1
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Lokanathan Balaji S, De Bragança S, Balaguer-Pérez F, Northall S, Wilkinson OJ, Aicart-Ramos C, Seetaloo N, Sobott F, Moreno-Herrero F, Dillingham MS. DNA binding and bridging by human CtIP in the healthy and diseased states. Nucleic Acids Res 2024; 52:8303-8319. [PMID: 38922686 DOI: 10.1093/nar/gkae538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 06/05/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
The human DNA repair factor CtIP helps to initiate the resection of double-stranded DNA breaks for repair by homologous recombination, in part through its ability to bind and bridge DNA molecules. However, CtIP is a natively disordered protein that bears no apparent similarity to other DNA-binding proteins and so the structural basis for these activities remains unclear. In this work, we have used bulk DNA binding, single molecule tracking, and DNA bridging assays to study wild-type and variant CtIP proteins to better define the DNA binding domains and the effects of mutations associated with inherited human disease. Our work identifies a monomeric DNA-binding domain in the C-terminal region of CtIP. CtIP binds non-specifically to DNA and can diffuse over thousands of nucleotides. CtIP-mediated bridging of distant DNA segments is observed in single-molecule magnetic tweezers experiments. However, we show that binding alone is insufficient for DNA bridging, which also requires tetramerization via the N-terminal domain. Variant CtIP proteins associated with Seckel and Jawad syndromes display impaired DNA binding and bridging activities. The significance of these findings in the context of facilitating DNA break repair is discussed.
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Affiliation(s)
- Shreya Lokanathan Balaji
- DNA:Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Sara De Bragança
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049, Spain
| | - Francisco Balaguer-Pérez
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049, Spain
| | - Sarah Northall
- DNA:Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Oliver John Wilkinson
- DNA:Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Clara Aicart-Ramos
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049, Spain
| | - Neeleema Seetaloo
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Frank Sobott
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049, Spain
| | - Mark Simon Dillingham
- DNA:Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
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2
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Chua GNL, Liu S. When Force Met Fluorescence: Single-Molecule Manipulation and Visualization of Protein-DNA Interactions. Annu Rev Biophys 2024; 53:169-191. [PMID: 38237015 DOI: 10.1146/annurev-biophys-030822-032904] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Myriad DNA-binding proteins undergo dynamic assembly, translocation, and conformational changes while on DNA or alter the physical configuration of the DNA substrate to control its metabolism. It is now possible to directly observe these activities-often central to the protein function-thanks to the advent of single-molecule fluorescence- and force-based techniques. In particular, the integration of fluorescence detection and force manipulation has unlocked multidimensional measurements of protein-DNA interactions and yielded unprecedented mechanistic insights into the biomolecular processes that orchestrate cellular life. In this review, we first introduce the different experimental geometries developed for single-molecule correlative force and fluorescence microscopy, with a focus on optical tweezers as the manipulation technique. We then describe the utility of these integrative platforms for imaging protein dynamics on DNA and chromatin, as well as their unique capabilities in generating complex DNA configurations and uncovering force-dependent protein behaviors. Finally, we give a perspective on the future directions of this emerging research field.
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Affiliation(s)
- Gabriella N L Chua
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, New York, USA;
- Tri-Institutional PhD Program in Chemical Biology, New York, New York, USA
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, New York, USA;
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3
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Liu Z, van Veen E, Sánchez H, Solano B, Palmero Moya FJ, McCluskey KA, Ramírez Montero D, van Laar T, Dekker NH. A Biophysics Toolbox for Reliable Data Acquisition and Processing in Integrated Force-Confocal Fluorescence Microscopy. ACS PHOTONICS 2024; 11:1592-1603. [PMID: 38645993 PMCID: PMC11027178 DOI: 10.1021/acsphotonics.3c01739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/01/2024] [Accepted: 03/01/2024] [Indexed: 04/23/2024]
Abstract
Integrated single-molecule force-fluorescence spectroscopy setups allow for simultaneous fluorescence imaging and mechanical force manipulation and measurements on individual molecules, providing comprehensive dynamic and spatiotemporal information. Dual-beam optical tweezers (OT) combined with a confocal scanning microscope form a force-fluorescence spectroscopy apparatus broadly used to investigate various biological processes, in particular, protein:DNA interactions. Such experiments typically involve imaging of fluorescently labeled proteins bound to DNA and force spectroscopy measurements of trapped individual DNA molecules. Here, we present a versatile state-of-the-art toolbox including the preparation of protein:DNA complex samples, design of a microfluidic flow cell incorporated with OT, automation of OT-confocal scanning measurements, and the development and implementation of a streamlined data analysis package for force and fluorescence spectroscopy data processing. Its components can be adapted to any commercialized or home-built dual-beam OT setup equipped with a confocal scanning microscope, which will facilitate single-molecule force-fluorescence spectroscopy studies on a large variety of biological systems.
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Affiliation(s)
- Zhaowei Liu
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Edo van Veen
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Humberto Sánchez
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Belén Solano
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Francisco J. Palmero Moya
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Kaley A. McCluskey
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Daniel Ramírez Montero
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Theo van Laar
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Nynke H. Dekker
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
- Clarendon
Laboratory, Department of Physics, University
of Oxford, Oxford OX1 3PU, U.K.
- Kavli
Institute of Nanoscience Discovery, University
of Oxford, Dorothy Crowfoot
Hodgkin Building, Oxford OX1 3QU, U.K.
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4
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Scheiderer L, von der Emde H, Hesselink M, Weber M, Hell SW. MINSTED tracking of single biomolecules. Nat Methods 2024; 21:569-573. [PMID: 38480903 PMCID: PMC11009101 DOI: 10.1038/s41592-024-02209-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 02/13/2024] [Indexed: 04/13/2024]
Abstract
Here we show that MINSTED localization, a method whereby the position of a fluorophore is identified with precisely controlled beams of a STED microscope, tracks fluorophores and hence labeled biomolecules with nanometer/millisecond spatiotemporal precision. By updating the position for each detected photon, MINSTED recognizes fluorophore steps of 16 nm within <250 μs using about 13 photons. The power of MINSTED tracking is demonstrated by resolving the stepping of the motor protein kinesin-1 walking on microtubules and switching protofilaments.
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Affiliation(s)
- Lukas Scheiderer
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Henrik von der Emde
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Mira Hesselink
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Michael Weber
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Stefan W Hell
- Department of Optical Nanoscopy, Max Planck Institute for Medical Research, Heidelberg, Germany.
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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5
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Chatterjee S, Chaubet L, van den Berg A, Mukhortava A, Gulkis M, Çağlayan M. Uncovering nick DNA binding by LIG1 at the single-molecule level. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.28.587287. [PMID: 38586032 PMCID: PMC10996606 DOI: 10.1101/2024.03.28.587287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
DNA ligases repair the strand breaks are made continually and naturally throughout the genome, if left unrepaired and allowed to persist, they can lead to genome instability in the forms of lethal double-strand (ds) breaks, deletions, and duplications. DNA ligase 1 (LIG1) joins Okazaki fragments during the replication machinery and seals nicks at the end of most DNA repair pathways. Yet, how LIG1 recognizes its target substrate is entirely missing. Here, we uncover the dynamics of nick DNA binding by LIG1 at the single-molecule level. Our findings reveal that LIG1 binds to dsDNA both specifically and non-specifically and exhibits diffusive behavior to form a stable complex at the nick. Furthermore, by comparing with the LIG1 C-terminal protein, we demonstrate that the N-terminal non-catalytic region promotes binding enriched at nick sites and facilitates an efficient nick search process by promoting 1D diffusion along the DNA. Our findings provide a novel single-molecule insight into the nick binding by LIG1, which is critical to repair broken phosphodiester bonds in the DNA backbone to maintain genome integrity.
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6
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Madariaga-Marcos J, Aldag P, Kauert DJ, Seidel R. Correlated Single-Molecule Magnetic Tweezers and Fluorescence Measurements of DNA-Enzyme Interactions. Methods Mol Biol 2024; 2694:421-449. [PMID: 37824016 DOI: 10.1007/978-1-0716-3377-9_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Combining force spectroscopy and fluorescence microscopy provides a substantial improvement to the single-molecule toolbox by allowing simultaneous manipulation and orthogonal characterizations of the conformations, interactions, and activity of biomolecular complexes. Here, we describe a combined magnetic tweezers and total internal reflection fluorescence microscopy setup to carry out correlated single-molecule fluorescence spectroscopy and force/twisting experiments. We apply the setup to reveal the DNA interactions of the CRISPR-Cas surveillance complex Cascade. Single-molecule fluorescence of a labeled Cascade allows to follow the DNA association and dissociation of the protein. Simultaneously, the magnetic tweezers probe the DNA unwinding during R-loop formation by the bound Cascade complexes. Furthermore, the setup supports observation of 1D diffusion of protein complexes on stretched DNA molecules. This technique can be applied to study a vast range of protein-DNA interactions.
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Affiliation(s)
- Julene Madariaga-Marcos
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany
| | - Pierre Aldag
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany
| | - Dominik J Kauert
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany
| | - Ralf Seidel
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany.
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7
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Malinowska AM, van Mameren J, Peterman EJG, Wuite GJL, Heller I. Introduction to Optical Tweezers: Background, System Designs, and Applications. Methods Mol Biol 2024; 2694:3-28. [PMID: 37823997 DOI: 10.1007/978-1-0716-3377-9_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Optical tweezers are a means to manipulate objects with light. With the technique, microscopically small objects can be held and steered, allowing for accurate measurement of the forces applied to these objects. Optical tweezers can typically obtain a nanometer spatial resolution, a picoNewton force resolution, and a millisecond time resolution, which makes the technique well suited for the study of biological processes from the single-cell down to the single-molecule level. In this chapter, we aim to provide an introduction to the use of optical tweezers for single-molecule analyses. We start from 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. Finally, we will provide an overview of the broad applications in context of biological research, with the emphasis on the measurement modes, experimental assays, and possible combinations with fluorescence microscopy techniques.
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Affiliation(s)
- Agata M Malinowska
- LaserLaB Amsterdam and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Joost van Mameren
- Institute of Physics, University of Amsterdam, Amsterdam, The Netherlands
| | - Erwin J G Peterman
- LaserLaB Amsterdam and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Gijs J L Wuite
- LaserLaB Amsterdam and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Iddo Heller
- LaserLaB Amsterdam and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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8
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Guo J, Kang X, Chen K, Li Z, Wang G, Gao X, Liu Y. Arbitrary combinations of helical-conical optical beams in free space. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2024; 41:11-18. [PMID: 38175125 DOI: 10.1364/josaa.506476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/10/2023] [Indexed: 01/05/2024]
Abstract
Helical-conical optical beams (HCOBs) have attracted considerable interest due to their peculiar optical features. Their characteristic helical light intensity distribution has exerted unprecedented advantages in many fields, but multiple combinations of HCOBs have not been reported due to the limitations of algorithms and light field modulation techniques. We propose and experimentally demonstrate arbitrary combinations of multiple HCOBs in free space to construct hybrid HCOB arrays. The similarity between the experimental results and the numerical simulation results is 94.22%. The initial orientation of the HCOBs is flexibly tuned by the rotation factor β, and the optical pen is used to combine the HCOBs. This approach allows multiple parameters in the array to be precisely tuned, including the type, number, and position of HCOBs, adding more design flexibility. The constructed HCOB arrays have a higher degree of modulation freedom and may find applications in fields where dynamic control is in high demand, including optical tweezers, biological cell sorting, and multiparticle manipulation.
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9
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Liu S, Fan X, Qu Z, Fang C, Feng C, Zhao X, Wang JL. Improving the multi-functionality of optical tweezers with FPGA integration. APPLIED OPTICS 2024; 63:255-262. [PMID: 38175028 DOI: 10.1364/ao.505998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/29/2023] [Indexed: 01/05/2024]
Abstract
The development of optical tweezers aims to extend their operating function and pattern. However, excessive programming can lead to a decrease in the system's operating speed and introduce bugs or data transmission delays. In this study, we present a time-shared optical tweezers system that allows for parallel operation of multiple functions. To enable efficient data transmission, we employ a queue structure and a buffer. To assess the system's performance, we utilize a biological sample in conjunction with the optical tweezers system and scanning imaging technique. We quantify the trapping parameter while concurrently running power stabilization programs. As a result, the standard deviation of the measured stiffness is reduced by 60% in the x and y directions and 30% in the z direction, indicating a significant improvement in calibration precision. Throughout the program execution, the system maintains an operating rate of 110 kHz, and the data are continuously updated in real time on the host. The system's performance demonstrates its potential for quantification and morphological reconstruction of biological samples.
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10
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Xu X, Qiu K, Tian Z, Aryal C, Rowan F, Chen R, Sun Y, Diao J. Probing the dynamic crosstalk of lysosomes and mitochondria with structured illumination microscopy. Trends Analyt Chem 2023; 169:117370. [PMID: 37928815 PMCID: PMC10621629 DOI: 10.1016/j.trac.2023.117370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Structured illumination microscopy (SIM) is a super-resolution technology for imaging living cells and has been used for studying the dynamics of lysosomes and mitochondria. Recently, new probes and analyzing methods have been developed for SIM imaging, enabling the quantitative analysis of these subcellular structures and their interactions. This review provides an overview of the working principle and advances of SIM, as well as the organelle-targeting principles and types of fluorescence probes, including small molecules, metal complexes, nanoparticles, and fluorescent proteins. Additionally, quantitative methods based on organelle morphology and distribution are outlined. Finally, the review provides an outlook on the current challenges and future directions for improving the combination of SIM imaging and image analysis to further advance the study of organelles. We hope that this review will be useful for researchers working in the field of organelle research and help to facilitate the development of SIM imaging and analysis techniques.
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Affiliation(s)
- Xiuqiong Xu
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Kangqiang Qiu
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Zhiqi Tian
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Chinta Aryal
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Fiona Rowan
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Rui Chen
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Yujie Sun
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
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11
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Lu S, Chemla YR. Optical traps induce fluorophore photobleaching by two-photon excitation. Biophys J 2023; 122:4316-4325. [PMID: 37828742 PMCID: PMC10698272 DOI: 10.1016/j.bpj.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/20/2023] [Accepted: 10/10/2023] [Indexed: 10/14/2023] Open
Abstract
Techniques combining optical tweezers with fluorescence microscopy have become increasingly popular. Unfortunately, the high-power, infrared lasers used to create optical traps can have a deleterious effect on dye stability. Previous studies have shown that dye photobleaching is enhanced by absorption of visible fluorescence excitation plus infrared trap photons, a process that can be significantly reduced by minimizing simultaneous exposure to both light sources. Here, we report another photobleaching pathway that results from direct excitation by the trapping laser alone. Our results show that this trap-induced fluorescence loss is a two-photon absorption process, as demonstrated by a quadratic dependence on the intensity of the trapping laser. We further show that, under conditions typical of many trap-based experiments, fluorescence emission of certain fluorophores near the trap focus can drop by 90% within 1 min. We investigate how photostability is affected by the choice of dye molecule, excitation and emission wavelength, and labeled molecule. Finally, we discuss the different photobleaching pathways in combined trap-fluorescence measurements, which guide the selection of optimal dyes and conditions for more robust experimental protocols.
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Affiliation(s)
- Suoang Lu
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Yann R Chemla
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois; Center of the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois.
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12
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Zhu Y, You M, Shi Y, Huang H, Wei Z, He T, Xiong S, Wang Z, Cheng X. Optofluidic Tweezers: Efficient and Versatile Micro/Nano-Manipulation Tools. MICROMACHINES 2023; 14:1326. [PMID: 37512637 PMCID: PMC10384111 DOI: 10.3390/mi14071326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 06/21/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023]
Abstract
Optical tweezers (OTs) can transfer light momentum to particles, achieving the precise manipulation of particles through optical forces. Due to the properties of non-contact and precise control, OTs have provided a gateway for exploring the mysteries behind nonlinear optics, soft-condensed-matter physics, molecular biology, and analytical chemistry. In recent years, OTs have been combined with microfluidic chips to overcome their limitations in, for instance, speed and efficiency, creating a technology known as "optofluidic tweezers." This paper describes static OTs briefly first. Next, we overview recent developments in optofluidic tweezers, summarizing advancements in capture, manipulation, sorting, and measurement based on different technologies. The focus is on various kinds of optofluidic tweezers, such as holographic optical tweezers, photonic-crystal optical tweezers, and waveguide optical tweezers. Moreover, there is a continuing trend of combining optofluidic tweezers with other techniques to achieve greater functionality, such as antigen-antibody interactions and Raman tweezers. We conclude by summarizing the main challenges and future directions in this research field.
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Affiliation(s)
- Yuchen Zhu
- Institute of Precision Optical Engineering, School of Physics Science and Engineering, Tongji University, Shanghai 200092, China
- MOE Key Laboratory of Advanced Micro-Structured Materials, Shanghai 200092, China
- Shanghai Institute of Intelligent Science and Technology, Tongji University, Shanghai 200092, China
- Shanghai Frontiers Science Center of Digital Optics, Shanghai 200092, China
| | - Minmin You
- National Key Laboratory of Advanced Micro and Nano Manufacture Technology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuzhi Shi
- Institute of Precision Optical Engineering, School of Physics Science and Engineering, Tongji University, Shanghai 200092, China
- MOE Key Laboratory of Advanced Micro-Structured Materials, Shanghai 200092, China
- Shanghai Institute of Intelligent Science and Technology, Tongji University, Shanghai 200092, China
- Shanghai Frontiers Science Center of Digital Optics, Shanghai 200092, China
| | - Haiyang Huang
- Institute of Precision Optical Engineering, School of Physics Science and Engineering, Tongji University, Shanghai 200092, China
- MOE Key Laboratory of Advanced Micro-Structured Materials, Shanghai 200092, China
- Shanghai Institute of Intelligent Science and Technology, Tongji University, Shanghai 200092, China
- Shanghai Frontiers Science Center of Digital Optics, Shanghai 200092, China
| | - Zeyong Wei
- Institute of Precision Optical Engineering, School of Physics Science and Engineering, Tongji University, Shanghai 200092, China
- MOE Key Laboratory of Advanced Micro-Structured Materials, Shanghai 200092, China
- Shanghai Institute of Intelligent Science and Technology, Tongji University, Shanghai 200092, China
- Shanghai Frontiers Science Center of Digital Optics, Shanghai 200092, China
| | - Tao He
- Institute of Precision Optical Engineering, School of Physics Science and Engineering, Tongji University, Shanghai 200092, China
- MOE Key Laboratory of Advanced Micro-Structured Materials, Shanghai 200092, China
- Shanghai Institute of Intelligent Science and Technology, Tongji University, Shanghai 200092, China
- Shanghai Frontiers Science Center of Digital Optics, Shanghai 200092, China
| | - Sha Xiong
- School of Automation, Central South University, Changsha 410083, China
| | - Zhanshan Wang
- Institute of Precision Optical Engineering, School of Physics Science and Engineering, Tongji University, Shanghai 200092, China
- MOE Key Laboratory of Advanced Micro-Structured Materials, Shanghai 200092, China
- Shanghai Institute of Intelligent Science and Technology, Tongji University, Shanghai 200092, China
- Shanghai Frontiers Science Center of Digital Optics, Shanghai 200092, China
| | - Xinbin Cheng
- Institute of Precision Optical Engineering, School of Physics Science and Engineering, Tongji University, Shanghai 200092, China
- MOE Key Laboratory of Advanced Micro-Structured Materials, Shanghai 200092, China
- Shanghai Institute of Intelligent Science and Technology, Tongji University, Shanghai 200092, China
- Shanghai Frontiers Science Center of Digital Optics, Shanghai 200092, China
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13
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Louis B, Huang CH, Camacho R, Scheblykin IG, Sugiyama T, Kudo T, Melendez M, Delgado-Buscalioni R, Masuhara H, Hofkens J, Bresoli-Obach R. Unravelling 3D Dynamics and Hydrodynamics during Incorporation of Dielectric Particles to an Optical Trapping Site. ACS NANO 2023; 17:3797-3808. [PMID: 36800201 PMCID: PMC10623636 DOI: 10.1021/acsnano.2c11753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Mapping of the spatial and temporal motion of particles inside an optical field is critical for understanding and further improvement of the 3D spatio-temporal control over their optical trapping dynamics. However, it is not trivial to capture the 3D motion, and most imaging systems only capture a 2D projection of the 3D motion, in which the information about the axial movement is not directly available. In this work, we resolve the 3D incorporation trajectories of 200 nm fluorescent polystyrene particles in an optical trapping site under different optical experimental conditions using a recently developed widefield multiplane microscope (imaging volume of 50 × 50 × 4 μm3). The particles are gathered at the focus following some preferential 3D channels that show a shallow cone distribution. We demonstrate that the radial and the axial flow speed components depend on the axial distance from the focus, which is directly related to the scattering/gradient optical forces. While particle velocities and trajectories are mainly determined by the trapping laser profile, they cannot be completely explained without considering collective effects resulting from hydrodynamic forces.
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Affiliation(s)
- Boris Louis
- Molecular
Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Leuven 3001, Belgium
- Center
for Cellular Imaging, Core Facilities, the Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 5A-7A, Box 413, Gothenburg 40530, Sweden
| | - Chih-Hao Huang
- Department
of Applied Chemistry, National Yang Ming
Chiao Tung University, 1001 Ta Hsueh Road, Hsinchu 300093, Taiwan
| | - Rafael Camacho
- Center
for Cellular Imaging, Core Facilities, the Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 5A-7A, Box 413, Gothenburg 40530, Sweden
| | - Ivan G. Scheblykin
- Division
of Chemical Physics and NanoLund, Lund University, Kemicentrum Naturvetarvägen
16, P.O. Box 124, Lund 22100, Sweden
| | - Teruki Sugiyama
- Department
of Applied Chemistry, National Yang Ming
Chiao Tung University, 1001 Ta Hsueh Road, Hsinchu 300093, Taiwan
- Division
of Materials Science, Nara Institute of
Science and Technology, 8916-5 Takayamacho, Ikoma, Nara 630-0101, Japan
| | - Tetsuhiro Kudo
- Department
of Applied Chemistry, National Yang Ming
Chiao Tung University, 1001 Ta Hsueh Road, Hsinchu 300093, Taiwan
| | - Marc Melendez
- Departamento
de Física Teórica de la Materia Condensada, Institut
for Condensed Matter (IFIMAC), Universidad
Autónoma de Madrid, Campus de Cantoblanco, Madrid 28049, Spain
| | - Rafael Delgado-Buscalioni
- Departamento
de Física Teórica de la Materia Condensada, Institut
for Condensed Matter (IFIMAC), Universidad
Autónoma de Madrid, Campus de Cantoblanco, Madrid 28049, Spain
| | - Hiroshi Masuhara
- Department
of Applied Chemistry, National Yang Ming
Chiao Tung University, 1001 Ta Hsueh Road, Hsinchu 300093, Taiwan
- Center
for Emergent Functional Matter Science, National Yang Ming Chiao Tung University, 1001 Ta Hsueh Road, Hsinchu 300093, Taiwan
| | - Johan Hofkens
- Molecular
Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Leuven 3001, Belgium
- Max
Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
| | - Roger Bresoli-Obach
- Molecular
Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Leuven 3001, Belgium
- AppLightChem,
Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, Barcelona, Catalunya 08017, Spain
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14
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Xu L, Halma MTJ, Wuite GJL. Unravelling How Single-Stranded DNA Binding Protein Coordinates DNA Metabolism Using Single-Molecule Approaches. Int J Mol Sci 2023; 24:ijms24032806. [PMID: 36769124 PMCID: PMC9917605 DOI: 10.3390/ijms24032806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/23/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023] Open
Abstract
Single-stranded DNA-binding proteins (SSBs) play vital roles in DNA metabolism. Proteins of the SSB family exclusively and transiently bind to ssDNA, preventing the DNA double helix from re-annealing and maintaining genome integrity. In the meantime, they interact and coordinate with various proteins vital for DNA replication, recombination, and repair. Although SSB is essential for DNA metabolism, proteins of the SSB family have been long described as accessory players, primarily due to their unclear dynamics and mechanistic interaction with DNA and its partners. Recently-developed single-molecule tools, together with biochemical ensemble techniques and structural methods, have enhanced our understanding of the different coordination roles that SSB plays during DNA metabolism. In this review, we discuss how single-molecule assays, such as optical tweezers, magnetic tweezers, Förster resonance energy transfer, and their combinations, have advanced our understanding of the binding dynamics of SSBs to ssDNA and their interaction with other proteins partners. We highlight the central coordination role that the SSB protein plays by directly modulating other proteins' activities, rather than as an accessory player. Many possible modes of SSB interaction with protein partners are discussed, which together provide a bigger picture of the interaction network shaped by SSB.
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15
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Haghizadeh A, Iftikhar M, Dandpat SS, Simpson T. Looking at Biomolecular Interactions through the Lens of Correlated Fluorescence Microscopy and Optical Tweezers. Int J Mol Sci 2023; 24:2668. [PMID: 36768987 PMCID: PMC9916863 DOI: 10.3390/ijms24032668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/19/2022] [Accepted: 01/26/2023] [Indexed: 02/01/2023] Open
Abstract
Understanding complex biological events at the molecular level paves the path to determine mechanistic processes across the timescale necessary for breakthrough discoveries. While various conventional biophysical methods provide some information for understanding biological systems, they often lack a complete picture of the molecular-level details of such dynamic processes. Studies at the single-molecule level have emerged to provide crucial missing links to understanding complex and dynamic pathways in biological systems, which are often superseded by bulk biophysical and biochemical studies. Latest developments in techniques combining single-molecule manipulation tools such as optical tweezers and visualization tools such as fluorescence or label-free microscopy have enabled the investigation of complex and dynamic biomolecular interactions at the single-molecule level. In this review, we present recent advances using correlated single-molecule manipulation and visualization-based approaches to obtain a more advanced understanding of the pathways for fundamental biological processes, and how this combination technique is facilitating research in the dynamic single-molecule (DSM), cell biology, and nanomaterials fields.
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16
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Halma MTJ, Tuszynski JA, Wuite GJL. Optical tweezers for drug discovery. Drug Discov Today 2023; 28:103443. [PMID: 36396117 DOI: 10.1016/j.drudis.2022.103443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 09/23/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022]
Abstract
The time taken and the cost of producing novel therapeutic drugs presents a significant burden - a typical target-based drug discovery process involves computational screening of drug libraries, compound assays and expensive clinical trials. This review summarises the value of dynamic conformational information obtained by optical tweezers and how this information can target 'undruggable' proteins. Optical tweezers provide insights into the link between biological mechanisms and structural conformations, which can be used in drug discovery. Developing workflows including software and sample preparation will improve throughput, enabling adoption of optical tweezers in biopharma. As a complementary tool, optical tweezers increase the number of drug candidates, improve the understanding of a target's complex structural dynamics and elucidate interactions between compounds and their targets.
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Affiliation(s)
- Matthew T J Halma
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands; LUMICKS B.V, Paalbergweg 3, 1105 AG Amsterdam, The Netherlands
| | - Jack A Tuszynski
- Department of Physics, University of Alberta, 116 St 85 Ave, Edmonton, Alberta T6G 2R3, Canada
| | - Gijs J L Wuite
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands.
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17
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Optical Tweezers to Force Information out of Biological and Synthetic Systems One Molecule at a Time. BIOPHYSICA 2022. [DOI: 10.3390/biophysica2040047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Over the last few decades, in vitro single-molecule manipulation techniques have enabled the use of force and displacement as controlled variables in biochemistry. Measuring the effect of mechanical force on the real-time kinetics of a biological process gives us access to the rates, equilibrium constants and free-energy landscapes of the mechanical steps of the reaction; this information is not accessible by ensemble assays. Optical tweezers are the current method of choice in single-molecule manipulation due to their versatility, high force and spatial and temporal resolutions. The aim of this review is to describe the contributions of our lab in the single-molecule manipulation field. We present here several optical tweezers assays refined in our laboratory to probe the dynamics and mechano-chemical properties of biological molecular motors and synthetic molecular devices at the single-molecule level.
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18
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Favre-Bulle IA, Scott EK. Optical tweezers across scales in cell biology. Trends Cell Biol 2022; 32:932-946. [PMID: 35672197 PMCID: PMC9588623 DOI: 10.1016/j.tcb.2022.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 01/21/2023]
Abstract
Optical tweezers (OT) provide a noninvasive approach for delivering minute physical forces to targeted objects. Controlling such forces in living cells or in vitro preparations allows for the measurement and manipulation of numerous processes relevant to the form and function of cells. As such, OT have made important contributions to our understanding of the structures of proteins and nucleic acids, the interactions that occur between microscopic structures within cells, the choreography of complex processes such as mitosis, and the ways in which cells interact with each other. In this review, we highlight recent contributions made to the field of cell biology using OT and provide basic descriptions of the physics, the methods, and the equipment that made these studies possible.
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Affiliation(s)
- Itia A Favre-Bulle
- Queensland Brain Institute, The University of Queensland, 4067, Brisbane, Australia; School of Mathematics and Physics, The University of Queensland, 4067, Brisbane, Australia.
| | - Ethan K Scott
- Queensland Brain Institute, The University of Queensland, 4067, Brisbane, Australia; Department of Anatomy and Physiology, School of Biomedical Sciences, The University of Melbourne, Parkville, VIC 3010, Australia.
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19
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Yoon Y, Kim HS, Yoon S, Yeon KM, Kim J. Precipitation-based microscale enzyme reactors coupled with porous and adhesive elastomer for effective bacterial decontamination and membrane antifouling on-demand. ENVIRONMENTAL RESEARCH 2022; 212:113407. [PMID: 35523281 DOI: 10.1016/j.envres.2022.113407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 06/14/2023]
Abstract
Bacterial contamination of water environments can cause various troubles in various areas. As one of potential solutions, we develop enzyme-immobilized elastomer, and demonstrate the uses of enzyme reactions on-demand for effective microbial decontamination and antifouling. Asymmetrically-structured elastomer is prepared by combining two polydimethylsiloxane (PDMS) layers with different degrees of crosslinking: highly-crosslinked and lightly-crosslinked PDMS layers. At the surface of highly-crosslinked PDMS layer, porous structure with average diameter of 842 nm is formed by dissolving pre-packed and entrapped latex beads. Lightly-crosslinked PDMS on the other side, due to its adhesive nature, enables iterative attachments on various materials under either dry or wet condition. Glucose oxidase (GOx) is immobilized by using the pores at the surface of highly-crosslinked PDMS matrix via a ship-in-a-bottle protocol of precipitation-based microscale enzyme reactor (p-MER), which consists of GOx adsorption, precipitation and chemical crosslinking (EAPC). As a result, crosslinked enzyme aggregates (CLEAs) of GOx not only are well entrapped within many pores of highly-crosslinked PDMS layer (ship-in-bottle) but also cover the external surface of matrix, both of which are well connected together. Highly-interconnected network of CLEAs themselves effectively prevents enzyme leaching, which shows the 25% residual activity of GOx under shaking at 200 rpm for 156 days after 48% initial drop of loosely-bound p-MER after 4 days. In presence of glucose, the underwater attachment of biocatalytic elastomer demonstrates the generation of hydrogen peroxide via p-MER-catalyzed glucose oxidation, exhibiting effective biocidal activities against both gram-positive S. aureus and gram-negative E. coli. Adhesion-induced GOx-catalyzed reaction also alleviates the biofouling of membrane, suggesting its extendibility to various engineering systems being suffered by biofouling. This study of biocatalytic elastomer has demonstrated its new opportunities for the facile and on-demand enzyme-catalyzed reactions in various environmental applications, such as bactericidal treatment, water treatment/purification, and pollutant degradation.
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Affiliation(s)
- YoungChul Yoon
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Han Sol Kim
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Seji Yoon
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Kyung-Min Yeon
- Engineering Center, Samsung C&T Corporation, Tower B, 26, Sangil-ro, 6- gil, Gangdong-gu, Seoul, Republic of Korea.
| | - Jungbae Kim
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea.
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20
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Wang G, Kang X, Sun X, Li Z, Li Y, Chen K, Zhang N, Gao X, Zhuang S. Generation of perfect optical vortex arrays by an optical pen. OPTICS EXPRESS 2022; 30:31959-31970. [PMID: 36242267 DOI: 10.1364/oe.464473] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/02/2022] [Indexed: 06/16/2023]
Abstract
Recently, perfect optical vortexes (POVs) have attracted substantial attention, because they have an orbital angular momentum (OAM) and the beam diameter is independent of the topological charges. There are numerous innovative results that have been found by modulating the POV optical field. However, methods for controlling the arbitrary parameters of POV are lacking. In this paper, we use the optical pen to overcome this problem. The optical pen is a high-precision optical field modulation method construction based on the relationship between the optical path difference and phase. Based on this method, we have achieved POV arrays with controllable arbitrary parameters in free space, including the spatial position, numbers, topological charges, beam diameter, and amplitude. This work can be applied not only in the fields of optical tweezers, particle manipulation, and super-resolution microscopic imaging, but also will promote the development of optical communication, quantum information coding, and so on.
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21
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Chen Z, Cai Z, Liu W, Yan Z. Optical trapping and manipulation for single-particle spectroscopy and microscopy. J Chem Phys 2022; 157:050901. [DOI: 10.1063/5.0086328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Optical tweezers can control the position and orientation of individual colloidal particles in solution. Such control is often desirable but challenging for single-particle spectroscopy and microscopy, especially at the nanoscale. Functional nanoparticles that are optically trapped and manipulated in a three-dimensional (3D) space can serve as freestanding nanoprobes, which provide unique prospects of sensing and mapping the surrounding environment of the nanoparticles and studying their interactions with biological systems. In this perspective, we will first describe the optical forces underlying the optical trapping and manipulation of microscopic particles, then review the combinations and applications of different spectroscopy and microscopy techniques with optical tweezers. Finally, we will discuss the challenges of performing spectroscopy and microscopy on single nanoparticles with optical tweezers, the possible routes to address these challenges, and the new opportunities that will arise.
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Affiliation(s)
- Zhenzhen Chen
- The University of North Carolina at Chapel Hill, United States of America
| | - Zhewei Cai
- Clarkson University, United States of America
| | - Wenbo Liu
- The University of North Carolina at Chapel Hill, United States of America
| | - Zijie Yan
- University of North Carolina at Chapel Hill, United States of America
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22
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Paul B, Chaubet L, Verver DE, Montoya G. Mechanics of CRISPR-Cas12a and engineered variants on λ-DNA. Nucleic Acids Res 2022; 50:5208-5225. [PMID: 34951457 PMCID: PMC9122593 DOI: 10.1093/nar/gkab1272] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 12/26/2022] Open
Abstract
Cas12a is an RNA-guided endonuclease that is emerging as a powerful genome-editing tool. Here, we selected a target site on bacteriophage λ-DNA and used optical tweezers combined with fluorescence to provide mechanistic insight into wild type Cas12a and three engineered variants, where the specific dsDNA and the unspecific ssDNA cleavage are dissociated (M1 and M2) and a third one which nicks the target DNA (M3). At low forces wtCas12a and the variants display two main off-target binding sites, while on stretched dsDNA at higher forces numerous binding events appear driven by the mechanical distortion of the DNA and partial matches to the crRNA. The multiple binding events onto dsDNA at high tension do not lead to cleavage, which is observed on the target site at low forces when the DNA is flexible. In addition, activity assays also show that the preferential off-target sites for this crRNA are not cleaved by wtCas12a, indicating that λ-DNA is only severed at the target site. Our single molecule data indicate that the Cas12a scaffold presents singular mechanical properties, which could be used to generate new endonucleases with biomedical and biotechnological applications.
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Affiliation(s)
- Bijoya Paul
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen, Blegdamsvej 3-B, Copenhagen 2200, Denmark
| | - Loïc Chaubet
- LUMICKS, Pilotenstraat 41, 1059 CH, Amsterdam, The Netherlands
| | | | - Guillermo Montoya
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences University of Copenhagen, Blegdamsvej 3-B, Copenhagen 2200, Denmark
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23
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Meijering AEC, Sarlós K, Nielsen CF, Witt H, Harju J, Kerklingh E, Haasnoot GH, Bizard AH, Heller I, Broedersz CP, Liu Y, Peterman EJG, Hickson ID, Wuite GJL. Nonlinear mechanics of human mitotic chromosomes. Nature 2022; 605:545-550. [PMID: 35508652 PMCID: PMC9117150 DOI: 10.1038/s41586-022-04666-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 03/21/2022] [Indexed: 12/26/2022]
Abstract
In preparation for mitotic cell division, the nuclear DNA of human cells is compacted into individualized, X-shaped chromosomes1. This metamorphosis is driven mainly by the combined action of condensins and topoisomerase IIα (TOP2A)2,3, and has been observed using microscopy for over a century. Nevertheless, very little is known about the structural organization of a mitotic chromosome. Here we introduce a workflow to interrogate the organization of human chromosomes based on optical trapping and manipulation. This allows high-resolution force measurements and fluorescence visualization of native metaphase chromosomes to be conducted under tightly controlled experimental conditions. We have used this method to extensively characterize chromosome mechanics and structure. Notably, we find that under increasing mechanical load, chromosomes exhibit nonlinear stiffening behaviour, distinct from that predicted by classical polymer models4. To explain this anomalous stiffening, we introduce a hierarchical worm-like chain model that describes the chromosome as a heterogeneous assembly of nonlinear worm-like chains. Moreover, through inducible degradation of TOP2A5 specifically in mitosis, we provide evidence that TOP2A has a role in the preservation of chromosome compaction. The methods described here open the door to a wide array of investigations into the structure and dynamics of both normal and disease-associated chromosomes.
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Affiliation(s)
- Anna E C Meijering
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Kata Sarlós
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Christian F Nielsen
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Hannes Witt
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Janni Harju
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Emma Kerklingh
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Guus H Haasnoot
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Anna H Bizard
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Iddo Heller
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Chase P Broedersz
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| | - Ying Liu
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Erwin J G Peterman
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Ian D Hickson
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark.
| | - Gijs J L Wuite
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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24
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Liu J, Gu Q, Du W, Feng Z, Zhang Q, Tian Y, Luo K, Gong Q, Tian X. Nucleolar RNA in action: Ultrastructure revealed during protein translation through a terpyridyl manganese(II) complex. Biosens Bioelectron 2022; 203:114058. [DOI: 10.1016/j.bios.2022.114058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/21/2021] [Accepted: 01/28/2022] [Indexed: 11/02/2022]
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25
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Hörnblad A, Remeseiro S. Epigenetics, Enhancer Function and 3D Chromatin Organization in Reprogramming to Pluripotency. Cells 2022; 11:cells11091404. [PMID: 35563711 PMCID: PMC9105757 DOI: 10.3390/cells11091404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 12/22/2022] Open
Abstract
Genome architecture, epigenetics and enhancer function control the fate and identity of cells. Reprogramming to induced pluripotent stem cells (iPSCs) changes the transcriptional profile and chromatin landscape of the starting somatic cell to that of the pluripotent cell in a stepwise manner. Changes in the regulatory networks are tightly regulated during normal embryonic development to determine cell fate, and similarly need to function in cell fate control during reprogramming. Switching off the somatic program and turning on the pluripotent program involves a dynamic reorganization of the epigenetic landscape, enhancer function, chromatin accessibility and 3D chromatin topology. Within this context, we will review here the current knowledge on the processes that control the establishment and maintenance of pluripotency during somatic cell reprogramming.
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Affiliation(s)
- Andreas Hörnblad
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, 901 87 Umeå, Sweden
- Correspondence: (A.H.); (S.R.)
| | - Silvia Remeseiro
- Umeå Centre for Molecular Medicine (UCMM), Umeå University, 901 87 Umeå, Sweden
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, 901 87 Umeå, Sweden
- Correspondence: (A.H.); (S.R.)
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26
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Geldhof JJ, Malinowska AM, Wuite GJL, Peterman EJG, Heller I. Temperature Quantification and Temperature Control in Optical Tweezers. Methods Mol Biol 2022; 2478:123-140. [PMID: 36063321 DOI: 10.1007/978-1-0716-2229-2_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Optical tweezers are widely used to investigate biomolecules and biomolecular interactions. In these investigations, the biomolecules of interest are typically coupled to microscopic beads that can be optically trapped. Since high-intensity laser beams are required to trap such microscopic beads, laser-induced heating due to optical absorption is typically unavoidable. This chapter discusses how to identify, quantify, and control thermal effects in optical tweezers. We provide a brief overview of the reported causes and effects of unwanted heating in optical tweezers systems. Specific details are provided on methods to perform a temperature-independent trap calibration procedure. Finally, an effective temperature-control system is presented, and we discuss the operation of this system as well as the methods to measure the temperature at the optically trapped particle.
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Affiliation(s)
- Joost J Geldhof
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Agata M Malinowska
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Erwin J G Peterman
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Iddo Heller
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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27
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Bi L, Qin Z, Hou XM, Modesti M, Sun B. Simultaneous Mechanical and Fluorescence Detection of Helicase-Catalyzed DNA Unwinding. Methods Mol Biol 2022; 2478:329-347. [PMID: 36063326 DOI: 10.1007/978-1-0716-2229-2_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Helicases are ubiquitous molecular motor proteins that utilize the energy derived from the hydrolysis of nucleoside triphosphates (NTPs) to transiently convert the duplex form of nucleic acids to single-stranded intermediates for many biological processes. These enzymes play vital roles in nearly all aspects of nucleic acid metabolism, such as DNA repair and RNA splicing. Understanding helicase's functional roles requires methods to dissect the mechanisms of motor proteins at the molecular level. In the past three decades, there has been a large increase in the application of single-molecule approaches to investigate helicases. These techniques, such as optical tweezers and single-molecule fluorescence, offer capabilities to monitor helicase motions with unprecedented spatiotemporal resolution, to apply quantitative forces to probe the chemo-mechanical activities of these motors and to resolve helicase heterogeneity at the single-molecule level. In this chapter, we describe a single-molecule method that combines optical tweezers with confocal fluorescence microscopy to study helicase-catalyzed DNA unwinding. Using Bloom syndrome protein (BLM), a multifunctional helicase that maintains genome stability, as an example, we show that this method allows for the simultaneous detection of displacement, force and fluorescence signals of a single DNA molecule during unwinding in real time, leading to the discovery of a distinct bidirectional unwinding mode of BLM that is activated by a single-stranded DNA binding protein called replication protein A (RPA). We provide detailed instructions on how to prepare two DNA templates to be used in the assays, purify the BLM and RPA proteins, perform single-molecule experiments, and acquire and analyse the data.
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Affiliation(s)
- Lulu Bi
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zhenheng Qin
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xi-Miao Hou
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Mauro Modesti
- Cancer Research Center of Marseille, Marseille, France
| | - Bo Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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28
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Meijering AEC, Bakx JAM, Man T, Heller I, Wuite GJL, Peterman EJG. Implementation of 3D Multi-Color Fluorescence Microscopy in a Quadruple Trap Optical Tweezers System. Methods Mol Biol 2022; 2478:75-100. [PMID: 36063319 DOI: 10.1007/978-1-0716-2229-2_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Recent advances in the design and measurement capabilities of optical tweezers instruments, and especially the combination with multi-color fluorescence detection, have accommodated a dramatic increase in the versatility of optical trapping. Quadruple (Q)-trap optical tweezers are an excellent example of such an advance, by providing three-dimensional control over two constructs and thereby enabling for example DNA-DNA braiding. However, the implementation of fluorescence detection in such a Q-trapping system poses several challenges: (1) since typical samples span a distance in the order of tens of micrometers, it requires imaging of a large field of view, (2) in order to capture fast molecular dynamics, fast imaging with single-molecule sensitivity is desired, (3) in order to study three-dimensional objects, it could be needed to detect emission light at different axial heights while keeping the objective lens and thus the optically trapped microspheres in a fixed position. In this chapter, we describe design guidelines for a fluorescence imaging module on a Q-trap system that overcomes these challenges and provide a step-by-step description for construction and alignment of such a system. Finally, we present detailed instructions for proof-of-concept experiments that can be used to validate and highlight the capabilities of the instruments.
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Affiliation(s)
- Anna E C Meijering
- Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, Amsterdam, The Netherlands
| | - Julia A M Bakx
- Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, Amsterdam, The Netherlands
| | - Tianlong Man
- Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, Amsterdam, The Netherlands
| | - Iddo Heller
- Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, Amsterdam, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, Amsterdam, The Netherlands
| | - Erwin J G Peterman
- Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, Amsterdam, The Netherlands.
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29
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Shepherd JW, Leake MC. The End Restraint Method for Mechanically Perturbing Nucleic Acids In Silico. Methods Mol Biol 2022; 2476:249-262. [PMID: 35635708 DOI: 10.1007/978-1-0716-2221-6_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Far from being a passive information store, the genome is a mechanically dynamic and diverse system in which torsion and tension fluctuate and combine to determine structure and help regulate gene expression. Much of this mechanical perturbation is due to molecular machines such as topoisomerases which must stretch and twist DNA as part of various functions including DNA repair and replication. While the broad-scale mechanical response of nucleic acids to tension and torsion is well characterized, detail at the single base pair level is beyond the limits of even super-resolution imaging. Here, we present a straightforward, flexible, and extensible umbrella-sampling protocol to twist and stretch nucleic acids in silico using the popular biomolecular simulation package Amber-though the principles we describe are applicable also to other packages such as GROMACS. We discuss how to set up the simulation system, decide force fields and solvation models, and equilibrate. We then introduce the torsionally constrained stretching protocol, and finally we present some analysis techniques we have used to characterize structural motif formation. Rather than defining forces or fictional pseudoatoms, we instead define a fixed translation of specified atoms between each umbrella-sampling step, which allows comparison with experiment without needing to estimate applied forces by simply using the fractional end-to-end displacement as a comparison metric. We hope that this easy-to-implement solution will be valuable for interrogating optical and magnetic tweezers data on nucleic acids at base pair resolution.
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Affiliation(s)
| | - Mark C Leake
- Departments of Physics and Biology, University of York, York, UK
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30
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Man T, Geldhof JJ, Peterman EJG, Wuite GJL, Heller I. One-Dimensional STED Microscopy in Optical Tweezers. Methods Mol Biol 2022; 2478:101-122. [PMID: 36063320 DOI: 10.1007/978-1-0716-2229-2_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Optical tweezers and fluorescence microscopy are powerful methods for investigating the mechanical and structural properties of biomolecules and for studying the dynamics of the biomolecular processes that these molecules are involved in. Here we provide an outline of the concurrent use of optical tweezers and fluorescence microscopy for analyzing biomolecular processes. In particular, we focus on the use of super-resolution microscopy in optical tweezers, which allows visualization of molecules at the higher molecular densities that are typically encountered in living systems. We provide specific details on the alignment procedures of the optical pathways for confocal fluorescence microscopy and 1D-STED microscopy and elaborate on how to diagnose and correct optical aberrations and STED phase plate misalignments.
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Affiliation(s)
- Tianlong Man
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Joost J Geldhof
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Erwin J G Peterman
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Iddo Heller
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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31
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Bocanegra R, Plaza G A I, Ibarra B. In vitro single-molecule manipulation studies of viral DNA replication. Enzymes 2021; 49:115-148. [PMID: 34696830 DOI: 10.1016/bs.enz.2021.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Faithfull replication of genomic information relies on the coordinated activity of the multi-protein machinery known as the replisome. Several constituents of the replisome operate as molecular motors that couple thermal and chemical energy to a mechanical task. Over the last few decades, in vitro single-molecule manipulation techniques have been used to monitor and manipulate mechanically the activities of individual molecular motors involved in DNA replication with nanometer, millisecond, and picoNewton resolutions. These studies have uncovered the real-time kinetics of operation of these biological systems, the nature of their transient intermediates, and the processes by which they convert energy to work (mechano-chemistry), ultimately providing new insights into their inner workings of operation not accessible by ensemble assays. In this chapter, we describe two of the most widely used single-molecule manipulation techniques for the study of DNA replication, optical and magnetic tweezers, and their application in the study of the activities of proteins involved in viral DNA replication.
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Affiliation(s)
- Rebeca Bocanegra
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, Madrid, Spain
| | - Ismael Plaza G A
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, Madrid, Spain
| | - Borja Ibarra
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, Madrid, Spain.
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32
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Abstract
Condensation and faithful separation of the genome are crucial for the cellular life cycle. During chromosome segregation, mechanical forces generated by the mitotic spindle pull apart the sister chromatids. The mechanical nature of this process has motivated a lot of research interest into the mechanical properties of mitotic chromosomes. Although their fundamental mechanical characteristics are known, it still remains unclear how these characteristics emerge from the structure of the mitotic chromosome. Recent advances in genomics, computational and super-resolution microscopy techniques have greatly promoted our understanding of the chromosomal structure and have motivated us to review the mechanical characteristics of chromosomes in light of the current structural insights. In this review, we will first introduce the current understanding of the chromosomal structure, before reviewing characteristic mechanical properties such as the Young's modulus and the bending modulus of mitotic chromosomes. Then we will address the approaches used to relate mechanical properties to the structure of chromosomes and we will also discuss how mechanical characterization can aid in elucidating their structure. Finally, future challenges, recent developments and emergent questions in this research field will be discussed.
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33
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Kamit A, Tseng C, Kudo T, Sugiyama T, Hofkens J, Bresolí‐Obach R, Masuhara H. Unraveling the three‐dimensional morphology and dynamics of the optically evolving polystyrene nanoparticle assembly using dual‐objective lens microscopy. J CHIN CHEM SOC-TAIP 2021. [DOI: 10.1002/jccs.202100275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Abdullah Kamit
- Department of Applied Chemistry and Center for Emergent Functional Matter Science National Yang Ming Chao Tung University Hsinchu Taiwan
| | - Ching‐Shiang Tseng
- Department of Applied Chemistry and Center for Emergent Functional Matter Science National Yang Ming Chao Tung University Hsinchu Taiwan
| | - Tetsuhiro Kudo
- Department of Applied Chemistry and Center for Emergent Functional Matter Science National Yang Ming Chao Tung University Hsinchu Taiwan
- Laser Science Laboratory Toyota Technological University Nagoya Japan
| | - Teruki Sugiyama
- Department of Applied Chemistry and Center for Emergent Functional Matter Science National Yang Ming Chao Tung University Hsinchu Taiwan
- Division of Materials Science, Graduate School of Science and Technology Nara Institute of Science and Technology Ikoma Nara Japan
| | - Johan Hofkens
- Department of Chemistry Katholieke Universiteit Leuven Leuven Belgium
- Max‐Planck‐Institute for Polymer Research Mainz Germany
| | - Roger Bresolí‐Obach
- Department of Applied Chemistry and Center for Emergent Functional Matter Science National Yang Ming Chao Tung University Hsinchu Taiwan
- Department of Chemistry Katholieke Universiteit Leuven Leuven Belgium
| | - Hiroshi Masuhara
- Department of Applied Chemistry and Center for Emergent Functional Matter Science National Yang Ming Chao Tung University Hsinchu Taiwan
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34
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Chew K, Zhao L. Interactions of Mitochondrial Transcription Factor A with DNA Damage: Mechanistic Insights and Functional Implications. Genes (Basel) 2021; 12:genes12081246. [PMID: 34440420 PMCID: PMC8393399 DOI: 10.3390/genes12081246] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 12/17/2022] Open
Abstract
Mitochondria have a plethora of functions in eukaryotic cells, including cell signaling, programmed cell death, protein cofactor synthesis, and various aspects of metabolism. The organelles carry their own genomic DNA, which encodes transfer and ribosomal RNAs and crucial protein subunits in the oxidative phosphorylation system. Mitochondria are vital for cellular and organismal functions, and alterations of mitochondrial DNA (mtDNA) have been linked to mitochondrial disorders and common human diseases. As such, how the cell maintains the integrity of the mitochondrial genome is an important area of study. Interactions of mitochondrial proteins with mtDNA damage are critically important for repairing, regulating, and signaling mtDNA damage. Mitochondrial transcription factor A (TFAM) is a key player in mtDNA transcription, packaging, and maintenance. Due to the extensive contact of TFAM with mtDNA, it is likely to encounter many types of mtDNA damage and secondary structures. This review summarizes recent research on the interaction of human TFAM with different forms of non-canonical DNA structures and discusses the implications on mtDNA repair and packaging.
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35
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Spakman D, Bakx JAM, Biebricher AS, Peterman EJG, Wuite GJL, King GA. Unravelling the mechanisms of Type 1A topoisomerases using single-molecule approaches. Nucleic Acids Res 2021; 49:5470-5492. [PMID: 33963870 PMCID: PMC8191776 DOI: 10.1093/nar/gkab239] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/19/2021] [Accepted: 05/05/2021] [Indexed: 12/14/2022] Open
Abstract
Topoisomerases are essential enzymes that regulate DNA topology. Type 1A family topoisomerases are found in nearly all living organisms and are unique in that they require single-stranded (ss)DNA for activity. These enzymes are vital for maintaining supercoiling homeostasis and resolving DNA entanglements generated during DNA replication and repair. While the catalytic cycle of Type 1A topoisomerases has been long-known to involve an enzyme-bridged ssDNA gate that allows strand passage, a deeper mechanistic understanding of these enzymes has only recently begun to emerge. This knowledge has been greatly enhanced through the combination of biochemical studies and increasingly sophisticated single-molecule assays based on magnetic tweezers, optical tweezers, atomic force microscopy and Förster resonance energy transfer. In this review, we discuss how single-molecule assays have advanced our understanding of the gate opening dynamics and strand-passage mechanisms of Type 1A topoisomerases, as well as the interplay of Type 1A topoisomerases with partner proteins, such as RecQ-family helicases. We also highlight how these assays have shed new light on the likely functional roles of Type 1A topoisomerases in vivo and discuss recent developments in single-molecule technologies that could be applied to further enhance our understanding of these essential enzymes.
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Affiliation(s)
- Dian Spakman
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Julia A M Bakx
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Andreas S Biebricher
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Erwin J G Peterman
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Graeme A King
- Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
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Zhang Y, Zhou Y, Tang X, Wang Z, Zhang Y, Liu Z, Zhang J, Yang J, Yuan L. Mode division multiplexing for multiple particles noncontact simultaneous trap. OPTICS LETTERS 2021; 46:3017-3020. [PMID: 34197368 DOI: 10.1364/ol.426229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/18/2021] [Indexed: 06/13/2023]
Abstract
We propose and demonstrate an optical trap on the basis of a normal single-mode fiber (SMF), which is used to trap two particles in the axial direction at the same time without contact based on mode division multiplexing technology. We design and manufacture a tapered fiber probe. The LP11 mode beam is excited by docking a normal SMF to a 980 nm SMF with a 2 µm offset. Then the beams of LP01 and LP11 are both transmitted in the fiber. To converge the LP11 mode beam, a SMF with a tapered end is used to produce a cage for trapping the first microparticle. This particle acts as a lens to converge the LP01 mode beam to trap the second microparticle. We verify the feasibility of trapping two particles simultaneously through simulation. With this function, the proposed optical trap is easier to manipulate different individual particles for comparison and testing, which can promote the development of the biological, biophysical, colloidal, and soft matter fields.
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37
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Jarillo J, Ibarra B, Cao-García FJ. DNA replication: In vitro single-molecule manipulation data analysis and models. Comput Struct Biotechnol J 2021; 19:3765-3778. [PMID: 34285777 PMCID: PMC8267548 DOI: 10.1016/j.csbj.2021.06.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 11/05/2022] Open
Abstract
Data analysis allows to extract information from the noisy single-molecule data. Models provide insight in the underlying biochemical processes. Ligands can activate or inhibit DNA replication and DNA unwinding.
DNA replication is a key biochemical process of the cell cycle. In the last years, analysis of in vitro single-molecule DNA replication events has provided new information that cannot be obtained with ensembles studies. Here, we introduce crucial techniques for the proper analysis and modelling of DNA replication in vitro single-molecule manipulation data. Specifically, we review some of the main methods to analyze and model the real-time kinetics of the two main molecular motors of the replisome: DNA polymerase and DNA helicase. Our goal is to facilitate access to and understanding of these techniques to promotetheir use in the study of DNA replication at the single-molecule level. A proper analysis of single-molecule data is crucial to obtain a detailed picture of, among others, the kinetics rates, equilibrium contants and conformational changes of the system under study. The techniques presented here have been used or can be adapted to study the operation of other proteins involved in nucleic acids metabolism.
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Affiliation(s)
- Javier Jarillo
- University of Namur, Institute of Life-Earth-Environment, Namur Center for Complex Systems, Rue de Bruxelles 61, 5000 Namur, Belgium
| | - Borja Ibarra
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, C/ Faraday 9, 28049 Madrid, Spain
| | - Francisco Javier Cao-García
- Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, C/ Faraday 9, 28049 Madrid, Spain.,Departamento de Estructura de la Materia, Física Térmica y Electrónica, Universidad Complutense de Madrid, Pza. de Ciencias, 1, 28040 Madrid, Spain
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38
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Bocanegra R, Ismael Plaza GA, Pulido CR, Ibarra B. DNA replication machinery: Insights from in vitro single-molecule approaches. Comput Struct Biotechnol J 2021; 19:2057-2069. [PMID: 33995902 PMCID: PMC8085672 DOI: 10.1016/j.csbj.2021.04.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/03/2021] [Accepted: 04/03/2021] [Indexed: 11/16/2022] Open
Abstract
The replisome is the multiprotein molecular machinery that replicates DNA. The replisome components work in precise coordination to unwind the double helix of the DNA and replicate the two strands simultaneously. The study of DNA replication using in vitro single-molecule approaches provides a novel quantitative understanding of the dynamics and mechanical principles that govern the operation of the replisome and its components. ‘Classical’ ensemble-averaging methods cannot obtain this information. Here we describe the main findings obtained with in vitro single-molecule methods on the performance of individual replisome components and reconstituted prokaryotic and eukaryotic replisomes. The emerging picture from these studies is that of stochastic, versatile and highly dynamic replisome machinery in which transient protein-protein and protein-DNA associations are responsible for robust DNA replication.
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Affiliation(s)
- Rebeca Bocanegra
- IMDEA Nanociencia, Faraday 9, Campus Cantoblanco, 28049 Madrid, Spain
| | - G A Ismael Plaza
- IMDEA Nanociencia, Faraday 9, Campus Cantoblanco, 28049 Madrid, Spain
| | - Carlos R Pulido
- IMDEA Nanociencia, Faraday 9, Campus Cantoblanco, 28049 Madrid, Spain
| | - Borja Ibarra
- IMDEA Nanociencia, Faraday 9, Campus Cantoblanco, 28049 Madrid, Spain
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39
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Biology on track: single-molecule visualisation of protein dynamics on linear DNA substrates. Essays Biochem 2021; 65:5-16. [PMID: 33236762 DOI: 10.1042/ebc20200019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 12/14/2022]
Abstract
Single-molecule fluorescence imaging techniques have become important tools in biological research to gain mechanistic insights into cellular processes. These tools provide unique access to the dynamic and stochastic behaviour of biomolecules. Single-molecule tools are ideally suited to study protein-DNA interactions in reactions reconstituted from purified proteins. The use of linear DNA substrates allows for the study of protein-DNA interactions with observation of the movement and behaviour of DNA-translocating proteins over long distances. Single-molecule studies using long linear DNA substrates have revealed unanticipated insights on the dynamics of multi-protein systems. In this review, we provide an overview of recent methodological advances, including the construction of linear DNA substrates. We highlight the versatility of these substrates by describing their application in different single-molecule fluorescence techniques, with a focus on in vitro reconstituted systems. We discuss insights from key experiments on DNA curtains, DNA-based molecular motor proteins, and multi-protein systems acting on DNA that relied on the use of long linear substrates and single-molecule visualisation. The quality and customisability of linear DNA substrates now allows the insertion of modifications, such as nucleosomes, to create conditions mimicking physiologically relevant crowding and complexity. Furthermore, the current technologies will allow future studies on the real-time visualisation of the interfaces between DNA maintenance processes such as replication and transcription.
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40
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Bustamante CJ, Chemla YR, Liu S, Wang MD. Optical tweezers in single-molecule biophysics. NATURE REVIEWS. METHODS PRIMERS 2021; 1:25. [PMID: 34849486 PMCID: PMC8629167 DOI: 10.1038/s43586-021-00021-6] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/12/2021] [Indexed: 12/15/2022]
Abstract
Optical tweezers have become the method of choice in single-molecule manipulation studies. In this Primer, we first review the physical principles of optical tweezers and the characteristics that make them a powerful tool to investigate single molecules. We then introduce the modifications of the method to extend the measurement of forces and displacements to torques and angles, and to develop optical tweezers with single-molecule fluorescence detection capabilities. We discuss force and torque calibration of these instruments, their various modes of operation and most common experimental geometries. We describe the type of data obtained in each experimental design and their analyses. This description is followed by a survey of applications of these methods to the studies of protein-nucleic acid interactions, protein/RNA folding and molecular motors. We also discuss data reproducibility, the factors that lead to the data variability among different laboratories and the need to develop field standards. We cover the current limitations of the methods and possible ways to optimize instrument operation, data extraction and analysis, before suggesting likely areas of future growth.
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Affiliation(s)
- Carlos J. Bustamante
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Physics, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- Kavli Energy NanoScience Institute, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Yann R. Chemla
- Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
| | - Michelle D. Wang
- Department of Physics, Laboratory of Atomic and Solid State Physics, Howard Hughes Medical Institute, Cornell University, Ithaca, NY, USA
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41
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Yuan Z, Zhang D, Yu F, Ma Y, Liu Y, Li X, Wang H. Precise sequencing of single protected-DNA fragment molecules for profiling of protein distribution and assembly on DNA. Chem Sci 2021; 12:2039-2049. [PMID: 34163966 PMCID: PMC8179319 DOI: 10.1039/d0sc01742f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 12/31/2020] [Indexed: 11/21/2022] Open
Abstract
Multiple DNA-interacting protein molecules are often dynamically distributed and/or assembled along a DNA molecule to adapt to their intricate functions temporally. However, analytical technology for measuring such binding behaviours is still missing. Here, we demonstrate the unique capacity of a supernuclease for a highly efficient cutting of the unprotected-DNA segments and with complete preservation of the protein-occluded DNA segments at near single-nucleotide resolution. By exploring this high-resolution cutting, an unprecedented assay that allows a precise sequencing of single protected-DNA fragment molecules (SPDFMS) was developed. As relevant applications, relevant information was gained on the respective distribution/assembly patterns and coordinated displacement of single-stranded DNA-binding protein and recombinase RecA, two model proteins, on DNA. Benefiting from this assay, we also for the first time provide direct measurement of the length of single RecA nucleofilaments, showing the predominant stoichiometry of 5-7 RecA monomers per RecA nucleofilament under physiologically relevant conditions. This innovative assay appears as a promising analytical tool for studying diverse protein-DNA interactions implicated in DNA replication, transcription, recombination, repair, and gene editing.
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Affiliation(s)
- Zheng Yuan
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences Beijing 100085 P. R. China +86 10 62849600 +86 10 62849600
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Dapeng Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences Beijing 100085 P. R. China +86 10 62849600 +86 10 62849600
- Institute of Environment and Health, Hangzhou, Institute for Advanced Study, UCAS Hangzhou 310000 P. R. China
| | - Fangzhi Yu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences Beijing 100085 P. R. China +86 10 62849600 +86 10 62849600
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Yangde Ma
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Yan Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences Beijing 100085 P. R. China +86 10 62849600 +86 10 62849600
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Xiangjun Li
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences Beijing 100085 P. R. China +86 10 62849600 +86 10 62849600
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
- Institute of Environment and Health, Jianghan University Wuhan Hubei 430056 P. R. China
- Institute of Environment and Health, Hangzhou, Institute for Advanced Study, UCAS Hangzhou 310000 P. R. China
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42
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Auer JMT, Stoddart JJ, Christodoulou I, Lima A, Skouloudaki K, Hall HN, Vukojević V, Papadopoulos DK. Of numbers and movement - understanding transcription factor pathogenesis by advanced microscopy. Dis Model Mech 2020; 13:dmm046516. [PMID: 33433399 PMCID: PMC7790199 DOI: 10.1242/dmm.046516] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Transcription factors (TFs) are life-sustaining and, therefore, the subject of intensive research. By regulating gene expression, TFs control a plethora of developmental and physiological processes, and their abnormal function commonly leads to various developmental defects and diseases in humans. Normal TF function often depends on gene dosage, which can be altered by copy-number variation or loss-of-function mutations. This explains why TF haploinsufficiency (HI) can lead to disease. Since aberrant TF numbers frequently result in pathogenic abnormalities of gene expression, quantitative analyses of TFs are a priority in the field. In vitro single-molecule methodologies have significantly aided the identification of links between TF gene dosage and transcriptional outcomes. Additionally, advances in quantitative microscopy have contributed mechanistic insights into normal and aberrant TF function. However, to understand TF biology, TF-chromatin interactions must be characterised in vivo, in a tissue-specific manner and in the context of both normal and altered TF numbers. Here, we summarise the advanced microscopy methodologies most frequently used to link TF abundance to function and dissect the molecular mechanisms underlying TF HIs. Increased application of advanced single-molecule and super-resolution microscopy modalities will improve our understanding of how TF HIs drive disease.
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Affiliation(s)
- Julia M T Auer
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 1XU, UK
| | - Jack J Stoddart
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 1XU, UK
| | | | - Ana Lima
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 1XU, UK
| | | | - Hildegard N Hall
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 1XU, UK
| | - Vladana Vukojević
- Center for Molecular Medicine (CMM), Department of Clinical Neuroscience, Karolinska Institutet, 17176 Stockholm, Sweden
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43
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Madariaga-Marcos J, Corti R, Hormeño S, Moreno-Herrero F. Characterizing microfluidic approaches for a fast and efficient reagent exchange in single-molecule studies. Sci Rep 2020; 10:18069. [PMID: 33093484 PMCID: PMC7581773 DOI: 10.1038/s41598-020-74523-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 09/21/2020] [Indexed: 11/09/2022] Open
Abstract
Single-molecule experiments usually take place in flow cells. This experimental approach is essential for experiments requiring a liquid environment, but is also useful to allow the exchange of reagents before or during measurements. This is crucial in experiments that need to be triggered by ligands or require a sequential addition of proteins. Home-fabricated flow cells using two glass coverslips and a gasket made of paraffin wax are a widespread approach. The volume of the flow cell can be controlled by modifying the dimensions of the channel while the reagents are introduced using a syringe pump. In this system, high flow rates disturb the biological system, whereas lower flow rates lead to the generation of a reagent gradient in the flow cell. For very precise measurements it is thus desirable to have a very fast exchange of reagents with minimal diffusion. We propose the implementation of multistream laminar microfluidic cells with two inlets and one outlet, which achieve a minimum fluid switching time of 0.25 s. We additionally define a phenomenological expression to predict the boundary switching time for a particular flow cell cross section. Finally, we study the potential applicability of the platform to study kinetics at the single molecule level.
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Affiliation(s)
- Julene Madariaga-Marcos
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Roberta Corti
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy.,Department of Materials Science, University of Milano-Bicocca, Milan, Italy
| | - Silvia Hormeño
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain.
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44
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Hidalgo-Soria M, Barkai E. Hitchhiker model for Laplace diffusion processes. Phys Rev E 2020; 102:012109. [PMID: 32794941 DOI: 10.1103/physreve.102.012109] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 06/17/2020] [Indexed: 06/11/2023]
Abstract
Brownian motion is a Gaussian process describing normal diffusion with a variance increasing linearly with time. Recently, intracellular single-molecule tracking experiments have recorded exponentially decaying propagators, a phenomenon called Laplace diffusion. Inspired by these developments we study a many-body approach, called the Hitchhiker model, providing a microscopic description of the widely observed behavior. Our model explains how Laplace diffusion is controlled by size fluctuations of single molecules, independently of the diffusion law which they follow. By means of numerical simulations Laplace diffusion is recovered and we show how single-molecule tracking and data analysis, in a many-body system, is highly nontrivial as tracking of a single particle or many in parallel yields vastly different estimates for the diffusivity. We quantify the differences between these two commonly used approaches, showing how the single-molecule estimate of diffusivity is larger if compared to the full tagging method.
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Affiliation(s)
- M Hidalgo-Soria
- Department of Physics, Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - E Barkai
- Department of Physics, Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
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45
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Qiu K, Du Y, Liu J, Guan JL, Chao H, Diao J. Super-resolution observation of lysosomal dynamics with fluorescent gold nanoparticles. Theranostics 2020; 10:6072-6081. [PMID: 32483439 PMCID: PMC7254985 DOI: 10.7150/thno.42134] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 04/30/2020] [Indexed: 02/05/2023] Open
Abstract
Because lysosomes play critical roles in multiple cellular functions and are associated with many diseases, studying them at the subcellular level could elucidate their functionality and support the discovery of therapeutic drugs for treating those diseases. The commonly used dyes for super-resolution imaging of lysosomes are the commercial molecular LysoTrackers. But the tolerance to changes in the lysosomal microenvironment and to lysosomal membrane permeabilization (LMP) and the photostability of the LysoTrackers are worrisome. The purpose of our study was to evaluate the feasibility of performing a fluorescent gold nanoprobe for super-resolution observation of lysosomal dynamics in living cells and compare it to the commercial LysoTrackers. Methods: The nanoprobe Cy5@Au NP contained three parts: a bio-inert gold core, a biocompatible polyethylene glycol spacer, and a fluorophore cyanine 5. Structured illumination microscopy (SIM) was employed to capture the fluorescence of Cy5@Au NPs in cells. The tolerance assays to changes in the lysosomal microenvironment and to LMP, the photobleaching assay, and the long-term lysosomes labelling assay of Cy5@Au NPs were compared with commercial LysoTrackers. The super-resolution observation of lysosomal dynamics with Cy5@Au NPs was performed. Results: Cy5@Au NPs can light up lysosomes specifically under SIM. Compared with commercial lysosomal molecular probes, Cy5@Au NPs exhibited stronger tolerance in lysosomes during various treatments, and changes in the lysosomal microenvironment and LMP did not cause Cy5@Au NPs to lose track of their targets. Cy5@Au NPs demonstrated an excellent anti-photobleaching ability, and a long-term labelling assay revealed that they could label lysosomes more than 3 d. Biological events of lysosomes such as the kiss-and-run process, fusion, fission, and mitophagy were recorded with the fluorescent Cy5@Au NPs under SIM. Conclusions: The nanoprobe Cy5@Au NP was successfully used as a lysosomal probe for the super-resolution observation in living cells and found to overcome the limitations of commercial LysoTrackers. Our results thus confirm that nanoparticles can be useful tools for subcellular super-resolution imaging and highlight new avenues for using nanoparticles in biology.
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46
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Meijering AEC, Biebricher AS, Sitters G, Brouwer I, Peterman EJG, Wuite GJL, Heller I. Imaging unlabeled proteins on DNA with super-resolution. Nucleic Acids Res 2020; 48:e34. [PMID: 32016413 PMCID: PMC7102996 DOI: 10.1093/nar/gkaa061] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 12/24/2019] [Accepted: 01/24/2020] [Indexed: 02/06/2023] Open
Abstract
Fluorescence microscopy is invaluable to a range of biomolecular analysis approaches. The required labeling of proteins of interest, however, can be challenging and potentially perturb biomolecular functionality as well as cause imaging artefacts and photo bleaching issues. Here, we introduce inverse (super-resolution) imaging of unlabeled proteins bound to DNA. In this new method, we use DNA-binding fluorophores that transiently label bare DNA but not protein-bound DNA. In addition to demonstrating diffraction-limited inverse imaging, we show that inverse Binding-Activated Localization Microscopy or 'iBALM' can resolve biomolecular features smaller than the diffraction limit. The current detection limit is estimated to lie at features between 5 and 15 nm in size. Although the current image-acquisition times preclude super-resolving fast dynamics, we show that diffraction-limited inverse imaging can reveal molecular mobility at ∼0.2 s temporal resolution and that the method works both with DNA-intercalating and non-intercalating dyes. Our experiments show that such inverse imaging approaches are valuable additions to the single-molecule toolkit that relieve potential limitations posed by labeling.
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Affiliation(s)
- Anna E C Meijering
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Andreas S Biebricher
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Gerrit Sitters
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Ineke Brouwer
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Erwin J G Peterman
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Iddo Heller
- Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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47
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Abstract
Opto-thermoelectric tweezers present a new paradigm for optical trapping and manipulation of particles using low-power and simple optics. New real-life applications of opto-thermoelectric tweezers in areas such as biophysics, microfluidics, and nanomanufacturing will require them to have large-scale and high-throughput manipulation capabilities in complex environments. Here, we present opto-thermoelectric speckle tweezers, which use speckle field consisting of many randomly distributed thermal hotspots that arise from an optical speckle pattern to trap multiple particles over large areas. By further integrating the speckle tweezers with a microfluidic system, we experimentally demonstrate their application for size-based nanoparticle filtration. With their low-power operation, simplicity, and versatility, opto-thermoelectric speckle tweezers will broaden the applications of optical manipulation techniques.
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Affiliation(s)
- Abhay Kotnala
- Walker Department of Mechanical Engineering, Materials Science and Engineering Program and Texas Materials Institute, The University of Texas at Austin, Austin, TX 78712, USA
| | - Pavana Siddhartha Kollipara
- Walker Department of Mechanical Engineering, Materials Science and Engineering Program and Texas Materials Institute, The University of Texas at Austin, Austin, TX 78712, USA
| | - Yuebing Zheng
- Walker Department of Mechanical Engineering, Materials Science and Engineering Program and Texas Materials Institute, The University of Texas at Austin, Austin, TX 78712, USA
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48
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Liang Y, Yan S, Wang Z, Li R, Cai Y, He M, Yao B, Lei M. Simultaneous optical trapping and imaging in the axial plane: a review of current progress. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2020; 83:032401. [PMID: 31995793 DOI: 10.1088/1361-6633/ab7175] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Optical trapping has become a powerful tool in numerous fields such as biology, physics, chemistry, etc. In conventional optical trapping systems, trapping and imaging share the same objective lens, confining the region of observation to the focal plane. For the capture of optical trapping processes occurring in other planes, especially the axial plane (the one containing the z-axis), many methods have been proposed to achieve this goal. Here, we review the methods of acquiring the axial-plane information from which axial plane trapping is observed and discuss their advantages and limitations. To overcome the limitations existing in these methods, we developed an optical tweezers system that allows for simultaneous optical trapping and imaging in the axial plane. The versatility and usefulness of the system in axial-plane trapping and imaging are demonstrated by investigating its trapping performance with various optical fields, including Bessel, Airy, and snake-like beams. The potential applications of the reported technique are suggested to several research fields, including optical pulling, longitudinal optical binding, tomographic phase microscopy (TPM), and super-resolution microscopy.
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Affiliation(s)
- Yansheng Liang
- Shaanxi Key Laboratory of Quantum Information and Quantum Optoelectronic Devices, School of Science, Xi'an Jiaotong University, Xi'an 710049, People's Republic of China
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49
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Simultaneous sensing and imaging of individual biomolecular complexes enabled by modular DNA-protein coupling. Commun Chem 2020; 3:20. [PMID: 36703465 PMCID: PMC9814868 DOI: 10.1038/s42004-020-0267-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 01/17/2020] [Indexed: 01/29/2023] Open
Abstract
Many proteins form dynamic complexes with DNA, RNA, and other proteins, which often involves protein conformational changes that are key to function. Yet, methods to probe these critical dynamics are scarce. Here we combine optical tweezers with fluorescence imaging to simultaneously monitor the conformation of individual proteins and their binding to partner proteins. Central is a protein-DNA coupling strategy, which uses exonuclease digestion and partial re-synthesis to generate DNA overhangs of different lengths, and ligation to oligo-labeled proteins. It provides up to 40 times higher coupling yields than existing protocols and enables new fluorescence-tweezers assays, which require particularly long and strong DNA handles. We demonstrate the approach by detecting the emission of a tethered fluorescent protein and of a molecular chaperone (trigger factor) complexed with its client. We conjecture that our strategy will be an important tool to study conformational dynamics within larger biomolecular complexes.
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50
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Fang H, Yao S, Chen Q, Liu C, Cai Y, Geng S, Bai Y, Tian Z, Zacharias AL, Takebe T, Chen Y, Guo Z, He W, Diao J. De Novo-Designed Near-Infrared Nanoaggregates for Super-Resolution Monitoring of Lysosomes in Cells, in Whole Organoids, and in Vivo. ACS NANO 2019; 13:14426-14436. [PMID: 31799834 PMCID: PMC7255917 DOI: 10.1021/acsnano.9b08011] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
As the cleaners of cells, lysosomes play an important role in circulating organic matter within cells, recovering damaged organelles, and removing waste via endocytosis. Because lysosome dysfunction is associated with various diseases-lysosomal storage diseases, inherited diseases, rheumatoid arthritis, and even shock-it is vital to monitor the movement of lysosomes in cells and in vivo. To that purpose, a method of optical imaging, super-resolution imaging technology (e.g., SIM and STORM), can overcome the limitations of traditional optical imaging and afford a range of possibilities for fluorescence imaging. However, the short wavelength excitation and easy photobleaching of super-resolution fluorescence probes somewhat problematize super-resolution imaging. As described herein, we designed a low-toxicity, photostable, near-infrared small molecule fluorescence probe HD-Br for use in the super-resolution imaging of lysosomes. The interaction of lysosomes and mitochondria was dynamically traced while using the probe's properties to label the lysosomes. Because the probe has the optimal near-infrared excitation and emission wavelengths, liver organoid 3D imaging and Caenorhabditis elegans imaging were also performed. Altogether, our findings indicate valuable approaches and techniques for super-resolution 3D and in vivo imaging.
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Affiliation(s)
- Hongbao Fang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023 (P. R. China)
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267 (USA)
| | - Shankun Yao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023 (P. R. China)
| | - Qixin Chen
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267 (USA)
| | - Chunyan Liu
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 (USA)
| | - Yuqi Cai
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 (USA)
| | - Shanshan Geng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023 (P. R. China)
| | - Yang Bai
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023 (P. R. China)
| | - Zhiqi Tian
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267 (USA)
| | - Amanda L. Zacharias
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 (USA)
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267 (USA)
| | - Takanori Takebe
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 (USA)
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 (USA)
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 (USA)
- Division of Endocrinology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 (USA)
- Institute of Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510 (Japan)
| | - Yuncong Chen
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023 (P. R. China)
| | - Zijian Guo
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023 (P. R. China)
| | - Weijiang He
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023 (P. R. China)
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267 (USA)
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