stiffness, 10-10 to 10-8 N/m), which has been challenging. This paper intuitively demonstrates the remarkable functionality to sort out single gold nanoparticles with radii ranging from 30 to 50 nm, as well as 100- and 150-nm polystyrene nanoparticles, with single nanometer precision. The quasi-Bessel optical profile and the loosely overdamped potential wells in the microchannel enable those aforementioned nanoparticles to be separated, positioned, and microscopically oscillated. This work reveals an unprecedentedly meaningful damping scenario that enriches our fundamental understanding of particle kinetics in intriguing optical systems, and offers new opportunities for tumor targeting, intracellular imaging, and sorting small particles such as viruses and DNA.
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Affiliation(s)
- Yuzhi Shi
- School of Mechanical Engineering, Xi’an Jiao Tong University, Xi’an 710049, China
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Sha Xiong
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore
- Corresponding author. (S.X.); (C.-W.Q.); (A.Q.L.)
| | - Lip Ket Chin
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Jingbo Zhang
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Wee Ser
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Jiuhui Wu
- School of Mechanical Engineering, Xi’an Jiao Tong University, Xi’an 710049, China
| | - Tianning Chen
- School of Mechanical Engineering, Xi’an Jiao Tong University, Xi’an 710049, China
| | - Zhenchuan Yang
- National Key Laboratory of Science and Technology on Micro/Nano Fabrication Institute of Microelectronics, Peking University, Beijing 100871, China
| | - Yilong Hao
- National Key Laboratory of Science and Technology on Micro/Nano Fabrication Institute of Microelectronics, Peking University, Beijing 100871, China
| | - Bo Liedberg
- Centre for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Peng Huat Yap
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
| | - Din Ping Tsai
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Cheng-Wei Qiu
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore 117583, Singapore
- SZU-NUS Collaborative Innovation Center for Optoelectronic Science and Technology, Shenzhen University, Shenzhen 518060, China
- Corresponding author. (S.X.); (C.-W.Q.); (A.Q.L.)
| | - Ai Qun Liu
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore
- National Key Laboratory of Science and Technology on Micro/Nano Fabrication Institute of Microelectronics, Peking University, Beijing 100871, China
- Corresponding author. (S.X.); (C.-W.Q.); (A.Q.L.)
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76
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Sarlós K, Biebricher A, Petermann EJG, Wuite GJL, Hickson ID. Knotty Problems during Mitosis: Mechanistic Insight into the Processing of Ultrafine DNA Bridges in Anaphase. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2017; 82:187-195. [PMID: 29167280 DOI: 10.1101/sqb.2017.82.033647] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
To survive and proliferate, cells have to faithfully segregate their newly replicated genomic DNA to the two daughter cells. However, the sister chromatids of mitotic chromosomes are frequently interlinked by so-called ultrafine DNA bridges (UFBs) that are visible in the anaphase of mitosis. UFBs can only be detected by the proteins bound to them and not by staining with conventional DNA dyes. These DNA bridges are presumed to represent entangled sister chromatids and hence pose a threat to faithful segregation. A failure to accurately unlink UFB DNA results in chromosome segregation errors and binucleation. This, in turn, compromises genome integrity, which is a hallmark of cancer. UFBs are actively removed during anaphase, and most known UFB-associated proteins are enzymes involved in DNA repair in interphase. However, little is known about the mitotic activities of these enzymes or the exact DNA structures present on UFBs. We focus on the biology of UFBs, with special emphasis on their underlying DNA structure and the decatenation machineries that process UFBs.
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Affiliation(s)
- Kata Sarlós
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Andreas Biebricher
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Erwin J G Petermann
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Ian D Hickson
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen N, Denmark
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77
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Black JW, Kamenetska M, Ganim Z. An Optical Tweezers Platform for Single Molecule Force Spectroscopy in Organic Solvents. NANO LETTERS 2017; 17:6598-6605. [PMID: 28972764 DOI: 10.1021/acs.nanolett.7b02413] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Observation at the single molecule level has been a revolutionary tool for molecular biophysics and materials science, but single molecule studies of solution-phase chemistry are less widespread. In this work we develop an experimental platform for solution-phase single molecule force spectroscopy in organic solvents. This optical-tweezer-based platform was designed for broad chemical applicability and utilizes optically trapped core-shell microspheres, synthetic polymer tethers, and click chemistry linkages formed in situ. We have observed stable optical trapping of the core-shell microspheres in ten different solvents, and single molecule link formation in four different solvents. These experiments demonstrate how to use optical tweezers for single molecule force application in the study of solution-phase chemistry.
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Affiliation(s)
- Jacob W Black
- Department of Chemistry, Yale University , 350 Edwards St., New Haven, Connecticut 06520, United States
| | - Maria Kamenetska
- Department of Chemistry, Yale University , 350 Edwards St., New Haven, Connecticut 06520, United States
| | - Ziad Ganim
- Department of Chemistry, Yale University , 350 Edwards St., New Haven, Connecticut 06520, United States
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78
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Mechanically switching single-molecule fluorescence of GFP by unfolding and refolding. Proc Natl Acad Sci U S A 2017; 114:11052-11056. [PMID: 29073015 DOI: 10.1073/pnas.1704937114] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Green fluorescent protein (GFP) variants are widely used as genetically encoded fluorescent fusion tags, and there is an increasing interest in engineering their structure to develop in vivo optical sensors, such as for optogenetics and force transduction. Ensemble experiments have shown that the fluorescence of GFP is quenched upon denaturation. Here we study the dependence of fluorescence on protein structure by driving single molecules of GFP into different conformational states with optical tweezers and simultaneously probing the chromophore with fluorescence. Our results show that fluorescence is lost during the earliest events in unfolding, 3.5 ms before secondary structure is disrupted. No fluorescence is observed from the unfolding intermediates or the ensemble of compact and extended states populated during refolding. We further demonstrate that GFP can be mechanically switched between emissive and dark states. These data definitively establish that complete structural integrity is necessary to observe single-molecule fluorescence of GFP.
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79
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Liu Q, Zhao Y, Ding M, Yao W, Fan X, Shen D. Wavelength- and OAM-tunable vortex laser with a reflective volume Bragg grating. OPTICS EXPRESS 2017; 25:23312-23319. [PMID: 29041632 DOI: 10.1364/oe.25.023312] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Vortex beams carrying orbital angular momentum (OAM) have been recently investigated intensely in optical communication systems, as using OAM mode multiplexing simultaneously with other conventional multiplexing techniques is the key to further expand data capacity. This article demonstrates a wavelength- and OAM-tunable vortex laser at 1.6 µm in an Er:YAG system. For the first time to the best of our knowledge, a reflective volume Bragg grating (VBG) was theoretically and experimentally proved to be an effective OAM-preserving wavelength selector inside the laser cavity. A z-shaped laser cavity employing a VBG as a folding mirror was constructed for the direct generation of vortex beams, and we finally obtained wavelength-tunable beams of five OAM states (0, ± ħ, and ± 2ħ) with a narrow bandwidth less than 0.04 nm. This laser supplies a new way for optical communication by combining the spatial degree of freedom for multiplexing information channels with the conventionally used wavelength domains in packable and robust resonant cavity.
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80
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Soltys JN, Meyer SA, Schumann H, Gibson EA, Restrepo D, Bennett JL. Determining the Spatial Relationship of Membrane-Bound Aquaporin-4 Autoantibodies by STED Nanoscopy. Biophys J 2017; 112:1692-1702. [PMID: 28445760 DOI: 10.1016/j.bpj.2017.03.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 03/07/2017] [Accepted: 03/15/2017] [Indexed: 02/05/2023] Open
Abstract
Determining the spatial relationship of individual proteins in dense assemblies remains a challenge for superresolution nanoscopy. The organization of aquaporin-4 (AQP4) into large plasma membrane assemblies provides an opportunity to image membrane-bound AQP4 antibodies (AQP4-IgG) and evaluate changes in their spatial distribution due to alterations in AQP4 isoform expression and AQP4-IgG epitope specificity. Using stimulated emission depletion nanoscopy, we imaged secondary antibody labeling of monoclonal AQP4-IgGs with differing epitope specificity bound to isolated tetramers (M1-AQP4) and large orthogonal arrays of AQP4 (M23-AQP4). Imaging secondary antibodies bound to M1-AQP4 allowed us to infer the size of individual AQP4-IgG binding events. This information was used to model the assembly of larger AQP4-IgG complexes on M23-AQP4 arrays. A scoring algorithm was generated from these models to characterize the spatial arrangement of bound AQP4-IgG antibodies, yielding multiple epitope-specific patterns of bound antibodies on M23-AQP4 arrays. Our results delineate an approach to infer spatial relationships within protein arrays using stimulated emission depletion nanoscopy, offering insight into how information on single antibody fluorescence events can be used to extract information from dense protein assemblies under a biologic context.
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Affiliation(s)
- John N Soltys
- Medical Scientist Training and Neuroscience Graduate Training Programs, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Stephanie A Meyer
- Department of Bioengineering, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Hannah Schumann
- Department of Neurology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Emily A Gibson
- Department of Bioengineering, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Diego Restrepo
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Jeffrey L Bennett
- Department of Neurology, University of Colorado Anschutz Medical Campus, Aurora, Colorado; Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, Colorado.
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81
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Yeh JW, Szeto K. Electrophoretic stretching and imaging of single native chromatin fibers in nanoslits. BIOMICROFLUIDICS 2017; 11:044108. [PMID: 28794818 PMCID: PMC5526712 DOI: 10.1063/1.4996340] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/16/2017] [Indexed: 05/16/2023]
Abstract
Stretching single chromosomal DNA fibers in nanofluidic devices has become a valuable tool for studying the genome and more recently the epigenome. Although nanofluidic technology has been extensively used in single molecular DNA analysis, compared to bare DNA, much less work has been done to elongate chromatin, and only a few studies utilize more biologically relevant samples such as native eukaryotic chromatin. Here, we provide a method for stretching and imaging individual chromatin fibers within a micro- and nanofluidic device. This device was used to electrophoretically stretch and image single native chromatin fibers extracted from human cancer cells (HeLa cells) by attaching the chromatin to microspheres held at the entrance of a nanoslit. To further demonstrate the potential of this device in epigenetics, histone modification H3k79me2 was optically detected by fluorescence microscopy.
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Affiliation(s)
- Jia-Wei Yeh
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
| | - Kylan Szeto
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
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82
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Interfacing 3D magnetic twisting cytometry with confocal fluorescence microscopy to image force responses in living cells. Nat Protoc 2017; 12:1437-1450. [PMID: 28686583 DOI: 10.1038/nprot.2017.042] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Cells and tissues can undergo a variety of biological and structural changes in response to mechanical forces. Only a few existing techniques are available for quantification of structural changes at high resolution in response to forces applied along different directions. 3D-magnetic twisting cytometry (3D-MTC) is a technique for applying local mechanical stresses to living cells. Here we describe a protocol for interfacing 3D-MTC with confocal fluorescence microscopy. In 3D-MTC, ferromagnetic beads are bound to the cell surface via surface receptors, followed by their magnetization in any desired direction. A magnetic twisting field in a different direction is then applied to generate rotational shear stresses in any desired direction. This protocol describes how to combine magnetic-field-induced mechanical stimulation with confocal fluorescence microscopy and provides an optional extension for super-resolution imaging using stimulated emission depletion (STED) nanoscopy. This technology allows for rapid real-time acquisition of a living cell's mechanical responses to forces via specific receptors and for quantifying structural and biochemical changes in the same cell using confocal fluorescence microscopy or STED. The integrated 3D-MTC-microscopy platform takes ∼20 d to construct, and the experimental procedures require ∼4 d when carried out by a life sciences graduate student.
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83
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Abstract
Living cells and tissues experience physical forces and chemical stimuli in a human body. The process of converting mechanical forces into biochemical activities and gene expression is mechanochemical transduction or mechanotransduction. Significant advances have been made in understanding mechanotransduction at cellular and molecular levels over the last two decades. However, major challenges remain in elucidating how a living cell integrates signals from mechanotransduction with chemical signals to regulate gene expression and to generate coherent biological responses in living tissues in physiological conditions and diseases.
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Affiliation(s)
- Ning Wang
- School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; Department of Mechanical Science and Engineering, College of Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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84
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Kotnala A, Zheng Y, Fu J, Cheng W. Microfluidic-based high-throughput optical trapping of nanoparticles. LAB ON A CHIP 2017; 17:2125-2134. [PMID: 28561826 PMCID: PMC5533511 DOI: 10.1039/c7lc00286f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Optical tweezers have emerged as a powerful tool for multiparametric analysis of individual nanoparticles with single-molecule sensitivity. However, its inherent low-throughput characteristic remains a major obstacle to its applications within and beyond the laboratory. This limitation is further exacerbated when working with low concentration nanoparticle samples. Here, we present a microfluidic-based optical tweezers system that can 'actively' deliver nanoparticles to a designated microfluidic region for optical trapping and analysis. The active microfluidic delivery of nanoparticles results in significantly improved throughput and efficiency for optical trapping of nanoparticles. We observed a more than tenfold increase in optical trapping throughput for nanoparticles as compared to conventional systems at the same nanoparticle concentration. To demonstrate the utility of this microfluidic-based optical tweezers system, we further used back-focal plane interferometry coupled with a trapping laser for the precise quantitation of nanoparticle size without prior knowledge of the refractive index of nanoparticles. The development of this microfluidic-based active optical tweezers system thus opens the door to high-throughput multiparametric analysis of nanoparticles using precision optical traps in the future.
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Affiliation(s)
- Abhay Kotnala
- Department of Pharmaceutical Sciences, University of Michigan, 428 church street, Ann Arbor, MI 48109, USA
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85
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Syrjänen JL, Heller I, Candelli A, Davies OR, Peterman EJG, Wuite GJL, Pellegrini L. Single-molecule observation of DNA compaction by meiotic protein SYCP3. eLife 2017; 6. [PMID: 28287952 PMCID: PMC5348128 DOI: 10.7554/elife.22582] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 03/04/2017] [Indexed: 12/14/2022] Open
Abstract
In a previous paper (Syrjänen et al., 2014), we reported the first structural characterisation of a synaptonemal complex (SC) protein, SYCP3, which led us to propose a model for its role in chromosome compaction during meiosis. As a component of the SC lateral element, SYCP3 has a critical role in defining the specific chromosome architecture required for correct meiotic progression. In the model, the reported compaction of chromosomal DNA caused by SYCP3 would result from its ability to bridge distant sites on a DNA molecule with the DNA-binding domains located at each end of its strut-like structure. Here, we describe a single-molecule assay based on optical tweezers, fluorescence microscopy and microfluidics that, in combination with bulk biochemical data, provides direct visual evidence for our proposed mechanism of SYCP3-mediated chromosome organisation. DOI:http://dx.doi.org/10.7554/eLife.22582.001
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Affiliation(s)
- Johanna L Syrjänen
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Iddo Heller
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,LaserLaB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Andrea Candelli
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,LaserLaB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Owen R Davies
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, United Kingdom
| | - Erwin J G Peterman
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,LaserLaB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,LaserLaB, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Luca Pellegrini
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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86
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Kamagata K, Murata A, Itoh Y, Takahashi S. Characterization of facilitated diffusion of tumor suppressor p53 along DNA using single-molecule fluorescence imaging. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2017. [DOI: 10.1016/j.jphotochemrev.2017.01.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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87
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Norregaard K, Metzler R, Ritter CM, Berg-Sørensen K, Oddershede LB. Manipulation and Motion of Organelles and Single Molecules in Living Cells. Chem Rev 2017; 117:4342-4375. [PMID: 28156096 DOI: 10.1021/acs.chemrev.6b00638] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The biomolecule is among the most important building blocks of biological systems, and a full understanding of its function forms the scaffold for describing the mechanisms of higher order structures as organelles and cells. Force is a fundamental regulatory mechanism of biomolecular interactions driving many cellular processes. The forces on a molecular scale are exactly in the range that can be manipulated and probed with single molecule force spectroscopy. The natural environment of a biomolecule is inside a living cell, hence, this is the most relevant environment for probing their function. In vivo studies are, however, challenged by the complexity of the cell. In this review, we start with presenting relevant theoretical tools for analyzing single molecule data obtained in intracellular environments followed by a description of state-of-the art visualization techniques. The most commonly used force spectroscopy techniques, namely optical tweezers, magnetic tweezers, and atomic force microscopy, are described in detail, and their strength and limitations related to in vivo experiments are discussed. Finally, recent exciting discoveries within the field of in vivo manipulation and dynamics of single molecule and organelles are reviewed.
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Affiliation(s)
- Kamilla Norregaard
- Cluster for Molecular Imaging, Department of Biomedical Science and Department of Clinical Physiology, Nuclear Medicine and PET, Rigshospitalet, University of Copenhagen , 2200 Copenhagen, Denmark
| | - Ralf Metzler
- Institute for Physics & Astronomy, University of Potsdam , 14476 Potsdam-Golm, Germany
| | - Christine M Ritter
- Niels Bohr Institute, University of Copenhagen , 2100 Copenhagen, Denmark
| | | | - Lene B Oddershede
- Niels Bohr Institute, University of Copenhagen , 2100 Copenhagen, Denmark
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88
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Block J, Witt H, Candelli A, Peterman EJG, Wuite GJL, Janshoff A, Köster S. Nonlinear Loading-Rate-Dependent Force Response of Individual Vimentin Intermediate Filaments to Applied Strain. PHYSICAL REVIEW LETTERS 2017; 118:048101. [PMID: 28186786 DOI: 10.1103/physrevlett.118.048101] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Indexed: 06/06/2023]
Abstract
The mechanical properties of eukaryotic cells are to a great extent determined by the cytoskeleton, a composite network of different filamentous proteins. Among these, intermediate filaments (IFs) are exceptional in their molecular architecture and mechanical properties. Here we directly record stress-strain curves of individual vimentin IFs using optical traps and atomic force microscopy. We find a strong loading rate dependence of the mechanical response, supporting the hypothesis that IFs could serve to protect eukaryotic cells from fast, large deformations. Our experimental results show different unfolding regimes, which we can quantitatively reproduce by an elastically coupled system of multiple two-state elements.
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Affiliation(s)
- Johanna Block
- Institute for X-Ray Physics, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
| | - Hannes Witt
- Institute of Physical Chemistry, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
| | - Andrea Candelli
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, Netherlands
- LUMICKS B.V., 1081 HV Amsterdam, Netherlands
| | - Erwin J G Peterman
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, Netherlands
| | - Andreas Janshoff
- Institute of Physical Chemistry, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
| | - Sarah Köster
- Institute for X-Ray Physics, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
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89
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Yuyama KI, Marcelis L, Su PM, Chung WS, Masuhara H. Photocontrolled Supramolecular Assembling of Azobenzene-Based Biscalix[4]arenes upon Starting and Stopping Laser Trapping. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:755-763. [PMID: 28033013 DOI: 10.1021/acs.langmuir.6b03780] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Laser trapping in chemistry covers various studies ranging from single molecules, nanoparticles, and quantum dots to crystallization and liquid-liquid phase separation of amino acids. In this work, a supramolecular assembly of azobenzene-based biscalix[4]arene is generated in ethyl acetate using laser trapping; its nucleation and growth are elucidated. No trapping behavior was observed when a 1064 nm laser beam was focused inside of the solution; however, interesting assembling phenomena were induced when it was shined at the air/solution interface. A single disk having two layers was first prepared at the focal point of ∼1 μm and then expanded to the size of a few tens of micrometers, although no optical force was exerted outside of the focal volume. Upon switching the trapping laser off, needles were generated at the outer layer of the assembly, giving a stable sea urchin-like morphology to the generated assembly. At a 30-50% dilution of the initial solution in ethyl acetate, a mushroom-like morphology was also observed. Laser trapping-induced assembly of azobenzene-based biscalix[4]arene was quite different from the sharp-ellipsoidal aggregates obtained by the spontaneous evaporation of the solution. These trapping phenomena were specifically observed for biscalix[4]arene in the trans conformation of azo-benzene moiety but not for the cis-form, suggesting that the laser trapping of this azobenzene-based biscalix[4]arene is photocontrollable. Dynamics and mechanism of the supramolecular assembling are considered, referring to laser trapping-induced nucleation and liquid-liquid phase separation of amino acids.
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Affiliation(s)
- Ken-Ichi Yuyama
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University , Hsinchu 30010, Taiwan
| | - Lionel Marcelis
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University , Hsinchu 30010, Taiwan
| | - Pei-Mei Su
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University , Hsinchu 30010, Taiwan
| | - Wen-Sheng Chung
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University , Hsinchu 30010, Taiwan
| | - Hiroshi Masuhara
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University , Hsinchu 30010, Taiwan
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90
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Hauser M, Wojcik M, Kim D, Mahmoudi M, Li W, Xu K. Correlative Super-Resolution Microscopy: New Dimensions and New Opportunities. Chem Rev 2017; 117:7428-7456. [PMID: 28045508 DOI: 10.1021/acs.chemrev.6b00604] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Correlative microscopy, the integration of two or more microscopy techniques performed on the same sample, produces results that emphasize the strengths of each technique while offsetting their individual weaknesses. Light microscopy has historically been a central method in correlative microscopy due to its widespread availability, compatibility with hydrated and live biological samples, and excellent molecular specificity through fluorescence labeling. However, conventional light microscopy can only achieve a resolution of ∼300 nm, undercutting its advantages in correlations with higher-resolution methods. The rise of super-resolution microscopy (SRM) over the past decade has drastically improved the resolution of light microscopy to ∼10 nm, thus creating exciting new opportunities and challenges for correlative microscopy. Here we review how these challenges are addressed to effectively correlate SRM with other microscopy techniques, including light microscopy, electron microscopy, cryomicroscopy, atomic force microscopy, and various forms of spectroscopy. Though we emphasize biological studies, we also discuss the application of correlative SRM to materials characterization and single-molecule reactions. Finally, we point out current limitations and discuss possible future improvements and advances. We thus demonstrate how a correlative approach adds new dimensions of information and provides new opportunities in the fast-growing field of SRM.
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Affiliation(s)
- Meghan Hauser
- Department of Chemistry, University of California , Berkeley, California 94720, United States
| | - Michal Wojcik
- Department of Chemistry, University of California , Berkeley, California 94720, United States
| | - Doory Kim
- Department of Chemistry, University of California , Berkeley, California 94720, United States
| | - Morteza Mahmoudi
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Wan Li
- Department of Chemistry, University of California , Berkeley, California 94720, United States
| | - Ke Xu
- Department of Chemistry, University of California , Berkeley, California 94720, United States.,Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
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91
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Whitley K, Comstock M, Chemla Y. High-Resolution Optical Tweezers Combined With Single-Molecule Confocal Microscopy. Methods Enzymol 2017; 582:137-169. [PMID: 28062033 PMCID: PMC5540136 DOI: 10.1016/bs.mie.2016.10.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We describe the design, construction, and application of an instrument combining dual-trap, high-resolution optical tweezers and a confocal microscope. This hybrid instrument allows nanomechanical manipulation and measurement simultaneously with single-molecule fluorescence detection. We present the general design principles that overcome the challenges of maximizing optical trap resolution while maintaining single-molecule fluorescence sensitivity, and provide details on the construction and alignment of the instrument. This powerful new tool is just beginning to be applied to biological problems. We present step-by-step instructions on an application of this technique that highlights the instrument's capabilities, detecting conformational dynamics in a nucleic acid-processing enzyme.
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Affiliation(s)
- K.D. Whitley
- University of Illinois at Urbana–Champaign, Urbana, IL, United States
| | - M.J. Comstock
- Michigan State University, East Lansing, MI, United States
| | - Y.R. Chemla
- University of Illinois at Urbana–Champaign, Urbana, IL, United States,Center for the Physics of Living Cells, University of Illinois at Urbana–Champaign, Urbana, IL, United States,Corresponding author:
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92
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Bugiel M, Jannasch A, Schäffer E. Implementation and Tuning of an Optical Tweezers Force-Clamp Feedback System. Methods Mol Biol 2017; 1486:109-136. [PMID: 27844427 DOI: 10.1007/978-1-4939-6421-5_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Feedback systems can be used to control the value of a system variable. In optical tweezers, active feedback is often implemented to either keep the position or tension applied to a single biomolecule constant. Here, we describe the implementation of the latter: an optical force-clamp setup that can be used to study the motion of processive molecular motors under a constant load. We describe the basics of a software-implemented proportional-integral-derivative (PID) controller, how to tune it, and how to determine its optimal feedback rate. Limitations, possible feed-forward applications, and extensions into two- and three-dimensional optical force clamps are discussed. The feedback is ultimately limited by thermal fluctuations and the compliance of the involved molecules. To investigate a particular mechanical process, understanding the basics and limitations of the feedback system will be helpful for choosing the proper feedback hardware, for optimizing the system parameters, and for the design of the experiment.
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Affiliation(s)
- Michael Bugiel
- Center for Plant Molecular Biology, Universität Tübingen, Auf der Morgenstelle 32, D-72076, Tübingen, Germany
| | - Anita Jannasch
- Center for Plant Molecular Biology, Universität Tübingen, Auf der Morgenstelle 32, D-72076, Tübingen, Germany
| | - Erik Schäffer
- Center for Plant Molecular Biology, Universität Tübingen, Auf der Morgenstelle 32, D-72076, Tübingen, Germany.
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93
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Heller I, Laurens N, Vorselen D, Broekmans OD, Biebricher AS, King GA, Brouwer I, Wuite GJL, Peterman EJG. Versatile Quadruple-Trap Optical Tweezers for Dual DNA Experiments. Methods Mol Biol 2017; 1486:257-272. [PMID: 27844431 DOI: 10.1007/978-1-4939-6421-5_9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Optical manipulation techniques provide researchers the powerful ability to directly move, probe and interrogate molecular complexes. Quadruple optical trapping is an emerging method for optical manipulation and force spectroscopy that has found its primary use in studying dual DNA interactions, but is certainly not limited to DNA investigations. The key benefit of quadruple optical trapping is that two molecular strands can be manipulated independently and simultaneously. The molecular geometries of the strands can thus be controlled and their interactions can be quantified by force measurements. Accurate control of molecular geometry is of critical importance for the analysis of, for example, protein-mediated DNA-bridging, which plays an important role in DNA compaction. Here, we describe the design of a dedicated and robust quadruple optical trapping-instrument. This instrument can be switched straightforwardly to a high-resolution dual trap and it is integrated with microfluidics and single-molecule fluorescence microscopy, making it a highly versatile tool for correlative single-molecule analysis of a wide range of biomolecular systems.
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Affiliation(s)
- Iddo Heller
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Niels Laurens
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Daan Vorselen
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Onno D Broekmans
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Andreas S Biebricher
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Graeme A King
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Ineke Brouwer
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Erwin J G Peterman
- Department of Physics and Astronomy and LaserLab, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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94
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Liu Q, Zhang B, Qi S, Li Y, Fan X, Zhao Y, Zhou W, Shen D. Integration of helicity-control and pulse-modulation for vortex laser based on a black phosphorus plate. OPTICS EXPRESS 2016; 24:30031-30037. [PMID: 28059388 DOI: 10.1364/oe.24.030031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Using a home-made black phosphorus plate (BPP) as handedness controller and Q-switch modulator synchronously, a ~1.6 µm pulsed vortex laser with well-determined handedness is demonstrated in this letter. Stable vortex pulses of LG0, + 1, LG0,-1, LG0, + 2 and LG0,-2 modes were respectively achieved from compact resonant cavities in this experiment. Such pulsed vortex laser should have promising applications in various fields based on its simple structure, controllable handedness, and carried orbital angular momentum.
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95
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Hashemi Shabestari M, Meijering AEC, Roos WH, Wuite GJL, Peterman EJG. Recent Advances in Biological Single-Molecule Applications of Optical Tweezers and Fluorescence Microscopy. Methods Enzymol 2016; 582:85-119. [PMID: 28062046 DOI: 10.1016/bs.mie.2016.09.047] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Over the past two decades, single-molecule techniques have evolved into robust tools to study many fundamental biological processes. The combination of optical tweezers with fluorescence microscopy and microfluidics provides a powerful single-molecule manipulation and visualization technique that has found widespread application in biology. In this combined approach, the spatial (~nm) and temporal (~ms) resolution, as well as the force scale (~pN) accessible to optical tweezers is complemented with the power of fluorescence microscopy. Thereby, it provides information on the local presence, identity, spatial dynamics, and conformational dynamics of single biomolecules. Together, these techniques allow comprehensive studies of, among others, molecular motors, protein-protein and protein-DNA interactions, biomolecular conformational changes, and mechanotransduction pathways. In this chapter, recent applications of fluorescence microscopy in combination with optical trapping are discussed. After an introductory section, we provide a description of instrumentation together with the current capabilities and limitations of the approaches. Next we summarize recent studies that applied this combination of techniques in biological systems and highlight some representative biological assays to mark the exquisite opportunities that optical tweezers combined with fluorescence microscopy provide.
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Affiliation(s)
| | | | - W H Roos
- Moleculaire Biofysica, Zernike Institute, Rijksuniversiteit Groningen, Groningen, The Netherlands
| | - G J L Wuite
- Vrije Universiteit, Amsterdam, The Netherlands
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96
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Single-molecule studies of high-mobility group B architectural DNA bending proteins. Biophys Rev 2016; 9:17-40. [PMID: 28303166 PMCID: PMC5331113 DOI: 10.1007/s12551-016-0236-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 10/19/2016] [Indexed: 11/23/2022] Open
Abstract
Protein–DNA interactions can be characterized and quantified using single molecule methods such as optical tweezers, magnetic tweezers, atomic force microscopy, and fluorescence imaging. In this review, we discuss studies that characterize the binding of high-mobility group B (HMGB) architectural proteins to single DNA molecules. We show how these studies are able to extract quantitative information regarding equilibrium binding as well as non-equilibrium binding kinetics. HMGB proteins play critical but poorly understood roles in cellular function. These roles vary from the maintenance of chromatin structure and facilitation of ribosomal RNA transcription (yeast high-mobility group 1 protein) to regulatory and packaging roles (human mitochondrial transcription factor A). We describe how these HMGB proteins bind, bend, bridge, loop and compact DNA to perform these functions. We also describe how single molecule experiments observe multiple rates for dissociation of HMGB proteins from DNA, while only one rate is observed in bulk experiments. The measured single-molecule kinetics reveals a local, microscopic mechanism by which HMGB proteins alter DNA flexibility, along with a second, much slower macroscopic rate that describes the complete dissociation of the protein from DNA.
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97
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Direct and precise length measurement of single, stretched DNA fragments by dynamic molecular combing and STED nanoscopy. Anal Bioanal Chem 2016; 408:6453-9. [DOI: 10.1007/s00216-016-9764-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 06/25/2016] [Accepted: 07/04/2016] [Indexed: 11/25/2022]
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98
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Chemla YR. High‐resolution, hybrid optical trapping methods, and their application to nucleic acid processing proteins. Biopolymers 2016; 105:704-14. [DOI: 10.1002/bip.22880] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 05/12/2016] [Accepted: 05/16/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Yann R. Chemla
- Department of Physics, Center for the Physics of Living Cells, Center for Biophysics and Quantitative BiologyUniversity of IllinoisUrbana‐Champaign
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99
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Sliding sleeves of XRCC4-XLF bridge DNA and connect fragments of broken DNA. Nature 2016; 535:566-9. [PMID: 27437582 DOI: 10.1038/nature18643] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/13/2016] [Indexed: 12/11/2022]
Abstract
Non-homologous end joining (NHEJ) is the primary pathway for repairing DNA double-strand breaks (DSBs) in mammalian cells. Such breaks are formed, for example, during gene-segment rearrangements in the adaptive immune system or by cancer therapeutic agents. Although the core components of the NHEJ machinery are known, it has remained difficult to assess the specific roles of these components and the dynamics of bringing and holding the fragments of broken DNA together. The structurally similar XRCC4 and XLF proteins are proposed to assemble as highly dynamic filaments at (or near) DSBs. Here we show, using dual- and quadruple-trap optical tweezers combined with fluorescence microscopy, how human XRCC4, XLF and XRCC4-XLF complexes interact with DNA in real time. We find that XLF stimulates the binding of XRCC4 to DNA, forming heteromeric complexes that diffuse swiftly along the DNA. Moreover, we find that XRCC4-XLF complexes robustly bridge two independent DNA molecules and that these bridges are able to slide along the DNA. These observations suggest that XRCC4-XLF complexes form mobile sleeve-like structures around DNA that can reconnect the broken ends very rapidly and hold them together. Understanding the dynamics and regulation of this mechanism will lead to clarification of how NHEJ proteins are involved in generating chromosomal translocations.
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100
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Abulikemu A, Yusufu T, Mamuti R, Araki S, Miyamoto K, Omatsu T. Octave-band tunable optical vortex parametric oscillator. OPTICS EXPRESS 2016; 24:15204-15211. [PMID: 27410798 DOI: 10.1364/oe.24.015204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We developed an octave-band tunable optical vortex laser based on a 532 nm optical vortex pumped optical parametric oscillator with a simple linear-cavity configuration by employing cascaded non-critical phase-matching LiB3O5 crystals. The optical vortex output was tunable from 735 to 1903 nm. For a pump energy of 9 mJ, an optical vortex pulse energy of 0.24-2.36 mJ was obtained, corresponding to an optical-optical efficiency of 0.3-26%.
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