1
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Qian J, Cartee A, Xu W, Yan Y, Wang B, Artsimovitch I, Dunlap D, Finzi L. Reciprocating RNA Polymerase batters through roadblocks. Nat Commun 2024; 15:3193. [PMID: 38609371 PMCID: PMC11014978 DOI: 10.1038/s41467-024-47531-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 04/04/2024] [Indexed: 04/14/2024] Open
Abstract
RNA polymerases must transit through protein roadblocks to produce full-length transcripts. Here we report real-time measurements of Escherichia coli RNA polymerase passing through different barriers. As intuitively expected, assisting forces facilitated, and opposing forces hindered, RNA polymerase passage through lac repressor protein bound to natural binding sites. Force-dependent differences were significant at magnitudes as low as 0.2 pN and were abolished in the presence of the transcript cleavage factor GreA, which rescues backtracked RNA polymerase. In stark contrast, opposing forces promoted passage when the rate of RNA polymerase backtracking was comparable to, or faster than the rate of dissociation of the roadblock, particularly in the presence of GreA. Our experiments and simulations indicate that RNA polymerase may transit after roadblocks dissociate, or undergo cycles of backtracking, recovery, and ramming into roadblocks to pass through. We propose that such reciprocating motion also enables RNA polymerase to break protein-DNA contacts that hold RNA polymerase back during promoter escape and RNA chain elongation. This may facilitate productive transcription in vivo.
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Affiliation(s)
- Jin Qian
- Physics Department, Emory University, Atlanta, GA, USA
| | | | - Wenxuan Xu
- Physics Department, Emory University, Atlanta, GA, USA
| | - Yan Yan
- Physics Department, Emory University, Atlanta, GA, USA
| | - Bing Wang
- The Center for RNA Biology and Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Irina Artsimovitch
- The Center for RNA Biology and Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - David Dunlap
- Physics Department, Emory University, Atlanta, GA, USA
| | - Laura Finzi
- Physics Department, Emory University, Atlanta, GA, USA.
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2
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Bauer MS, Gruber S, Hausch A, Melo MCR, Gomes PSFC, Nicolaus T, Milles LF, Gaub HE, Bernardi RC, Lipfert J. Single-molecule force stability of the SARS-CoV-2-ACE2 interface in variants-of-concern. NATURE NANOTECHNOLOGY 2024; 19:399-405. [PMID: 38012274 DOI: 10.1038/s41565-023-01536-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 09/26/2023] [Indexed: 11/29/2023]
Abstract
Mutations in SARS-CoV-2 have shown effective evasion of population immunity and increased affinity to the cellular receptor angiotensin-converting enzyme 2 (ACE2). However, in the dynamic environment of the respiratory tract, forces act on the binding partners, which raises the question of whether not only affinity but also force stability of the SARS-CoV-2-ACE2 interaction might be a selection factor for mutations. Using magnetic tweezers, we investigate the impact of amino acid substitutions in variants of concern (Alpha, Beta, Gamma and Delta) and on force-stability and bond kinetic of the receptor-binding domain-ACE2 interface at a single-molecule resolution. We find a higher affinity for all of the variants of concern (>fivefold) compared with the wild type. In contrast, Alpha is the only variant of concern that shows higher force stability (by 17%) compared with the wild type. Using molecular dynamics simulations, we rationalize the mechanistic molecular origins of this increase in force stability. Our study emphasizes the diversity of contributions to the transmissibility of variants and establishes force stability as one of the several factors for fitness. Understanding fitness advantages opens the possibility for the prediction of probable mutations, allowing a rapid adjustment of therapeutics, vaccines and intervention measures.
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Affiliation(s)
- Magnus S Bauer
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Sophia Gruber
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany
| | - Adina Hausch
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany
- Center for Protein Assemblies, TUM School of Natural Sciences, Technical University of Munich, Munich, Germany
| | | | | | - Thomas Nicolaus
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany
| | - Lukas F Milles
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Hermann E Gaub
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany
| | | | - Jan Lipfert
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany.
- Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands.
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3
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Croquette V, Orero JV, Rieu M, Allemand JF. Magnetic tweezers principles and promises. Methods Enzymol 2024; 694:1-49. [PMID: 38492947 DOI: 10.1016/bs.mie.2024.01.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2024]
Abstract
Magnetic tweezers have become popular with the outbreak of single molecule micromanipulation: catching a single molecule of DNA, RNA or a single protein and applying mechanical constrains using micron-size magnetic beads and magnets turn out to be easy. Various factors have made this possible: the fact that manufacturers have been preparing these beads to catch various biological entities-the ease of use provided by magnets which apply a force or a torque at a distance thus inside a flow cell-some chance: since the forces so generated are in the right range to stretch a single molecule. This is a little less true for torque. Finally, one feature which also appears very important is the simplicity of their calibration using Brownian motion. Here we start by describing magnetic tweezers used routinely in our laboratory where we have tried to develop a device as simple as possible so that the experimentalist can really focus on the biological aspect of the biomolecules that he/she is interested in. We discuss the implications of the various components and their important features. Next, we summarize what is easy to achieve and what is less easy. Then we refer to contributions by other groups who have brought valuable insights to improve magnetic tweezers.
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Affiliation(s)
- Vincent Croquette
- Laboratoire de Physique de l'École normale supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université Paris-Diderot, Sorbonne Paris Cité, Paris, France; ESPCI Paris, Université PSL, Paris, France.
| | - Jessica Valle Orero
- Laboratoire de Physique de l'École normale supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université Paris-Diderot, Sorbonne Paris Cité, Paris, France; The American University of Paris, Paris, France
| | - Martin Rieu
- Department of Physics, New Biochemistry Building, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Jean-François Allemand
- Laboratoire de Physique de l'École normale supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université Paris-Diderot, Sorbonne Paris Cité, Paris, France
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4
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Gaire S, Bhandari R, Pegg I, Sarkar A. Horizontal magnetic tweezers and its applications in single molecule micromanipulation experiments. Methods Enzymol 2024; 694:191-207. [PMID: 38492951 DOI: 10.1016/bs.mie.2023.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2024]
Abstract
Magnetic tweezers (MTs) have become indispensable tools for gaining mechanistic insights into the behavior of DNA-processing enzymes and acquiring detailed, high-resolution data on the mechanical properties of DNA. Currently, MTs have two distinct designs: vertical and horizontal (or transverse) configurations. While the vertical design and its applications have been extensively documented, there is a noticeable gap in comprehensive information pertaining to the design details, experimental procedures, and types of studies conducted with horizontal MTs. This article aims to address this gap by providing a concise overview of the fundamental principles underlying transverse MTs. It will explore the multifaceted applications of this technique as an exceptional instrument for scrutinizing DNA and its interactions with DNA-binding proteins at the single-molecule level.
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Affiliation(s)
- Santosh Gaire
- Department of Physics, The Catholic University of America, Washington, DC, United States; Vitreous State Laboratory, The Catholic University of America, Washington, DC, United States.
| | - Rajendra Bhandari
- Department of Physics, The Catholic University of America, Washington, DC, United States; Vitreous State Laboratory, The Catholic University of America, Washington, DC, United States
| | - Ian Pegg
- Department of Physics, The Catholic University of America, Washington, DC, United States; Vitreous State Laboratory, The Catholic University of America, Washington, DC, United States
| | - Abhijit Sarkar
- Department of Physics, The Catholic University of America, Washington, DC, United States; Vitreous State Laboratory, The Catholic University of America, Washington, DC, United States
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5
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Dohnalová H, Seifert M, Matoušková E, Klein M, Papini FS, Lipfert J, Dulin D, Lankaš F. Temperature-Dependent Twist of Double-Stranded RNA Probed by Magnetic Tweezer Experiments and Molecular Dynamics Simulations. J Phys Chem B 2024; 128:664-675. [PMID: 38197365 PMCID: PMC10823466 DOI: 10.1021/acs.jpcb.3c06280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/11/2024]
Abstract
RNA plays critical roles in the transmission and regulation of genetic information and is increasingly used in biomedical and biotechnological applications. Functional RNAs contain extended double-stranded regions, and the structure of double-stranded RNA (dsRNA) has been revealed at high resolution. However, the dependence of the properties of the RNA double helix on environmental effects, notably temperature, is still poorly understood. Here, we use single-molecule magnetic tweezer measurements to determine the dependence of the dsRNA twist on temperature. We find that dsRNA unwinds with increasing temperature, even more than DNA, with ΔTwRNA = -14.4 ± 0.7°/(°C·kbp), compared to ΔTwDNA = -11.0 ± 1.2°/(°C·kbp). All-atom molecular dynamics (MD) simulations using a range of nucleic acid force fields, ion parameters, and water models correctly predict that dsRNA unwinds with rising temperature but significantly underestimate the magnitude of the effect. These MD data, together with additional MD simulations involving DNA and DNA-RNA hybrid duplexes, reveal a linear correlation between the twist temperature decrease and the helical rise, in line with DNA but at variance with RNA experimental data. We speculate that this discrepancy might be caused by some unknown bias in the RNA force fields tested or by as yet undiscovered transient alternative structures in the RNA duplex. Our results provide a baseline to model more complex RNA assemblies and to test and develop new parametrizations for RNA simulations. They may also inspire physical models of the temperature-dependent dsRNA structure.
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Affiliation(s)
- Hana Dohnalová
- Department
of Informatics and Chemistry, University
of Chemistry and Technology Prague, Technická 5, 166 28 Praha
6, Czech Republic
| | - Mona Seifert
- Junior
Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg, Cauerstr. 3, Erlangen 91058, Germany
| | - Eva Matoušková
- Department
of Informatics and Chemistry, University
of Chemistry and Technology Prague, Technická 5, 166 28 Praha
6, Czech Republic
| | - Misha Klein
- Department
of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, Amsterdam 1081 HV, The Netherlands
| | - Flávia S. Papini
- Junior
Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg, Cauerstr. 3, Erlangen 91058, Germany
| | - Jan Lipfert
- Soft
Condensed Matter and Biophysics, Department of Physics and Debye Institute, Utrecht University, Utrecht 3584 CC, The Netherlands
| | - David Dulin
- Junior
Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg, Cauerstr. 3, Erlangen 91058, Germany
- Department
of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, Amsterdam 1081 HV, The Netherlands
| | - Filip Lankaš
- Department
of Informatics and Chemistry, University
of Chemistry and Technology Prague, Technická 5, 166 28 Praha
6, Czech Republic
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6
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Jung J, Kim S, Rah SH, Lee J, Shon MJ. Force-fluorescence setup for observing protein-DNA interactions under load. Methods Enzymol 2024; 694:137-165. [PMID: 38492949 DOI: 10.1016/bs.mie.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2024]
Abstract
This chapter explores advanced single-molecule techniques for studying protein-DNA interactions, particularly focusing on Replication Protein A (RPA) using a force-fluorescence setup. It combines magnetic tweezers (MT) with total internal reflection fluorescence (TIRF) microscopy, enabling detailed observation of DNA behavior under mechanical stress. The chapter details the use of DNA hairpins and bare DNA to examine RPA's binding dynamics and its influence on DNA's mechanical properties. This approach provides deeper insights into RPA's role in DNA replication, repair, and recombination, highlighting its significance in maintaining genomic stability.
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Affiliation(s)
- Jaehun Jung
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Subin Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Sang-Hyun Rah
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Jayil Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea; Institute of Basic Science Center for Genomic Integrity, Ulsan, Republic of Korea
| | - Min Ju Shon
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea.
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7
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Brouwer TB, Kaczmarczyk A, Zarguit I, Pham C, Dame RT, van Noort J. Unravelling DNA Organization with Single-Molecule Force Spectroscopy Using Magnetic Tweezers. Methods Mol Biol 2024; 2819:535-572. [PMID: 39028523 DOI: 10.1007/978-1-0716-3930-6_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Genomes carry the genetic blueprint of all living organisms. Their organization requires strong condensation as well as carefully regulated accessibility to specific genes for proper functioning of their hosts. The study of the structure and dynamics of the proteins that organize the genome has benefited tremendously from the development of single-molecule force spectroscopy techniques that allow for real-time, nanometer accuracy measurements of the compaction of DNA and manipulation with pico-Newton scale forces. Magnetic tweezers, in particular, have the unique ability to complement such force spectroscopy with the control over the linking number of the DNA molecule, which plays an important role when DNA-organizing proteins form or release wraps, loops, and bends in DNA. Here, we describe all the necessary steps to prepare DNA substrates for magnetic tweezers experiments, assemble flow cells, tether DNA to a magnetic bead inside a flow cell, and manipulate and record the extension of such DNA tethers. Furthermore, we explain how mechanical parameters of nucleoprotein filaments can be extracted from the data.
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Affiliation(s)
- Thomas B Brouwer
- Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - Artur Kaczmarczyk
- Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - Ilias Zarguit
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Chi Pham
- Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - Remus T Dame
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - John van Noort
- Leiden Institute of Physics, Leiden University, Leiden, The Netherlands.
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands.
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8
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Lin SN, Qin L, Taris KKH, Wuite GJL, Dame RT. Unravelling the Biophysical Properties of Chromatin Proteins and DNA Using Acoustic Force Spectroscopy. Methods Mol Biol 2024; 2819:519-534. [PMID: 39028522 DOI: 10.1007/978-1-0716-3930-6_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Acoustic force spectroscopy (AFS) is a single-molecule micromanipulation technique that uses sound waves to exert force on surface-tethered DNA molecules in a microfluidic chamber. As large numbers of individual protein-DNA complexes are tracked in parallel, AFS provides insight into the individual properties of such complexes as well as their population averages. In this chapter, we describe in detail how to perform AFS experiments specifically on bare DNA, protein-DNA complexes, and how to extract their (effective) persistence length and contour length from force-extension relations.
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Affiliation(s)
- Szu-Ning Lin
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
- Department of Physics and Astronomy, VU University Amsterdam, Amsterdam, The Netherlands
| | - Liang Qin
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Kees-Karel H Taris
- Department of Physics and Astronomy, VU University Amsterdam, Amsterdam, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy, VU University Amsterdam, Amsterdam, The Netherlands
| | - Remus T Dame
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands.
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands.
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9
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Dulin D. An Introduction to Magnetic Tweezers. Methods Mol Biol 2024; 2694:375-401. [PMID: 37824014 DOI: 10.1007/978-1-0716-3377-9_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Magnetic tweezers are a single-molecule force and torque spectroscopy technique that enable the mechanical interrogation in vitro of biomolecules, such as nucleic acids and proteins. They use a magnetic field originating from either permanent magnets or electromagnets to attract a magnetic particle, thus stretching the tethering biomolecule. They nicely complement other force spectroscopy techniques such as optical tweezers and atomic force microscopy (AFM) as they operate as a very stable force clamp, enabling long-duration experiments over a very broad range of forces spanning from 10 fN to 1 nN, with 1-10 milliseconds time and sub-nanometer spatial resolution. Their simplicity, robustness, and versatility have made magnetic tweezers a key technique within the field of single-molecule biophysics, being broadly applied to study the mechanical properties of, e.g., nucleic acids, genome processing molecular motors, protein folding, and nucleoprotein filaments. Furthermore, magnetic tweezers allow for high-throughput single-molecule measurements by tracking hundreds of biomolecules simultaneously both in real-time and at high spatiotemporal resolution. Magnetic tweezers naturally combine with surface-based fluorescence spectroscopy techniques, such as total internal reflection fluorescence microscopy, enabling correlative fluorescence and force/torque spectroscopy on biomolecules. This chapter presents an introduction to magnetic tweezers including a description of the hardware, the theory behind force calibration, its spatiotemporal resolution, combining it with other techniques, and a (non-exhaustive) overview of biological applications.
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Affiliation(s)
- David Dulin
- LaserLaB Amsterdam and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, Netherlands.
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10
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Yang ZY, Jiang WY, Ran SY. Reductant-dependent DNA-templated silver nanoparticle formation kinetics. Phys Chem Chem Phys 2023; 25:23197-23206. [PMID: 37605826 DOI: 10.1039/d3cp02623j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
DNA molecules have been demonstrated to be good templates for producing silver nanoparticles (AgNPs), with the advantages of well-controlled sizes, shapes, and properties. Revealing the formation kinetics of DNA-templated AgNPs is crucial for their efficient synthesis. Herein, using magnetic tweezers, we studied the reduction kinetics of the Ag+-DNA structure and the subsequent nucleation kinetics by adding NaBH4, L-ascorbic acid, and sodium citrate solutions. At [Ag+] = 0.01 mM, the addition of NaBH4 solution with the same concentration resulted in the restoration of DNA. In contrast, by increasing the [NaBH4]/[Ag+] ratio (r) to 10 and 100, the DNA extension initially decreased rapidly and then increased, indicating nucleation-dissolution kinetics. With AgNO3 solutions of higher concentrations (0.1 mM and 1 mM), direct particle nucleation and growth kinetics were observed by adding a tenfold (r = 10) or a hundredfold (r = 100) amount of NaBH4, which were evidenced by a significant reduction in DNA extension. The reductant dependence of the kinetics was further investigated. Addition of L-ascorbic acid to the DNA-Ag+ solution yielded an increase-decrease kinetics that was different from that caused by NaBH4, suggesting that nucleation was not initially favored due to the lack of sufficient Ag atoms; while sodium citrate showed a weak nucleation-promoting ability to form AgNPs. We discussed the findings within the framework of classical nucleation theory, in which the supersaturation of the Ag atom is strongly influenced by multiple factors (including the reducing ability of the reductant), resulting in different kinetics.
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Affiliation(s)
- Zi-Yang Yang
- Department of Physics, Wenzhou University, Wenzhou 325035, China.
| | - Wen-Yan Jiang
- Department of Physics, Wenzhou University, Wenzhou 325035, China.
| | - Shi-Yong Ran
- Department of Physics, Wenzhou University, Wenzhou 325035, China.
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11
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Liu CP, Yu Z, Xiong J, Hu J, Song A, Ding D, Yu C, Yang N, Wang M, Yu J, Hou P, Zeng K, Li Z, Zhang Z, Zhang X, Li W, Zhang Z, Zhu B, Li G, Xu RM. Structural insights into histone binding and nucleosome assembly by chromatin assembly factor-1. Science 2023; 381:eadd8673. [PMID: 37616371 PMCID: PMC11186048 DOI: 10.1126/science.add8673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 07/19/2023] [Indexed: 08/26/2023]
Abstract
Chromatin inheritance entails de novo nucleosome assembly after DNA replication by chromatin assembly factor-1 (CAF-1). Yet direct knowledge about CAF-1's histone binding mode and nucleosome assembly process is lacking. In this work, we report the crystal structure of human CAF-1 in the absence of histones and the cryo-electron microscopy structure of CAF-1 in complex with histones H3 and H4. One histone H3-H4 heterodimer is bound by one CAF-1 complex mainly through the p60 subunit and the acidic domain of the p150 subunit. We also observed a dimeric CAF-1-H3-H4 supercomplex in which two H3-H4 heterodimers are poised for tetramer assembly and discovered that CAF-1 facilitates right-handed DNA wrapping of H3-H4 tetramers. These findings signify the involvement of DNA in H3-H4 tetramer formation and suggest a right-handed nucleosome precursor in chromatin replication.
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Affiliation(s)
- Chao-Pei Liu
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhenyu Yu
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jun Xiong
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jie Hu
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Aoqun Song
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Dongbo Ding
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Cong Yu
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences; Hangzhou, Zhejiang 310024, China
| | - Na Yang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of Tianjin, Nankai University, Tianjin 300353, China
| | - Mingzhu Wang
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
| | - Juan Yu
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Peini Hou
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Kangning Zeng
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhenyu Li
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuqiang Zhang
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xinzheng Zhang
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Li
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Department of Pediatrics and Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Bing Zhu
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Guohong Li
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui-Ming Xu
- National Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences; Hangzhou, Zhejiang 310024, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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12
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Lin YY, Brouns T, Kolbeck PJ, Vanderlinden W, Lipfert J. High-yield ligation-free assembly of DNA constructs with nucleosome positioning sequence repeats for single-molecule manipulation assays. J Biol Chem 2023; 299:104874. [PMID: 37257819 PMCID: PMC10404619 DOI: 10.1016/j.jbc.2023.104874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/08/2023] [Accepted: 05/16/2023] [Indexed: 06/02/2023] Open
Abstract
Force and torque spectroscopy have provided unprecedented insights into the mechanical properties, conformational transitions, and dynamics of DNA and DNA-protein complexes, notably nucleosomes. Reliable single-molecule manipulation measurements require, however, specific and stable attachment chemistries to tether the molecules of interest. Here, we present a functionalization strategy for DNA that enables high-yield production of constructs for torsionally constrained and very stable attachment. The method is based on two subsequent PCRs: first ∼380 bp long DNA strands are generated that contain multiple labels, which are used as "megaprimers" in a second PCR to generate ∼kbp long double-stranded DNA constructs with multiple labels at the respective ends. To achieve high-force stability, we use dibenzocyclooctyne-based click chemistry for covalent attachment to the surface and biotin-streptavidin coupling to the bead. The resulting tethers are torsionally constrained and extremely stable under load, with an average lifetime of 70 ± 3 h at 45 pN. The high yield of the approach enables nucleosome reconstitution by salt dialysis on the functionalized DNA, and we demonstrate proof-of-concept measurements on nucleosome assembly statistics and inner turn unwrapping under force. We anticipate that our approach will facilitate a range of studies of DNA interactions and nucleoprotein complexes under forces and torques.
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Affiliation(s)
- Yi-Yun Lin
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany; Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Tine Brouns
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany; Division of Molecular Imaging and Photonics, KU Leuven, Leuven, Belgium
| | - Pauline J Kolbeck
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany; Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands
| | - Willem Vanderlinden
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany; Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands.
| | - Jan Lipfert
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany; Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands.
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13
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A conformational transition of the D'D3 domain primes von Willebrand factor for multimerization. Blood Adv 2022; 6:5198-5209. [PMID: 36069828 PMCID: PMC9631632 DOI: 10.1182/bloodadvances.2022006978] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 05/17/2022] [Indexed: 11/26/2022] Open
Abstract
Magnetic tweezers reveal a pH-dependent destabilization of the D3 interface priming VWF for multimerization by exposing Cys1099 and Cys1142. The stability of the D3 interface is increased by FVIII, suggesting a binding site within the D3 submodules.
Von Willebrand factor (VWF) is a multimeric plasma glycoprotein that is critically involved in hemostasis. Biosynthesis of long VWF concatemers in the endoplasmic reticulum and the trans-Golgi is still not fully understood. We use the single-molecule force spectroscopy technique magnetic tweezers to analyze a previously hypothesized conformational change in the D′D3 domain crucial for VWF multimerization. We find that the interface formed by submodules C8-3, TIL3, and E3 wrapping around VWD3 can open and expose 2 buried cysteines, Cys1099 and Cys1142, that are vital for multimerization. By characterizing the conformational change at varying levels of force, we can quantify the kinetics of the transition and stability of the interface. We find a pronounced destabilization of the interface on lowering the pH from 7.4 to 6.2 and 5.5. This is consistent with initiation of the conformational change that enables VWF multimerization at the D′D3 domain by a decrease in pH in the trans-Golgi network and Weibel-Palade bodies. Furthermore, we find a stabilization of the interface in the presence of coagulation factor VIII, providing evidence for a previously hypothesized binding site in submodule C8-3. Our findings highlight the critical role of the D′D3 domain in VWF biosynthesis and function, and we anticipate our methodology to be applicable to study other, similar conformational changes in VWF and beyond.
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14
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Abstract
Single-molecule magnetic tweezers deliver magnetic force and torque to single target molecules, permitting the study of dynamic changes in biomolecular structures and their interactions. Because the magnetic tweezer setups can generate magnetic fields that vary slowly over tens of millimeters-far larger than the nanometer scale of the single molecule events being observed-this technique can maintain essentially constant force levels during biochemical experiments while generating a biologically meaningful force on the order of 1-100 pN. When using bead-tether constructs to pull on single molecules, smaller magnetic beads and shorter submicrometer tethers improve dynamic response times and measurement precision. In addition, employing high-speed cameras, stronger light sources, and a graphics programming unit permits true high-resolution single-molecule magnetic tweezers that can track nanometer changes in target molecules on a millisecond or even submillisecond time scale. The unique force-clamping capacity of the magnetic tweezer technique provides a way to conduct measurements under near-equilibrium conditions and directly map the energy landscapes underlying various molecular phenomena. High-resolution single-molecule magnetic tweezers can thus be used to monitor crucial conformational changes in single-protein molecules, including those involved in mechanotransduction and protein folding. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Hyun-Kyu Choi
- Wallace H. Coulter Department of Biomedical Engineering and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Hyun Gyu Kim
- School of Biological Sciences and Institute for Molecular Biology and Genetics, Seoul National University, Seoul, South Korea;
| | - Min Ju Shon
- Department of Physics and School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science & Technology (POSTECH), Pohang, South Korea;
| | - Tae-Young Yoon
- School of Biological Sciences and Institute for Molecular Biology and Genetics, Seoul National University, Seoul, South Korea;
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15
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Magnetic tweezers: development and use in single-molecule research. Biotechniques 2022; 72:65-72. [PMID: 35037472 DOI: 10.2144/btn-2021-0104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The use of magnetic tweezers for single-molecule micromanipulation has evolved rapidly since its introduction approximately 30 years ago. Magnetic tweezers have provided important insights into the dynamic activity of DNA-processing enzymes, as well as detailed, high-resolution information on the mechanical properties of DNA. These successes have been enabled by major advancements in the hardware and software components of these devices. These developments now allow for a much richer mechanistic understanding of the functions and mechanisms of DNA-binding enzymes. In this review, the authors briefly discuss the fundamental principles of magnetic tweezers and describe the advancements that have made it a superlative tool for investigating, at the single-molecule level, DNA and its interactions with DNA-binding proteins.
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16
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Moon HM, Park JS, Lee IB, Kang YI, Jung HJ, An D, Shin Y, Kim MJ, Kim HI, Song JJ, Kim J, Lee NK, Hong SC. Cisplatin fastens chromatin irreversibly even at a high chloride concentration. Nucleic Acids Res 2021; 49:12035-12047. [PMID: 34865121 PMCID: PMC8643659 DOI: 10.1093/nar/gkab922] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 09/12/2021] [Accepted: 09/28/2021] [Indexed: 12/17/2022] Open
Abstract
Cisplatin is one of the most potent anti-cancer drugs developed so far. Recent studies highlighted several intriguing roles of histones in cisplatin's anti-cancer effect. Thus, the effect of nucleosome formation should be considered to give a better account of the anti-cancer effect of cisplatin. Here we investigated this important issue via single-molecule measurements. Surprisingly, the reduced activity of cisplatin under [NaCl] = 180 mM, corresponding to the total concentration of cellular ionic species, is still sufficient to impair the integrity of a nucleosome by retaining its condensed structure firmly, even against severe mechanical and chemical disturbances. Our finding suggests that such cisplatin-induced fastening of chromatin can inhibit nucleosome remodelling required for normal biological functions. The in vitro chromatin transcription assay indeed revealed that the transcription activity was effectively suppressed in the presence of cisplatin. Our direct physical measurements on cisplatin-nucleosome adducts suggest that the formation of such adducts be the key to the anti-cancer effect by cisplatin.
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Affiliation(s)
- Hyeon-Min Moon
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Korea.,Department of Physics, Korea University, Seoul 02841, Korea
| | - Jin-Sung Park
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Korea
| | - Il-Buem Lee
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Korea.,Department of Physics, Korea University, Seoul 02841, Korea
| | - Young-Im Kang
- Department of Physics, Korea University, Seoul 02841, Korea
| | - Hae Jun Jung
- Department of Physics, Korea University, Seoul 02841, Korea
| | - Dongju An
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Yumi Shin
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Min Ji Kim
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Hugh I Kim
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Ji-Joon Song
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Jaehoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Nam-Kyung Lee
- Department of Physics, Sejong University, Seoul 05006, Korea
| | - Seok-Cheol Hong
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Korea.,Department of Physics, Korea University, Seoul 02841, Korea
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17
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Liang L, Ma K, Wang Z, Janissen R, Yu Z. Dynamics and inhibition of MLL1 CXXC domain on DNA revealed by single-molecule quantification. Biophys J 2021; 120:3283-3291. [PMID: 34280370 DOI: 10.1016/j.bpj.2021.03.045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 02/09/2021] [Accepted: 03/11/2021] [Indexed: 02/05/2023] Open
Abstract
CpG islands recruit MLL1 via the CXXC domain to modulate chromatin structure and regulate gene expression. The amino acid motif of CXXC also plays a pivotal role in MLL1's structure and function and serves as a target for drug design. In addition, the CpG pattern in an island governs spatially dependent collaboration among CpGs in recruiting epigenetic enzymes. However, current studies using short DNA fragments cannot probe the dynamics of CXXC on long DNA with crowded CpG motifs. Here, we used single-molecule magnetic tweezers to examine the binding dynamics of MLL1's CXXC domain on a long DNA with a CpG island. The mechanical strand separation assay allows profiling of protein-DNA complexes and reports force-dependent unfolding times. Further design of a hairpin detector reveals the unfolding time of individual CXXC-CpG complexes. Finally, in a proof of concept we demonstrate the inhibiting effect of dimethyl fumarate on the CXXC-DNA complexes by measuring the dose response curve of the unfolding time. This demonstrates the potential feasibility of using single-molecule strand separation as a label-free detector in drug discovery and chemical biology.
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Affiliation(s)
- Lin Liang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, China
| | - Kangkang Ma
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, China
| | - Zeyu Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, China
| | - Richard Janissen
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft, South-Holland, The Netherlands
| | - Zhongbo Yu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, China.
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18
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Kolbeck PJ, Vanderlinden W, Gemmecker G, Gebhardt C, Lehmann M, Lak A, Nicolaus T, Cordes T, Lipfert J. Molecular structure, DNA binding mode, photophysical properties and recommendations for use of SYBR Gold. Nucleic Acids Res 2021; 49:5143-5158. [PMID: 33905507 PMCID: PMC8136779 DOI: 10.1093/nar/gkab265] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/29/2021] [Accepted: 04/05/2021] [Indexed: 01/08/2023] Open
Abstract
SYBR Gold is a commonly used and particularly bright fluorescent DNA stain, however, its chemical structure is unknown and its binding mode to DNA remains controversial. Here, we solve the structure of SYBR Gold by NMR and mass spectrometry to be [2-[N-(3-dimethylaminopropyl)-N-propylamino]-4-[2,3-dihydro-3-methyl-(benzo-1,3-thiazol-2-yl)-methylidene]-1-phenyl-quinolinium] and determine its extinction coefficient. We quantitate SYBR Gold binding to DNA using two complementary approaches. First, we use single-molecule magnetic tweezers (MT) to determine the effects of SYBR Gold binding on DNA length and twist. The MT assay reveals systematic lengthening and unwinding of DNA by 19.1° ± 0.7° per molecule upon binding, consistent with intercalation, similar to the related dye SYBR Green I. We complement the MT data with spectroscopic characterization of SYBR Gold. The data are well described by a global binding model for dye concentrations ≤2.5 μM, with parameters that quantitatively agree with the MT results. The fluorescence increases linearly with the number of intercalated SYBR Gold molecules up to dye concentrations of ∼2.5 μM, where quenching and inner filter effects become relevant. In summary, we provide a mechanistic understanding of DNA-SYBR Gold interactions and present practical guidelines for optimal DNA detection and quantitative DNA sensing applications using SYBR Gold.
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Affiliation(s)
- Pauline J Kolbeck
- Department of Physics and Center for NanoScience, LMU Munich, Amalienstrasse 54, 80799 Munich, Germany
| | - Willem Vanderlinden
- Department of Physics and Center for NanoScience, LMU Munich, Amalienstrasse 54, 80799 Munich, Germany
| | - Gerd Gemmecker
- Bavarian NMR Center (BNMRZ), Department of Chemistry, Technical University of Munich, Garching, Germany
| | - Christian Gebhardt
- Physical and Synthetic Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Martin Lehmann
- Plant Molecular Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Aidin Lak
- Department of Physics and Center for NanoScience, LMU Munich, Amalienstrasse 54, 80799 Munich, Germany
| | - Thomas Nicolaus
- Department of Physics and Center for NanoScience, LMU Munich, Amalienstrasse 54, 80799 Munich, Germany
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Jan Lipfert
- Department of Physics and Center for NanoScience, LMU Munich, Amalienstrasse 54, 80799 Munich, Germany
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19
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Liang L, Wang Z, Qu L, Huang W, Guo S, Guan X, Zhang W, Sun F, Yuan H, Zou H, Liu H, Yu Z. Single-molecule multiplexed profiling of protein-DNA complexes using magnetic tweezers. J Biol Chem 2021; 296:100327. [PMID: 33493518 PMCID: PMC7949110 DOI: 10.1016/j.jbc.2021.100327] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 01/10/2021] [Accepted: 01/21/2021] [Indexed: 01/14/2023] Open
Abstract
Epigenetics, such as the dynamic interplay between DNA methylation and demethylation, play diverse roles in critical cellular events. Enzymatic activity at CpG sites, where cytosines are methylated or demethylated, is known to be influenced by the density of CpGs, methylation states, and the flanking sequences of a CpG site. However, how the relevant enzymes are recruited to and recognize their target DNA is less clear. Moreover, although DNA-binding epigenetic enzymes are ideal targets for therapeutic intervention, these targets have been rarely exploited. Single-molecule techniques offer excellent capabilities to probe site-specific protein-DNA interactions and unravel the dynamics. Here, we develop a single-molecule approach that allows multiplexed profiling of protein-DNA complexes using magnetic tweezers. When a DNA hairpin with multiple binding sites is unzipping, strand separation pauses at the positions bound by a protein. We can thus measure site-specific binding probabilities and dissociation time directly. Taking the TET1 CXXC domain as an example, we show that TET1 CXXC binds multiple CpG motifs with various flanking nucleotides or different methylation patterns in an AT-rich DNA. We are able to establish for the first time, at nanometer resolution, that TET1 CXXC prefers G/C flanked CpG motif over C/G, A/T, or T/A flanked ones. CpG methylation strengthens TET1 CXXC recruitment but has little effect on dissociation time. Finally, we demonstrate that TET1 CXXC can distinguish five CpG clusters in a CpG island with crowded binding motifs. We anticipate that the feasibility of single-molecule multiplexed profiling assays will contribute to the understanding of protein-DNA interactions.
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Affiliation(s)
- Lin Liang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, China
| | - Zeyu Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, China
| | - Lihua Qu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, China
| | - Wei Huang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, China
| | - Shuang Guo
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, China
| | - Xiangchen Guan
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, China
| | - Wei Zhang
- Tianjin Key Laboratory of Optoelectronic Sensor and Sensing Network Technology, Institute of Modern Optics, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, China
| | - Fuping Sun
- Tianjin Key Laboratory of Optoelectronic Sensor and Sensing Network Technology, Institute of Modern Optics, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, China
| | - Hongrui Yuan
- Tianjin Key Laboratory of Optoelectronic Sensor and Sensing Network Technology, Institute of Modern Optics, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, China
| | - Huiru Zou
- Central Laboratory of Tianjin Stomatological Hospital, The Affiliated Stomatological Hospital of Nankai University, Tianjin, China
| | - Haitao Liu
- Tianjin Key Laboratory of Optoelectronic Sensor and Sensing Network Technology, Institute of Modern Optics, College of Electronic Information and Optical Engineering, Nankai University, Tianjin, China
| | - Zhongbo Yu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, China.
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20
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余 平. The Effect of Magnetic Field Direction on the Extension Noise in Magnetic Tweezers Measurement. Biophysics (Nagoya-shi) 2021. [DOI: 10.12677/biphy.2021.91001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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21
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Agarwal R, Duderstadt KE. Multiplex flow magnetic tweezers reveal rare enzymatic events with single molecule precision. Nat Commun 2020; 11:4714. [PMID: 32948754 PMCID: PMC7501243 DOI: 10.1038/s41467-020-18456-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 08/21/2020] [Indexed: 02/08/2023] Open
Abstract
The application of forces and torques on the single molecule level has transformed our understanding of the dynamic properties of biomolecules, but rare intermediates have remained difficult to characterize due to limited throughput. Here, we describe a method that provides a 100-fold improvement in the throughput of force spectroscopy measurements with topological control, which enables routine imaging of 50,000 single molecules and a 100 million reaction cycles in parallel. This improvement enables detection of rare events in the life cycle of the cell. As a demonstration, we characterize the supercoiling dynamics and drug-induced DNA break intermediates of topoisomerases. To rapidly quantify distinct classes of dynamic behaviors and rare events, we developed a software platform with an automated feature classification pipeline. The method and software can be readily adapted for studies of a broad range of complex, multistep enzymatic pathways in which rare intermediates have escaped classification due to limited throughput.
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Affiliation(s)
- Rohit Agarwal
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
- Physik Department, Technische Universität München, Garching, Germany
| | - Karl E Duderstadt
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany.
- Physik Department, Technische Universität München, Garching, Germany.
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22
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Carrasco C, Pastrana CL, Aicart-Ramos C, Leuba SH, Khan S, Moreno-Herrero F. Dynamics of DNA nicking and unwinding by the RepC-PcrA complex. Nucleic Acids Res 2020; 48:2013-2025. [PMID: 31930301 PMCID: PMC7038956 DOI: 10.1093/nar/gkz1200] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 12/10/2019] [Accepted: 12/18/2019] [Indexed: 01/22/2023] Open
Abstract
The rolling-circle replication is the most common mechanism for the replication of small plasmids carrying antibiotic resistance genes in Gram-positive bacteria. It is initiated by the binding and nicking of double-stranded origin of replication by a replication initiator protein (Rep). Duplex unwinding is then performed by the PcrA helicase, whose processivity is critically promoted by its interaction with Rep. How Rep and PcrA proteins interact to nick and unwind the duplex is not fully understood. Here, we have used magnetic tweezers to monitor PcrA helicase unwinding and its relationship with the nicking activity of Staphylococcus aureus plasmid pT181 initiator RepC. Our results indicate that PcrA is a highly processive helicase prone to stochastic pausing, resulting in average translocation rates of 30 bp s-1, while a typical velocity of 50 bp s-1 is found in the absence of pausing. Single-strand DNA binding protein did not affect PcrA translocation velocity but slightly increased its processivity. Analysis of the degree of DNA supercoiling required for RepC nicking, and the time between RepC nicking and DNA unwinding, suggests that RepC and PcrA form a protein complex on the DNA binding site before nicking. A comprehensive model that rationalizes these findings is presented.
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Affiliation(s)
- Carolina Carrasco
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049 Cantoblanco, Madrid, Spain
| | - Cesar L Pastrana
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049 Cantoblanco, Madrid, Spain
| | - Clara Aicart-Ramos
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049 Cantoblanco, Madrid, Spain
| | - Sanford H Leuba
- Departments of Cell Biology and Bioengineering, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Pittsburgh, PA 15213, USA
| | - Saleem A Khan
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA 15219, USA
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049 Cantoblanco, Madrid, Spain
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23
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Multiplexed protein force spectroscopy reveals equilibrium protein folding dynamics and the low-force response of von Willebrand factor. Proc Natl Acad Sci U S A 2019; 116:18798-18807. [PMID: 31462494 PMCID: PMC6754583 DOI: 10.1073/pnas.1901794116] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Single-molecule force spectroscopy has provided unprecedented insights into protein folding, force regulation, and function. So far, the field has relied primarily on atomic force microscope and optical tweezers assays that, while powerful, are limited in force resolution, throughput, and require feedback for constant force measurements. Here, we present a modular approach based on magnetic tweezers (MT) for highly multiplexed protein force spectroscopy. Our approach uses elastin-like polypeptide linkers for the specific attachment of proteins, requiring only short peptide tags on the protein of interest. The assay extends protein force spectroscopy into the low force (<1 pN) regime and enables parallel and ultra-stable measurements at constant forces. We present unfolding and refolding data for the small, single-domain protein ddFLN4, commonly used as a molecular fingerprint in force spectroscopy, and for the large, multidomain dimeric protein von Willebrand factor (VWF) that is critically involved in primary hemostasis. For both proteins, our measurements reveal exponential force dependencies of unfolding and refolding rates. We directly resolve the stabilization of the VWF A2 domain by Ca2+ and discover transitions in the VWF C domain stem at low forces that likely constitute the first steps of VWF's mechano-activation. Probing the force-dependent lifetime of biotin-streptavidin bonds, we find that monovalent streptavidin constructs with specific attachment geometry are significantly more force stable than commercial, multivalent streptavidin. We expect our modular approach to enable multiplexed force-spectroscopy measurements for a wide range of proteins, in particular in the physiologically relevant low-force regime.
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24
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Lee M, Shin S, Uhm H, Hong H, Kirk J, Hyun K, Kulikowicz T, Kim J, Ahn B, Bohr VA, Hohng S. Multiple RPAs make WRN syndrome protein a superhelicase. Nucleic Acids Res 2019; 46:4689-4698. [PMID: 29668972 PMCID: PMC5961295 DOI: 10.1093/nar/gky272] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 04/11/2018] [Indexed: 02/01/2023] Open
Abstract
RPA is known to stimulate the helicase activity of Werner syndrome protein (WRN), but the exact stimulation mechanism is not understood. We use single-molecule FRET and magnetic tweezers to investigate the helicase activity of WRN and its stimulation by RPA. We show that WRN alone is a weak helicase which repetitively unwind just a few tens of base pairs, but that binding of multiple RPAs to the enzyme converts WRN into a superhelicase that unidirectionally unwinds double-stranded DNA more than 1 kb. Our study provides a good case in which the activity and biological functions of the enzyme may be fundamentally altered by the binding of cofactors.
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Affiliation(s)
- Mina Lee
- Center for Nano-Bio Measurement, Korea Research Institute of Standards and Science, Daejeon, Republic of Korea
| | - Soochul Shin
- Department of Physics and Astronomy, Institute of Applied Physics, National Center of Creative Research Initiatives, Seoul National University, Seoul, Republic of Korea
| | - Heesoo Uhm
- Department of Physics and Astronomy, Institute of Applied Physics, National Center of Creative Research Initiatives, Seoul National University, Seoul, Republic of Korea
| | - Heesun Hong
- Department of Physics and Astronomy, Institute of Applied Physics, National Center of Creative Research Initiatives, Seoul National University, Seoul, Republic of Korea
| | - Jaewon Kirk
- Department of Physics and Astronomy, Institute of Applied Physics, National Center of Creative Research Initiatives, Seoul National University, Seoul, Republic of Korea
| | - Kwangbeom Hyun
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Tomasz Kulikowicz
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jaehoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Byungchan Ahn
- Department of Life Sciences, University of Ulsan, Ulsan, Republic of Korea
| | - Vilhelm A Bohr
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Sungchul Hohng
- Department of Physics and Astronomy, Institute of Applied Physics, National Center of Creative Research Initiatives, Seoul National University, Seoul, Republic of Korea
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25
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Shon MJ, Rah SH, Yoon TY. Submicrometer elasticity of double-stranded DNA revealed by precision force-extension measurements with magnetic tweezers. SCIENCE ADVANCES 2019; 5:eaav1697. [PMID: 31206015 PMCID: PMC6561745 DOI: 10.1126/sciadv.aav1697] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 05/03/2019] [Indexed: 05/07/2023]
Abstract
Submicrometer elasticity of double-stranded DNA (dsDNA) governs nanoscale bending of DNA segments and their interactions with proteins. Single-molecule force spectroscopy, including magnetic tweezers (MTs), is an important tool for studying DNA mechanics. However, its application to short DNAs under 1 μm is limited. We developed an MT-based method for precise force-extension measurements in the 100-nm regime that enables in situ correction of the error in DNA extension measurement, and normalizes the force variability across beads by exploiting DNA hairpins. The method reduces the lower limit of tractable dsDNA length down to 198 base pairs (bp) (67 nm), an order-of-magnitude improvement compared to conventional tweezing experiments. Applying this method and the finite worm-like chain model we observed an essentially constant persistence length across the chain lengths studied (198 bp to 10 kbp), which steeply depended on GC content and methylation. This finding suggests a potential sequence-dependent mechanism for short-DNA elasticity.
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Affiliation(s)
- Min Ju Shon
- School of Biological Sciences and Institute for Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
- Corresponding author. (T.-Y.Y.); (M.J.S.)
| | - Sang-Hyun Rah
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Tae-Young Yoon
- School of Biological Sciences and Institute for Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
- Corresponding author. (T.-Y.Y.); (M.J.S.)
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26
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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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27
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Focused clamping of a single neuronal SNARE complex by complexin under high mechanical tension. Nat Commun 2018; 9:3639. [PMID: 30194295 PMCID: PMC6128827 DOI: 10.1038/s41467-018-06122-3] [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: 05/30/2018] [Accepted: 08/14/2018] [Indexed: 01/10/2023] Open
Abstract
Neuronal soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) catalyze synaptic vesicle fusion with presynaptic membranes through the formation of SNARE complexes. Complexin (Cpx) is the only presynaptic protein that tightly binds to SNAREs and regulates membrane fusion, but how it modulates the energy landscape of SNARE complex assembly, especially under mechanical tension on the complex, remains unclear. Here, using magnetic tweezers, we report how Cpx interacts with single SNARE complexes. The effects of Cpx manifest only under high mechanical tensions above 13 pN. Cpx stabilizes the central four-helix bundle of SNARE motifs and, at the same time, prevents the complete zippering of SNAREs by inhibiting linker-domain assembly. These results suggest that Cpx generates a focused clamp for the neuronal SNARE complex in a linker-open conformation. Our results provide a hint as to how Cpx cooperates with neuronal SNAREs to prime synaptic vesicles in preparation for synchronous neurotransmitter release. The SNARE complex enables the fusion of synaptic vesicles with presynaptic membrane via a zippering process that is modulated by the protein complexin, though the precise mechanism remains unclear. Here, the authors used magnetic tweezers to show how complexin prepares a SNARE complex for fusion under mechanical tension.
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28
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Dutta S, Benetatos P. Inequivalence of fixed-force and fixed-extension statistical ensembles for a flexible polymer tethered to a planar substrate. SOFT MATTER 2018; 14:6857-6866. [PMID: 30101250 DOI: 10.1039/c8sm01321g] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Recent advances in single macromolecule experiments have sparked interest in the ensemble dependence of force-extension relations. The thermodynamic limit may not be attainable for such systems, which leads to inequivalence of the fixed-force and the fixed-extension ensembles. We consider an ideal Gaussian chain described by the Edwards Hamiltonian with one end tethered to a rigid planar substrate. We analytically calculate the force-extension relation in the two ensembles and we show their inequivalence, which is caused by the confinement of the polymer to half space. The inequivalence is quite remarkable for strong compressional forces. We also perform Monte-Carlo simulations of a tethered wormlike chain with contour length 20 times its persistence length, which corresponds to experiments measuring the conformations of DNA tethered to a wall. The simulations confirm the ensemble inequivalence and qualitatively agree with the analytical predictions of the Gaussian model. Our analysis shows that confinement due to tethering causes ensemble inequivalence, irrespective of the polymer model.
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Affiliation(s)
- Sandipan Dutta
- Center for Soft and Living Matter, Institute for Basic Science, Ulsan 44919, Korea
| | - Panayotis Benetatos
- Department of Physics, Kyungpook National University, 80 Daehakro, Bukgu, Daegu 41566, Korea.
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29
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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.
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30
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Lin SN, Qin L, Wuite GJL, Dame RT. Unraveling the Biophysical Properties of Chromatin Proteins and DNA Using Acoustic Force Spectroscopy. Methods Mol Biol 2018; 1837:301-316. [PMID: 30109617 DOI: 10.1007/978-1-4939-8675-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Acoustic Force Spectroscopy (AFS) is a single-molecule micromanipulation technique that uses sound waves to exert force on surface-tethered DNA molecules in a microfluidic chamber. As large numbers of individual protein-DNA complexes are tracked in parallel, AFS provides insight into the individual properties of such complexes as well as their population averages. In this chapter, we describe in detail how to perform AFS experiments specifically on bare DNA, protein-DNA complexes, and how to extract their (effective) persistence length and contour length from force-extension relations.
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Affiliation(s)
- Szu-Ning Lin
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.,Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Liang Qin
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Gijs J L Wuite
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| | - Remus T Dame
- Leiden Institute of Chemistry and Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands.
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31
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Martín-García B, Martín-González A, Carrasco C, Hernández-Arriaga AM, Ruíz-Quero R, Díaz-Orejas R, Aicart-Ramos C, Moreno-Herrero F, Oliva MA. The TubR-centromere complex adopts a double-ring segrosome structure in Type III partition systems. Nucleic Acids Res 2018; 46:5704-5716. [PMID: 29762781 PMCID: PMC6009700 DOI: 10.1093/nar/gky370] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 04/27/2018] [Indexed: 11/26/2022] Open
Abstract
In prokaryotes, the centromere is a specialized segment of DNA that promotes the assembly of the segrosome upon binding of the Centromere Binding Protein (CBP). The segrosome structure exposes a specific surface for the interaction of the CBP with the motor protein that mediates DNA movement during cell division. Additionally, the CBP usually controls the transcriptional regulation of the segregation system as a cell cycle checkpoint. Correct segrosome functioning is therefore indispensable for accurate DNA segregation. Here, we combine biochemical reconstruction and structural and biophysical analysis to bring light to the architecture of the segrosome complex in Type III partition systems. We present the particular features of the centromere site, tubC, of the model system encoded in Clostridium botulinum prophage c-st. We find that the split centromere site contains two different iterons involved in the binding and spreading of the CBP, TubR. The resulting nucleoprotein complex consists of a novel double-ring structure that covers part of the predicted promoter. Single molecule data provides a mechanism for the formation of the segrosome structure based on DNA bending and unwinding upon TubR binding.
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Affiliation(s)
- Bárbara Martín-García
- Department of Structural and Chemical Biology, CSIC-Centro de Investigaciones Biológicas, Madrid 28040, Spain
| | | | - Carolina Carrasco
- Department of Macromolecular Structures, CSIC-Centro Nacional de Biotecnología, Madrid 28049, Spain
| | - Ana M Hernández-Arriaga
- Department of Structural and Chemical Biology, CSIC-Centro de Investigaciones Biológicas, Madrid 28040, Spain
| | - Rubén Ruíz-Quero
- Department of Structural and Chemical Biology, CSIC-Centro de Investigaciones Biológicas, Madrid 28040, Spain
| | - Ramón Díaz-Orejas
- Department of Structural and Chemical Biology, CSIC-Centro de Investigaciones Biológicas, Madrid 28040, Spain
| | - Clara Aicart-Ramos
- Department of Macromolecular Structures, CSIC-Centro Nacional de Biotecnología, Madrid 28049, Spain
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, CSIC-Centro Nacional de Biotecnología, Madrid 28049, Spain
| | - María A Oliva
- Department of Structural and Chemical Biology, CSIC-Centro de Investigaciones Biológicas, Madrid 28040, Spain
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32
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Madariaga-Marcos J, Hormeño S, Pastrana CL, Fisher GLM, Dillingham MS, Moreno-Herrero F. Force determination in lateral magnetic tweezers combined with TIRF microscopy. NANOSCALE 2018; 10:4579-4590. [PMID: 29461549 PMCID: PMC5831119 DOI: 10.1039/c7nr07344e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 12/07/2017] [Indexed: 06/08/2023]
Abstract
Combining single-molecule techniques with fluorescence microscopy has attracted much interest because it allows the correlation of mechanical measurements with directly visualized DNA : protein interactions. In particular, its combination with total internal reflection fluorescence microscopy (TIRF) is advantageous because of the high signal-to-noise ratio this technique achieves. This, however, requires stretching long DNA molecules across the surface of a flow cell to maximize polymer exposure to the excitation light. In this work, we develop a module to laterally stretch DNA molecules at a constant force, which can be easily implemented in regular or combined magnetic tweezers (MT)-TIRF setups. The pulling module is further characterized in standard flow cells of different thicknesses and glass capillaries, using two types of micrometer size superparamagnetic beads, long DNA molecules, and a home-built device to rotate capillaries with mrad precision. The force range achieved by the magnetic pulling module was between 0.1 and 30 pN. A formalism for estimating forces in flow-stretched tethered beads is also proposed, and the results compared with those of lateral MT, demonstrating that lateral MT achieve higher forces with lower dispersion. Finally, we show the compatibility with TIRF microscopy and the parallelization of measurements by characterizing DNA binding by the centromere-binding protein ParB from Bacillus subtilis. Simultaneous MT pulling and fluorescence imaging demonstrate the non-specific binding of BsParB on DNA under conditions restrictive to condensation.
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Affiliation(s)
- J. Madariaga-Marcos
- Department of Macromolecular Structures , Centro Nacional de Biotecnología , Consejo Superior de Investigaciones Científicas , 28049 Cantoblanco , Madrid , Spain .
| | - S. Hormeño
- Department of Macromolecular Structures , Centro Nacional de Biotecnología , Consejo Superior de Investigaciones Científicas , 28049 Cantoblanco , Madrid , Spain .
| | - C. L. Pastrana
- Department of Macromolecular Structures , Centro Nacional de Biotecnología , Consejo Superior de Investigaciones Científicas , 28049 Cantoblanco , Madrid , Spain .
| | - G. L. M. Fisher
- DNA:Protein Interactions Unit , School of Biochemistry , Biomedical Sciences Building , University of Bristol , Bristol , BS8 1TD , UK
| | - M. S. Dillingham
- DNA:Protein Interactions Unit , School of Biochemistry , Biomedical Sciences Building , University of Bristol , Bristol , BS8 1TD , UK
| | - F. Moreno-Herrero
- Department of Macromolecular Structures , Centro Nacional de Biotecnología , Consejo Superior de Investigaciones Científicas , 28049 Cantoblanco , Madrid , Spain .
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33
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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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34
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Brouwer TB, Kaczmarczyk A, Pham C, van Noort J. Unraveling DNA Organization with Single-Molecule Force Spectroscopy Using Magnetic Tweezers. Methods Mol Biol 2018; 1837:317-349. [PMID: 30109618 DOI: 10.1007/978-1-4939-8675-0_17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Genomes carry the genetic blueprint of all living organisms. Their organization requires strong condensation as well as carefully regulated accessibility to specific genes for proper functioning of their hosts. The study of the structure and dynamics of the proteins that organize the genome has benefited tremendously from the development of single-molecule force spectroscopy techniques that allow for real-time, nanometer accuracy measurements of the compaction of DNA and manipulation with pico-Newton scale forces. Magnetic tweezers in particular have the unique ability to complement such force spectroscopy with the control over the linking number of the DNA molecule, which plays an important role when DNA organizing proteins form or release wraps, loops, and bends in DNA. Here, we describe all the necessary steps to prepare DNA substrates for magnetic tweezers experiments, assemble flow cells, tether DNA to magnetics bead inside flow cell, and manipulate and record the extension of such DNA tethers. Furthermore, we explain how mechanical parameters of nucleo-protein filaments can be extracted from the data.
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Affiliation(s)
- Thomas B Brouwer
- Huygens-Kamerlingh Onnes Laboratory, Leiden Institute of Physics, Leiden University, Niels Bohrweg 2, Leiden, CA, The Netherlands
| | - Artur Kaczmarczyk
- Huygens-Kamerlingh Onnes Laboratory, Leiden Institute of Physics, Leiden University, Niels Bohrweg 2, Leiden, CA, The Netherlands
| | - Chi Pham
- Huygens-Kamerlingh Onnes Laboratory, Leiden Institute of Physics, Leiden University, Niels Bohrweg 2, Leiden, CA, The Netherlands
| | - John van Noort
- Huygens-Kamerlingh Onnes Laboratory, Leiden Institute of Physics, Leiden University, Niels Bohrweg 2, Leiden, CA, The Netherlands.
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35
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Kriegel F, Vanderlinden W, Nicolaus T, Kardinal A, Lipfert J. Measuring Single-Molecule Twist and Torque in Multiplexed Magnetic Tweezers. Methods Mol Biol 2018; 1814:75-98. [PMID: 29956228 DOI: 10.1007/978-1-4939-8591-3_6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Magnetic tweezers permit application of precisely calibrated stretching forces to nucleic acid molecules tethered between a surface and superparamagnetic beads. In addition, magnetic tweezers can control the tethers' twist. Here, we focus on recent extensions of the technique that expand the capabilities of conventional magnetic tweezers by enabling direct measurements of single-molecule torque and twist. Magnetic torque tweezers (MTT) still control the DNA or RNA tether's twist, but directly measure molecular torque by monitoring changes in the equilibrium rotation angle upon overwinding and underwinding of the tether. In freely orbiting magnetic tweezers (FOMT), one end of the tether is allowed to rotate freely, while still applying stretching forces and monitoring rotation angle. Both MTT and FOMT have provided unique insights into the mechanical properties, structural transitions, and interactions of DNA and RNA. Here, we provide step-by-step protocols to carry out FOMT and MTT measurements. In particular, we focus on multiplexed measurements, i.e., measurements that record data for multiple nucleic acid tethers at the same time, to improve statistics and to facilitate the observation of rare events.
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Affiliation(s)
- Franziska Kriegel
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, Munich, Germany
| | - Willem Vanderlinden
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, Munich, Germany.,Division of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven-University of Leuven, Leuven, Belgium
| | - Thomas Nicolaus
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, Munich, Germany
| | - Angelika Kardinal
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, Munich, Germany
| | - Jan Lipfert
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, Munich, Germany.
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36
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Liu C, Kubo K, Wang E, Han KS, Yang F, Chen G, Escobedo FA, Coates GW, Chen P. Single polymer growth dynamics. Science 2017; 358:352-355. [DOI: 10.1126/science.aan6837] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 09/11/2017] [Indexed: 11/02/2022]
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37
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Kamsma D, Wuite GJL. Single-Molecule Measurements Using Acoustic Force Spectroscopy (AFS). Methods Mol Biol 2017; 1665:341-351. [PMID: 28940078 DOI: 10.1007/978-1-4939-7271-5_18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
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38
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Kriegel F, Ermann N, Forbes R, Dulin D, Dekker NH, Lipfert J. Probing the salt dependence of the torsional stiffness of DNA by multiplexed magnetic torque tweezers. Nucleic Acids Res 2017; 45:5920-5929. [PMID: 28460037 PMCID: PMC5449586 DOI: 10.1093/nar/gkx280] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 04/28/2017] [Indexed: 12/14/2022] Open
Abstract
The mechanical properties of DNA fundamentally constrain and enable the storage and transmission of genetic information and its use in DNA nanotechnology. Many properties of DNA depend on the ionic environment due to its highly charged backbone. In particular, both theoretical analyses and direct single-molecule experiments have shown its bending stiffness to depend on salt concentration. In contrast, the salt-dependence of the twist stiffness of DNA is much less explored. Here, we employ optimized multiplexed magnetic torque tweezers to study the torsional stiffness of DNA under varying salt conditions as a function of stretching force. At low forces (<3 pN), the effective torsional stiffness is ∼10% smaller for high salt conditions (500 mM NaCl or 10 mM MgCl2) compared to lower salt concentrations (20 mM NaCl and 100 mM NaCl). These differences, however, can be accounted for by taking into account the known salt dependence of the bending stiffness. In addition, the measured high-force (6.5 pN) torsional stiffness values of C = 103 ± 4 nm are identical, within experimental errors, for all tested salt concentration, suggesting that the intrinsic torsional stiffness of DNA does not depend on salt.
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Affiliation(s)
- Franziska Kriegel
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, Amalienstrasse 54, 80799 Munich, Germany
| | - Niklas Ermann
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, Amalienstrasse 54, 80799 Munich, Germany
| | - Ruaridh Forbes
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - David Dulin
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.,Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Hartmannstrasse 14, 91052 Erlangen, Germany
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jan Lipfert
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, Amalienstrasse 54, 80799 Munich, Germany
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39
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Burnham DR, Nijholt B, De Vlaminck I, Quan J, Yusufzai T, Dekker C. Annealing helicase HARP closes RPA-stabilized DNA bubbles non-processively. Nucleic Acids Res 2017; 45:4687-4695. [PMID: 28334870 PMCID: PMC5416776 DOI: 10.1093/nar/gkx147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 02/27/2017] [Indexed: 02/06/2023] Open
Abstract
We investigate the mechanistic nature of the Snf2 family protein HARP, mutations of which are responsible for Schimke immuno-osseous dysplasia. Using a single-molecule magnetic tweezers assay, we construct RPA-stabilized DNA bubbles within torsionally constrained DNA to investigate the annealing action of HARP on a physiologically relevant substrate. We find that HARP closes RPA-stabilized bubbles in a slow reaction, taking on the order of tens of minutes for ∼600 bp of DNA to be re-annealed. The data indicate that DNA re-anneals through the removal of RPA, which is observed as clear steps in the bubble-closing traces. The dependence of the closing rate on both ionic strength and HARP concentration indicates that removal of RPA occurs via an association-dissociation mechanism where HARP does not remain associated with the DNA. The enzyme exhibits classical Michaelis–Menten kinetics and acts cooperatively with a Hill coefficient of 3 ± 1. Our work also allows the determination of some important features of RPA-bubble structures at low supercoiling, including the existence of multiple bubbles and that RPA molecules are mis-registered on the two strands.
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Affiliation(s)
- Daniel R Burnham
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, 2629 HZ, The Netherlands
| | - Bas Nijholt
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, 2629 HZ, The Netherlands
| | - Iwijn De Vlaminck
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, 2629 HZ, The Netherlands
| | - Jinhua Quan
- Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA
| | - Timur Yusufzai
- Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, 2629 HZ, The Netherlands
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40
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Hodeib S, Raj S, Manosas M, Zhang W, Bagchi D, Ducos B, Fiorini F, Kanaan J, Le Hir H, Allemand J, Bensimon D, Croquette V. A mechanistic study of helicases with magnetic traps. Protein Sci 2017; 26:1314-1336. [PMID: 28474797 PMCID: PMC5477542 DOI: 10.1002/pro.3187] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 04/29/2017] [Accepted: 05/02/2017] [Indexed: 01/08/2023]
Abstract
Helicases are a broad family of enzymes that separate nucleic acid double strand structures (DNA/DNA, DNA/RNA, or RNA/RNA) and thus are essential to DNA replication and the maintenance of nucleic acid integrity. We review the picture that has emerged from single molecule studies of the mechanisms of DNA and RNA helicases and their interactions with other proteins. Many features have been uncovered by these studies that were obscured by bulk studies, such as DNA strands switching, mechanical (rather than biochemical) coupling between helicases and polymerases, helicase-induced re-hybridization and stalled fork rescue.
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Affiliation(s)
- Samar Hodeib
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| | - Saurabh Raj
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| | - Maria Manosas
- Departament de Física FonamentalFacultat de Física, Universitat de BarcelonaBarcelona08028Spain
- CIBER‐BBN de BioingenieriaBiomateriales y Nanomedicina, Instituto de Sanidad Carlos IIIMadridSpain
| | - Weiting Zhang
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| | - Debjani Bagchi
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
- Present address: Physics DepartmentFaculty of Science, The M.S. University of BarodaVadodaraGujarat390002India
| | - Bertrand Ducos
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| | - Francesca Fiorini
- Univ Lyon, Molecular Microbiology and Structural Biochemistry, MMSB‐IBCP UMR5086 CNRS/Lyon1Lyon Cedex 769367France
| | - Joanne Kanaan
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| | - Hervé Le Hir
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| | - Jean‐François Allemand
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
| | - David Bensimon
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
- Department of Chemistry and BiochemistryUniversity of California Los AngelesLos AngelesCalifornia90095
| | - Vincent Croquette
- Laboratoire de physique statistiqueDépartement de physique de l'ENS, École normale supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS75005ParisFrance
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS)Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University75005ParisFrance
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41
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Nomidis SK, Kriegel F, Vanderlinden W, Lipfert J, Carlon E. Twist-Bend Coupling and the Torsional Response of Double-Stranded DNA. PHYSICAL REVIEW LETTERS 2017; 118:217801. [PMID: 28598642 DOI: 10.1103/physrevlett.118.217801] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Indexed: 06/07/2023]
Abstract
Recent magnetic tweezers experiments have reported systematic deviations of the twist response of double-stranded DNA from the predictions of the twistable wormlike chain model. Here we show, by means of analytical results and computer simulations, that these discrepancies can be resolved if a coupling between twist and bend is introduced. We obtain an estimate of 40±10 nm for the twist-bend coupling constant. Our simulations are in good agreement with high-resolution, magnetic-tweezers torque data. Although the existence of twist-bend coupling was predicted long ago [J. Marko and E. Siggia, Macromolecules 27, 981 (1994)MAMOBX0024-929710.1021/ma00082a015], its effects on the mechanical properties of DNA have been so far largely unexplored. We expect that this coupling plays an important role in several aspects of DNA statics and dynamics.
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Affiliation(s)
- Stefanos K Nomidis
- KU Leuven, Institute for Theoretical Physics, Celestijnenlaan 200D, 3001 Leuven, Belgium
- Flemish Institute for Technological Research (VITO), Boeretang 200, B-2400 Mol, Belgium
| | - Franziska Kriegel
- Department of Physics, Nanosystems Initiative Munich, and Center for NanoScience, LMU Munich, Amalienstrasse 54, 80799 Munich, Germany
| | - Willem Vanderlinden
- Department of Physics, Nanosystems Initiative Munich, and Center for NanoScience, LMU Munich, Amalienstrasse 54, 80799 Munich, Germany
- KU Leuven, Division of Molecular Imaging and Photonics, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Jan Lipfert
- Department of Physics, Nanosystems Initiative Munich, and Center for NanoScience, LMU Munich, Amalienstrasse 54, 80799 Munich, Germany
| | - Enrico Carlon
- KU Leuven, Institute for Theoretical Physics, Celestijnenlaan 200D, 3001 Leuven, Belgium
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42
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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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43
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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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44
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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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45
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Pastrana CL, Carrasco C, Akhtar P, Leuba SH, Khan SA, Moreno-Herrero F. Force and twist dependence of RepC nicking activity on torsionally-constrained DNA molecules. Nucleic Acids Res 2016; 44:8885-8896. [PMID: 27488190 PMCID: PMC5062986 DOI: 10.1093/nar/gkw689] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/22/2016] [Indexed: 11/14/2022] Open
Abstract
Many bacterial plasmids replicate by an asymmetric rolling-circle mechanism that requires sequence-specific recognition for initiation, nicking of one of the template DNA strands and unwinding of the duplex prior to subsequent leading strand DNA synthesis. Nicking is performed by a replication-initiation protein (Rep) that directly binds to the plasmid double-stranded origin and remains covalently bound to its substrate 5′-end via a phosphotyrosine linkage. It has been proposed that the inverted DNA sequences at the nick site form a cruciform structure that facilitates DNA cleavage. However, the role of Rep proteins in the formation of this cruciform and the implication for its nicking and religation functions is unclear. Here, we have used magnetic tweezers to directly measure the DNA nicking and religation activities of RepC, the replication initiator protein of plasmid pT181, in plasmid sized and torsionally-constrained linear DNA molecules. Nicking by RepC occurred only in negatively supercoiled DNA and was force- and twist-dependent. Comparison with a type IB topoisomerase in similar experiments highlighted a relatively inefficient religation activity of RepC. Based on the structural modeling of RepC and on our experimental evidence, we propose a model where RepC nicking activity is passive and dependent upon the supercoiling degree of the DNA substrate.
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Affiliation(s)
- Cesar L Pastrana
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049 Cantoblanco, Madrid, Spain
| | - Carolina Carrasco
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049 Cantoblanco, Madrid, Spain
| | - Parvez Akhtar
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA 15219, USA
| | - Sanford H Leuba
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Saleem A Khan
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA 15219, USA
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049 Cantoblanco, Madrid, Spain
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46
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Berghuis BA, Köber M, van Laar T, Dekker NH. High-throughput, high-force probing of DNA-protein interactions with magnetic tweezers. Methods 2016; 105:90-8. [DOI: 10.1016/j.ymeth.2016.03.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/23/2016] [Accepted: 03/29/2016] [Indexed: 12/19/2022] Open
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47
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Hodeib S, Raj S, Manosas M, Zhang W, Bagchi D, Ducos B, Allemand JF, Bensimon D, Croquette V. Single molecule studies of helicases with magnetic tweezers. Methods 2016; 105:3-15. [DOI: 10.1016/j.ymeth.2016.06.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/31/2016] [Accepted: 06/20/2016] [Indexed: 10/21/2022] Open
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48
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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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49
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Abstract
In all organisms, DNA molecules are tightly compacted into a dynamic 3D nucleoprotein complex. In bacteria, this compaction is governed by the family of nucleoid-associated proteins (NAPs). Under conditions of stress and starvation, an NAP called Dps (DNA-binding protein from starved cells) becomes highly up-regulated and can massively reorganize the bacterial chromosome. Although static structures of Dps-DNA complexes have been documented, little is known about the dynamics of their assembly. Here, we use fluorescence microscopy and magnetic-tweezers measurements to resolve the process of DNA compaction by Dps. Real-time in vitro studies demonstrated a highly cooperative process of Dps binding characterized by an abrupt collapse of the DNA extension, even under applied tension. Surprisingly, we also discovered a reproducible hysteresis in the process of compaction and decompaction of the Dps-DNA complex. This hysteresis is extremely stable over hour-long timescales despite the rapid binding and dissociation rates of Dps. A modified Ising model is successfully applied to fit these kinetic features. We find that long-lived hysteresis arises naturally as a consequence of protein cooperativity in large complexes and provides a useful mechanism for cells to adopt unique epigenetic states.
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50
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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.
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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.
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