101
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Oliveira L, Campos WH, Rocha MS. Optical Trapping and Manipulation of Superparamagnetic Beads Using Annular-Shaped Beams. Methods Protoc 2018. [PMCID: PMC6481052 DOI: 10.3390/mps1040044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We propose an optical tweezers setup based on an annular-shaped laser beam that is efficient to trap 2.8 μm-diameter superparamagnetic particles. The optical trapping of such particles was fully characterized, and a direct absolute comparison with a geometrical optics model was performed. With this comparison, we were able to show that light absorption by the superparamagnetic particles is negligible for our annular beam tweezers, differing from the case of conventional Gaussian beam tweezers, in which laser absorption by the beads makes stable trapping difficult. In addition, the trap stiffness of the annular beam tweezers increases with the laser power and with the bead distance from the coverslip surface. While this first result is expected and similar to that achieved for conventional Gaussian tweezers, which use ordinary dielectric beads, the second result is quite surprising and different from the ordinary case, suggesting that spherical aberration is much less important in our annular beam geometry. The results obtained here provide new insights into the development of hybrid optomagnetic tweezers, which can apply simultaneously optical and magnetic forces on the same particles.
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102
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Basoli F, Giannitelli SM, Gori M, Mozetic P, Bonfanti A, Trombetta M, Rainer A. Biomechanical Characterization at the Cell Scale: Present and Prospects. Front Physiol 2018; 9:1449. [PMID: 30498449 PMCID: PMC6249385 DOI: 10.3389/fphys.2018.01449] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 09/24/2018] [Indexed: 12/12/2022] Open
Abstract
The rapidly growing field of mechanobiology demands for robust and reproducible characterization of cell mechanical properties. Recent achievements in understanding the mechanical regulation of cell fate largely rely on technological platforms capable of probing the mechanical response of living cells and their physico–chemical interaction with the microenvironment. Besides the established family of atomic force microscopy (AFM) based methods, other approaches include optical, magnetic, and acoustic tweezers, as well as sensing substrates that take advantage of biomaterials chemistry and microfabrication techniques. In this review, we introduce the available methods with an emphasis on the most recent advances, and we discuss the challenges associated with their implementation.
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Affiliation(s)
- Francesco Basoli
- Department of Engineering, Università Campus Bio-Medico di Roma, Rome, Italy
| | | | - Manuele Gori
- Department of Engineering, Università Campus Bio-Medico di Roma, Rome, Italy
| | - Pamela Mozetic
- Center for Translational Medicine, International Clinical Research Center, St. Anne's University Hospital, Brno, Czechia
| | - Alessandra Bonfanti
- Department of Engineering, University of Cambridge, Cambridge, United Kingdom
| | - Marcella Trombetta
- Department of Engineering, Università Campus Bio-Medico di Roma, Rome, Italy
| | - Alberto Rainer
- Department of Engineering, Università Campus Bio-Medico di Roma, Rome, Italy.,Institute for Photonics and Nanotechnologies, National Research Council, Rome, Italy
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103
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Xiao Z, Khojah R, Chooljian M, Conte RL, Schneider JD, Fitzell K, Chopdekar RV, Wang Y, Scholl A, Chang J, Carman GP, Bokor J, Di Carlo D, Candler RN. Cytocompatible magnetostrictive microstructures for nano- and microparticle manipulation on linear strain response piezoelectrics. ACTA ACUST UNITED AC 2018. [DOI: 10.1088/2399-7532/aae4d7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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104
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Zhang S, Shakiba N, Chen Y, Zhang Y, Tian P, Singh J, Chamberlain MD, Satkauskas M, Flood AG, Kherani NP, Yu S, Zandstra PW, Wheeler AR. Patterned Optoelectronic Tweezers: A New Scheme for Selecting, Moving, and Storing Dielectric Particles and Cells. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1803342. [PMID: 30307718 DOI: 10.1002/smll.201803342] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Indexed: 06/08/2023]
Abstract
Optical micromanipulation has become popular for a wide range of applications. In this work, a new type of optical micromanipulation platform, patterned optoelectronic tweezers (p-OET), is introduced. In p-OET devices, the photoconductive layer (that is continuous in a conventional OET device) is patterned, forming regions in which the electrode layer is locally exposed. It is demonstrated that micropatterns in the photoconductive layer are useful for repelling unwanted particles/cells, and also for keeping selected particles/cells in place after turning off the light source, minimizing light-induced heating. To clarify the physical mechanism behind these effects, systematic simulations are carried out, which indicate the existence of strong nonuniform electric fields at the boundary of micropatterns. The simulations are consistent with experimental observations, which are explored for a wide variety of geometries and conditions. It is proposed that the new technique may be useful for myriad applications in the rapidly growing area of optical micromanipulation.
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Affiliation(s)
- Shuailong Zhang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, M5S 3G9, Canada
| | - Nika Shakiba
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, M5S 3G9, Canada
| | - Yujie Chen
- State Key Laboratory of Optoelectronic Materials and Technologies, School of Electronics and Information Technology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yanfeng Zhang
- State Key Laboratory of Optoelectronic Materials and Technologies, School of Electronics and Information Technology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Pengfei Tian
- Institute for Electric Light Sources, Fudan University, Shanghai, 200433, China
| | - Jastaranpreet Singh
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, M5S 3G9, Canada
| | - M Dean Chamberlain
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, M5S 3G9, Canada
| | - Monika Satkauskas
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada
| | - Andrew G Flood
- Department of Electrical and Computer Engineering, University of Toronto, Toronto, ON, M5S 3G4, Canada
| | - Nazir P Kherani
- Department of Electrical and Computer Engineering, University of Toronto, Toronto, ON, M5S 3G4, Canada
- Department of Materials Science and Engineering, University of Toronto, Toronto, ON, M5S 3E4, Canada
| | - Siyuan Yu
- State Key Laboratory of Optoelectronic Materials and Technologies, School of Electronics and Information Technology, Sun Yat-sen University, Guangzhou, 510275, China
- Photonics Group, Merchant Venturers School of Engineering, University of Bristol, Bristol, BS81UB, UK
| | - Peter W Zandstra
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, M5S 3G9, Canada
- Medicine by Design, University of Toronto, Toronto, ON, M5S 3G9, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Aaron R Wheeler
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, M5S 3G9, Canada
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105
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Ostrofet E, Papini FS, Dulin D. Correction-free force calibration for magnetic tweezers experiments. Sci Rep 2018; 8:15920. [PMID: 30374099 PMCID: PMC6206022 DOI: 10.1038/s41598-018-34360-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 10/12/2018] [Indexed: 11/09/2022] Open
Abstract
Magnetic tweezers are a powerful technique to perform high-throughput and high-resolution force spectroscopy experiments at the single-molecule level. The camera-based detection of magnetic tweezers enables the observation of hundreds of magnetic beads in parallel, and therefore the characterization of the mechanochemical behavior of hundreds of nucleic acids and enzymes. However, magnetic tweezers experiments require an accurate force calibration to extract quantitative data, which is limited to low forces if the deleterious effect of the finite camera open shutter time (τsh) is not corrected. Here, we provide a simple method to perform correction-free force calibration for high-throughput magnetic tweezers at low image acquisition frequency (fac). By significantly reducing τsh to at least 4-fold the characteristic times of the tethered magnetic bead, we accurately evaluated the variance of the magnetic bead position along the axis parallel to the magnetic field, estimating the force with a relative error of ~10% (standard deviation), being only limited by the bead-to-bead difference. We calibrated several magnets - magnetic beads configurations, covering a force range from ~50 fN to ~60 pN. In addition, for the presented configurations, we provide a table with the mathematical expressions that describe the force as a function of the magnets position.
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Affiliation(s)
- Eugen Ostrofet
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich Alexander University Erlangen-Nürnberg (FAU), Hartmannstr. 14, 91052, Erlangen, Germany
| | - Flávia Stal Papini
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich Alexander University Erlangen-Nürnberg (FAU), Hartmannstr. 14, 91052, Erlangen, Germany
| | - David Dulin
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich Alexander University Erlangen-Nürnberg (FAU), Hartmannstr. 14, 91052, Erlangen, Germany.
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106
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Ghosh S, Chatterjee A, Bhattacharya S. Accelerated Construction of Kinetic Network Model of Biomolecules Using Steered Molecular Dynamics. J Chem Theory Comput 2018; 14:5393-5405. [PMID: 30212629 DOI: 10.1021/acs.jctc.8b00398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new class of rare event acceleration techniques based on steered molecular dynamics (SMD) simulations is introduced. A stretching force applied on a biomolecule causes it to access large end-to-end distances. Under these conditions the biomolecule undergoes rapid conformational changes that are rare at zero-force conditions. A theory describing kinetics of a biomolecule at various stretching forces is presented. Using the theory, a master-Markov state model (master-MSM) is constructed from rates frequently accessed over a small range of force conditions. The master-MSM is shown to be applicable over a wide range of force conditions. We demonstrate application of the theory to three different biomolecular systems, namely, deca-alanine, TBA (thrombin binding aptamer), and a RNA hairpin. The master-MSM is used to estimate the kinetics at zero-force conditions, i.e., on the unbiased free-energy landscape, resulting inasmuch as 2-6 orders-of-magnitude speed-up over standard molecular dynamics.
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Affiliation(s)
- Susmita Ghosh
- Department of Physics , Indian Institute of Technology Guwahati , Guwahati , India 781039
| | - Abhijit Chatterjee
- Department of Chemical Engineering , Indian Institute of Technology Bombay , Mumbai , India 400076
| | - Swati Bhattacharya
- Department of Chemical Engineering , Indian Institute of Technology Bombay , Mumbai , India 400076
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107
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Zemánek J, Michálek T, Hurák Z. Phase-shift feedback control for dielectrophoretic micromanipulation. LAB ON A CHIP 2018; 18:1793-1801. [PMID: 29796529 DOI: 10.1039/c8lc00113h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In this paper, we present a novel approach to noncontact micromanipulation by controlled dielectrophoresis (DEP). To steer micro-objects in the desired way, the solutions reported in the literature use either DEP cages or amplitude modulation of the voltages applied to the electrodes. In contrast, we modulate the phases, that is, we control the phase shifts of the voltages applied to the electrodes, which simplifies the hardware implementation and extends the set of feasible forces. Furthermore, we introduce an innovative micro-electrode array layout, composed of four sectors with parallel (colinear) electrodes, which is capable of inducing an arbitrary movement in the manipulation area and is easy to fabricate using just an affordable one-layer technology. We then propose a closed-loop cascade control strategy based on real-time numerical optimization and deploy it to our experimental set-up. Numerical simulations and laboratory experiments demonstrate the manipulation capabilities such as positioning and steering of one or several microscopic objects (microspheres with a diameter of 50 μm) and even bringing two objects together and then separating them again. The results from simulations and experiments are compared and the positioning accuracy is evaluated in the whole manipulation area. The error in position is 8 μm in the worst case, which corresponds to 16% of the microsphere size or 0.7% of the manipulation range.
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Affiliation(s)
- Jiří Zemánek
- Department of Control Engineering, Faculty of Electrical Engineering, Czech Technical University in Prague, Karlovo Namesti 13, 121 35, Prague, Czech Republic.
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108
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King G, Biebricher AS, Heller I, Peterman EJG, Wuite GJL. Quantifying Local Molecular Tension Using Intercalated DNA Fluorescence. NANO LETTERS 2018; 18:2274-2281. [PMID: 29473755 PMCID: PMC6023266 DOI: 10.1021/acs.nanolett.7b04842] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 02/14/2018] [Indexed: 05/25/2023]
Abstract
The ability to measure mechanics and forces in biological nanostructures, such as DNA, proteins and cells, is of great importance as a means to analyze biomolecular systems. However, current force detection methods often require specialized instrumentation. Here, we present a novel and versatile method to quantify tension in molecular systems locally and in real time, using intercalated DNA fluorescence. This approach can report forces over a range of at least ∼0.5-65 pN with a resolution of 1-3 pN, using commercially available intercalating dyes and a general-purpose fluorescence microscope. We demonstrate that the method can be easily implemented to report double-stranded (ds)DNA tension in any single-molecule assay that is compatible with fluorescence microscopy. This is particularly useful for multiplexed techniques, where measuring applied force in parallel is technically challenging. Moreover, tension measurements based on local dye binding offer the unique opportunity to determine how an applied force is distributed locally within biomolecular structures. Exploiting this, we apply our method to quantify the position-dependent force profile along the length of flow-stretched DNA and reveal that stretched and entwined DNA molecules-mimicking catenated DNA structures in vivo-display transient DNA-DNA interactions. The method reported here has obvious and broad applications for the study of DNA and DNA-protein interactions. Additionally, we propose that it could be employed to measure forces in any system to which dsDNA can be tethered, for applications including protein unfolding, chromosome mechanics, cell motility, and DNA nanomachines.
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109
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Min D, Jefferson RE, Qi Y, Wang JY, Arbing MA, Im W, Bowie JU. Unfolding of a ClC chloride transporter retains memory of its evolutionary history. Nat Chem Biol 2018; 14:489-496. [PMID: 29581582 PMCID: PMC6038805 DOI: 10.1038/s41589-018-0025-4] [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: 09/13/2017] [Accepted: 02/12/2018] [Indexed: 11/12/2022]
Abstract
ClC chloride channels and transporters are important for chloride homeostasis in species from bacteria to human. Mutations in ClC proteins cause genetically inherited diseases, some of which are likely to have folding defects. The ClC proteins present a challenging and unusual biological folding problem because they are large membrane proteins possessing a complex architecture with many re-entrant helices that go only part way through membrane and loop back out. Here we were able to examine the unfolding of the E. coli ClC transporter, ClC-ec1, using single-molecule forced unfolding methods. We find that the protein can be separated into two stable halves that unfold independently. The independence of the two domains is consistent with an evolutionary model in which the two halves arose from independent folding subunits that later fused together. Maintaining smaller folding domains of lesser complexity within large membrane proteins may be an advantageous strategy to avoid misfolding traps.
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Affiliation(s)
- Duyoung Min
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.,UCLA-DOE and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Robert E Jefferson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.,UCLA-DOE and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yifei Qi
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Jing Yang Wang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.,UCLA-DOE and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Mark A Arbing
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.,UCLA-DOE and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Wonpil Im
- Departments of Biological Sciences and Bioengineering, Lehigh University, Bethlehem, PA, USA
| | - James U Bowie
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA. .,UCLA-DOE and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA.
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110
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Seol Y, Neuman KC. Combined Magnetic Tweezers and Micro-mirror Total Internal Reflection Fluorescence Microscope for Single-Molecule Manipulation and Visualization. Methods Mol Biol 2018; 1665:297-316. [PMID: 28940076 PMCID: PMC5672814 DOI: 10.1007/978-1-4939-7271-5_16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Magnetic tweezers is a versatile yet simple single-molecule manipulation technique that has been used to study a broad range of nucleic acids and nucleic acid-based molecular motors. In this chapter, we combine micro-mirror-based total internal reflection microscopy with a magnetic tweezers instrument, permitting simultaneous single-molecule visualization and mechanical manipulation. We provide a simple method to calibrate the evanescent wave penetration depth via supercoiling of DNA with a fluorescent nanodiamond-labeled magnetic bead and a complementary method employing a surface-immobilized fluorescent nanodiamond.
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Affiliation(s)
- Yeonee Seol
- Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Building 50, Room 3517, 50 South Drive, Bethesda, 20892, MD, USA
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Building 50, Room 3517, 50 South Drive, Bethesda, 20892, MD, USA.
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111
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van Mameren J, Wuite GJL, Heller I. Introduction to Optical Tweezers: Background, System Designs, and Commercial Solutions. Methods Mol Biol 2018; 1665:3-23. [PMID: 28940061 DOI: 10.1007/978-1-4939-7271-5_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Optical tweezers are a means to manipulate objects with light. With the technique, microscopically small objects can be held and steered, while forces on the trapped objects can be accurately measured and exerted. Optical tweezers can typically obtain a nanometer spatial resolution, a picoNewton force resolution, and a millisecond time resolution, which makes them excellently suited to study biological processes from the single-cell down to the single-molecule level. In this chapter, we will provide an introduction on the use of optical tweezers in single-molecule approaches. We will introduce the basic principles and methodology involved in optical trapping, force calibration, and force measurements. Next we describe the components of an optical tweezers setup and their experimental relevance in single-molecule approaches. Finally, we provide a concise overview of commercial optical tweezers systems. Commercial systems are becoming increasingly available and provide access to single-molecule optical tweezers experiments without the need for a thorough background in physics.
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Affiliation(s)
- Joost van Mameren
- Institute of Physics, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Gijs J L Wuite
- LaserLaB and Department of Physics and Astronomy, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands.
| | - Iddo Heller
- LaserLaB and Department of Physics and Astronomy, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
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112
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Xu Y. Nanofluidics: A New Arena for Materials Science. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:1702419. [PMID: 29094401 DOI: 10.1002/adma.201702419] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 07/04/2017] [Indexed: 06/07/2023]
Abstract
A significant growth of research in nanofluidics is achieved over the past decade, but the field is still facing considerable challenges toward the transition from the current physics-centered stage to the next application-oriented stage. Many of these challenges are associated with materials science, so the field of nanofluidics offers great opportunities for materials scientists to exploit. In addition, the use of unusual effects and ultrasmall confined spaces of well-defined nanofluidic environments would offer new mechanisms and technologies to manipulate nanoscale objects as well as to synthesize novel nanomaterials in the liquid phase. Therefore, nanofluidics will be a new arena for materials science. In the past few years, burgeoning progress has been made toward this trend, as overviewed in this article, including materials and methods for fabricating nanofluidic devices, nanofluidics with functionalized surfaces and functional material components, as well as nanofluidics for manipulating nanoscale materials and fabricating new nanomaterials. Many critical challenges as well as fantastic opportunities in this arena lie ahead. Some of those, which are of particular interest, are also discussed.
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Affiliation(s)
- Yan Xu
- Department of Chemical Engineering, Graduate School of Engineering, Osaka Prefecture University, 1-2, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8570, Japan
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113
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Zhang X, Song C, Ma G, Wei W. Mechanical determination of particle–cell interactions and the associated biomedical applications. J Mater Chem B 2018; 6:7129-7143. [DOI: 10.1039/c8tb01590b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mechanical determination of particle–cell interactions and the associated biomedical applications.
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Affiliation(s)
- Xiao Zhang
- State Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- P. R. China
| | - Cui Song
- State Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- P. R. China
| | - Guanghui Ma
- State Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- P. R. China
| | - Wei Wei
- State Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- P. R. China
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114
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Johnson KC, Clemmens E, Mahmoud H, Kirkpatrick R, Vizcarra JC, Thomas WE. A multiplexed magnetic tweezer with precision particle tracking and bi-directional force control. J Biol Eng 2017; 11:47. [PMID: 29213305 PMCID: PMC5712100 DOI: 10.1186/s13036-017-0091-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 11/22/2017] [Indexed: 11/17/2022] Open
Abstract
Background In the past two decades, methods have been developed to measure the mechanical properties of single biomolecules. One of these methods, Magnetic tweezers, is amenable to aquisition of data on many single molecules simultaneously, but to take full advantage of this "multiplexing" ability, it is necessary to simultaneously incorprorate many capabilities that ahve been only demonstrated separately. Methods Our custom built magnetic tweezer combines high multiplexing, precision bead tracking, and bi-directional force control into a flexible and stable platform for examining single molecule behavior. This was accomplished using electromagnets, which provide high temporal control of force while achieving force levels similar to permanent magnets via large paramagnetic beads. Results Here we describe the instrument and its ability to apply 2–260 pN of force on up to 120 beads simultaneously, with a maximum spatial precision of 12 nm using a variety of bead sizes and experimental techniques. We also demonstrate a novel method for increasing the precision of force estimations on heterogeneous paramagnetic beads using a combination of density separation and bi-directional force correlation which reduces the coefficient of variation of force from 27% to 6%. We then use the instrument to examine the force dependence of uncoiling and recoiling velocity of type 1 fimbriae from Eschericia coli (E. coli) bacteria, and see similar results to previous studies. Conclusion This platform provides a simple, effective, and flexible method for efficiently gathering single molecule force spectroscopy measurements.
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Affiliation(s)
- Keith C Johnson
- Mechanical Engineering, University of Washington, Seattle, USA
| | | | - Hani Mahmoud
- Bioengineering, University of Washington, Seattle, USA
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115
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Hermans N, Huisman JJ, Brouwer TB, Schächner C, van Heusden GPH, Griesenbeck J, van Noort J. Toehold-enhanced LNA probes for selective pull down and single-molecule analysis of native chromatin. Sci Rep 2017; 7:16721. [PMID: 29196662 PMCID: PMC5711847 DOI: 10.1038/s41598-017-16864-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 11/19/2017] [Indexed: 12/18/2022] Open
Abstract
The organization of DNA into chromatin is thought to regulate gene expression in eukaryotes. To study its structure in vitro, there is a need for techniques that can isolate specific chromosomal loci of natively assembled chromatin. Current purification methods often involve chemical cross-linking to preserve the chromatin composition. However, such cross-linking may affect the native structure. It also impedes single molecule force spectroscopy experiments, which have been instrumental to probe chromatin folding. Here we present a method for the incorporation of affinity tags, such as biotin, into native nucleoprotein fragments based on their DNA sequence, and subsequent single molecule analysis by magnetic tweezers. DNA oligos with several Locked Nucleic Acid (LNA) nucleotides are shown to selectively bind to target DNA at room temperature, mediated by a toehold end in the target, allowing for selective purification of DNA fragments. The stability of the probe-target hybrid is sufficient to withstand over 65 pN of force. We employ these probes to obtain force-extension curves of native chromatin fragments of the 18S ribosomal DNA from the yeast Saccharomyces cerevisiae. These experiments yield valuable insights in the heterogeneity in structure and composition of natively assembled chromatin at the single-molecule level.
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Affiliation(s)
- Nicolaas Hermans
- Leiden Institute of Physics, Huygens-Kamerlingh Onnes Laboratory, Niels Bohrweg, 2 2333 CA, Leiden, The Netherlands
| | - Juriën Jori Huisman
- Leiden Institute of Physics, Huygens-Kamerlingh Onnes Laboratory, Niels Bohrweg, 2 2333 CA, Leiden, The Netherlands
| | - Thomas Bauke Brouwer
- Leiden Institute of Physics, Huygens-Kamerlingh Onnes Laboratory, Niels Bohrweg, 2 2333 CA, Leiden, The Netherlands
| | - Christopher Schächner
- Universität Regensburg, Biochemie-Zentrum Regensburg (BZR), Institut für Biochemie, Genetik und Mikrobiologie, Lehrstuhl Biochemie III, 93053, Regensburg, Germany
| | - G Paul H van Heusden
- Department of Molecular and Developmental Genetics, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Joachim Griesenbeck
- Universität Regensburg, Biochemie-Zentrum Regensburg (BZR), Institut für Biochemie, Genetik und Mikrobiologie, Lehrstuhl Biochemie III, 93053, Regensburg, Germany
| | - John van Noort
- Leiden Institute of Physics, Huygens-Kamerlingh Onnes Laboratory, Niels Bohrweg, 2 2333 CA, Leiden, The Netherlands.
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116
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Eeftens J, Dekker C. Catching DNA with hoops—biophysical approaches to clarify the mechanism of SMC proteins. Nat Struct Mol Biol 2017; 24:1012-1020. [DOI: 10.1038/nsmb.3507] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/18/2017] [Indexed: 12/11/2022]
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117
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Abstract
The active transport of cargo molecules within cells is essential for life. Developing synthetic strategies for cargo control in living or inanimate thermal systems could lead to powerful tools to manipulate chemical gradients at the microscale and thus drive processes out of equilibrium to realize work. Here we demonstrate a colloidal analog of the complex biological shuttles responsible for molecular trafficking in cells. Our colloidal shuttles consist of magneto-dielectric particles that are loaded with cargo particles or living cells through size-selective dielectrophoretic trapping using electrical fields. The loaded colloidal shuttle can be transported with magnetic field gradients before cargo is released at the target location by switching off the electrical field. Such spatiotemporal control over the distribution of chemically active cargo in a reversible fashion can be potentially exploited for fundamental biological research or for the development of novel technologies for advanced cell culturing, drug discovery and medical diagnosis. Biological shuttles efficiently traffic molecules in cells, inspiring the development of synthetic analogs. Here, the authors create colloidal shuttles that collect, transport, and deliver cargo particles and cells under the control of external electrical and magnetic fields.
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118
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Zhao X, Zeng X, Lu C, Yan J. Studying the mechanical responses of proteins using magnetic tweezers. NANOTECHNOLOGY 2017; 28:414002. [PMID: 28766506 DOI: 10.1088/1361-6528/aa837e] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The mechanical stability of proteins has been extensively studied using AFM as a single-molecule force spectroscopy method. While this has led to many important results, these studies have been mainly limited to fast unfolding at a high-force regime due to the rapid mechanical drift in most AFM stretching experiments. Therefore, there is a gap between the knowledge obtained at a high-force regime and the mechanical properties of proteins at a lower force regime which is often more physiologically relevant. Recent studies have demonstrated that this gap can be addressed by stretching single protein molecules using magnetic tweezers, due to the excellent mechanical stability this technology offers. Here we review magnetic tweezers technology and its current application in studies of the force-dependent stability and interactions of proteins.
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Affiliation(s)
- Xiaodan Zhao
- Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, 117411, Singapore
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119
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Vilhena JG, Gnecco E, Pawlak R, Moreno-Herrero F, Meyer E, Pérez R. Stick-Slip Motion of ssDNA over Graphene. J Phys Chem B 2017; 122:840-846. [PMID: 28945092 DOI: 10.1021/acs.jpcb.7b06952] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We have performed molecular dynamics simulations of nanomanipulation experiments on short single-stranded DNA chains elastically driven on a graphene surface. After a brief transient, reproducible stick-slip cycles are observed on chains made by 10 units of thymine, cytosine, adenine, and guanine. The cycles have the periodicity of the graphene substrate, and take place via an intermediate stage, appearing as a dip in the sawtooth variations of lateral force recorded while the chains are manipulated. Guanine presents remarkable differences from the other bases, since a lower number of nucleotides are prone to stick to the substrate in this case. Nevertheless, the magnitudes of static friction and lateral stiffness are similar for all chains (30 pN and 0.7 N/m per adsorbed nucleotide respectively).
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Affiliation(s)
- J G Vilhena
- Department of Macromolecular Structures, Centro Nacional de Biotecnologa, Consejo Superior de Investigaciones Cientficas , 28049 Cantoblanco, Madrid, Spain.,Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid , E-28049 Madrid, Spain
| | - Enrico Gnecco
- Otto Schott Institute of Materials Research, Friedrich Schiller University Jena , D-07742 Jena, Germany
| | - Rémy Pawlak
- Department of Physics, University of Basel , Klingelbergstrasse 82, 4056 Basel, Switzerland
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnologa, Consejo Superior de Investigaciones Cientficas , 28049 Cantoblanco, Madrid, Spain
| | - Ernst Meyer
- Department of Physics, University of Basel , Klingelbergstrasse 82, 4056 Basel, Switzerland
| | - Rubén Pérez
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid , E-28049 Madrid, Spain.,Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid , E-28049 Madrid, Spain
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120
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Pirrotta A, Solomon GC, Franco I, Troisi A. Excitonic Coupling Modulated by Mechanical Stimuli. J Phys Chem Lett 2017; 8:4326-4332. [PMID: 28837767 DOI: 10.1021/acs.jpclett.7b01828] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Understanding energy transfer is of vital importance in a diverse range of applications from biological systems to photovoltaics. The ability to tune excitonic coupling in any of these systems, however, is generally limited. In this work, we have simulated a new class of single-molecule spectroscopy in which force microscopy is used to control the excitonic coupling between chromophores. Here we demonstrate that the excitonic coupling can be controlled by mechanical manipulation of the molecule (perylenediimide dimers and terrylenediimide-perylenediimide heterodimers) and can be tuned over a broad range of values (0.02-0.15 eV) that correspond to different regimes of exciton dynamics going from the folded to the elongated structure of the dimer. In all of the systems considered here, the switching from high to low coupling takes place simultaneously with the mechanical deformation detected by a strong increase and subsequent decay of the force. These simulations suggest that single-molecule force spectroscopy can be used to understand and eventually aid the design of excitonic devices.
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Affiliation(s)
- Alessandro Pirrotta
- Nano-Science Center and Department of Chemistry, University of Copenhagen , 2100 Copenhagen Ø, Denmark
| | - Gemma C Solomon
- Nano-Science Center and Department of Chemistry, University of Copenhagen , 2100 Copenhagen Ø, Denmark
| | - Ignacio Franco
- Department of Chemistry, University of Rochester , Rochester, New York 14627-0216, United States
| | - Alessandro Troisi
- Department of Chemistry, University of Liverpool , L69 7DZ Liverpool, United Kingdom
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121
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You H, Le S, Chen H, Qin L, Yan J. Single-molecule Manipulation of G-quadruplexes by Magnetic Tweezers. J Vis Exp 2017. [PMID: 28994776 DOI: 10.3791/56328] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Non-canonical nucleic acid secondary structure G-quadruplexes (G4) are involved in diverse cellular processes, such as DNA replication, transcription, RNA processing, and telomere elongation. During these processes, various proteins bind and resolve G4 structures to perform their function. As the function of G4 often depends on the stability of its folded structure, it is important to investigate how G4 binding proteins regulate the stability of G4. This work presents a method to manipulate single G4 molecules using magnetic tweezers, which enables studies of the regulation of G4 binding proteins on a single G4 molecule in real time. In general, this method is suitable for a wide scope of applications in studies for proteins/ligands interactions and regulations on various DNA or RNA secondary structures.
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Affiliation(s)
- Huijuan You
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology;
| | - Shimin Le
- Mechanobiology Institute, National University of Singapore; Department of Physics, National University of Singapore
| | - Hu Chen
- Mechanobiology Institute, National University of Singapore; Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University
| | - Linyan Qin
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore; Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University; Center for Bioimaging Sciences, National University of Singapore;
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122
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Lin L, Peng X, Mao Z, Wei X, Xie C, Zheng Y. Interfacial-entropy-driven thermophoretic tweezers. LAB ON A CHIP 2017; 17:3061-3070. [PMID: 28805878 DOI: 10.1039/c7lc00432j] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Directed migration of particles and molecules in a temperature gradient field, which is known as thermophoresis or the Soret effect, is of fundamental importance for mass transfer in colloid science and life sciences. However, thermophoretic tweezers that enable versatile particle manipulation have remained elusive due to the complex underlying physical forces in thermophoresis and the lack of general thermophilic particles above room temperature. Herein, we exploit entropic response and permittivity gradient at the particle-solvent interface to optically generated thermal gradient to achieve the thermophoretic trapping and dynamic manipulation of charged particles over an optothermal-responsive substrate. Engineering the interfacial properties, i.e., the surface charge of particles and the ionic strength of the solvent, further enhances the trapping efficiency. Through the rational design of optothermal potential profiles and substrate geometries, we have achieved various tweezing functionalities, including particle assembly, alignment, rotation and guiding, as well as precise transport of single nanoparticles. Based on the general concept of entropic change of polarized molecules structured at the particle-solvent interlayer, the thermophoretic tweezers are applicable to various types of particles, biological cells, and molecules and a wide range of solvents.
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Affiliation(s)
- Linhan Lin
- Department of Mechanical Engineering, The University of Texas at Austin, Austin, TX 78712, USA.
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123
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124
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Wu M, Yadav R, Pal N, Lu HP. Manipulating motions of targeted single cells in solution by an integrated double-ring magnetic tweezers imaging microscope. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2017; 88:073703. [PMID: 28764529 DOI: 10.1063/1.4995362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Controlling and manipulating living cell motions in solution hold a high promise in developing new biotechnology and biological science. Here, we developed a magnetic tweezers device that employs a combination of two permanent magnets in up-down double-ring configuration axially fitting with a microscopic objective, allowing a picoNewton (pN) bidirectional force and motion control on the sample beyond a single upward pulling direction. The experimental force calibration and magnetic field simulation using finite element method magnetics demonstrate that the designed magnetic tweezers covers a linear-combined pN force with positive-negative polarization changes in a tenability of sub-pN scale, which can be utilized to further achieve motion manipulation by shifting the force balance. We demonstrate an application of the up-down double-ring magnetic tweezers for single cell manipulation, showing that the cells with internalized paramagnetic beads can be selectively picked up and guided in a controlled fine motion.
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Affiliation(s)
- Meiling Wu
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, USA
| | - Rajeev Yadav
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, USA
| | - Nibedita Pal
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, USA
| | - H Peter Lu
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, USA
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125
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Understanding the mechanical response of double-stranded DNA and RNA under constant stretching forces using all-atom molecular dynamics. Proc Natl Acad Sci U S A 2017. [PMID: 28634300 DOI: 10.1073/pnas.1705642114] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Multiple biological processes involve the stretching of nucleic acids (NAs). Stretching forces induce local changes in the molecule structure, inhibiting or promoting the binding of proteins, which ultimately affects their functionality. Understanding how a force induces changes in the structure of NAs at the atomic level is a challenge. Here, we use all-atom, microsecond-long molecular dynamics to simulate the structure of dsDNA and dsRNA subjected to stretching forces up to 20 pN. We determine all of the elastic constants of dsDNA and dsRNA and provide an explanation for three striking differences in the mechanical response of these two molecules: the threefold softer stretching constant obtained for dsRNA, the opposite twist-stretch coupling, and its nontrivial force dependence. The lower dsRNA stretching resistance is linked to its more open structure, whereas the opposite twist-stretch coupling of both molecules is due to the very different evolution of molecules' interstrand distance with the stretching force. A reduction of this distance leads to overwinding in dsDNA. In contrast, dsRNA is not able to reduce its interstrand distance and can only elongate by unwinding. Interstrand distance is directly correlated with the slide base-pair parameter and its different behavior in dsDNA and dsRNA traced down to changes in the sugar pucker angle of these NAs.
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126
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Zahn C, Keller S, Toro-Nahuelpan M, Dorscht P, Gross W, Laumann M, Gekle S, Zimmermann W, Schüler D, Kress H. Measurement of the magnetic moment of single Magnetospirillum gryphiswaldense cells by magnetic tweezers. Sci Rep 2017; 7:3558. [PMID: 28620230 PMCID: PMC5472611 DOI: 10.1038/s41598-017-03756-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 05/03/2017] [Indexed: 11/26/2022] Open
Abstract
Magnetospirillum gryphiswaldense is a helix-shaped magnetotactic bacterium that synthesizes iron-oxide nanocrystals, which allow navigation along the geomagnetic field. The bacterium has already been thoroughly investigated at the molecular and cellular levels. However, the fundamental physical property enabling it to perform magnetotaxis, its magnetic moment, remains to be elucidated at the single cell level. We present a method based on magnetic tweezers; in combination with Stokesian dynamics and Boundary Integral Method calculations, this method allows the simultaneous measurement of the magnetic moments of multiple single bacteria. The method is demonstrated by quantifying the distribution of the individual magnetic moments of several hundred cells of M. gryphiswaldense. In contrast to other techniques for measuring the average magnetic moment of bacterial populations, our method accounts for the size and the helical shape of each individual cell. In addition, we determined the distribution of the saturation magnetic moments of the bacteria from electron microscopy data. Our results are in agreement with the known relative magnetization behavior of the bacteria. Our method can be combined with single cell imaging techniques and thus can address novel questions about the functions of components of the molecular magnetosome biosynthesis machinery and their correlation with the resulting magnetic moment.
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Affiliation(s)
- C Zahn
- Biological Physics, Department of Physics, University of Bayreuth, Bayreuth, Germany
| | - S Keller
- Biological Physics, Department of Physics, University of Bayreuth, Bayreuth, Germany
| | - M Toro-Nahuelpan
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Planegg-Martinsried, Germany
| | - P Dorscht
- Biological Physics, Department of Physics, University of Bayreuth, Bayreuth, Germany
| | - W Gross
- Biological Physics, Department of Physics, University of Bayreuth, Bayreuth, Germany
| | - M Laumann
- Theoretical Physics I, Department of Physics, University of Bayreuth, Bayreuth, Germany
| | - S Gekle
- Biofluid Simulation and Modeling, Department of Physics, University of Bayreuth, Bayreuth, Germany
| | - W Zimmermann
- Theoretical Physics I, Department of Physics, University of Bayreuth, Bayreuth, Germany
| | - D Schüler
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany
| | - H Kress
- Biological Physics, Department of Physics, University of Bayreuth, Bayreuth, Germany.
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127
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Timonen JVI, Grzybowski BA. Tweezing of Magnetic and Non-Magnetic Objects with Magnetic Fields. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2017; 29:1603516. [PMID: 28198579 DOI: 10.1002/adma.201603516] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 10/06/2016] [Indexed: 06/06/2023]
Abstract
Although strong magnetic fields cannot be conveniently "focused" like light, modern microfabrication techniques enable preparation of microstructures with which the field gradients - and resulting magnetic forces - can be localized to very small dimensions. This ability provides the foundation for magnetic tweezers which in their classical variant can address magnetic targets. More recently, the so-called negative magnetophoretic tweezers have also been developed which enable trapping and manipulations of completely nonmagnetic particles provided that they are suspended in a high-magnetic-susceptibility liquid. These two modes of magnetic tweezing are complimentary techniques tailorable for different types of applications. This Progress Report provides the theoretical basis for both modalities and illustrates their specific uses ranging from the manipulation of colloids in 2D and 3D, to trapping of living cells, control of cell function, experiments with single molecules, and more.
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Affiliation(s)
- Jaakko V I Timonen
- Department of Applied Physics, Aalto University School of Science, Espoo, 02150, Finland
| | - Bartosz A Grzybowski
- Center for Soft and Living Matter, Ulsan National Institute of Science and Technology, Ulsan, 44919, South Korea
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, 44919, South Korea
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128
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Jiang C, Kaul N, Campbell J, Meyhofer E. A novel dual-color bifocal imaging system for single-molecule studies. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2017; 88:053705. [PMID: 28571404 DOI: 10.1063/1.4983648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In this paper, we report the design and implementation of a dual-color bifocal imaging (DBI) system that is capable of acquiring two spectrally distinct, spatially registered images of objects located in either same or two distinct focal planes. We achieve this by separating an image into two channels with distinct chromatic properties and independently focusing both images onto a single CCD camera. The two channels in our device are registered with subpixel accuracy, and long-term stability of the registered images with nanometer-precision was accomplished by reducing the drift of the images to ∼5 nm. We demonstrate the capabilities of our DBI system by imaging biomolecules labeled with spectrally distinct dyes and micro- and nano-sized spheres located in different focal planes.
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Affiliation(s)
- Chang Jiang
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Neha Kaul
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Jenna Campbell
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Edgar Meyhofer
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
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129
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Single-stranded nucleic acid elasticity arises from internal electrostatic tension. Proc Natl Acad Sci U S A 2017; 114:5095-5100. [PMID: 28461493 DOI: 10.1073/pnas.1701132114] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Understanding of the conformational ensemble of flexible polyelectrolytes, such as single-stranded nucleic acids (ssNAs), is complicated by the interplay of chain backbone entropy and salt-dependent electrostatic repulsions. Molecular elasticity measurements are sensitive probes of the statistical conformation of polymers and have elucidated ssNA conformation at low force, where electrostatic repulsion leads to a strong excluded volume effect, and at high force, where details of the backbone structure become important. Here, we report measurements of ssDNA and ssRNA elasticity in the intermediate-force regime, corresponding to 5- to 100-pN forces and 50-85% extension. These data are explained by a modified wormlike chain model incorporating an internal electrostatic tension. Fits to the elastic data show that the internal tension decreases with salt, from [Formula: see text]5 pN under 5 mM ionic strength to near zero at 1 M. This decrease is quantitatively described by an analytical model of electrostatic screening that ascribes to the polymer an effective charge density that is independent of force and salt. Our results thus connect microscopic chain physics to elasticity and structure at intermediate scales and provide a framework for understanding flexible polyelectrolyte elasticity across a broad range of relative extensions.
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130
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Conteduca D, Dell'Olio F, Krauss TF, Ciminelli C. Photonic and Plasmonic Nanotweezing of Nano- and Microscale Particles. APPLIED SPECTROSCOPY 2017; 71:367-390. [PMID: 28287314 DOI: 10.1177/0003702816684839] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The ability to manipulate and sense biological molecules is important in many life science domains, such as single-molecule biophysics, the development of new drugs and cancer detection. Although the manipulation of biological matter at the nanoscale continues to be a challenge, several types of nanotweezers based on different technologies have recently been demonstrated to address this challenge. In particular, photonic and plasmonic nanotweezers are attracting a strong research effort especially because they are efficient and stable, they offer fast response time, and avoid any direct physical contact with the target object to be trapped, thus preventing its disruption or damage. In this paper, we critically review photonic and plasmonic resonant technologies for biomolecule trapping, manipulation, and sensing at the nanoscale, with a special emphasis on hybrid photonic/plasmonic nanodevices allowing a very strong light-matter interaction. The state-of-the-art of competing technologies, e.g., electronic, magnetic, acoustic and carbon nanotube-based nanotweezers, and a description of their applications are also included.
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131
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Ghosh S, Chatterjee A, Bhattacharya S. Time-Dependent Markov State Models for Single Molecule Force Spectroscopy. J Chem Theory Comput 2017; 13:957-962. [DOI: 10.1021/acs.jctc.6b01094] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Susmita Ghosh
- Department
of Physics, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Abhijit Chatterjee
- Department
of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Swati Bhattacharya
- Department
of Physics, Indian Institute of Technology Guwahati, Guwahati 781039, India
- Department
of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai 400076, India
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132
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Silva EF, Bazoni RF, Ramos EB, Rocha MS. DNA-doxorubicin interaction: New insights and peculiarities. Biopolymers 2017; 107. [PMID: 27718222 DOI: 10.1002/bip.22998] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 09/25/2016] [Accepted: 10/05/2016] [Indexed: 12/18/2022]
Abstract
We have investigated the interaction of the DNA molecule with the anticancer drug doxorubicin (doxo) by using three different experimental techniques: single molecule stretching, single molecule imaging, and dynamic light scattering. Such techniques allowed us to get new insights on the mechanical behavior of the DNA-doxo complexes as well as on the physical chemistry of the interaction. First, the contour length data obtained from single molecule stretching were used to extract the physicochemical parameters of the DNA-doxo interaction under different buffer conditions. This analysis has proven that the physical chemistry of such interaction can be modulated by changing the ionic strength of the surrounding buffer. In particular we have found that at low ionc strengths doxo interacts with DNA by simple intercalation (no aggregation) and/or by forming bound dimers. For high ionic strengths, otherwise, doxo-doxo self-association is enhanced, giving rise to the formation of bound doxo aggregates composed by 3 to 4 molecules along the double-helix. On the other hand, the results obtained for the persistence length of the DNA-doxo complexes is strongly force-dependent, presenting different behaviors when measured with stretching or non-stretching techniques.
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Affiliation(s)
- E F Silva
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - R F Bazoni
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - E B Ramos
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - M S Rocha
- Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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133
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Ryu JK, Jahn R, Yoon TY. Review: Progresses in understanding N-ethylmaleimide sensitive factor (NSF) mediated disassembly of SNARE complexes. Biopolymers 2017; 105:518-31. [PMID: 27062050 DOI: 10.1002/bip.22854] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/19/2016] [Accepted: 04/06/2016] [Indexed: 11/09/2022]
Abstract
N-ethylmaleimide sensitive factor (NSF) is a key protein of intracellular membrane traffic. NSF is a highly conserved protein belonging to the ATPases associated with other activities (AAA+ proteins). AAA+ share common domains and all transduce ATP hydrolysis into major conformational movements that are used to carry out conformational work on client proteins. Together with its cofactor SNAP, NSF is specialized on disassembling highly stable SNARE complexes that form after each membrane fusion event. Although essential for all eukaryotic cells, however, the details of this reaction have long been enigmatic. Recently, major progress has been made in both elucidating the structure of NSF/SNARE complexes and in understanding the reaction mechanism. Advances in both cryo EM and single molecule measurements suggest that NSF, together with its cofactor SNAP, imposes a tight grip on the SNARE complex. After ATP hydrolysis and phosphate release, it then builds up mechanical tension that is ultimately used to rip apart the SNAREs in a single burst. Because the AAA domains are extremely well-conserved, the molecular mechanism elucidated for NSF is presumably shared by many other AAA+ ATPases. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 518-531, 2016.
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Affiliation(s)
- Je-Kyung Ryu
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, CJ, 2628, the Netherlands
| | - Reinhard Jahn
- Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, 37077, Germany
| | - Tae-Young Yoon
- Center for Nanomedicine, Institute for Basic Science (IBS) and Y-IBS Institute, Yonsei University, Seoul, 03722, South Korea
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134
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Norregaard K, Metzler R, Ritter CM, Berg-Sørensen K, Oddershede LB. Manipulation and Motion of Organelles and Single Molecules in Living Cells. Chem Rev 2017; 117:4342-4375. [PMID: 28156096 DOI: 10.1021/acs.chemrev.6b00638] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The biomolecule is among the most important building blocks of biological systems, and a full understanding of its function forms the scaffold for describing the mechanisms of higher order structures as organelles and cells. Force is a fundamental regulatory mechanism of biomolecular interactions driving many cellular processes. The forces on a molecular scale are exactly in the range that can be manipulated and probed with single molecule force spectroscopy. The natural environment of a biomolecule is inside a living cell, hence, this is the most relevant environment for probing their function. In vivo studies are, however, challenged by the complexity of the cell. In this review, we start with presenting relevant theoretical tools for analyzing single molecule data obtained in intracellular environments followed by a description of state-of-the art visualization techniques. The most commonly used force spectroscopy techniques, namely optical tweezers, magnetic tweezers, and atomic force microscopy, are described in detail, and their strength and limitations related to in vivo experiments are discussed. Finally, recent exciting discoveries within the field of in vivo manipulation and dynamics of single molecule and organelles are reviewed.
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Affiliation(s)
- Kamilla Norregaard
- Cluster for Molecular Imaging, Department of Biomedical Science and Department of Clinical Physiology, Nuclear Medicine and PET, Rigshospitalet, University of Copenhagen , 2200 Copenhagen, Denmark
| | - Ralf Metzler
- Institute for Physics & Astronomy, University of Potsdam , 14476 Potsdam-Golm, Germany
| | - Christine M Ritter
- Niels Bohr Institute, University of Copenhagen , 2100 Copenhagen, Denmark
| | | | - Lene B Oddershede
- Niels Bohr Institute, University of Copenhagen , 2100 Copenhagen, Denmark
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135
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Srivastava N, Kay RR, Kabla AJ. Method to study cell migration under uniaxial compression. Mol Biol Cell 2017; 28:809-816. [PMID: 28122819 PMCID: PMC5349787 DOI: 10.1091/mbc.e16-08-0575] [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: 08/09/2016] [Revised: 12/06/2016] [Accepted: 01/17/2017] [Indexed: 12/23/2022] Open
Abstract
A method is described for imposing mechanical compression on individual cells while monitoring their morphology and migratory phenotype. A compression of the order of 500 Pa flattens the cells by up to 50% and triggers a transition in the mode of migration. This approach is convenient for studying mechanotransduction in confined environments. The chemical, physical, and mechanical properties of the extracellular environment have a strong effect on cell migration. Aspects such as pore size or stiffness of the matrix influence the selection of the mechanism used by cells to propel themselves, including by pseudopods or blebbing. How a cell perceives its environment and how such a cue triggers a change in behavior are largely unknown, but mechanics is likely to be involved. Because mechanical conditions are often controlled by modifying the composition of the environment, separating chemical and physical contributions is difficult and requires multiple controls. Here we propose a simple method to impose a mechanical compression on individual cells without altering the composition of the matrix. Live imaging during compression provides accurate information about the cell's morphology and migratory phenotype. Using Dictyostelium as a model, we observe that a compression of the order of 500 Pa flattens the cells under gel by up to 50%. This uniaxial compression directly triggers a transition in the mode of migration from primarily pseudopodial to bleb driven in <30 s. This novel device is therefore capable of influencing cell migration in real time and offers a convenient approach with which to systematically study mechanotransduction in confined environments.
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Affiliation(s)
- Nishit Srivastava
- Department of Engineering, University of Cambridge, Cambridge CB2 1PZ, United Kingdom
| | - Robert R Kay
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Alexandre J Kabla
- Department of Engineering, University of Cambridge, Cambridge CB2 1PZ, United Kingdom
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136
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Abstract
Microrheology provides a technique to probe the local viscoelastic properties and dynamics of soft materials at the microscopic level by observing the motion of tracer particles embedded within them. It is divided into passive and active microrheology according to the force exerted on the embedded particles. Particles are driven by thermal fluctuations in passive microrheology, and the linear viscoelasticity of samples can be obtained on the basis of the generalized Stokes-Einstein equation. In active microrheology, tracer particles are controlled by external forces, and measurements can be extended to the nonlinear regime. Microrheology techniques have many advantages such as the need for only small sample amounts and a wider measurable frequency range. In particular, microrheology is able to examine the spatial heterogeneity of samples at the microlevel, which is not possible using traditional rheology. Therefore, microrheology has considerable potential for studying the local mechanical properties and dynamics of soft matter, particularly complex fluids, including solutions, dispersions, and other colloidal systems. Food products such as emulsions, foams, or gels are complex fluids with multiple ingredients and phases. Their macroscopic properties, such as stability and texture, are closely related to the structure and mechanical properties at the microlevel. In this article, the basic principles and methods of microrheology are reviewed, and the latest developments and achievements of microrheology in the field of food science are presented.
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Affiliation(s)
- Nan Yang
- Glyn O. Phillips Hydrocolloid Research Centre, School of Food and Biological Engineering, and Hubei Collaborative Innovation Centre for Industrial Fermentation, Hubei University of Technology, Wuhan 430068, China;
| | - Ruihe Lv
- Glyn O. Phillips Hydrocolloid Research Centre, School of Food and Biological Engineering, and Hubei Collaborative Innovation Centre for Industrial Fermentation, Hubei University of Technology, Wuhan 430068, China;
| | - Junji Jia
- School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Katsuyoshi Nishinari
- Glyn O. Phillips Hydrocolloid Research Centre, School of Food and Biological Engineering, and Hubei Collaborative Innovation Centre for Industrial Fermentation, Hubei University of Technology, Wuhan 430068, China;
| | - Yapeng Fang
- Glyn O. Phillips Hydrocolloid Research Centre, School of Food and Biological Engineering, and Hubei Collaborative Innovation Centre for Industrial Fermentation, Hubei University of Technology, Wuhan 430068, China;
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137
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Frykholm K, Nyberg LK, Westerlund F. Exploring DNA–protein interactions on the single DNA molecule level using nanofluidic tools. Integr Biol (Camb) 2017; 9:650-661. [DOI: 10.1039/c7ib00085e] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
This review highlights the use of nanofluidic channels for studying DNA–protein interactions on the single DNA molecule level.
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Affiliation(s)
- Karolin Frykholm
- Department of Biology and Biological Engineering
- Chalmers University of Technology
- Gothenburg
- Sweden
| | - Lena K. Nyberg
- Department of Biology and Biological Engineering
- Chalmers University of Technology
- Gothenburg
- Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering
- Chalmers University of Technology
- Gothenburg
- Sweden
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138
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Pud S, Chao SH, Belkin M, Verschueren D, Huijben T, van Engelenburg C, Dekker C, Aksimentiev A. Mechanical Trapping of DNA in a Double-Nanopore System. NANO LETTERS 2016; 16:8021-8028. [PMID: 27960493 PMCID: PMC5523128 DOI: 10.1021/acs.nanolett.6b04642] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Nanopores have become ubiquitous components of systems for single-molecule manipulation and detection, in particular DNA sequencing where electric field driven translocation of DNA through a nanopore is used to read out the DNA molecule. Here, we present a double-pore system where two nanopores are drilled in parallel through the same solid-state membrane, which offers new opportunities for DNA manipulation. Our experiments and molecular dynamics simulations show that simultaneous electrophoretic capture of a DNA molecule by the two nanopores mechanically traps the molecule, increasing its residence time within the nanopores by orders of magnitude. Remarkably, by using two unequal-sized nanopores, the pore of DNA entry and exit can be discerned from the ionic current blockades, and the translocation direction can be precisely controlled by small differences in the effective force applied to DNA. The mechanical arrest of DNA translocation using a double-pore system can be straightforwardly integrated into any solid-state nanopore platform, including those using optical or transverse-current readouts.
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Affiliation(s)
- Sergii Pud
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Shu-Han Chao
- Department of Physics, University of Illinois at Urbana—Champaign, Urbana, Illinois 61801, United States
| | - Maxim Belkin
- Department of Physics, University of Illinois at Urbana—Champaign, Urbana, Illinois 61801, United States
| | - Daniel Verschueren
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Teun Huijben
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Casper van Engelenburg
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana—Champaign, Urbana, Illinois 61801, United States
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139
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Hashim H, Maruyama H, Masuda T, Arai F. Manipulation and Immobilization of a Single Fluorescence Nanosensor for Selective Injection into Cells. SENSORS 2016; 16:s16122041. [PMID: 27916931 PMCID: PMC5191022 DOI: 10.3390/s16122041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 11/21/2016] [Accepted: 11/29/2016] [Indexed: 12/15/2022]
Abstract
Manipulation and injection of single nanosensors with high cell viability is an emerging field in cell analysis. We propose a new method using fluorescence nanosensors with a glass nanoprobe and optical control of the zeta potential. The nanosensor is fabricated by encapsulating a fluorescence polystyrene nanobead into a lipid layer with 1,3,3-trimethylindolino-6'-nitrobenzopyrylospiran (SP), which is a photochromic material. The nanobead contains iron oxide nanoparticles and a temperature-sensitive fluorescent dye, Rhodamine B. The zeta potential of the nanosensor switches between negative and positive by photo-isomerization of SP with ultraviolet irradiation. The positively-charged nanosensor easily adheres to a negatively-charged glass nanoprobe, is transported to a target cell, and then adheres to the negatively-charged cell membrane. The nanosensor is then injected into the cytoplasm by heating with a near-infrared (NIR) laser. As a demonstration, a single 750 nm nanosensor was picked-up using a glass nanoprobe with optical control of the zeta potential. Then, the nanosensor was transported and immobilized onto a target cell membrane. Finally, it was injected into the cytoplasm using a NIR laser. The success rates of pick-up and cell immobilization of the nanosensor were 75% and 64%, respectively. Cell injection and cell survival rates were 80% and 100%, respectively.
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Affiliation(s)
- Hairulazwan Hashim
- Department of Micro-Nano Systems Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan.
- Faculty of Engineering Technology, Universiti Tun Hussein Onn Malaysia, 86400 Parit Raja, Batu Pahat, Johor, Malaysia.
| | - Hisataka Maruyama
- Department of Micro-Nano Systems Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan.
| | - Taisuke Masuda
- Department of Micro-Nano Systems Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan.
| | - Fumihito Arai
- Department of Micro-Nano Systems Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan.
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140
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Shamsudhin N, Tao Y, Sort J, Jang B, Degen CL, Nelson BJ, Pané S. Magnetometry of Individual Polycrystalline Ferromagnetic Nanowires. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:6363-6369. [PMID: 27690370 DOI: 10.1002/smll.201602338] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 08/25/2016] [Indexed: 06/06/2023]
Abstract
Ferromagnetic nanowires are finding use as untethered sensors and actuators for probing micro- and nanoscale biophysical phenomena, such as for localized sensing and application of forces and torques on biological samples, for tissue heating through magnetic hyperthermia, and for microrheology. Quantifying the magnetic properties of individual isolated nanowires is crucial for such applications. Dynamic cantilever magnetometry is used to measure the magnetic properties of individual sub-500 nm diameter polycrystalline nanowires of Ni and Ni80 Co20 fabricated by template-assisted electrochemical deposition. The values are compared with bulk, ensemble measurements when the nanowires are still embedded within their growth matrix. It is found that single-particle and ensemble measurements of nanowires yield significantly different results that reflect inter-nanowire interactions and chemical modifications of the sample during the release process from the growth matrix. The results highlight the importance of performing single-particle characterization for objects that will be used as individual magnetic nanoactuators or nanosensors in biomedical applications.
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Affiliation(s)
- Naveen Shamsudhin
- Multi-Scale Robotics Laboratory, ETH Zurich, Zurich, 8092, Switzerland
| | - Ye Tao
- Department of Physics, ETH Zurich, Zurich, 8092, Switzerland
| | - Jordi Sort
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Departament de Física, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, 08193, Spain
| | - Bumjin Jang
- Multi-Scale Robotics Laboratory, ETH Zurich, Zurich, 8092, Switzerland
| | | | - Bradley J Nelson
- Multi-Scale Robotics Laboratory, ETH Zurich, Zurich, 8092, Switzerland
| | - Salvador Pané
- Multi-Scale Robotics Laboratory, ETH Zurich, Zurich, 8092, Switzerland
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141
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Rinklin P, Krause HJ, Wolfrum B. On-chip electromagnetic tweezers - 3-dimensional particle actuation using microwire crossbar arrays. LAB ON A CHIP 2016; 16:4749-4758. [PMID: 27847939 DOI: 10.1039/c6lc00887a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Emerging miniaturization technologies for biological and bioengineering applications require precise control over position and actuation of microparticles. While many of these applications call for high-throughput approaches, common tools for particle manipulation, such as magnetic or optical tweezers, suffer from low parallelizability. To address this issue, we introduce a chip-based platform that enables flexible three-dimensional control over individual magnetic microparticles. Our system relies on microwire crossbar arrays for simultaneous generation of magnetic and dielectric forces, which actuate the particles along highly localized traps. We demonstrate the precise spatiotemporal control of individual particles by tracing complex trajectories in three dimensions and investigate the forces that can be generated along different axes. Furthermore, we show that our approach for particle actuation can be parallelized by simultaneously controlling the position and movement of 16 particles in parallel.
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Affiliation(s)
- Philipp Rinklin
- Institute of Bioelectronics (ICS-8/PGI-8), Forschungszentrum Jülich, 52425 Jülich, Germany and Neuroelectronics, Munich School of Bioengineering, Department of Electrical and Computer Engineering, Technical University of Munich, Boltzmannstraße 11, D-85748 Garching, Germany.
| | - Hans-Joachim Krause
- Institute of Bioelectronics (ICS-8/PGI-8), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Bernhard Wolfrum
- Institute of Bioelectronics (ICS-8/PGI-8), Forschungszentrum Jülich, 52425 Jülich, Germany and Neuroelectronics, Munich School of Bioengineering, Department of Electrical and Computer Engineering, Technical University of Munich, Boltzmannstraße 11, D-85748 Garching, Germany.
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142
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Single-molecule studies of high-mobility group B architectural DNA bending proteins. Biophys Rev 2016; 9:17-40. [PMID: 28303166 PMCID: PMC5331113 DOI: 10.1007/s12551-016-0236-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 10/19/2016] [Indexed: 11/23/2022] Open
Abstract
Protein–DNA interactions can be characterized and quantified using single molecule methods such as optical tweezers, magnetic tweezers, atomic force microscopy, and fluorescence imaging. In this review, we discuss studies that characterize the binding of high-mobility group B (HMGB) architectural proteins to single DNA molecules. We show how these studies are able to extract quantitative information regarding equilibrium binding as well as non-equilibrium binding kinetics. HMGB proteins play critical but poorly understood roles in cellular function. These roles vary from the maintenance of chromatin structure and facilitation of ribosomal RNA transcription (yeast high-mobility group 1 protein) to regulatory and packaging roles (human mitochondrial transcription factor A). We describe how these HMGB proteins bind, bend, bridge, loop and compact DNA to perform these functions. We also describe how single molecule experiments observe multiple rates for dissociation of HMGB proteins from DNA, while only one rate is observed in bulk experiments. The measured single-molecule kinetics reveals a local, microscopic mechanism by which HMGB proteins alter DNA flexibility, along with a second, much slower macroscopic rate that describes the complete dissociation of the protein from DNA.
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143
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Sitters G, Laurens N, de Rijk EJ, Kress H, Peterman EJG, Wuite GJL. Optical Pushing: A Tool for Parallelized Biomolecule Manipulation. Biophys J 2016; 110:44-50. [PMID: 26745408 DOI: 10.1016/j.bpj.2015.11.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 10/25/2015] [Accepted: 11/17/2015] [Indexed: 01/05/2023] Open
Abstract
The ability to measure and manipulate single molecules has greatly advanced the field of biophysics. Yet, the addition of more single-molecule tools that enable one to measure in a parallel fashion is important to diversify the questions that can be addressed. Here we present optical pushing (OP), a single-molecule technique that is used to exert forces on many individual biomolecules tethered to microspheres using a single collimated laser beam. Forces ranging from a few femtoNewtons to several picoNewtons can be applied with a submillisecond response time. To determine forces exerted on the tethered particles by the laser, we analyzed their measured Brownian motion using, to our knowledge, a newly derived analytical model and numerical simulations. In the model, Brownian rotation of the microspheres is taken into account, which proved to be a critical component to correctly determine the applied forces. We used our OP technique to map the energy landscape of the protein-induced looping dynamics of DNA. OP can be used to apply loading rates in the range of 10(-4)-10(6) pN/s to many molecules at the same time, which makes it a tool suitable for dynamic force spectroscopy.
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Affiliation(s)
- Gerrit Sitters
- Department of Physics and Astronomy and LaserLaB, VU University Amsterdam, Amsterdam, The Netherlands
| | - Niels Laurens
- Department of Physics and Astronomy and LaserLaB, VU University Amsterdam, Amsterdam, The Netherlands
| | - Emilie J de Rijk
- Department of Physics and Astronomy and LaserLaB, VU University Amsterdam, Amsterdam, The Netherlands
| | - Holger Kress
- Experimental Physics I, University of Bayreuth, Bayreuth, Germany; Department of Applied Physics, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Erwin J G Peterman
- Department of Physics and Astronomy and LaserLaB, VU University Amsterdam, Amsterdam, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy and LaserLaB, VU University Amsterdam, Amsterdam, The Netherlands.
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144
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Matek C, Šulc P, Randisi F, Doye JPK, Louis AA. Coarse-grained modelling of supercoiled RNA. J Chem Phys 2016; 143:243122. [PMID: 26723607 DOI: 10.1063/1.4933066] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
We study the behaviour of double-stranded RNA under twist and tension using oxRNA, a recently developed coarse-grained model of RNA. Introducing explicit salt-dependence into the model allows us to directly compare our results to data from recent single-molecule experiments. The model reproduces extension curves as a function of twist and stretching force, including the buckling transition and the behaviour of plectoneme structures. For negative supercoiling, we predict denaturation bubble formation in plectoneme end-loops, suggesting preferential plectoneme localisation in weak base sequences. OxRNA exhibits a positive twist-stretch coupling constant, in agreement with recent experimental observations.
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Affiliation(s)
- Christian Matek
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom
| | - Petr Šulc
- Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - Ferdinando Randisi
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom
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145
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Dulin D, Cui TJ, Cnossen J, Docter MW, Lipfert J, Dekker NH. High Spatiotemporal-Resolution Magnetic Tweezers: Calibration and Applications for DNA Dynamics. Biophys J 2016; 109:2113-25. [PMID: 26588570 DOI: 10.1016/j.bpj.2015.10.018] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 10/05/2015] [Accepted: 10/13/2015] [Indexed: 11/16/2022] Open
Abstract
The observation of biological processes at the molecular scale in real time requires high spatial and temporal resolution. Magnetic tweezers are straightforward to implement, free of radiation or photodamage, and provide ample multiplexing capability, but their spatiotemporal resolution has lagged behind that of other single-molecule manipulation techniques, notably optical tweezers and AFM. Here, we present, to our knowledge, a new high-resolution magnetic tweezers apparatus. We systematically characterize the achievable spatiotemporal resolution for both incoherent and coherent light sources, different types and sizes of beads, and different types and lengths of tethered molecules. Using a bright coherent laser source for illumination and tracking at 6 kHz, we resolve 3 Å steps with a 1 s period for surface-melted beads and 5 Å steps with a 0.5 s period for double-stranded-dsDNA-tethered beads, in good agreement with a model of stochastic bead motion in the magnetic tweezers. We demonstrate how this instrument can be used to monitor the opening and closing of a DNA hairpin on millisecond timescales in real time, together with attendant changes in the hairpin dynamics upon the addition of deoxythymidine triphosphate. Our approach opens up the possibility of observing biological events at submillisecond timescales with subnanometer resolution using camera-based detection.
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Affiliation(s)
- David Dulin
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands.
| | - Tao Ju Cui
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Jelmer Cnossen
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Margreet W Docter
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Jan Lipfert
- Department of Physics, Nanosystems Initiative Munich and Center for Nanoscience, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands.
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146
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Jacobson DR, Saleh OA. Magnetic tweezers force calibration for molecules that exhibit conformational switching. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2016; 87:094302. [PMID: 27782545 DOI: 10.1063/1.4963321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
High spatial and temporal resolution magnetic tweezers experiments allow for the direct calibration of pulling forces applied to short biomolecules. In one class of experiments, a force is applied to a structured RNA or protein to induce an unfolding transition; when the force is maintained at particular values, the molecule can exhibit conformational switching between the folded and unfolded states or between intermediate states. Here, we analyze the degree to which common force calibration approaches, involving the fitting of model functions to the Allan variance or power spectral density of the bead trajectory, are biased by this conformational switching. We find significant effects in two limits: that of large molecular extension changes between the two states, in which alternative fitting functions must be used, and that of very fast switching kinetics, in which the force calibration cannot be recovered due to the slow diffusion time of the magnetic bead. We use simulations and high-resolution RNA hairpin data to show that most biophysical experiments do not occur in either of these limits.
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Affiliation(s)
- David R Jacobson
- Department of Physics, University of California, Santa Barbara, California 93106, USA
| | - Omar A Saleh
- Materials Department and BMSE Program, University of California, Santa Barbara, California 93106, USA
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147
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Fornander LH, Frykholm K, Fritzsche J, Araya J, Nevin P, Werner E, Çakır A, Persson F, Garcin EB, Beuning PJ, Mehlig B, Modesti M, Westerlund F. Visualizing the Nonhomogeneous Structure of RAD51 Filaments Using Nanofluidic Channels. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:8403-8412. [PMID: 27479732 DOI: 10.1021/acs.langmuir.6b01877] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
RAD51 is the key component of the homologous recombination pathway in eukaryotic cells and performs its task by forming filaments on DNA. In this study we investigate the physical properties of RAD51 filaments formed on DNA using nanofluidic channels and fluorescence microscopy. Contrary to the bacterial ortholog RecA, RAD51 forms inhomogeneous filaments on long DNA in vitro, consisting of several protein patches. We demonstrate that a permanent "kink" in the filament is formed where two patches meet if the stretch of naked DNA between the patches is short. The kinks are readily seen in the present microscopy approach but would be hard to identify using conventional single DNA molecule techniques where the DNA is more stretched. We also demonstrate that protein patches separated by longer stretches of bare DNA roll up on each other and this is visualized as transiently overlapping filaments. RAD51 filaments can be formed at several different conditions, varying the cation (Mg(2+) or Ca(2+)), the DNA substrate (single-stranded or double-stranded), and the RAD51 concentration during filament nucleation, and we compare the properties of the different filaments formed. The results provide important information regarding the physical properties of RAD51 filaments but also demonstrate that nanofluidic channels are perfectly suited to study protein-DNA complexes.
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Affiliation(s)
| | | | | | - Joshua Araya
- Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States
| | - Philip Nevin
- Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States
| | - Erik Werner
- Department of Physics, University of Gothenburg , 412 96 Gothenburg, Sweden
| | - Ali Çakır
- Department of Physics, University of Gothenburg , 412 96 Gothenburg, Sweden
| | - Fredrik Persson
- Department for Cell and Molecular Biology, Science for Life Laboratory, Uppsala University , 751 24 Uppsala, Sweden
| | - Edwige B Garcin
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université , 13273 Marseille, France
| | - Penny J Beuning
- Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States
| | - Bernhard Mehlig
- Department of Physics, University of Gothenburg , 412 96 Gothenburg, Sweden
| | - Mauro Modesti
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université , 13273 Marseille, France
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148
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Seol Y, Strub MP, Neuman KC. Single molecule measurements of DNA helicase activity with magnetic tweezers and t-test based step-finding analysis. Methods 2016; 105:119-27. [PMID: 27131595 PMCID: PMC4967025 DOI: 10.1016/j.ymeth.2016.04.030] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 04/25/2016] [Accepted: 04/27/2016] [Indexed: 01/26/2023] Open
Abstract
Magnetic tweezers is a versatile and easy to implement single-molecule technique that has become increasingly prevalent in the study of nucleic acid based molecular motors. Here, we provide a description of the magnetic tweezers instrument and guidelines for measuring and analyzing DNA helicase activity. Along with experimental methods, we describe a robust method of single-molecule trajectory analysis based on the Student's t-test that accommodates continuous transitions in addition to the discrete transitions assumed in most widely employed analysis routines. To illustrate the single-molecule unwinding assay and the analysis routine, we provide DNA unwinding measurements of Escherichia coli RecQ helicase under a variety of conditions (Na+, ATP, temperature, and DNA substrate geometry). These examples reveal that DNA unwinding measurements under various conditions can aid in elucidating the unwinding mechanism of DNA helicase but also emphasize that environmental effects on DNA helicase activity must be considered in relation to in vivo activity and mechanism.
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Affiliation(s)
- Yeonee Seol
- Laboratory of Single Molecule Biophysics, NHLBI, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Marie-Paule Strub
- Laboratory of Single Molecule Biophysics, NHLBI, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, NHLBI, National Institutes of Health, Bethesda, MD 20892, USA.
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149
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Liu AP. Biophysical Tools for Cellular and Subcellular Mechanical Actuation of Cell Signaling. Biophys J 2016; 111:1112-1118. [PMID: 27456131 DOI: 10.1016/j.bpj.2016.02.043] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 01/17/2016] [Accepted: 02/01/2016] [Indexed: 10/24/2022] Open
Abstract
The ability to spatially control cell signaling can help resolve fundamental biological questions. Optogenetic and chemical dimerization techniques along with fluorescent biosensors to report cell signaling activities have enabled researchers to both visualize and perturb biochemistry in living cells. A number of approaches based on mechanical actuation using force-field gradients have emerged as complementary technologies to manipulate cell signaling in real time. This review covers several technologies, including optical, magnetic, and acoustic control of cell signaling and behavior and highlights some studies that have led to novel insights. I will also discuss some future direction on repurposing mechanosensitive channel for mechanical actuation of spatial cell signaling.
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Affiliation(s)
- Allen P Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan; Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan; Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan; Biophysics Program, University of Michigan, Ann Arbor, Michigan.
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150
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Campàs O. A toolbox to explore the mechanics of living embryonic tissues. Semin Cell Dev Biol 2016; 55:119-30. [PMID: 27061360 PMCID: PMC4903887 DOI: 10.1016/j.semcdb.2016.03.011] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 03/15/2016] [Indexed: 01/03/2023]
Abstract
The sculpting of embryonic tissues and organs into their functional morphologies involves the spatial and temporal regulation of mechanics at cell and tissue scales. Decades of in vitro work, complemented by some in vivo studies, have shown the relevance of mechanical cues in the control of cell behaviors that are central to developmental processes, but the lack of methodologies enabling precise, quantitative measurements of mechanical cues in vivo have hindered our understanding of the role of mechanics in embryonic development. Several methodologies are starting to enable quantitative studies of mechanics in vivo and in situ, opening new avenues to explore how mechanics contributes to shaping embryonic tissues and how it affects cell behavior within developing embryos. Here we review the present methodologies to study the role of mechanics in living embryonic tissues, considering their strengths and drawbacks as well as the conditions in which they are most suitable.
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Affiliation(s)
- Otger Campàs
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106, USA; Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, CA 93106, USA; California Nanosystems Institute, University of California, Santa Barbara, CA 93106, USA.
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