1
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Kabtiyal P, Robbins A, Jergens E, Castro CE, Winter JO, Poirier MG, Johnston-Halperin E. Localized Plasmonic Heating for Single-Molecule DNA Rupture Measurements in Optical Tweezers. NANO LETTERS 2024; 24:3097-3103. [PMID: 38417053 DOI: 10.1021/acs.nanolett.3c04848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2024]
Abstract
To date, studies on the thermodynamic and kinetic processes that underlie biological function and nanomachine actuation in biological- and biology-inspired molecular constructs have primarily focused on photothermal heating of ensemble systems, highlighting the need for probes that are localized within the molecular construct and capable of resolving single-molecule response. Here we present an experimental demonstration of wavelength-selective, localized heating at the single-molecule level using the surface plasmon resonance of a 15 nm gold nanoparticle (AuNP). Our approach is compatible with force-spectroscopy measurements and can be applied to studies of the single-molecule thermodynamic properties of DNA origami nanomachines as well as biomolecular complexes. We further demonstrate wavelength selectivity and establish the temperature dependence of the reaction coordinate for base-pair disruption in the shear-rupture geometry, demonstrating the utility and flexibility of this approach for both fundamental studies of local (nanometer-scale) temperature gradients and rapid and multiplexed nanomachine actuation.
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Affiliation(s)
- Prerna Kabtiyal
- Department of Physics, The Ohio State University, Columbus, Ohio 43210, United States
| | - Ariel Robbins
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Elizabeth Jergens
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Carlos E Castro
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jessica O Winter
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, United States
| | - Michael G Poirier
- Department of Physics, The Ohio State University, Columbus, Ohio 43210, United States
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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2
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Burdík M, Kužela T, Fojtů D, Elisek P, Hrnčiřík J, Jašek R, Ingr M. Optical Tweezers Apparatus Based on a Cost-Effective IR Laser-Hardware and Software Description. SENSORS (BASEL, SWITZERLAND) 2024; 24:643. [PMID: 38276334 PMCID: PMC10818436 DOI: 10.3390/s24020643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 01/08/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024]
Abstract
Optical tweezers (OT), or optical traps, are a device for manipulating microscopic objects through a focused laser beam. They are used in various fields of physical and biophysical chemistry to identify the interactions between individual molecules and measure single-molecule forces. In this work, we describe the development of a homemade optical tweezers device based on a cost-effective IR diode laser, the hardware, and, in particular, the software controlling it. It allows us to control the instrument, calibrate it, and record and process the measured data. It includes the user interface design, peripherals control, recording, A/D conversion of the detector signals, evaluation of the calibration constants, and visualization of the results. Particular stress is put on the signal filtration from noise, where several methods were tested. The calibration experiments indicate a good sensitivity of the instrument that is thus ready to be used for various single-molecule measurements.
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Affiliation(s)
- Martin Burdík
- Department of Informatics and Artificial Intelligence, Faculty of Applied Informatics, Tomas Bata University in Zlín, Nad Stráněmi 4511, 760 05 Zlín, Czech Republic; (M.B.); (R.J.)
| | - Tomáš Kužela
- Department of Physics and Materials Engineering, Faculty of Technology, Tomas Bata University in Zlín, Nám. T. G. Masaryka 5555, 760 01 Zlín, Czech Republic; (P.E.); (J.H.); (M.I.)
| | - Dušan Fojtů
- Department of Computer and Communication Systems, Faculty of Applied Informatics, Tomas Bata University in Zlín, Nad Stráněmi 4511, 760 05 Zlín, Czech Republic;
| | - Petr Elisek
- Department of Physics and Materials Engineering, Faculty of Technology, Tomas Bata University in Zlín, Nám. T. G. Masaryka 5555, 760 01 Zlín, Czech Republic; (P.E.); (J.H.); (M.I.)
| | - Josef Hrnčiřík
- Department of Physics and Materials Engineering, Faculty of Technology, Tomas Bata University in Zlín, Nám. T. G. Masaryka 5555, 760 01 Zlín, Czech Republic; (P.E.); (J.H.); (M.I.)
| | - Roman Jašek
- Department of Informatics and Artificial Intelligence, Faculty of Applied Informatics, Tomas Bata University in Zlín, Nad Stráněmi 4511, 760 05 Zlín, Czech Republic; (M.B.); (R.J.)
| | - Marek Ingr
- Department of Physics and Materials Engineering, Faculty of Technology, Tomas Bata University in Zlín, Nám. T. G. Masaryka 5555, 760 01 Zlín, Czech Republic; (P.E.); (J.H.); (M.I.)
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3
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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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4
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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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5
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Tessmer I. The roles of non-productive complexes of DNA repair proteins with DNA lesions. DNA Repair (Amst) 2023; 129:103542. [PMID: 37453245 DOI: 10.1016/j.dnarep.2023.103542] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/30/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023]
Abstract
A multitude of different types of lesions is continuously introduced into the DNA inside our cells, and their rapid and efficient repair is fundamentally important for the maintenance of genomic stability and cellular viability. This is achieved by a number of DNA repair systems that each involve different protein factors and employ versatile strategies to target different types of DNA lesions. Intriguingly, specialized DNA repair proteins have also evolved to form non-functional complexes with their target lesions. These proteins allow the marking of innocuous lesions to render them visible for DNA repair systems and can serve to directly recruit DNA repair cascades. Moreover, they also provide links between different DNA repair mechanisms or even between DNA lesions and transcription regulation. I will focus here in particular on recent findings from single molecule analyses on the alkyltransferase-like protein ATL, which is believed to initiate nucleotide excision repair (NER) of non-native NER target lesions, and the base excision repair (BER) enzyme hOGG1, which recruits the oncogene transcription factor Myc to gene promoters under oxidative stress.
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Affiliation(s)
- Ingrid Tessmer
- Rudolf Virchow Center, University of Würzburg, Josef Schneider Str. 2, 97080 Würzburg, Germany
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6
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Abraham Punnoose J, Thomas KJ, Chandrasekaran AR, Vilcapoma J, Hayden A, Kilpatrick K, Vangaveti S, Chen A, Banco T, Halvorsen K. High-throughput single-molecule quantification of individual base stacking energies in nucleic acids. Nat Commun 2023; 14:631. [PMID: 36746949 PMCID: PMC9902561 DOI: 10.1038/s41467-023-36373-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 01/26/2023] [Indexed: 02/08/2023] Open
Abstract
Base stacking interactions between adjacent bases in DNA and RNA are important for many biological processes and in biotechnology applications. Previous work has estimated stacking energies between pairs of bases, but contributions of individual bases has remained unknown. Here, we use a Centrifuge Force Microscope for high-throughput single molecule experiments to measure stacking energies between adjacent bases. We found stacking energies strongest between purines (G|A at -2.3 ± 0.2 kcal/mol) and weakest between pyrimidines (C|T at -0.5 ± 0.1 kcal/mol). Hybrid stacking with phosphorylated, methylated, and RNA nucleotides had no measurable effect, but a fluorophore modification reduced stacking energy. We experimentally show that base stacking can influence stability of a DNA nanostructure, modulate kinetics of enzymatic ligation, and assess accuracy of force fields in molecular dynamics simulations. Our results provide insights into fundamental DNA interactions that are critical in biology and can inform design in biotechnology applications.
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Affiliation(s)
- Jibin Abraham Punnoose
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Kevin J Thomas
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | | | - Javier Vilcapoma
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Andrew Hayden
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Kacey Kilpatrick
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA.,Department of Chemistry, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Sweta Vangaveti
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Alan Chen
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA.,Department of Chemistry, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Thomas Banco
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA.
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7
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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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8
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Walker SD, Olivares AO. The activated ClpP peptidase forcefully grips a protein substrate. Biophys J 2022; 121:3907-3916. [PMID: 36045571 PMCID: PMC9674977 DOI: 10.1016/j.bpj.2022.08.042] [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: 04/29/2022] [Revised: 08/12/2022] [Accepted: 08/26/2022] [Indexed: 11/26/2022] Open
Abstract
ATPases associated with diverse cellular activities (AAA+) proteases power the maintenance of protein homeostasis by coupling ATP hydrolysis to mechanical protein unfolding, translocation, and ultimately degradation. Although ATPase activity drives a large portion of the mechanical work these molecular machines perform, how the peptidase contributes to the forceful denaturation and processive threading of substrates remains unknown. Here, using single-molecule optical trapping, we examine the mechanical activity of the caseinolytic peptidase P (ClpP) from Escherichia coli in the absence of a partner ATPase and in the presence of an activating small-molecule acyldepsipeptide. We demonstrate that ClpP grips protein substrate under mechanical loads exceeding 40 pN, which are greater than those observed for the AAA+ unfoldase ClpX and the AAA+ protease complexes ClpXP and ClpAP. We further characterize substrate-ClpP bond lifetimes and rupture forces under varying loads. We find that the resulting slip bond behavior does not depend on ClpP peptidase activity. In addition, we find that unloaded bond lifetimes between ClpP and protein substrate are on a timescale relevant to unfolding times (up to ∼160 s) for difficult to unfold model substrate proteins. These direct measurements of the substrate-peptidase bond under load define key properties required by AAA+ proteases to mechanically unfold and degrade protein substrates.
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Affiliation(s)
- Steven D Walker
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee; Chemical and Physical Biology Graduate Program, Vanderbilt University, Nashville, Tennessee
| | - Adrian O Olivares
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee.
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9
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Wu P, Qu S, Zeng X, Su N, Chen M, Yu Y. High- Q refractive index sensors based on all-dielectric metasurfaces. RSC Adv 2022; 12:21264-21269. [PMID: 35975043 PMCID: PMC9344899 DOI: 10.1039/d2ra02176e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/08/2022] [Indexed: 11/21/2022] Open
Abstract
Possessing fantastic abilities to freely manipulate electromagnetic waves on an ultrathin platform, metasurfaces have aroused intense interest in the academic circle. In this work, we present a high-sensitivity refractive index sensor excited by the guided mode of a two-dimensional periodic TiO2 dielectric grating structure. Numerical simulation results show that the optimized nanosensor can excite guided-mode resonance with an ultra-narrow linewidth of 0.19 nm. When the thickness of the biological layer is 20 nm, the sensitivity, Q factor, and FOM values of the nanosensor can reach 82.29 nm RIU−1, 3207.9, and 433.1, respectively. In addition, the device shows insensitivity to polarization and good tolerance to the angle of incident light. This demonstrates that the utilization of low-loss all-dielectric metasurfaces is an effective way to achieve ultra-sensitive biosensor detection. A high-sensitivity refractive index sensor excited by the 2D periodic TiO2 dielectric grating structure. The nanosensor can excite guided-mode resonance with a 0.19 nm ultra-narrow linewidth. Low loss all-dielectric metasurface allows ultra-sensitive biosensor detection.![]()
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Affiliation(s)
- Pinghui Wu
- Research Center for Photonic Technology, Fujian Provincial Key Laboratory for Advanced Micro-nano Photonics Technology and Devices & Key Laboratory of Information Functional Material for Fujian Higher Education, Quanzhou Normal University Quanzhou 362000 China
| | - Shuangcao Qu
- Research Center for Photonic Technology, Fujian Provincial Key Laboratory for Advanced Micro-nano Photonics Technology and Devices & Key Laboratory of Information Functional Material for Fujian Higher Education, Quanzhou Normal University Quanzhou 362000 China
| | - Xintao Zeng
- Research Center for Photonic Technology, Fujian Provincial Key Laboratory for Advanced Micro-nano Photonics Technology and Devices & Key Laboratory of Information Functional Material for Fujian Higher Education, Quanzhou Normal University Quanzhou 362000 China
| | - Ning Su
- Research Center for Photonic Technology, Fujian Provincial Key Laboratory for Advanced Micro-nano Photonics Technology and Devices & Key Laboratory of Information Functional Material for Fujian Higher Education, Quanzhou Normal University Quanzhou 362000 China
| | - Musheng Chen
- Research Center for Photonic Technology, Fujian Provincial Key Laboratory for Advanced Micro-nano Photonics Technology and Devices & Key Laboratory of Information Functional Material for Fujian Higher Education, Quanzhou Normal University Quanzhou 362000 China
| | - Yanzhong Yu
- Research Center for Photonic Technology, Fujian Provincial Key Laboratory for Advanced Micro-nano Photonics Technology and Devices & Key Laboratory of Information Functional Material for Fujian Higher Education, Quanzhou Normal University Quanzhou 362000 China
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10
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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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11
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Darcy M, Crocker K, Wang Y, Le JV, Mohammadiroozbahani G, Abdelhamid MAS, Craggs TD, Castro CE, Bundschuh R, Poirier MG. High-Force Application by a Nanoscale DNA Force Spectrometer. ACS NANO 2022; 16:5682-5695. [PMID: 35385658 PMCID: PMC9048690 DOI: 10.1021/acsnano.1c10698] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/28/2022] [Indexed: 05/06/2023]
Abstract
The ability to apply and measure high forces (>10 pN) on the nanometer scale is critical to the development of nanomedicine, molecular robotics, and the understanding of biological processes such as chromatin condensation, membrane deformation, and viral packaging. Established force spectroscopy techniques including optical traps, magnetic tweezers, and atomic force microscopy rely on micron-sized or larger handles to apply forces, limiting their applications within constrained geometries including cellular environments and nanofluidic devices. A promising alternative to these approaches is DNA-based molecular calipers. However, this approach is currently limited to forces on the scale of a few piconewtons. To study the force application capabilities of DNA devices, we implemented DNA origami nanocalipers with tunable mechanical properties in a geometry that allows application of force to rupture a DNA duplex. We integrated static and dynamic single-molecule characterization methods and statistical mechanical modeling to quantify the device properties including force output and dynamic range. We found that the thermally driven dynamics of the device are capable of applying forces of at least 20 piconewtons with a nanometer-scale dynamic range. These characteristics could eventually be used to study other biomolecular processes such as protein unfolding or to control high-affinity interactions in nanomechanical devices or molecular robots.
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Affiliation(s)
- Michael Darcy
- Department
of Physics, Department of Mechanical and Aerospace Engineering, Biophysics Graduate
Program, Department of Chemistry and Biochemistry, and Division of Hematology, Department
of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Kyle Crocker
- Department
of Physics, Department of Mechanical and Aerospace Engineering, Biophysics Graduate
Program, Department of Chemistry and Biochemistry, and Division of Hematology, Department
of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yuchen Wang
- Department
of Physics, Department of Mechanical and Aerospace Engineering, Biophysics Graduate
Program, Department of Chemistry and Biochemistry, and Division of Hematology, Department
of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jenny V. Le
- Department
of Physics, Department of Mechanical and Aerospace Engineering, Biophysics Graduate
Program, Department of Chemistry and Biochemistry, and Division of Hematology, Department
of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Golbarg Mohammadiroozbahani
- Department
of Physics, Department of Mechanical and Aerospace Engineering, Biophysics Graduate
Program, Department of Chemistry and Biochemistry, and Division of Hematology, Department
of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | | | - Timothy D. Craggs
- Department
of Chemistry, University of Sheffield, Sheffield S3 7HF, U.K.
| | - Carlos E. Castro
- Department
of Physics, Department of Mechanical and Aerospace Engineering, Biophysics Graduate
Program, Department of Chemistry and Biochemistry, and Division of Hematology, Department
of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Ralf Bundschuh
- Department
of Physics, Department of Mechanical and Aerospace Engineering, Biophysics Graduate
Program, Department of Chemistry and Biochemistry, and Division of Hematology, Department
of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Michael G. Poirier
- Department
of Physics, Department of Mechanical and Aerospace Engineering, Biophysics Graduate
Program, Department of Chemistry and Biochemistry, and Division of Hematology, Department
of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, United States
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12
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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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13
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Wilson H, Wang Q. Joint Detection of Change Points in Multichannel Single-Molecule Measurements. J Phys Chem B 2021; 125:13425-13435. [PMID: 34870418 DOI: 10.1021/acs.jpcb.1c08869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Recent developments in single-molecule measurement technology have expanded the capability to measure multiple parameters. These emergent modalities provide more holistic observations of complex biomolecular processes and call for new analysis methods to detect state changes in multichannel data. Here we develop an algorithm called MULLR (MUlti-channel Log-Likelihood Ratio test) to jointly identify change points in multichannel single-molecule measurements. MULLR is an extension of the popular single-channel implementation for change point detection based on a binary segmentation and log-likelihood ratio test framework. We validate the algorithm on simulated data and characterize the power of detection and false positive rate. We show that MULLR can identify change points in experimental multichannel data and naturally works with different noise statistics and time resolutions across channels. Further, we quantify the benefit of MULLR compared to single-channel analysis. We envision that the MULLR algorithm will be useful to a range of multiparameter single-molecule measurements.
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Affiliation(s)
- Hugh Wilson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08540, United States
| | - Quan Wang
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08540, United States
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14
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Lou Y, Ning X, Wu B, Pang Y. Optical trapping using transverse electromagnetic (TEM)-like mode in a coaxial nanowaveguide. FRONTIERS OF OPTOELECTRONICS 2021; 14:399-406. [PMID: 36637761 PMCID: PMC9743861 DOI: 10.1007/s12200-021-1134-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/22/2021] [Indexed: 06/13/2023]
Abstract
Optical traps have emerged as powerful tools for immobilizing and manipulating small particles in three dimensions. Fiber-based optical traps (FOTs) significantly simplify optical setup by creating trapping centers with single or multiple pieces of optical fibers. In addition, they inherit the flexibility and robustness of fiber-optic systems. However, trapping 10-nm-diameter nanoparticles (NPs) using FOTs remains challenging. In this study, we model a coaxial waveguide that works in the optical regime and supports a transverse electromagnetic (TEM)-like mode for NP trapping. Single NPs at waveguide front-end break the symmetry of TEM-like guided mode and lead to high transmission efficiency at far-field, thereby strongly altering light momentum and inducing a large-scale back-action on the particle. We demonstrate, via finite-difference time-domain (FDTD) simulations, that this FOT allows for trapping single 10-nm-diameter NPs at low power.
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Affiliation(s)
- Yuanhao Lou
- School of Optical and Electronic Information, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Xiongjie Ning
- School of Optical and Electronic Information, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Bei Wu
- School of Optical and Electronic Information, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Yuanjie Pang
- School of Optical and Electronic Information, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China.
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15
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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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16
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Banik D, Hamidinia M, Brzostek J, Wu L, Stephens HM, MacAry PA, Reinherz EL, Gascoigne NRJ, Lang MJ. Single Molecule Force Spectroscopy Reveals Distinctions in Key Biophysical Parameters of αβ T-Cell Receptors Compared with Chimeric Antigen Receptors Directed at the Same Ligand. J Phys Chem Lett 2021; 12:7566-7573. [PMID: 34347491 PMCID: PMC9082930 DOI: 10.1021/acs.jpclett.1c02240] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Chimeric antigen receptor (CAR) T-cell therapies exploit facile antibody-mediated targeting to elicit useful immune responses in patients. This work directly compares binding profiles of CAR and αβ T-cell receptors (TCR) with single cell and single molecule optical trap measurements against a shared ligand. DNA-tethered measurements of peptide-major histocompatibility complex (pMHC) ligand interaction in both CAR and TCR exhibit catch bonds with specific peptide agonist peaking at 25 and 14 pN, respectively. While a conformational transition is regularly seen in TCR-pMHC systems, that of CAR-pMHC systems is dissimilar, being infrequent, of lower magnitude, and irreversible. Slip bonds are observed with CD19-specific CAR T-cells and with a monoclonal antibody mapping to the MHC α2 helix but indifferent to the bound peptide. Collectively, these findings suggest that the CAR-pMHC interface underpins the CAR catch bond response to pMHC ligands in contradistinction to slip bonds for CARs targeting canonical ligands.
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Affiliation(s)
- Debasis Banik
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Maryam Hamidinia
- Translational
Immunology Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Translational
Cancer Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Department
of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Joanna Brzostek
- Translational
Immunology Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Translational
Cancer Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Department
of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Ling Wu
- Translational
Immunology Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Translational
Cancer Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Department
of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Hannah M. Stephens
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Paul A. MacAry
- Translational
Immunology Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Translational
Cancer Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Department
of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Ellis L. Reinherz
- Laboratory
of Immunobiology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, United States
- Department
of Medical Oncology, Dana-Farber Cancer Institute and Department of
Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Nicholas R. J. Gascoigne
- Translational
Immunology Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Translational
Cancer Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Department
of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Matthew J. Lang
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37235, United States
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17
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Magnetic Tweezers-Based Single-Molecule Assays to Study Interaction of E. coli SSB with DNA and RecQ Helicase. Methods Mol Biol 2021; 2281:93-115. [PMID: 33847954 DOI: 10.1007/978-1-0716-1290-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The ability of magnetic tweezers to apply forces and measure molecular displacements has resulted in its extensive use to study the activity of enzymes involved in various aspects of nucleic acid metabolism. These studies have led to the discovery of key aspects of protein-protein and protein-nucleic acid interaction, uncovering dynamic heterogeneities that are lost to ensemble averaging in bulk experiments. The versatility of magnetic tweezers lies in the possibility and ease of tracking multiple parallel single-molecule events to yield statistically relevant single-molecule data. Moreover, they allow tracking both fast millisecond dynamics and slow processes (spanning several hours). In this chapter, we present the protocols used to study the interaction between E. coli SSB, single-stranded DNA (ssDNA), and E. coli RecQ helicase using magnetic tweezers. In particular, we propose constant force and force modulation assays to investigate SSB binding to DNA, as well as to characterize various facets of RecQ helicase activity stimulation by SSB.
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18
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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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19
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Biochemistry: one molecule at a time. Essays Biochem 2021; 65:1-3. [PMID: 33860798 PMCID: PMC8056033 DOI: 10.1042/ebc20210015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 02/26/2021] [Accepted: 02/26/2021] [Indexed: 12/20/2022]
Abstract
Biological processes are orchestrated by complex networks of molecules. Conventional approaches for studying the action of biomolecules operate on a population level, averaging out any inhomogeneities within the ensemble. Investigating one biological macromolecule at a time allows researchers to directly probe individual behaviours, and thus characterise the intrinsic molecular heterogeneity of the system. Single-molecule methods have unravelled unexpected modes of action for many seemingly well-characterised biomolecules and often proved instrumental in understanding the intricate mechanistic basis of biological processes. This collection of reviews aims to showcase how single-molecule techniques can be used to address important biological questions and to inspire biochemists to ‘zoom in’ to the population and probe individual molecular behaviours, beyond the ensemble average. Furthermore, this issue of Essays in Biochemistry is the very first written and edited entirely by early career researchers, and so it also highlights the strength, diversity and excellence of the younger generation single-molecule scientists who drive this exciting field of research forward.
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20
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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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21
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Wack M, Wiegand T, Frischknecht F, Cavalcanti-Adam EA. An in vitro DNA Sensor-based Assay to Measure Receptor-specific Adhesion Forces of Eukaryotic Cells and Pathogens. Bio Protoc 2020; 10:e3733. [PMID: 33659394 DOI: 10.21769/bioprotoc.3733] [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: 01/21/2020] [Revised: 06/10/2020] [Accepted: 06/17/2020] [Indexed: 11/02/2022] Open
Abstract
Motility of eukaryotic cells or pathogens within tissues is mediated by the turnover of specific interactions with other cells or with the extracellular matrix. Biophysical characterization of these ligand-receptor adhesions helps to unravel the molecular mechanisms driving migration. Traction force microscopy or optical tweezers are typically used to measure the cellular forces exerted by cells on a substrate. However, the spatial resolution of traction force microscopy is limited to ~2 µm and performing experiments with optical traps is very time-consuming. Here we present the production of biomimetic surfaces that enable specific cell adhesion via synthetic ligands and at the same time monitor the transmitted forces by using molecular tension sensors. The ligands were coupled to double-stranded DNA probes with defined force thresholds for DNA unzipping. Receptor-mediated forces in the pN range are thereby semi-quantitatively converted into fluorescence signals, which can be detected by standard fluorescence microscopy at the resolution limit (~0.2 µm). The modular design of the assay allows to vary the presented ligands and the mechanical strength of the DNA probes, which provides a number of possibilities to probe the adhesion of different eukaryotic cell types and pathogens and is exemplified here with osteosarcoma cells and Plasmodium berghei Sporozoites.
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Affiliation(s)
- Maurizio Wack
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany
| | - Tina Wiegand
- Cellular Biophysics, Max Planck Institute for Medical Research, Heidelberg, Germany.,Institute for Physical Chemistry, Heidelberg University, Heidelberg, Germany
| | - Friedrich Frischknecht
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany
| | - E Ada Cavalcanti-Adam
- Cellular Biophysics, Max Planck Institute for Medical Research, Heidelberg, Germany.,Institute for Physical Chemistry, Heidelberg University, Heidelberg, Germany
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22
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Abstract
In recent decades, single particle tracking (SPT) has been developed into a sophisticated analytical approach involving complex instruments and data analysis schemes to extract information from time-resolved particle trajectories. Very often, mobility-related properties are extracted from these particle trajectories, as they often contain information about local interactions experienced by the particles while moving through the sample. This tutorial aims to provide a comprehensive overview about the accuracies that can be achieved when extracting mobility-related properties from 2D particle trajectories and how these accuracies depend on experimental parameters. Proper interpretation of SPT data requires an assessment of whether the obtained accuracies are sufficient to resolve the effect under investigation. This is demonstrated by calculating mean square displacement curves that show an apparent super- or subdiffusive behavior due to poor measurement statistics instead of the presence of true anomalous diffusion. Furthermore, the refinement of parameters involved in the design or analysis of SPT experiments is discussed and an approach is proposed in which square displacement distributions are inspected to evaluate the quality of SPT data and to extract information about the maximum distance over which particles should be tracked during the linking process.
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23
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Serov AS, Laurent F, Floderer C, Perronet K, Favard C, Muriaux D, Westbrook N, Vestergaard CL, Masson JB. Statistical Tests for Force Inference in Heterogeneous Environments. Sci Rep 2020; 10:3783. [PMID: 32123194 PMCID: PMC7052274 DOI: 10.1038/s41598-020-60220-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 02/05/2020] [Indexed: 01/22/2023] Open
Abstract
We devise a method to detect and estimate forces in a heterogeneous environment based on experimentally recorded stochastic trajectories. In particular, we focus on systems modeled by the heterogeneous overdamped Langevin equation. Here, the observed drift includes a "spurious” force term when the diffusivity varies in space. We show how Bayesian inference can be leveraged to reliably infer forces by taking into account such spurious forces of unknown amplitude as well as experimental sources of error. The method is based on marginalizing the force posterior over all possible spurious force contributions. The approach is combined with a Bayes factor statistical test for the presence of forces. The performance of our method is investigated analytically, numerically and tested on experimental data sets. The main results are obtained in a closed form allowing for direct exploration of their properties and fast computation. The method is incorporated into TRamWAy, an open-source software platform for automated analysis of biomolecule trajectories.
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Affiliation(s)
- Alexander S Serov
- Decision and Bayesian Computation, USR 3756 (C3BI/DBC) & Neuroscience department CNRS UMR 3751, Institut Pasteur, CNRS, Paris, France.
| | - François Laurent
- Decision and Bayesian Computation, USR 3756 (C3BI/DBC) & Neuroscience department CNRS UMR 3751, Institut Pasteur, CNRS, Paris, France
| | - Charlotte Floderer
- Infectious Disease Research Institute of Montpellier, CNRS UMR 9004, University of Montpellier, Montpellier, France
| | - Karen Perronet
- Laboratoire Charles Fabry, Université Paris-Saclay, Institut d'Optique Graduate School, CNRS UMR8501, 91127, Palaiseau Cedex, France
| | - Cyril Favard
- Infectious Disease Research Institute of Montpellier, CNRS UMR 9004, University of Montpellier, Montpellier, France
| | - Delphine Muriaux
- Infectious Disease Research Institute of Montpellier, CNRS UMR 9004, University of Montpellier, Montpellier, France
| | - Nathalie Westbrook
- Laboratoire Charles Fabry, Université Paris-Saclay, Institut d'Optique Graduate School, CNRS UMR8501, 91127, Palaiseau Cedex, France
| | - Christian L Vestergaard
- Decision and Bayesian Computation, USR 3756 (C3BI/DBC) & Neuroscience department CNRS UMR 3751, Institut Pasteur, CNRS, Paris, France.
| | - Jean-Baptiste Masson
- Decision and Bayesian Computation, USR 3756 (C3BI/DBC) & Neuroscience department CNRS UMR 3751, Institut Pasteur, CNRS, Paris, France.
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24
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Ma G, Hu C, Li S, Gao X, Li H, Hu X. Simultaneous, hybrid single-molecule method by optical tweezers and fluorescence. NANOTECHNOLOGY AND PRECISION ENGINEERING 2019. [DOI: 10.1016/j.npe.2019.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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25
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Chuang CY, Zammit M, Whitmore ML, Comstock MJ. Combined High-Resolution Optical Tweezers and Multicolor Single-Molecule Fluorescence with an Automated Single-Molecule Assembly Line. J Phys Chem A 2019; 123:9612-9620. [PMID: 31621318 DOI: 10.1021/acs.jpca.9b08282] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present an instrument that combines high-resolution optical tweezers and multicolor confocal fluorescence spectroscopy along with automated single-molecule assembly. The multicolor allows the simultaneous observation of multiple molecules or multiple degrees of freedom, which allows, for example, the observation of multiple proteins simultaneously within a complex. The instrument incorporates three fluorescence excitation lasers, with a reliable alignment scheme, which will allow three independent fluorescent probe or FRET measurements and also increases flexibility in the choice of fluorescent molecules. We demonstrate the ability to simultaneously measure angstrom-scale changes in tether extension and fluorescence signals. Simultaneous tweezers and fluorescence measurement are particularly challenging because of fluorophore photobleaching, even more so if multiple fluorophores are to be measured. Therefore, (1) fluorescence excitation and detection is interlaced with time-shared dual optical traps. (2) We investigated the photostability of common fluorophores. The mean number of photons emitted before bleaching was unaffected by the trap laser and decreased only slightly with increasing excitation laser intensity. Surprisingly, we found that Cy5 outperforms other commonly used fluorophores by more than fivefold. (3) We devised computer-controlled automation, which conserves fluorophore lifetime by quickly detecting fluorophore-labeled molecule binding, turning off lasers, and moving to add the next fluorophore-labeled component. The single-molecule assembly line enables the precise assembly of multimolecule complexes while preserving fluorophores.
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Affiliation(s)
- Cho-Ying Chuang
- Department of Physics and Astronomy , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Matthew Zammit
- Department of Physics and Astronomy , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Miles L Whitmore
- Department of Physics and Astronomy , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Matthew J Comstock
- Department of Physics and Astronomy , Michigan State University , East Lansing , Michigan 48824 , United States
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26
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Multi-parameter measurements of conformational dynamics in nucleic acids and nucleoprotein complexes. Methods 2019; 169:69-77. [PMID: 31228549 DOI: 10.1016/j.ymeth.2019.06.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 06/15/2019] [Accepted: 06/18/2019] [Indexed: 11/20/2022] Open
Abstract
Biological macromolecules undergo dynamic conformational changes. Single-molecule methods can track such structural rearrangements in real time. However, while the structure of large macromolecules may change along many degrees of freedom, single-molecule techniques only monitor a limited number of these axes of motion. Advanced single-molecule methods are being developed to track multiple degrees of freedom in nucleic acids and nucleoprotein complexes at high resolution, to enable better manipulation and control of the system under investigation, and to collect measurements in massively parallel fashion. Combining complementary single-molecule methods within the same assay also provides unique measurement opportunities. Implementations of magnetic and optical tweezers combined with fluorescence and FRET have demonstrated results unattainable by either technique alone. Augmenting other advanced single-molecule methods with fluorescence detection will allow us to better capture the multidimensional dynamics of nucleic acids and nucleoprotein complexes central to biology.
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27
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Desai VP, Frank F, Lee A, Righini M, Lancaster L, Noller HF, Tinoco I, Bustamante C. Co-temporal Force and Fluorescence Measurements Reveal a Ribosomal Gear Shift Mechanism of Translation Regulation by Structured mRNAs. Mol Cell 2019; 75:1007-1019.e5. [PMID: 31471187 DOI: 10.1016/j.molcel.2019.07.024] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 06/12/2019] [Accepted: 07/15/2019] [Indexed: 11/18/2022]
Abstract
The movement of ribosomes on mRNA is often interrupted by secondary structures that present mechanical barriers and play a central role in translation regulation. We investigate how ribosomes couple their internal conformational changes with the activity of translocation factor EF-G to unwind mRNA secondary structures using high-resolution optical tweezers with single-molecule fluorescence capability. We find that hairpin opening occurs during EF-G-catalyzed translocation and is driven by the forward rotation of the small subunit head. Modulating the magnitude of the hairpin barrier by force shows that ribosomes respond to strong barriers by shifting their operation to an alternative 7-fold-slower kinetic pathway prior to translocation. Shifting into a slow gear results from an allosteric switch in the ribosome that may allow it to exploit thermal fluctuations to overcome mechanical barriers. Finally, we observe that ribosomes occasionally open the hairpin in two successive sub-codon steps, revealing a previously unobserved translocation intermediate.
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Affiliation(s)
- Varsha P Desai
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Filipp Frank
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Antony Lee
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Physics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Maurizio Righini
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Laura Lancaster
- Department of Molecular, Cell, and Developmental Biology and Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Harry F Noller
- Department of Molecular, Cell, and Developmental Biology and Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Ignacio Tinoco
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Carlos Bustamante
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Physics, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Kavli Energy Nanoscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
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28
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Hanasaki I, Nemoto T, Tanaka YY. Soft trapping lasts longer: Dwell time of a Brownian particle varied by potential shape. Phys Rev E 2019; 99:022119. [PMID: 30934295 DOI: 10.1103/physreve.99.022119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Indexed: 06/09/2023]
Abstract
It is often regarded that the dwell time (or residence time, escape time, trapping duration) of trapped Brownian particles is described by the multiplication of two separate factors, i.e., the diffusive traveling time of the trapping domain size without taking into account the trapping force, and the stochastic event of overcoming the trapping energy by thermal one instantaneously. However, we show that the ratio of dwell time to the typical traveling time for the trapping domain size depends on the shape of the force field. The shape of the trapping potential affects this ratio even if the trapping energy gap is the same and the smooth potential has a single minimum. Our finding suggests the possible application of the potential shape to realize the desired trapping characteristics.
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Affiliation(s)
- Itsuo Hanasaki
- Institute of Engineering, Tokyo University of Agriculture and Technology, Naka-cho 2-24-16, Koganei, Tokyo 184-8588, Japan
| | - Takahiro Nemoto
- Philippe Meyer Institute for Theoretical Physics, Physics Department, École Normale Supérieure & PSL Research University, 24, rue Lhomond, 75231 Paris Cedex 05, France
| | - Yoshito Y Tanaka
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
- Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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29
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Abstract
B cells are essential to the adaptive immune system for providing the humoral immunity against cohorts of pathogens. The presentation of antigen to the B cell receptor (BCR) leads to the initiation of B cell activation, which is a process sensitive to the stiffness features of the substrates presenting the antigens. Mechanosensing of the B cells, potentiated through BCR signaling and the adhesion molecules, efficiently regulates B cell activation, proliferation and subsequent antibody responses. Defects in sensing of the antigen-presenting substrates can lead to the activation of autoreactive B cells in autoimmune diseases. The use of high-resolution, high-speed live-cell imaging along with the sophisticated biophysical materials, has uncovered the mechanisms underlying the initiation of B cell activation within seconds of its engagement with the antigen presenting substrates. In this chapter, we reviewed studies that have contributed to uncover the molecular mechanisms of B cell mechanosensing during the initiation of B cell activation.
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Affiliation(s)
- Samina Shaheen
- Center for life sciences, MOE Key Laboratory of Protein Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing Key Lab for Immunological Research on Chronic Diseases, School of Life Sciences, Institute for Immunology, Tsinghua University, Beijing, China
| | - Zhengpeng Wan
- Center for life sciences, MOE Key Laboratory of Protein Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing Key Lab for Immunological Research on Chronic Diseases, School of Life Sciences, Institute for Immunology, Tsinghua University, Beijing, China
| | - Kabeer Haneef
- Center for life sciences, MOE Key Laboratory of Protein Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing Key Lab for Immunological Research on Chronic Diseases, School of Life Sciences, Institute for Immunology, Tsinghua University, Beijing, China
| | - Yingyue Zeng
- Center for life sciences, MOE Key Laboratory of Protein Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing Key Lab for Immunological Research on Chronic Diseases, School of Life Sciences, Institute for Immunology, Tsinghua University, Beijing, China
| | - Wang Jing
- Center for life sciences, MOE Key Laboratory of Protein Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing Key Lab for Immunological Research on Chronic Diseases, School of Life Sciences, Institute for Immunology, Tsinghua University, Beijing, China
| | - Wanli Liu
- Center for life sciences, MOE Key Laboratory of Protein Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing Key Lab for Immunological Research on Chronic Diseases, School of Life Sciences, Institute for Immunology, Tsinghua University, Beijing, China.
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30
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Duss O, Stepanyuk GA, Grot A, O'Leary SE, Puglisi JD, Williamson JR. Real-time assembly of ribonucleoprotein complexes on nascent RNA transcripts. Nat Commun 2018; 9:5087. [PMID: 30504830 PMCID: PMC6269517 DOI: 10.1038/s41467-018-07423-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/26/2018] [Indexed: 12/22/2022] Open
Abstract
Cellular protein-RNA complexes assemble on nascent transcripts, but methods to observe transcription and protein binding in real time and at physiological concentrations are not available. Here, we report a single-molecule approach based on zero-mode waveguides that simultaneously tracks transcription progress and the binding of ribosomal protein S15 to nascent RNA transcripts during early ribosome biogenesis. We observe stable binding of S15 to single RNAs immediately after transcription for the majority of the transcripts at 35 °C but for less than half at 20 °C. The remaining transcripts exhibit either rapid and transient binding or are unable to bind S15, likely due to RNA misfolding. Our work establishes the foundation for studying transcription and its coupled co-transcriptional processes, including RNA folding, ligand binding, and enzymatic activity such as in coupling of transcription to splicing, ribosome assembly or translation. The early steps of ribosome assembly occur co-transcriptionally on the nascent ribosomal RNA. Here the authors demonstrate an approach that allows simultaneous monitoring of transcription and ribosomal protein assembly at the single-molecule level in real time.
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Affiliation(s)
- Olivier Duss
- Department of Integrative Structural and Computational Biology, Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Department of Structural Biology, Stanford University School of Medicine, CA, 94305, California, USA
| | - Galina A Stepanyuk
- Department of Integrative Structural and Computational Biology, Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Annette Grot
- Department of Research and Development, Pacific Biosciences Inc, Menlo Park, CA, 94025, USA
| | - Seán E O'Leary
- Department of Structural Biology, Stanford University School of Medicine, CA, 94305, California, USA.,Department of Biochemistry, University of California, Riverside, CA, 92521, USA
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, CA, 94305, California, USA.
| | - James R Williamson
- Department of Integrative Structural and Computational Biology, Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
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31
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Keya JJ, Kabir AMR, Inoue D, Sada K, Hess H, Kuzuya A, Kakugo A. Control of swarming of molecular robots. Sci Rep 2018; 8:11756. [PMID: 30082825 PMCID: PMC6079095 DOI: 10.1038/s41598-018-30187-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 07/17/2018] [Indexed: 12/19/2022] Open
Abstract
Recently we demonstrated swarming of a self-propelled biomolecular motor system microtubule (MT)-kinesin where interactions among thousands of motile MTs were regulated in a highly programmable fashion by using DNA as a processor. However, precise control of this potential system is yet to be achieved to optimize the swarm behavior. In this work, we systematically controlled swarming of MTs on kinesin adhered surface by different physicochemical parameters of MT-kinesin and DNA. Tuning the length of DNA sequences swarming was precisely controlled with thermodynamic and kinetic feasibility. In addition, swarming was regulated using different concentration of DNA crosslinkers. Reversibility of swarming was further controlled by changing the concentration of strand displacement DNA signal allowing dissociation of swarm. The control over the swarm was accompanied by variable stiffness of MTs successfully, providing translational and circular motion. Moreover, the morphology of swarm was also found to be changed not only depending on the stiffness but also body length of MTs. Such detail study of precise control of swarming would provide new insights in developing a promising molecular swarm robotic system with desired functions.
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Affiliation(s)
- Jakia Jannat Keya
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan
| | | | - Daisuke Inoue
- Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Kazuki Sada
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan
- Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Henry Hess
- Department of Biomedical Engineering, Columbia University, 1210 Amsterdam Ave., New York, NY, 10027, USA
| | - Akinori Kuzuya
- Department of Chemistry and Materials Engineering, Kansai University, Osaka, 564-8680, Japan.
| | - Akira Kakugo
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, 060-0810, Japan.
- Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.
- Department of Biomedical Engineering, Columbia University, 1210 Amsterdam Ave., New York, NY, 10027, USA.
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32
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Feng Y, Reinherz EL, Lang MJ. αβ T Cell Receptor Mechanosensing Forces out Serial Engagement. Trends Immunol 2018; 39:596-609. [PMID: 30060805 PMCID: PMC6154790 DOI: 10.1016/j.it.2018.05.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 05/15/2018] [Accepted: 05/31/2018] [Indexed: 11/08/2022]
Abstract
T lymphocytes use αβ T cell receptors (TCRs) to recognize
sparse antigenic peptides bound to MHC molecules (pMHCs) arrayed on
antigen-presenting cells (APCs). Contrary to conventional receptor–ligand
associations exemplified by antigen-antibody interactions, forces play a crucial
role in nonequilibrium mechanosensor-based T cell activation. Both T cell
motility and local cytoskeleton machinery exert forces (i.e., generate loads) on
TCR–pMHC bonds. We review biological features of the load-dependent
activation process as revealed by optical tweezers single molecule/single cell
and other biophysical measurements. The findings link pMHC-triggered TCRs to
single cytoskeletal motors; define the importance of energized anisotropic
(i.e., force direction dependent) activation; and characterize immunological
synapse formation as digital, revealing no serial requirement. The emerging
picture suggests new approaches for the monitoring and design of cytotoxic T
lymphocyte (CTL)-based immunotherapy.
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Affiliation(s)
- Yinnian Feng
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235, USA
| | - Ellis L Reinherz
- Laboratory of Immunobiology and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
| | - Matthew J Lang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37235, USA.
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33
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Lee SH. Optimal integration of wide field illumination and holographic optical tweezers for multimodal microscopy with ultimate flexibility and versatility. OPTICS EXPRESS 2018; 26:8049-8058. [PMID: 29715778 DOI: 10.1364/oe.26.008049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 03/04/2018] [Indexed: 05/29/2023]
Abstract
We introduce one-of-a-kind optical microscope that we have developed through optimized integration of wide-field and focused-light microscopies. This new instrument has accomplished operation of the same laser for both wide field illumination and holographic focused beam illumination interchangeably or simultaneously in a way scalable to multiple lasers. We have demonstrated its powerful capability by simultaneously carrying out Epi-fluorescence, total internal reflection fluorescence microscopy, selective plane illumination microscopy, and holographic optical tweezers with five lasers. Our instrument and the optical design will provide researchers across diverse fields, cell-biology and biophysics in particular, with a practical guidance to build an all-around multimodal microscope that will further inspire the development of novel hybrid microscopy experiments.
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34
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Ivanov IE, Lebel P, Oberstrass FC, Starr CH, Parente AC, Ierokomos A, Bryant Z. Multimodal Measurements of Single-Molecule Dynamics Using FluoRBT. Biophys J 2018; 114:278-282. [PMID: 29248150 PMCID: PMC5984952 DOI: 10.1016/j.bpj.2017.11.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 10/15/2017] [Accepted: 11/08/2017] [Indexed: 11/21/2022] Open
Abstract
Single-molecule methods provide direct measurements of macromolecular dynamics, but are limited by the number of degrees of freedom that can be followed at one time. High-resolution rotor bead tracking (RBT) measures DNA torque, twist, and extension, and can be used to characterize the structural dynamics of DNA and diverse nucleoprotein complexes. Here, we extend RBT to enable simultaneous monitoring of additional degrees of freedom. Fluorescence-RBT (FluoRBT) combines magnetic tweezers, infrared evanescent scattering, and single-molecule FRET imaging, providing real-time multiparameter measurements of complex molecular processes. We demonstrate the capabilities of FluoRBT by conducting simultaneous measurements of extension and FRET during opening and closing of a DNA hairpin under tension, and by observing simultaneous changes in FRET and torque during a transition between right-handed B-form and left-handed Z-form DNA under controlled supercoiling. We discover unanticipated continuous changes in FRET with applied torque, and also show how FluoRBT can facilitate high-resolution FRET measurements of molecular states, by using a mechanical signal as an independent temporal reference for aligning and averaging noisy fluorescence data. By combining mechanical measurements of global DNA deformations with FRET measurements of local conformational changes, FluoRBT will enable multidimensional investigations of systems ranging from DNA structures to large macromolecular machines.
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Affiliation(s)
- Ivan E Ivanov
- Department of Chemical Engineering, Stanford University, Stanford, California; Department of Bioengineering, Stanford University, Stanford, California
| | - Paul Lebel
- Department of Bioengineering, Stanford University, Stanford, California; Department of Applied Physics, Stanford University, Stanford, California
| | | | - Charles H Starr
- Department of Bioengineering, Stanford University, Stanford, California; Program in Biophysics, Stanford University, Stanford, California
| | - Angelica C Parente
- Department of Bioengineering, Stanford University, Stanford, California; Program in Biophysics, Stanford University, Stanford, California
| | - Athena Ierokomos
- Department of Bioengineering, Stanford University, Stanford, California; Program in Biophysics, Stanford University, Stanford, California
| | - Zev Bryant
- Department of Bioengineering, Stanford University, Stanford, California; Department of Structural Biology, Stanford University, Stanford, California.
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35
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Chang M, Oh J, Kim Y, Hohng S, Lee JB. Extended depth of field for single biomolecule optical imaging-force spectroscopy. OPTICS EXPRESS 2017; 25:32189-32197. [PMID: 29245882 DOI: 10.1364/oe.25.032189] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 12/01/2017] [Indexed: 06/07/2023]
Abstract
Real-time optical imaging combined with single-molecule manipulation broadens the horizons for acquiring information about the spatiotemporal localization and the mechanical details of target molecules. To obtain an optical signal outside the focal plane without unintended interruption of the force signal in single-molecule optical imaging-force spectroscopy, we developed an optical method to extend the depth of field in a high numerical aperture objective (≥ 1.2), required to visualize a single fluorophore. By axial scanning, using an electrically tunable lens with a fixed sample, we were successfully able to visualize the epidermal growth factor receptor (EGFR) moving along the three-dimensionally elongated filamentous actin bundles connecting cells (intercellular nanotube), while another EGFR on the intercellular nanotube was trapped by optical tweezers in living cells. Our approach is simple, fast and inexpensive, but it is powerful for imaging target molecules axially in single-molecule optical imaging-force spectroscopy.
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36
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Abstract
T lymphocytes use surface [Formula: see text] T-cell receptors (TCRs) to recognize peptides bound to MHC molecules (pMHCs) on antigen-presenting cells (APCs). How the exquisite specificity of high-avidity T cells is achieved is unknown but essential, given the paucity of foreign pMHC ligands relative to the ubiquitous self-pMHC array on an APC. Using optical traps, we determine physicochemical triggering thresholds based on load and force direction. Strikingly, chemical thresholds in the absence of external load require orders of magnitude higher pMHC numbers than observed physiologically. In contrast, force applied in the shear direction ([Formula: see text]10 pN per TCR molecule) triggers T-cell Ca2+ flux with as few as two pMHC molecules at the interacting surface interface with rapid positional relaxation associated with similarly directed motor-dependent transport via [Formula: see text]8-nm steps, behaviors inconsistent with serial engagement during initial TCR triggering. These synergistic directional forces generated during cell motility are essential for adaptive T-cell immunity against infectious pathogens and cancers.
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37
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Cervantes-Salguero K, Kawamata I, Nomura SIM, Murata S. Unzipping and shearing DNA with electrophoresed nanoparticles in hydrogels. Phys Chem Chem Phys 2017; 19:13414-13418. [PMID: 28513698 DOI: 10.1039/c7cp02214j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We show electric control of unzipping and shearing dehybridization of a DNA duplex anchored to a hydrogel. Tensile force is applied by electrophoresing (25 V cm-1) gold nanoparticles pulling the DNA duplex. The pulled DNA strand is gradually released from the hydrogel. The unzipping release rate is faster than shearing; for example, 3-fold for a 15 base pair duplex, which helps to design electrically driven DNA devices.
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Affiliation(s)
- Keitel Cervantes-Salguero
- Department of Robotics, Graduate School of Engineering, Tohoku University, 6-6-1 Aobayama, Sendai 980-8579, Japan.
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38
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Gunn KH, Marko JF, Mondragón A. An orthogonal single-molecule experiment reveals multiple-attempt dynamics of type IA topoisomerases. Nat Struct Mol Biol 2017; 24:484-490. [PMID: 28414321 PMCID: PMC5516274 DOI: 10.1038/nsmb.3401] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 03/17/2017] [Indexed: 12/19/2022]
Abstract
Topoisomerases are enzymes involved in maintaining the topological state of cellular DNA. Despite many structural, biophysical, and biochemical studies, their dynamic characteristics remain poorly understood. Recent single molecule experiments revealed that an important feature of the type IA topoisomerase mechanism is the presence of pauses between relaxation events. However, these experiments cannot determine whether the protein remains DNA bound during the pauses or the relationship between domain movements in the protein and topological changes in the DNA. By combining two orthogonal single molecule techniques, we observed that topoisomerase IA is constantly changing conformation and attempting to modify the topology of DNA, but only succeeds in a fraction of the attempts. Thus, its mechanism can be described as a series of DNA strand passage attempts that culminate in a successful relaxation event.
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Affiliation(s)
- Kathryn H Gunn
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
| | - John F Marko
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA.,Department of Physics and Astronomy, Northwestern University, Evanston, Illinois, USA
| | - Alfonso Mondragón
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
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39
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Sundaramoorthy S, Badaracco AG, Hirsch SM, Park JH, Davies T, Dumont J, Shirasu-Hiza M, Kummel AC, Canman JC. Low Efficiency Upconversion Nanoparticles for High-Resolution Coalignment of Near-Infrared and Visible Light Paths on a Light Microscope. ACS APPLIED MATERIALS & INTERFACES 2017; 9:7929-7940. [PMID: 28221018 PMCID: PMC5720688 DOI: 10.1021/acsami.6b15322] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The combination of near-infrared (NIR) and visible wavelengths in light microscopy for biological studies is increasingly common. For example, many fields of biology are developing the use of NIR for optogenetics, in which an NIR laser induces a change in gene expression and/or protein function. One major technical barrier in working with both NIR and visible light on an optical microscope is obtaining their precise coalignment at the imaging plane position. Photon upconverting particles (UCPs) can bridge this gap as they are excited by NIR light but emit in the visible range via an anti-Stokes luminescence mechanism. Here, two different UCPs have been identified, high-efficiency micro540-UCPs and lower efficiency nano545-UCPs, that respond to NIR light and emit visible light with high photostability even at very high NIR power densities (>25 000 Suns). Both of these UCPs can be rapidly and reversibly excited by visible and NIR light and emit light at visible wavelengths detectable with standard emission settings used for Green Fluorescent Protein (GFP), a commonly used genetically encoded fluorophore. However, the high efficiency micro540-UCPs were suboptimal for NIR and visible light coalignment, due to their larger size and spatial broadening from particle-to-particle energy transfer consistent with a long-lived excited state and saturated power dependence. In contrast, the lower efficiency nano-UCPs were superior for precise coalignment of the NIR beam with the visible light path (∼2 μm versus ∼8 μm beam broadening, respectively) consistent with limited particle-to-particle energy transfer, superlinear power dependence for emission, and much smaller particle size. Furthermore, the nano-UCPs were superior to a traditional two-camera method for NIR and visible light path alignment in an in vivo Infrared-Laser-Evoked Gene Operator (IR-LEGO) optogenetics assay in the budding yeast Saccharomyces cerevisiae. In summary, nano-UCPs are powerful new tools for coaligning NIR and visible light paths on a light microscope.
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Affiliation(s)
| | - Adrian Garcia Badaracco
- University of California, San Diego, Section of Chemical and Materials Science, La Jolla, CA 92093
| | - Sophia M. Hirsch
- University Medical Center, Dept. of Genetics and Development, New York, NY 10032
| | - Jun Hong Park
- University of California, San Diego, Section of Chemical and Materials Science, La Jolla, CA 92093
| | - Tim Davies
- Columbia University Medical Center, Dept. of Pathology and Cell Biology, New York, NY 10032
| | - Julien Dumont
- Institut Jacques Monod, CNRS, UMR 7592, University Paris Diderot, Sorbonne Paris Cité F-75205 Paris, France
| | - Mimi Shirasu-Hiza
- University Medical Center, Dept. of Genetics and Development, New York, NY 10032
| | - Andrew C. Kummel
- University of California, San Diego, Section of Chemical and Materials Science, La Jolla, CA 92093
| | - Julie C. Canman
- Columbia University Medical Center, Dept. of Pathology and Cell Biology, New York, NY 10032
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40
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Whitley K, Comstock M, Chemla Y. High-Resolution Optical Tweezers Combined With Single-Molecule Confocal Microscopy. Methods Enzymol 2017; 582:137-169. [PMID: 28062033 PMCID: PMC5540136 DOI: 10.1016/bs.mie.2016.10.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We describe the design, construction, and application of an instrument combining dual-trap, high-resolution optical tweezers and a confocal microscope. This hybrid instrument allows nanomechanical manipulation and measurement simultaneously with single-molecule fluorescence detection. We present the general design principles that overcome the challenges of maximizing optical trap resolution while maintaining single-molecule fluorescence sensitivity, and provide details on the construction and alignment of the instrument. This powerful new tool is just beginning to be applied to biological problems. We present step-by-step instructions on an application of this technique that highlights the instrument's capabilities, detecting conformational dynamics in a nucleic acid-processing enzyme.
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Affiliation(s)
- K.D. Whitley
- University of Illinois at Urbana–Champaign, Urbana, IL, United States
| | - M.J. Comstock
- Michigan State University, East Lansing, MI, United States
| | - Y.R. Chemla
- University of Illinois at Urbana–Champaign, Urbana, IL, United States,Center for the Physics of Living Cells, University of Illinois at Urbana–Champaign, Urbana, IL, United States,Corresponding author:
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41
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High-Resolution "Fleezers": Dual-Trap Optical Tweezers Combined with Single-Molecule Fluorescence Detection. Methods Mol Biol 2017; 1486:183-256. [PMID: 27844430 DOI: 10.1007/978-1-4939-6421-5_8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Recent advances in optical tweezers have greatly expanded their measurement capabilities. A new generation of hybrid instrument that combines nanomechanical manipulation with fluorescence detection-fluorescence optical tweezers, or "fleezers"-is providing a powerful approach to study complex macromolecular dynamics. Here, we describe a combined high-resolution optical trap/confocal fluorescence microscope that can simultaneously detect sub-nanometer displacements, sub-piconewton forces, and single-molecule fluorescence signals. The primary technical challenge to these hybrid instruments is how to combine both measurement modalities without sacrificing the sensitivity of either one. We present general design principles to overcome this challenge and provide detailed, step-by-step instructions to implement them in the construction and alignment of the instrument. Lastly, we present a set of protocols to perform a simple, proof-of-principle experiment that highlights the instrument capabilities.
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42
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A programmable DNA origami nanospring that reveals force-induced adjacent binding of myosin VI heads. Nat Commun 2016; 7:13715. [PMID: 27941751 PMCID: PMC5159853 DOI: 10.1038/ncomms13715] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 10/26/2016] [Indexed: 02/06/2023] Open
Abstract
Mechanosensitive biological nanomachines such as motor proteins and ion channels regulate diverse cellular behaviour. Combined optical trapping with single-molecule fluorescence imaging provides a powerful methodology to clearly characterize the mechanoresponse, structural dynamics and stability of such nanomachines. However, this system requires complicated experimental geometry, preparation and optics, and is limited by low data-acquisition efficiency. Here we develop a programmable DNA origami nanospring that overcomes these issues. We apply our nanospring to human myosin VI, a mechanosensory motor protein, and demonstrate nanometre-precision single-molecule fluorescence imaging of the individual motor domains (heads) under force. We observe force-induced transitions of myosin VI heads from non-adjacent to adjacent binding, which correspond to adapted roles for low-load and high-load transport, respectively. Our technique extends single-molecule studies under force and clarifies the effect of force on biological processes.
Characterizing the mechanical response of molecular motors involves the use of methods such as optical trapping to apply force. Here the authors develop a DNA origami nanospring to apply progressive force to human myosin VI, and discover that it adopts different stepping modes when subjected to low load or high load.
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43
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Duboc C, Fan J, Graves ET, Strick TR. Preparation of DNA Substrates and Functionalized Glass Surfaces for Correlative Nanomanipulation and Colocalization (NanoCOSM) of Single Molecules. Methods Enzymol 2016; 582:275-296. [PMID: 28062038 DOI: 10.1016/bs.mie.2016.09.048] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Simultaneous nanomanipulation and colocalization of single molecules (NanoCOSM) provides a unique opportunity to correlate the mechanical properties and activities of biomolecules with their conformational states or states of assembly as part of dynamic macromolecular complexes. This opens the door to real-time single-molecule analysis of the correlations between structure, function, and composition of large multicomponent protein complexes.
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Affiliation(s)
- C Duboc
- Institut Jacques Monod, Centre National de la Recherche Scientifique, University of Paris Diderot and Sorbonne Paris Cité, Paris, France
| | - J Fan
- Institut Jacques Monod, Centre National de la Recherche Scientifique, University of Paris Diderot and Sorbonne Paris Cité, Paris, France
| | - E T Graves
- Institut Jacques Monod, Centre National de la Recherche Scientifique, University of Paris Diderot and Sorbonne Paris Cité, Paris, France
| | - T R Strick
- Institut Jacques Monod, Centre National de la Recherche Scientifique, University of Paris Diderot and Sorbonne Paris Cité, Paris, France; Ecole Normale Supérieure, Institut de Biologie de l'ENS (iBENS), INSERM, CNRS, PSL Research University, Paris, France.
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44
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Manibog K, Yen CF, Sivasankar S. Measuring Force-Induced Dissociation Kinetics of Protein Complexes Using Single-Molecule Atomic Force Microscopy. Methods Enzymol 2016; 582:297-320. [PMID: 28062039 DOI: 10.1016/bs.mie.2016.08.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Proteins respond to mechanical force by undergoing conformational changes and altering the kinetics of their interactions. However, the biophysical relationship between mechanical force and the lifetime of protein complexes is not completely understood. In this chapter, we provide a step-by-step tutorial on characterizing the force-dependent regulation of protein interactions using in vitro and in vivo single-molecule force clamp measurements with an atomic force microscope (AFM). While we focus on the force-induced dissociation of E-cadherins, a critical cell-cell adhesion protein, the approaches described here can be readily adapted to study other protein complexes. We begin this chapter by providing a brief overview of theoretical models that describe force-dependent kinetics of biomolecular interactions. Next, we present step-by-step methods for measuring the response of single receptor-ligand bonds to tensile force in vitro. Finally, we describe methods for quantifying the mechanical response of single protein complexes on the surface of living cells. We describe general protocols for conducting such measurements, including sample preparation, AFM force clamp measurements, and data analysis. We also highlight critical limitations in current technologies and discuss solutions to these challenges.
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Affiliation(s)
- K Manibog
- Iowa State University, Ames, IA, United States; Ames Laboratory, U.S. Department of Energy, Ames, IA, United States
| | - C F Yen
- Iowa State University, Ames, IA, United States; Ames Laboratory, U.S. Department of Energy, Ames, IA, United States
| | - S Sivasankar
- Iowa State University, Ames, IA, United States; Ames Laboratory, U.S. Department of Energy, Ames, IA, United States.
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Zhang J, Yan Y, Samai S, Ginger DS. Dynamic Melting Properties of Photoswitch-Modified DNA: Shearing versus Unzipping. J Phys Chem B 2016; 120:10706-10713. [DOI: 10.1021/acs.jpcb.6b08297] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jie Zhang
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Yunqi Yan
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Soumyadyuti Samai
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - David S. Ginger
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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46
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Chemla YR. High‐resolution, hybrid optical trapping methods, and their application to nucleic acid processing proteins. Biopolymers 2016; 105:704-14. [DOI: 10.1002/bip.22880] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 05/12/2016] [Accepted: 05/16/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Yann R. Chemla
- Department of Physics, Center for the Physics of Living Cells, Center for Biophysics and Quantitative BiologyUniversity of IllinoisUrbana‐Champaign
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47
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The molecular choreography of protein synthesis: translational control, regulation, and pathways. Q Rev Biophys 2016; 49:e11. [PMID: 27658712 DOI: 10.1017/s0033583516000056] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Translation of proteins by the ribosome regulates gene expression, with recent results underscoring the importance of translational control. Misregulation of translation underlies many diseases, including cancer and many genetic diseases. Decades of biochemical and structural studies have delineated many of the mechanistic details in prokaryotic translation, and sketched the outlines of eukaryotic translation. However, translation may not proceed linearly through a single mechanistic pathway, but likely involves multiple pathways and branchpoints. The stochastic nature of biological processes would allow different pathways to occur during translation that are biased by the interaction of the ribosome with other translation factors, with many of the steps kinetically controlled. These multiple pathways and branchpoints are potential regulatory nexus, allowing gene expression to be tuned at the translational level. As research focus shifts toward eukaryotic translation, certain themes will be echoed from studies on prokaryotic translation. This review provides a general overview of the dynamic data related to prokaryotic and eukaryotic translation, in particular recent findings with single-molecule methods, complemented by biochemical, kinetic, and structural findings. We will underscore the importance of viewing the process through the viewpoints of regulation, translational control, and heterogeneous pathways.
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Long X, Parks JW, Stone MD. Integrated magnetic tweezers and single-molecule FRET for investigating the mechanical properties of nucleic acid. Methods 2016; 105:16-25. [PMID: 27320203 DOI: 10.1016/j.ymeth.2016.06.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 06/09/2016] [Accepted: 06/13/2016] [Indexed: 02/02/2023] Open
Abstract
Many enzymes promote structural changes in their nucleic acid substrates via application of piconewton forces over nanometer length scales. Magnetic tweezers (MT) is a single molecule force spectroscopy method widely used for studying the energetics of such mechanical processes. MT permits stable application of a wide range of forces and torques over long time scales with nanometer spatial resolution. However, in any force spectroscopy experiment, the ability to monitor structural changes in nucleic acids with nanometer sensitivity requires the system of interest to be held under high degrees of tension to improve signal to noise. This limitation prohibits measurement of structural changes within nucleic acids under physiologically relevant conditions of low stretching forces. To overcome this challenge, researchers have integrated a spatially sensitive fluorescence spectroscopy method, single molecule-FRET, with MT to allow simultaneous observation and manipulation of nanoscale structural transitions over a wide range of forces. Here, we describe a method for using this hybrid instrument to analyze the mechanical properties of nucleic acids. We expect that this method for analysis of nucleic acid structure will be easily adapted for experiments aiming to interrogate the mechanical responses of other biological macromolecules.
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Affiliation(s)
- Xi Long
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Joseph W Parks
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Michael D Stone
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA; Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA, USA.
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Chang JC, Fok PW, Chou T. Bayesian Uncertainty Quantification for Bond Energies and Mobilities Using Path Integral Analysis. Biophys J 2016; 109:966-74. [PMID: 26331254 DOI: 10.1016/j.bpj.2015.07.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 06/04/2015] [Accepted: 07/14/2015] [Indexed: 12/24/2022] Open
Abstract
Dynamic single-molecule force spectroscopy is often used to distort bonds. The resulting responses, in the form of rupture forces, work applied, and trajectories of displacements, are used to reconstruct bond potentials. Such approaches often rely on simple parameterizations of one-dimensional bond potentials, assumptions on equilibrium starting states, and/or large amounts of trajectory data. Parametric approaches typically fail at inferring complicated bond potentials with multiple minima, while piecewise estimation may not guarantee smooth results with the appropriate behavior at large distances. Existing techniques, particularly those based on work theorems, also do not address spatial variations in the diffusivity that may arise from spatially inhomogeneous coupling to other degrees of freedom in the macromolecule. To address these challenges, we develop a comprehensive empirical Bayesian approach that incorporates data and regularization terms directly into a path integral. All experimental and statistical parameters in our method are estimated directly from the data. Upon testing our method on simulated data, our regularized approach requires less data and allows simultaneous inference of both complex bond potentials and diffusivity profiles. Crucially, we show that the accuracy of the reconstructed bond potential is sensitive to the spatially varying diffusivity and accurate reconstruction can be expected only when both are simultaneously inferred. Moreover, after providing a means for self-consistently choosing regularization parameters from data, we derive posterior probability distributions, allowing for uncertainty quantification.
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Affiliation(s)
- Joshua C Chang
- Mathematical Biosciences Institute, The Ohio State University, Columbus, Ohio.
| | - Pak-Wing Fok
- Department of Mathematical Sciences, University of Delaware, Newark, Delaware.
| | - Tom Chou
- Departments of Biomathematics and Mathematics, University of California Los Angeles, Los Angeles, California.
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Song D, Graham TGW, Loparo JJ. A general approach to visualize protein binding and DNA conformation without protein labelling. Nat Commun 2016; 7:10976. [PMID: 26952553 PMCID: PMC4786781 DOI: 10.1038/ncomms10976] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 02/08/2016] [Indexed: 01/29/2023] Open
Abstract
Single-molecule manipulation methods, such as magnetic tweezers and flow stretching, generally use the measurement of changes in DNA extension as a proxy for examining interactions between a DNA-binding protein and its substrate. These approaches are unable to directly measure protein–DNA association without fluorescently labelling the protein, which can be challenging. Here we address this limitation by developing a new approach that visualizes unlabelled protein binding on DNA with changes in DNA conformation in a relatively high-throughput manner. Protein binding to DNA molecules sparsely labelled with Cy3 results in an increase in fluorescence intensity due to protein-induced fluorescence enhancement (PIFE), whereas DNA length is monitored under flow of buffer through a microfluidic flow cell. Given that our assay uses unlabelled protein, it is not limited to the low protein concentrations normally required for single-molecule fluorescence imaging and should be broadly applicable to studying protein–DNA interactions. Single-molecule imaging of protein-DNA association requires fluorescently labelled protein, which limits the protein concentration that can be used. Here the authors exploit protein induced fluorescent enhancement of DNA sparsely labelled with Cy3 to visualize protein binding and correlate it with changes in DNA conformation.
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Affiliation(s)
- Dan Song
- Harvard Biophysics Program, Harvard Medical School, Boston, Massachusetts 02115, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Seeley G. Mudd Room 204B, Boston, Massachusetts 02115, USA
| | - Thomas G W Graham
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Seeley G. Mudd Room 204B, Boston, Massachusetts 02115, USA.,Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Seeley G. Mudd Room 204B, Boston, Massachusetts 02115, USA
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