51
|
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.
Collapse
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.
| |
Collapse
|
52
|
Dissection of structural dynamics of chromatin fibers by single-molecule magnetic tweezers. BIOPHYSICS REPORTS 2018; 4:222-232. [PMID: 30310859 PMCID: PMC6153500 DOI: 10.1007/s41048-018-0064-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 07/18/2018] [Indexed: 12/01/2022] Open
Abstract
The accessibility of genomic DNA, as a key determinant of gene-related processes, is dependent on the packing density and structural dynamics of chromatin fiber. However, due to the highly dynamic and heterogeneous properties of chromatin fiber, it is technically challenging to study these properties of chromatin. Here, we report a strategy for dissecting the dynamics of chromatin fibers based on single-molecule magnetic tweezers. Using magnetic tweezers, we can manipulate the chromatin fiber and trace its extension during the folding and unfolding process under tension to investigate the dynamic structural transitions at single-molecule level. The highly accurate and reliable in vitro single-molecule strategy provides a new research platform to dissect the structural dynamics of chromatin fiber and its regulation by different epigenetic factors during gene expression.
Collapse
|
53
|
Calibration of force detection for arbitrarily shaped particles in optical tweezers. Sci Rep 2018; 8:10798. [PMID: 30018378 PMCID: PMC6050307 DOI: 10.1038/s41598-018-28876-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 06/28/2018] [Indexed: 11/08/2022] Open
Abstract
Force measurement with an optical trap requires calibration of it. With a suitable detector, such as a position-sensitive detector (PSD), it is possible to calibrate the detector so that the force can be measured for arbitrary particles and arbitrary beams without further calibration; such a calibration can be called an "absolute calibration". Here, we present a simple method for the absolute calibration of a PSD. Very often, paired position and force measurements are required, and even if synchronous measurements are possible with the position and force detectors used, knowledge of the force-position curve for the particle in the trap can be highly beneficial. Therefore, we experimentally demonstrate methods for determining the force-position curve with and without synchronous force and position measurements, beyond the Hookean (linear) region of the trap. Unlike the absolute calibration of the force and position detectors, the force-position curve depends on the particle and the trapping beam, and needs to be determined in each individual case. We demonstrate the robustness of our absolute calibration by measuring optical forces on microspheres as commonly trapped in optical tweezers, and other particles such a birefringent vaterite microspheres, red blood cells, and a deformable "blob".
Collapse
|
54
|
Copeland CR, Geist J, McGray CD, Aksyuk VA, Liddle JA, Ilic BR, Stavis SM. Subnanometer localization accuracy in widefield optical microscopy. LIGHT, SCIENCE & APPLICATIONS 2018; 7:31. [PMID: 30839614 PMCID: PMC6107003 DOI: 10.1038/s41377-018-0031-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 04/24/2018] [Accepted: 05/01/2018] [Indexed: 05/16/2023]
Abstract
The common assumption that precision is the limit of accuracy in localization microscopy and the typical absence of comprehensive calibration of optical microscopes lead to a widespread issue-overconfidence in measurement results with nanoscale statistical uncertainties that can be invalid due to microscale systematic errors. In this article, we report a comprehensive solution to this underappreciated problem. We develop arrays of subresolution apertures into the first reference materials that enable localization errors approaching the atomic scale across a submillimeter field. We present novel methods for calibrating our microscope system using aperture arrays and develop aberration corrections that reach the precision limit of our reference materials. We correct and register localization data from multiple colors and test different sources of light emission with equal accuracy, indicating the general applicability of our reference materials and calibration methods. In a first application of our new measurement capability, we introduce the concept of critical-dimension localization microscopy, facilitating tests of nanofabrication processes and quality control of aperture arrays. In a second application, we apply these stable reference materials to answer open questions about the apparent instability of fluorescent nanoparticles that commonly serve as fiducial markers. Our study establishes a foundation for subnanometer localization accuracy in widefield optical microscopy.
Collapse
Affiliation(s)
- Craig R. Copeland
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
- Maryland NanoCenter, University of Maryland, College Park, MD 20742 USA
| | - Jon Geist
- Engineering Physics Division, National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
| | - Craig D. McGray
- Engineering Physics Division, National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
| | - Vladimir A. Aksyuk
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
| | - J. Alexander Liddle
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
| | - B. Robert Ilic
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
| | - Samuel M. Stavis
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
| |
Collapse
|
55
|
Microrheology, advances in methods and insights. Adv Colloid Interface Sci 2018; 257:71-85. [PMID: 29859615 DOI: 10.1016/j.cis.2018.04.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 03/23/2018] [Accepted: 04/14/2018] [Indexed: 01/19/2023]
Abstract
Microrheology is an emerging technique that probes mechanical response of soft material at micro-scale. Generally, microrheology technique can be divided into active and passive versions. During last two decades, extensive efforts have been paid to improve both the experiment techniques and data analysis methods, especially about how to link consequential particle positions into trajectories. We review the recent advances in microrheology, including improvements in labeling, imaging, data acquiring, data processing and data interpretation. Some of the recent insights in soft matter and living systems gained by using this technique are given. Before these, we also give a very brief description of the basic principles of both active and passive microrheology techniques, and some details about optical particle tracking and DWS.
Collapse
|
56
|
van Oene MM, Ha S, Jager T, Lee M, Pedaci F, Lipfert J, Dekker NH. Quantifying the Precision of Single-Molecule Torque and Twist Measurements Using Allan Variance. Biophys J 2018; 114:1970-1979. [PMID: 29694873 DOI: 10.1016/j.bpj.2018.02.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 02/12/2018] [Accepted: 02/27/2018] [Indexed: 01/06/2023] Open
Abstract
Single-molecule manipulation techniques have provided unprecedented insights into the structure, function, interactions, and mechanical properties of biological macromolecules. Recently, the single-molecule toolbox has been expanded by techniques that enable measurements of rotation and torque, such as the optical torque wrench (OTW) and several different implementations of magnetic (torque) tweezers. Although systematic analyses of the position and force precision of single-molecule techniques have attracted considerable attention, their angle and torque precision have been treated in much less detail. Here, we propose Allan deviation as a tool to systematically quantitate angle and torque precision in single-molecule measurements. We apply the Allan variance method to experimental data from our implementations of (electro)magnetic torque tweezers and an OTW and find that both approaches can achieve a torque precision better than 1 pN · nm. The OTW, capable of measuring torque on (sub)millisecond timescales, provides the best torque precision for measurement times ≲10 s, after which drift becomes a limiting factor. For longer measurement times, magnetic torque tweezers with their superior stability provide the best torque precision. Use of the Allan deviation enables critical assessments of the torque precision as a function of measurement time across different measurement modalities and provides a tool to optimize measurement protocols for a given instrument and application.
Collapse
Affiliation(s)
- Maarten M van Oene
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Seungkyu Ha
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Tessa Jager
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Mina Lee
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Francesco Pedaci
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Jan Lipfert
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands; Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, Munich, Germany.
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
| |
Collapse
|
57
|
Fabian R, Tyson C, Tuma PL, Pegg I, Sarkar A. A Horizontal Magnetic Tweezers and Its Use for Studying Single DNA Molecules. MICROMACHINES 2018; 9:mi9040188. [PMID: 30424121 PMCID: PMC6187538 DOI: 10.3390/mi9040188] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 04/11/2018] [Accepted: 04/12/2018] [Indexed: 11/29/2022]
Abstract
We report the development of a magnetic tweezers that can be used to micromanipulate single DNA molecules by applying picoNewton (pN)-scale forces in the horizontal plane. The resulting force–extension data from our experiments show high-resolution detection of changes in the DNA tether’s extension: ~0.5 pN in the force and <10 nm change in extension. We calibrate our instrument using multiple orthogonal techniques including the well-characterized DNA overstretching transition. We also quantify the repeatability of force and extension measurements, and present data on the behavior of the overstretching transition under varying salt conditions. The design and experimental protocols are described in detail, which should enable straightforward reproduction of the tweezers.
Collapse
Affiliation(s)
- Roberto Fabian
- Department of Physics and Vitreous State Laboratory, The Catholic University of America, Washington, DC 20064, USA.
| | - Christopher Tyson
- Biomedical Engineering Department and Vitreous State Laboratory, The Catholic University of America, Washington, DC 20064, USA.
| | - Pamela L Tuma
- Department of Biology, The Catholic University of America, Washington, DC 20064, USA.
| | - Ian Pegg
- Department of Physics and Vitreous State Laboratory, The Catholic University of America, Washington, DC 20064, USA.
| | - Abhijit Sarkar
- Department of Physics and Vitreous State Laboratory, The Catholic University of America, Washington, DC 20064, USA.
| |
Collapse
|
58
|
Yu H, Yang Y, Yang Y, Zhang F, Wang S, Tao N. Tracking fast cellular membrane dynamics with sub-nm accuracy in the normal direction. NANOSCALE 2018; 10:5133-5139. [PMID: 29488990 PMCID: PMC5854544 DOI: 10.1039/c7nr09483c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Cellular membranes are important biomaterials with highly dynamic structures. Membrane dynamics plays an important role in numerous cellular processes, but precise tracking it is challenging due to the lack of tools with a highly sensitive and fast detection capability. Here we demonstrate a broad bandwidth optical imaging technique to measure cellular membrane displacements in the normal direction at sub-nm level detection limits and 20 μs temporal resolution (1 Hz-50 kHz). This capability allows us to study the intrinsic cellular membrane dynamics over a broad temporal and spatial spectrum. We measured the nanometer-scale stochastic fluctuations of the plasma membrane of HEK-293 cells, and found them to be highly dependent on the cytoskeletal structure of the cells. By analyzing the fluctuations, we further determine the mechanical properties of the cellular membranes. We anticipate that the method will contribute to the understanding of the basic cellular processes, and applications, such as mechanical phenotyping of cells at the single-cell level.
Collapse
Affiliation(s)
- Hui Yu
- Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yuting Yang
- Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yunze Yang
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, AZ 85287, USA
| | - Fenni Zhang
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, AZ 85287, USA
| | - Shaopeng Wang
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, AZ 85287, USA
| | - Nongjian Tao
- Biodesign Center for Bioelectronics and Biosensors, Arizona State University, Tempe, AZ 85287, USA
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| |
Collapse
|
59
|
Cerbino R. Quantitative optical microscopy of colloids: The legacy of Jean Perrin. Curr Opin Colloid Interface Sci 2018. [DOI: 10.1016/j.cocis.2018.03.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
|
60
|
Makarchuk S, Beyer N, Gaiddon C, Grange W, Hébraud P. Holographic Traction Force Microscopy. Sci Rep 2018; 8:3038. [PMID: 29445207 PMCID: PMC5813032 DOI: 10.1038/s41598-018-21206-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 01/31/2018] [Indexed: 01/14/2023] Open
Abstract
Traction Force Microscopy (TFM) computes the forces exerted at the surface of an elastic material by measuring induced deformations in volume. It is used to determine the pattern of the adhesion forces exerted by cells or by cellular assemblies grown onto a soft deformable substrate. Typically, colloidal particles are dispersed in the substrate and their displacement is monitored by fluorescent microscopy. As with any other fluorescent techniques, the accuracy in measuring a particule's position is ultimately limited by the number of evaluated fluorescent photons. Here, we present a TFM technique based on the detection of probe particle displacements by holographic tracking microscopy. We show that nanometer scale resolutions of the particle displacements can be obtained and determine the maximum volume fraction of markers in the substrate. We demonstrate the feasibility of the technique experimentally and measure the three-dimensional force fields exerted by colorectal cancer cells cultivated onto a polyacrylamide gel substrate.
Collapse
Affiliation(s)
- Stanislaw Makarchuk
- Université de Strasbourg, IPCMS/CNRS, UMR 7504, 23 rue du Loess, Strasbourg, 67034, France
| | - Nicolas Beyer
- Université de Strasbourg, IPCMS/CNRS, UMR 7504, 23 rue du Loess, Strasbourg, 67034, France
| | - Christian Gaiddon
- Université de Strasbourg, Inserm U1113, 3 avenue Molière, Strasbourg, 67200, France
| | - Wilfried Grange
- Université de Strasbourg, IPCMS/CNRS, UMR 7504, 23 rue du Loess, Strasbourg, 67034, France.
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France.
| | - Pascal Hébraud
- Université de Strasbourg, IPCMS/CNRS, UMR 7504, 23 rue du Loess, Strasbourg, 67034, France.
| |
Collapse
|
61
|
Bugiel M, Mitra A, Girardo S, Diez S, Schäffer E. Measuring Microtubule Supertwist and Defects by Three-Dimensional-Force-Clamp Tracking of Single Kinesin-1 Motors. NANO LETTERS 2018; 18:1290-1295. [PMID: 29380607 DOI: 10.1021/acs.nanolett.7b04971] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Three-dimensional (3D) nanometer tracking of single biomolecules provides important information about their biological function. However, existing microscopy approaches often have only limited spatial or temporal precision and do not allow the application of defined loads. Here, we developed and applied a high-precision 3D-optical-tweezers force clamp to track in vitro the 3D motion of single kinesin-1 motor proteins along microtubules. To provide the motors with unimpeded access to the whole microtubule lattice, we mounted the microtubules on topographic surface features generated by UV-nanoimprint lithography. Because kinesin-1 motors processively move along individual protofilaments, we could determine the number of protofilaments the microtubules were composed of by measuring the helical pitches of motor movement on supertwisted microtubules. Moreover, we were able to identify defects in microtubules, most likely arising from local changes in the protofilament number. While it is hypothesized that microtubule supertwist and defects can severely influence the function of motors and other microtubule-associated proteins, the presented method allows for the first time to fully map the microtubule lattice in situ. This mapping allows the correlation of motor-filament interactions with the microtubule fine-structure. With the additional ability to apply loads, we expect our 3D-optical-tweezers force clamp to become a valuable tool for obtaining a wide range of information from other biological systems, inaccessible by two-dimensional and/or ensemble measurements.
Collapse
Affiliation(s)
- Michael Bugiel
- Eberhard Karls Universität Tübingen, ZMBP , Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Aniruddha Mitra
- Technische Universität Dresden, B CUBE - Center for Molecular Bioengineering and Center for Advancing Electronics Dresden , Arnoldstrasse 18, 01307 Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics , Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Salvatore Girardo
- Technische Universität Dresden, BIOTEC - Center for Molecular and Cellular Bioengineering , Tatzberg 47/49, 01307 Dresden, Germany
| | - Stefan Diez
- Technische Universität Dresden, B CUBE - Center for Molecular Bioengineering and Center for Advancing Electronics Dresden , Arnoldstrasse 18, 01307 Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics , Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Erik Schäffer
- Eberhard Karls Universität Tübingen, ZMBP , Auf der Morgenstelle 32, 72076 Tübingen, Germany
| |
Collapse
|
62
|
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.
Collapse
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.
| |
Collapse
|
63
|
Kostiuk G, Dikic J, Schwarz FW, Sasnauskas G, Seidel R, Siksnys V. The dynamics of the monomeric restriction endonuclease BcnI during its interaction with DNA. Nucleic Acids Res 2017; 45:5968-5979. [PMID: 28453854 PMCID: PMC5449598 DOI: 10.1093/nar/gkx294] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 04/13/2017] [Indexed: 11/24/2022] Open
Abstract
Endonucleases that generate DNA double strand breaks often employ two independent subunits such that the active site from each subunit cuts either DNA strand. Restriction enzyme BcnI is a remarkable exception. It binds to the 5΄-CC/SGG-3΄ (where S = C or G, ‘/’ designates the cleavage position) target as a monomer forming an asymmetric complex, where a single catalytic center approaches the scissile phosphodiester bond in one of DNA strands. Bulk kinetic measurements have previously shown that the same BcnI molecule cuts both DNA strands at the target site without dissociation from the DNA. Here, we analyse the BcnI DNA binding and target recognition steps at the single molecule level. We find, using FRET, that BcnI adopts either ‘open’ or ‘closed’ conformation in solution. Next, we directly demonstrate that BcnI slides over long distances on DNA using 1D diffusion and show that sliding is accompanied by occasional jumping events, where the enzyme leaves the DNA and rebinds immediately at a distant site. Furthermore, we quantify the dynamics of the BcnI interactions with cognate and non-cognate DNA, and determine the preferred binding orientation of BcnI to the target site. These results provide new insights into the intricate dynamics of BcnI–DNA interactions.
Collapse
Affiliation(s)
- Georgij Kostiuk
- Institute of Biotechnology, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania
| | - Jasmina Dikic
- Molecular Biophysics group, Institute for Experimental Physics I, Universität Leipzig, Linnéstr. 5, 04103 Leipzig, Germany
| | - Friedrich W Schwarz
- BCUBE, Technische Universitaet Dresden, Arnoldstrasse 18, 01307 Dresden, Germany
| | - Giedrius Sasnauskas
- Institute of Biotechnology, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania
| | - Ralf Seidel
- Molecular Biophysics group, Institute for Experimental Physics I, Universität Leipzig, Linnéstr. 5, 04103 Leipzig, Germany
| | - Virginijus Siksnys
- Institute of Biotechnology, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania
| |
Collapse
|
64
|
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.
Collapse
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
| |
Collapse
|
65
|
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.
Collapse
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
| |
Collapse
|
66
|
Bugiel M, Jannasch A, Schäffer E. Implementation and Tuning of an Optical Tweezers Force-Clamp Feedback System. Methods Mol Biol 2017; 1486:109-136. [PMID: 27844427 DOI: 10.1007/978-1-4939-6421-5_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Feedback systems can be used to control the value of a system variable. In optical tweezers, active feedback is often implemented to either keep the position or tension applied to a single biomolecule constant. Here, we describe the implementation of the latter: an optical force-clamp setup that can be used to study the motion of processive molecular motors under a constant load. We describe the basics of a software-implemented proportional-integral-derivative (PID) controller, how to tune it, and how to determine its optimal feedback rate. Limitations, possible feed-forward applications, and extensions into two- and three-dimensional optical force clamps are discussed. The feedback is ultimately limited by thermal fluctuations and the compliance of the involved molecules. To investigate a particular mechanical process, understanding the basics and limitations of the feedback system will be helpful for choosing the proper feedback hardware, for optimizing the system parameters, and for the design of the experiment.
Collapse
Affiliation(s)
- Michael Bugiel
- Center for Plant Molecular Biology, Universität Tübingen, Auf der Morgenstelle 32, D-72076, Tübingen, Germany
| | - Anita Jannasch
- Center for Plant Molecular Biology, Universität Tübingen, Auf der Morgenstelle 32, D-72076, Tübingen, Germany
| | - Erik Schäffer
- Center for Plant Molecular Biology, Universität Tübingen, Auf der Morgenstelle 32, D-72076, Tübingen, Germany.
| |
Collapse
|
67
|
Rutkauskas M, Krivoy A, Szczelkun MD, Rouillon C, Seidel R. Single-Molecule Insight Into Target Recognition by CRISPR-Cas Complexes. Methods Enzymol 2016; 582:239-273. [PMID: 28062037 DOI: 10.1016/bs.mie.2016.10.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Ribonucleoprotein (RNP) complexes from CRISPR-Cas systems have attracted enormous interest since they can be easily and flexibly reprogrammed to target any desired locus for genome engineering and gene regulation applications. Basis for the programmability is a short RNA (crRNA) inside these complexes that recognizes the target nucleic acid by base pairing. For CRISPR-Cas systems that target double-stranded DNA this results in local DNA unwinding and formation of a so-called R-loop structure. Here we provide an overview how this target recognition mechanism can be dissected in great detail at the level of a single molecule. Specifically, we demonstrate how magnetic tweezers are applied to measure the local DNA unwinding at the target in real time. To this end we introduce the technique and the measurement principle. By studying modifications of the consensus target sequence, we show how different sequence elements contribute to the target recognition mechanism. From these data, a unified target recognition mechanism can be concluded for the RNPs Cascade and Cas9 from types I and II CRISPR-Cas systems. R-loop formation is hereby initiated on the target at an upstream element, called protospacer adjacent motif (PAM), from which the R-loop structure zips directionally toward the PAM-distal end of the target. At mismatch positions, the R-loop propagation stalls and further propagation competes with collapse of the structure. Upon full R-loop zipping conformational changes within the RNPs trigger degradation of the DNA target. This represents a shared labor mechanism in which zipping between nucleic acid strands is the actual target recognition mechanism while sensing of the R-loop arrival at the PAM-distal end just verifies the success of the full zipping.
Collapse
Affiliation(s)
- M Rutkauskas
- Molecular Biophysics Group, Institute for Experimental Physics I, Universität Leipzig, Leipzig, Germany
| | - A Krivoy
- Molecular Biophysics Group, Institute for Experimental Physics I, Universität Leipzig, Leipzig, Germany; Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - M D Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - C Rouillon
- Molecular Biophysics Group, Institute for Experimental Physics I, Universität Leipzig, Leipzig, Germany.
| | - R Seidel
- Molecular Biophysics Group, Institute for Experimental Physics I, Universität Leipzig, Leipzig, Germany.
| |
Collapse
|
68
|
Duboc C, Fan J, Graves ET, Strick TR. Preparation of DNA Substrates and Functionalized Glass Surfaces for Correlative Nanomanipulation and Colocalization (NanoCOSM) of Single Molecules. Methods Enzymol 2016; 582:275-296. [PMID: 28062038 DOI: 10.1016/bs.mie.2016.09.048] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Simultaneous nanomanipulation and colocalization of single molecules (NanoCOSM) provides a unique opportunity to correlate the mechanical properties and activities of biomolecules with their conformational states or states of assembly as part of dynamic macromolecular complexes. This opens the door to real-time single-molecule analysis of the correlations between structure, function, and composition of large multicomponent protein complexes.
Collapse
Affiliation(s)
- C Duboc
- Institut Jacques Monod, Centre National de la Recherche Scientifique, University of Paris Diderot and Sorbonne Paris Cité, Paris, France
| | - J Fan
- Institut Jacques Monod, Centre National de la Recherche Scientifique, University of Paris Diderot and Sorbonne Paris Cité, Paris, France
| | - E T Graves
- Institut Jacques Monod, Centre National de la Recherche Scientifique, University of Paris Diderot and Sorbonne Paris Cité, Paris, France
| | - T R Strick
- Institut Jacques Monod, Centre National de la Recherche Scientifique, University of Paris Diderot and Sorbonne Paris Cité, Paris, France; Ecole Normale Supérieure, Institut de Biologie de l'ENS (iBENS), INSERM, CNRS, PSL Research University, Paris, France.
| |
Collapse
|
69
|
Ding Y, Li C. Dual-color multiple-particle tracking at 50-nm localization and over 100-µm range in 3D with temporal focusing two-photon microscopy. BIOMEDICAL OPTICS EXPRESS 2016; 7:4187-4197. [PMID: 27867724 PMCID: PMC5102526 DOI: 10.1364/boe.7.004187] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 09/09/2016] [Accepted: 09/14/2016] [Indexed: 05/12/2023]
Abstract
Nanoscale particle tracking in three dimensions is crucial to directly observe dynamics of molecules and nanoparticles in living cells. Here we present a three-dimensional particle tracking method based on temporally focused two-photon excitation. Multiple particles are imaged at 30 frames/s in volume up to 180 × 180 × 100 µm3. The spatial localization precision can reach 50 nm. We demonstrate its capability of tracking fast swimming microbes at speed of ~200 µm/s. Two-photon dual-color tracking is achieved by simultaneously exciting two kinds of fluorescent beads at 800 nm to demonstrate its potential in molecular interaction studies. Our method provides a simple wide-field fluorescence imaging approach for deep multiple-particle tracking.
Collapse
Affiliation(s)
- Yu Ding
- Department of Physics, The University of Texas at El Paso, 500 W University Avenue, El Paso, TX 79968, USA
| | - Chunqiang Li
- Department of Physics, The University of Texas at El Paso, 500 W University Avenue, El Paso, TX 79968, USA
- Border Biomedical Research Center, The University of Texas at El Paso, 500 W University Avenue, El Paso, TX 79968, USA
| |
Collapse
|
70
|
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.
Collapse
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.
| |
Collapse
|
71
|
Pinto C, Kasaciunaite K, Seidel R, Cejka P. Human DNA2 possesses a cryptic DNA unwinding activity that functionally integrates with BLM or WRN helicases. eLife 2016; 5. [PMID: 27612385 PMCID: PMC5030094 DOI: 10.7554/elife.18574] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 09/08/2016] [Indexed: 12/13/2022] Open
Abstract
Human DNA2 (hDNA2) contains both a helicase and a nuclease domain within the same polypeptide. The nuclease of hDNA2 is involved in a variety of DNA metabolic processes. Little is known about the role of the hDNA2 helicase. Using bulk and single-molecule approaches, we show that hDNA2 is a processive helicase capable of unwinding kilobases of dsDNA in length. The nuclease activity prevents the engagement of the helicase by competing for the same substrate, hence prominent DNA unwinding by hDNA2 alone can only be observed using the nuclease-deficient variant. We show that the helicase of hDNA2 functionally integrates with BLM or WRN helicases to promote dsDNA degradation by forming a heterodimeric molecular machine. This collectively suggests that the hDNA2 motor promotes the enzyme's capacity to degrade dsDNA in conjunction with BLM or WRN and thus promote the repair of broken DNA. DOI:http://dx.doi.org/10.7554/eLife.18574.001
Collapse
Affiliation(s)
- Cosimo Pinto
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | | | - Ralf Seidel
- Institute of Experimental Physics I, University of Leipzig, Leipzig, Germany
| | - Petr Cejka
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| |
Collapse
|
72
|
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.
Collapse
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
| |
Collapse
|
73
|
Kemmerich FE, Kasaciunaite K, Seidel R. Modular magnetic tweezers for single-molecule characterizations of helicases. Methods 2016; 108:4-13. [PMID: 27402355 DOI: 10.1016/j.ymeth.2016.07.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/05/2016] [Accepted: 07/06/2016] [Indexed: 01/09/2023] Open
Abstract
Magnetic tweezers provide a versatile toolkit supporting the mechanistic investigation of helicases. In the present article, we show that custom magnetic tweezers setups are straightforward to construct and can easily be extended to provide adaptable platforms, capable of addressing a multitude of enquiries regarding the functions of these fascinating molecular machines. We first address the fundamental components of a basic magnetic tweezers scheme and review some previous results to demonstrate the versatility of this instrument. We then elaborate on several extensions to the basic magnetic tweezers scheme, and demonstrate their applications with data from ongoing research. As our methodological overview illustrates, magnetic tweezers are an extremely useful tool for the characterization of helicases and a custom built instrument can be specifically tailored to suit the experimenter's needs.
Collapse
Affiliation(s)
- Felix E Kemmerich
- Molecular Biophysics Group, Institute of Experimental Physics I, Universität Leipzig, 04103 Leipzig, Germany
| | - Kristina Kasaciunaite
- Molecular Biophysics Group, Institute of Experimental Physics I, Universität Leipzig, 04103 Leipzig, Germany
| | - Ralf Seidel
- Molecular Biophysics Group, Institute of Experimental Physics I, Universität Leipzig, 04103 Leipzig, Germany.
| |
Collapse
|
74
|
Probing the mechanical properties, conformational changes, and interactions of nucleic acids with magnetic tweezers. J Struct Biol 2016; 197:26-36. [PMID: 27368129 DOI: 10.1016/j.jsb.2016.06.022] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 05/06/2016] [Accepted: 06/28/2016] [Indexed: 11/21/2022]
Abstract
Nucleic acids are central to the storage and transmission of genetic information. Mechanical properties, along with their sequence, both enable and fundamentally constrain the biological functions of DNA and RNA. For small deformations from the equilibrium conformations, nucleic acids are well described by an isotropic elastic rod model. However, external forces and torsional strains can induce conformational changes, giving rise to a complex force-torque phase diagram. This review focuses on magnetic tweezers as a powerful tool to precisely determine both the elastic parameters and conformational transitions of nucleic acids under external forces and torques at the single-molecule level. We review several variations of magnetic tweezers, in particular conventional magnetic tweezers, freely orbiting magnetic tweezers and magnetic torque tweezers, and discuss their characteristic capabilities. We then describe the elastic rod model for DNA and RNA and discuss conformational changes induced by mechanical stress. The focus lies on the responses to torque and twist, which are crucial in the mechanics and interactions of nucleic acids and can directly be measured using magnetic tweezers. We conclude by highlighting several recent studies of nucleic acid-protein and nucleic acid-small-molecule interactions as further applications of magnetic tweezers and give an outlook of some exciting developments to come.
Collapse
|
75
|
Long X, Parks JW, Stone MD. Integrated magnetic tweezers and single-molecule FRET for investigating the mechanical properties of nucleic acid. Methods 2016; 105:16-25. [PMID: 27320203 DOI: 10.1016/j.ymeth.2016.06.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 06/09/2016] [Accepted: 06/13/2016] [Indexed: 02/02/2023] Open
Abstract
Many enzymes promote structural changes in their nucleic acid substrates via application of piconewton forces over nanometer length scales. Magnetic tweezers (MT) is a single molecule force spectroscopy method widely used for studying the energetics of such mechanical processes. MT permits stable application of a wide range of forces and torques over long time scales with nanometer spatial resolution. However, in any force spectroscopy experiment, the ability to monitor structural changes in nucleic acids with nanometer sensitivity requires the system of interest to be held under high degrees of tension to improve signal to noise. This limitation prohibits measurement of structural changes within nucleic acids under physiologically relevant conditions of low stretching forces. To overcome this challenge, researchers have integrated a spatially sensitive fluorescence spectroscopy method, single molecule-FRET, with MT to allow simultaneous observation and manipulation of nanoscale structural transitions over a wide range of forces. Here, we describe a method for using this hybrid instrument to analyze the mechanical properties of nucleic acids. We expect that this method for analysis of nucleic acid structure will be easily adapted for experiments aiming to interrogate the mechanical responses of other biological macromolecules.
Collapse
Affiliation(s)
- Xi Long
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Joseph W Parks
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Michael D Stone
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA; Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA, USA.
| |
Collapse
|
76
|
TrmBL2 from Pyrococcus furiosus Interacts Both with Double-Stranded and Single-Stranded DNA. PLoS One 2016; 11:e0156098. [PMID: 27214207 PMCID: PMC4877046 DOI: 10.1371/journal.pone.0156098] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 05/08/2016] [Indexed: 12/12/2022] Open
Abstract
In many hyperthermophilic archaea the DNA binding protein TrmBL2 or one of its homologues is abundantly expressed. TrmBL2 is thought to play a significant role in modulating the chromatin architecture in combination with the archaeal histone proteins and Alba. However, its precise physiological role is poorly understood. It has been previously shown that upon binding TrmBL2 covers double-stranded DNA, which leads to the formation of a thick and fibrous filament. Here we investigated the filament formation process as well as the stabilization of DNA by TrmBL2 from Pyroccocus furiosus in detail. We used magnetic tweezers that allow to monitor changes of the DNA mechanical properties upon TrmBL2 binding on the single-molecule level. Extended filaments formed in a cooperative manner and were considerably stiffer than bare double-stranded DNA. Unlike Alba, TrmBL2 did not form DNA cross-bridges. The protein was found to bind double- and single-stranded DNA with similar affinities. In mechanical disruption experiments of DNA hairpins this led to stabilization of both, the double- (before disruption) and the single-stranded (after disruption) DNA forms. Combined, these findings suggest that the biological function of TrmBL2 is not limited to modulating genome architecture and acting as a global repressor but that the protein acts additionally as a stabilizer of DNA secondary structure.
Collapse
|
77
|
Duboc C, Graves ET, Strick TR. Simple calibration of TIR field depth using the supercoiling response of DNA. Methods 2016; 105:56-61. [PMID: 27038746 DOI: 10.1016/j.ymeth.2016.03.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 03/29/2016] [Indexed: 11/29/2022] Open
Abstract
The combination of single-molecule fluorescence and nanomanipulation techniques into a single experimental platform enables one to carry out correlative analysis of the composition and the activity of complex, multicomponent molecular systems. Here we describe implementation and calibration of such a combined system allowing simultaneous single-molecule force spectroscopy and fluorescence imaging of proteins acting on the DNA using magnetic trapping coupled with fluorescence excitation based on a Total Internal Reflection (TIR), or evanescent, field. We propose a simple and robust in situ method for calibration of the TIR field depth against the mechanical properties of nanomanipulated DNA, and which is made possible by the fact that the magnetic bead used to trap and nanomanipulate DNA and measure its conformation also exhibits autofluorescence in the TIR field. Indeed, the fact that the bead size is on the 1-micron scale does not preclude sensitive probing of an intensity field which decays exponentially on the 0.1micron-scale. We demonstrate the usefulness of this approach by mapping out TIR field depth as a function of the angle of incidence of the illuminating laser at the glass-water interface and showing that one recovers the expected theoretical relationship between field depth and angle of incidence.
Collapse
Affiliation(s)
- Camille Duboc
- Institut Jacques Monod, Centre National de la Recherche Scientifique, University of Paris Diderot and Sorbonne Paris Cité, Paris, France
| | - Evan T Graves
- Institut Jacques Monod, Centre National de la Recherche Scientifique, University of Paris Diderot and Sorbonne Paris Cité, Paris, France
| | - Terence R Strick
- Institut Jacques Monod, Centre National de la Recherche Scientifique, University of Paris Diderot and Sorbonne Paris Cité, Paris, France; Ecole Normale Supérieure, Institut de Biologie de l'ENS (iBENS), INSERM, CNRS, PSL Research University, Paris, France.
| |
Collapse
|
78
|
Kemmerich FE, Daldrop P, Pinto C, Levikova M, Cejka P, Seidel R. Force regulated dynamics of RPA on a DNA fork. Nucleic Acids Res 2016; 44:5837-48. [PMID: 27016742 PMCID: PMC4937307 DOI: 10.1093/nar/gkw187] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 03/04/2016] [Indexed: 01/24/2023] Open
Abstract
Replication protein A (RPA) is a single-stranded DNA binding protein, involved in most aspects of eukaryotic DNA metabolism. Here, we study the behavior of RPA on a DNA substrate that mimics a replication fork. Using magnetic tweezers we show that both yeast and human RPA can open forked DNA when sufficient external tension is applied. In contrast, at low force, RPA becomes rapidly displaced by the rehybridization of the DNA fork. This process appears to be governed by the binding or the release of an RPA microdomain (toehold) of only few base-pairs length. This gives rise to an extremely rapid exchange dynamics of RPA at the fork. Fork rezipping rates reach up to hundreds of base-pairs per second, being orders of magnitude faster than RPA dissociation from ssDNA alone. Additionally, we show that RPA undergoes diffusive motion on ssDNA, such that it can be pushed over long distances by a rezipping fork. Generally the behavior of both human and yeast RPA homologs is very similar. However, in contrast to yeast RPA, the dissociation of human RPA from ssDNA is greatly reduced at low Mg2+ concentrations, such that human RPA can melt DNA in absence of force.
Collapse
Affiliation(s)
- Felix E Kemmerich
- Institute of Experimental Physics I, Universität Leipzig, Linnéstr. 5, 04103 Leipzig, Germany Institute for Molecular Cell Biology, University of Münster, Schlossplatz 5, D-48149 Münster, Germany
| | - Peter Daldrop
- Institute for Molecular Cell Biology, University of Münster, Schlossplatz 5, D-48149 Münster, Germany
| | - Cosimo Pinto
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Maryna Levikova
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Petr Cejka
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Ralf Seidel
- Institute of Experimental Physics I, Universität Leipzig, Linnéstr. 5, 04103 Leipzig, Germany Institute for Molecular Cell Biology, University of Münster, Schlossplatz 5, D-48149 Münster, Germany
| |
Collapse
|
79
|
Daldrop P, Brutzer H, Huhle A, Kauert DJ, Seidel R. Extending the range for force calibration in magnetic tweezers. Biophys J 2016; 108:2550-2561. [PMID: 25992733 DOI: 10.1016/j.bpj.2015.04.011] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 04/10/2015] [Accepted: 04/14/2015] [Indexed: 12/11/2022] Open
Abstract
Magnetic tweezers are a wide-spread tool used to study the mechanics and the function of a large variety of biomolecules and biomolecular machines. This tool uses a magnetic particle and a strong magnetic field gradient to apply defined forces to the molecule of interest. Forces are typically quantified by analyzing the lateral fluctuations of the biomolecule-tethered particle in the direction perpendicular to the applied force. Since the magnetic field pins the anisotropy axis of the particle, the lateral fluctuations follow the geometry of a pendulum with a short pendulum length along and a long pendulum length perpendicular to the field lines. Typically, the short pendulum geometry is used for force calibration by power-spectral-density (PSD) analysis, because the movement of the bead in this direction can be approximated by a simple translational motion. Here, we provide a detailed analysis of the fluctuations according to the long pendulum geometry and show that for this direction, both the translational and the rotational motions of the particle have to be considered. We provide analytical formulas for the PSD of this coupled system that agree well with PSDs obtained in experiments and simulations and that finally allow a faithful quantification of the magnetic force for the long pendulum geometry. We furthermore demonstrate that this methodology allows the calibration of much larger forces than the short pendulum geometry in a tether-length-dependent manner. In addition, the accuracy of determination of the absolute force is improved. Our force calibration based on the long pendulum geometry will facilitate high-resolution magnetic-tweezers experiments that rely on short molecules and large forces, as well as highly parallelized measurements that use low frame rates.
Collapse
Affiliation(s)
- Peter Daldrop
- Institute for Molecular Cell Biology, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Hergen Brutzer
- Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Alexander Huhle
- Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Dominik J Kauert
- Institute for Molecular Cell Biology, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Ralf Seidel
- Institute for Molecular Cell Biology, Westfälische Wilhelms-Universität Münster, Münster, Germany; Biotechnology Center, Technische Universität Dresden, Dresden, Germany; Institute for Experimental Physics I, Universität Leipzig, Leipzig, Germany.
| |
Collapse
|
80
|
Kemmerich FE, Swoboda M, Kauert DJ, Grieb MS, Hahn S, Schwarz FW, Seidel R, Schlierf M. Simultaneous Single-Molecule Force and Fluorescence Sampling of DNA Nanostructure Conformations Using Magnetic Tweezers. NANO LETTERS 2016; 16:381-6. [PMID: 26632021 DOI: 10.1021/acs.nanolett.5b03956] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
We present a hybrid single-molecule technique combining magnetic tweezers and Förster resonance energy transfer (FRET) measurements. Through applying external forces to a paramagnetic sphere, we induce conformational changes in DNA nanostructures, which are detected in two output channels simultaneously. First, by tracking a magnetic bead with high spatial and temporal resolution, we observe overall DNA length changes along the force axis. Second, the measured FRET efficiency between two fluorescent probes monitors local conformational changes. The synchronized orthogonal readout in different observation channels will facilitate deciphering the complex mechanisms of biomolecular machines.
Collapse
Affiliation(s)
- Felix E Kemmerich
- Institute for Molecular Cell Biology, University of Münster , 48149 Münster, Germany
- Institute of Experimental Physics I, Universität Leipzig , 04103 Leipzig, Germany
| | - Marko Swoboda
- B CUBE - Center for Molecular Bioengineering, TU Dresden , 01307 Dresden, Germany
| | - Dominik J Kauert
- Institute for Molecular Cell Biology, University of Münster , 48149 Münster, Germany
- Institute of Experimental Physics I, Universität Leipzig , 04103 Leipzig, Germany
| | - M Svea Grieb
- B CUBE - Center for Molecular Bioengineering, TU Dresden , 01307 Dresden, Germany
| | - Steffen Hahn
- B CUBE - Center for Molecular Bioengineering, TU Dresden , 01307 Dresden, Germany
| | - Friedrich W Schwarz
- B CUBE - Center for Molecular Bioengineering, TU Dresden , 01307 Dresden, Germany
- cfaed - Center for Advancing Electronics Dresden, TU Dresden , 01307 Dresden, Germany
| | - Ralf Seidel
- Institute for Molecular Cell Biology, University of Münster , 48149 Münster, Germany
- Institute of Experimental Physics I, Universität Leipzig , 04103 Leipzig, Germany
| | - Michael Schlierf
- B CUBE - Center for Molecular Bioengineering, TU Dresden , 01307 Dresden, Germany
| |
Collapse
|
81
|
Simple horizontal magnetic tweezers for micromanipulation of single DNA molecules and DNA-protein complexes. Biotechniques 2016; 60:21-7. [PMID: 26757808 DOI: 10.2144/000114369] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 09/08/2015] [Indexed: 12/16/2022] Open
Abstract
We report the development of a simple-to-implement magnetic force transducer that can apply a wide range of piconewton (pN) scale forces on single DNA molecules and DNA-protein complexes in the horizontal plane. The resulting low-noise force-extension data enable very high-resolution detection of changes in the DNA tether's extension: ~0.05 pN in force and <10 nm change in extension. We have also verified that we can manipulate DNA in near equilibrium conditions through the wide range of forces by ramping the force from low to high and back again, and observing minimal hysteresis in the molecule's force response. Using a calibration technique based on Stokes' drag law, we have confirmed our force measurements from DNA force-extension experiments obtained using the fluctuation-dissipation theorem applied to transverse fluctuations of the magnetic microsphere. We present data on the force-distance characteristics of a DNA molecule complexed with histones. The results illustrate how the tweezers can be used to study DNA binding proteins at the single molecule level.
Collapse
|
82
|
Untangling reaction pathways through modern approaches to high-throughput single-molecule force-spectroscopy experiments. Curr Opin Struct Biol 2015; 34:116-22. [PMID: 26434413 DOI: 10.1016/j.sbi.2015.08.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 08/06/2015] [Accepted: 08/10/2015] [Indexed: 11/22/2022]
Abstract
Single-molecule experiments provide a unique means for real-time observation of the activity of individual biomolecular machines. Through such techniques, insights into the mechanics of for example, polymerases, helicases, and packaging motors have been gleaned. Here we describe the recent advances in single-molecule force spectroscopy instrumentation that have facilitated high-throughput acquisition at high spatiotemporal resolution. The large datasets attained by such methods can capture rare but important events, and contain information regarding stochastic behaviors covering many orders of magnitude in time. We further discuss analysis of such data sets, and with a special focus on the pause states described in the general literature on RNA polymerase pausing we compare and contrast the signatures of different reaction pathways.
Collapse
|
83
|
Directional R-Loop Formation by the CRISPR-Cas Surveillance Complex Cascade Provides Efficient Off-Target Site Rejection. Cell Rep 2015; 10:1534-1543. [PMID: 25753419 DOI: 10.1016/j.celrep.2015.01.067] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 01/09/2015] [Accepted: 01/28/2015] [Indexed: 11/21/2022] Open
Abstract
CRISPR-Cas systems provide bacteria and archaea with adaptive immunity against foreign nucleic acids. In type I CRISPR-Cas systems, invading DNA is detected by a large ribonucleoprotein surveillance complex called Cascade. The crRNA component of Cascade is used to recognize target sites in foreign DNA (protospacers) by formation of an R-loop driven by base-pairing complementarity. Using single-molecule supercoiling experiments with near base-pair resolution, we probe here the mechanism of R-loop formation and detect short-lived R-loop intermediates on off-target sites bearing single mismatches. We show that R-loops propagate directionally starting from the protospacer-adjacent motif (PAM). Upon reaching a mismatch, R-loop propagation stalls and collapses in a length-dependent manner. This unambiguously demonstrates that directional zipping of the R-loop accomplishes efficient target recognition by rapidly rejecting binding to off-target sites with PAM-proximal mutations. R-loops that reach the protospacer end become locked to license DNA degradation by the auxiliary Cas3 nuclease/helicase without further target verification.
Collapse
|