1
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Chen P, Li G, Li W. Nucleosome Dynamics Derived at the Single-Molecule Level Bridges Its Structures and Functions. JACS AU 2024; 4:866-876. [PMID: 38559720 PMCID: PMC10976579 DOI: 10.1021/jacsau.3c00658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 04/04/2024]
Abstract
Nucleosome, the building block of chromatin, plays pivotal roles in all DNA-related processes. While cryogenic-electron microscopy (cryo-EM) has significantly advanced our understanding of nucleosome structures, the emerging field of single-molecule force spectroscopy is illuminating their dynamic properties. This technique is crucial for revealing how nucleosome behavior is influenced by chaperones, remodelers, histone variants, and post-translational modifications, particularly in their folding and unfolding mechanisms under tension. Such insights are vital for deciphering the complex interplay in nucleosome assembly and structural regulation, highlighting the nucleosome's versatility in response to DNA activities. In this Perspective, we aim to consolidate the latest advancements in nucleosome dynamics, with a special focus on the revelations brought forth by single-molecule manipulation. Our objective is to highlight the insights gained from studying nucleosome dynamics through this innovative approach, emphasizing the transformative impact of single-molecule manipulation techniques in the field of chromatin research.
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Affiliation(s)
- Ping Chen
- National
Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation
and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China
- Department
of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory
for Tumor Invasion and Metastasis, Capital
Medical University, Beijing 100069, P. R. China
| | - Guohong Li
- National
Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation
and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China
- University
of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Wei Li
- National
Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation
and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China
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2
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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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3
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Madariaga-Marcos J, Aldag P, Kauert DJ, Seidel R. Correlated Single-Molecule Magnetic Tweezers and Fluorescence Measurements of DNA-Enzyme Interactions. Methods Mol Biol 2024; 2694:421-449. [PMID: 37824016 DOI: 10.1007/978-1-0716-3377-9_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Combining force spectroscopy and fluorescence microscopy provides a substantial improvement to the single-molecule toolbox by allowing simultaneous manipulation and orthogonal characterizations of the conformations, interactions, and activity of biomolecular complexes. Here, we describe a combined magnetic tweezers and total internal reflection fluorescence microscopy setup to carry out correlated single-molecule fluorescence spectroscopy and force/twisting experiments. We apply the setup to reveal the DNA interactions of the CRISPR-Cas surveillance complex Cascade. Single-molecule fluorescence of a labeled Cascade allows to follow the DNA association and dissociation of the protein. Simultaneously, the magnetic tweezers probe the DNA unwinding during R-loop formation by the bound Cascade complexes. Furthermore, the setup supports observation of 1D diffusion of protein complexes on stretched DNA molecules. This technique can be applied to study a vast range of protein-DNA interactions.
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Affiliation(s)
- Julene Madariaga-Marcos
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany
| | - Pierre Aldag
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany
| | - Dominik J Kauert
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany
| | - Ralf Seidel
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany.
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4
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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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5
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Wang Y, Wang H, Zhang S, Yang Z, Shi X, Zhang L. Exploration of the Character Representation of DNA Chiral Conformations and Deformations via a Curved Surface Discrete Frenet Frame. Int J Mol Sci 2023; 25:4. [PMID: 38203177 PMCID: PMC10778681 DOI: 10.3390/ijms25010004] [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: 11/20/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024] Open
Abstract
While undergoing structural deformation, DNA experiences changes in the interactions between its internal base pairs, presenting challenges to conventional elastic methods. To address this, we propose the Discrete Critical State (DCS) model in this paper. This model combines surface discrete frame theory with gauge theory and Landau phase transition theory to investigate DNA's structural deformation, phase transitions, and chirality. Notably, the DCS model considers both the internal interactions within DNA and formulates an overall equation using unified physical and geometric parameters. By employing the discrete frame, we derive the evolution of physical quantities along the helical axis of DNA, including geodesic curvature, geodesic torsion, and others. Our findings indicate that B-DNA has a significantly lower free energy density compared to Z-DNA, which is in agreement with experimental observations. This research reveals that the direction of base pairs is primarily governed by the geodesic curve within the helical plane, aligning closely with the orientation of the base pairs. Moreover, the geodesic curve has a profound influence on the arrangement of base pairs at the microscopic level and effectively regulates the configuration and geometry of DNA through macroscopic-level free energy considerations.
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Affiliation(s)
- Ying Wang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China; (Y.W.); (H.W.); (S.Z.); (Z.Y.)
| | - He Wang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China; (Y.W.); (H.W.); (S.Z.); (Z.Y.)
| | - Shengli Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China; (Y.W.); (H.W.); (S.Z.); (Z.Y.)
| | - Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China; (Y.W.); (H.W.); (S.Z.); (Z.Y.)
| | - Xuguang Shi
- College of Science, Beijing Forestry University, Beijing 100083, China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China; (Y.W.); (H.W.); (S.Z.); (Z.Y.)
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6
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Kauert DJ, Madariaga-Marcos J, Rutkauskas M, Wulfken A, Songailiene I, Sinkunas T, Siksnys V, Seidel R. The energy landscape for R-loop formation by the CRISPR-Cas Cascade complex. Nat Struct Mol Biol 2023:10.1038/s41594-023-01019-2. [PMID: 37415009 DOI: 10.1038/s41594-023-01019-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/11/2023] [Indexed: 07/08/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) sequences and CRISPR-associated (Cas) genes comprise CIRSPR-Cas effector complexes, which have revolutionized gene editing with their ability to target specific genomic loci using CRISPR RNA (crRNA) complementarity. Recognition of double-stranded DNA targets proceeds via DNA unwinding and base pairing between crRNA and the DNA target strand, forming an R-loop structure. Full R-loop extension is a prerequisite for subsequent DNA cleavage. However, the recognition of unintended sequences with multiple mismatches has limited therapeutic applications and is still poorly understood on a mechanistic level. Here we set up ultrafast DNA unwinding experiments on the basis of plasmonic DNA origami nanorotors to study R-loop formation by the Cascade effector complex in real time, close to base-pair resolution. We resolve a weak global downhill bias of the forming R-loop, followed by a steep uphill bias for the final base pairs. We also show that the energy landscape is modulated by base flips and mismatches. These findings suggest that Cascade-mediated R-loop formation occurs on short timescales in submillisecond single base-pair steps, but on longer timescales in six base-pair intermediate steps, in agreement with the structural periodicity of the crRNA-DNA hybrid.
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Affiliation(s)
- Dominik J Kauert
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany
| | | | - Marius Rutkauskas
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany
| | - Alexander Wulfken
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany
| | - Inga Songailiene
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Tomas Sinkunas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Virginijus Siksnys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Ralf Seidel
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, Leipzig, Germany.
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7
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Galvin CJ, Hobson M, Meng JX, Ierokomos A, Ivanov IE, Berger JM, Bryant Z. Single-molecule dynamics of DNA gyrase in evolutionarily distant bacteria Mycobacterium tuberculosis and Escherichia coli. J Biol Chem 2023; 299:103003. [PMID: 36775125 PMCID: PMC10130225 DOI: 10.1016/j.jbc.2023.103003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
DNA gyrase is an essential nucleoprotein motor present in all bacteria and is a major target for antibiotic treatment of Mycobacterium tuberculosis (MTB) infection. Gyrase hydrolyzes ATP to add negative supercoils to DNA using a strand passage mechanism that has been investigated using biophysical and biochemical approaches. To analyze the dynamics of substeps leading to strand passage, single-molecule rotor bead tracking (RBT) has been used previously to follow real-time supercoiling and conformational transitions in Escherichia coli (EC) gyrase. However, RBT has not yet been applied to gyrase from other pathogenically relevant bacteria, and it is not known whether substeps are conserved across evolutionarily distant species. Here, we compare gyrase supercoiling dynamics between two evolutionarily distant bacterial species, MTB and EC. We used RBT to measure supercoiling rates, processivities, and the geometries and transition kinetics of conformational states of purified gyrase proteins in complex with DNA. Our results show that E. coli and MTB gyrases are both processive, with the MTB enzyme displaying velocities ∼5.5× slower than the EC enzyme. Compared with EC gyrase, MTB gyrase also more readily populates an intermediate state with DNA chirally wrapped around the enzyme, in both the presence and absence of ATP. Our substep measurements reveal common features in conformational states of EC and MTB gyrases interacting with DNA but also suggest differences in populations and transition rates that may reflect distinct cellular needs between these two species.
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Affiliation(s)
- Cooper J Galvin
- Program in Biophysics, Stanford University, Stanford, California, USA; Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Matthew Hobson
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Athena Ierokomos
- Program in Biophysics, Stanford University, Stanford, California, USA; Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Ivan E Ivanov
- Department of Bioengineering, Stanford University, Stanford, California, USA; Department of Chemical Engineering, Stanford University, Stanford, California, USA
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Zev Bryant
- Program in Biophysics, Stanford University, Stanford, California, USA; Department of Bioengineering, Stanford University, Stanford, California, USA; Department of Structural Biology, Stanford University Medical Center, Stanford, California, USA.
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8
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Haydell M, Ma Y. DNA Origami: Recent Progress and Applications. Methods Mol Biol 2023; 2639:3-19. [PMID: 37166708 DOI: 10.1007/978-1-0716-3028-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
This chapter explores the basic concept of DNA origami and its various types. By showing the progress made in structural DNA nanotechnology during the last 15 years, the chapter draws attention to the capability of DNA origami to construct complex structures in both 2D and 3D level. As well as looking at a few examples of dynamic DNA nanostructures, the chapter also explores the possible applications of DNA origami in different fields, such as biological computing, nanorobotics, and DNA walkers.
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Affiliation(s)
- Michael Haydell
- Chemical Biology and Medicinal Chemistry Unit, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Yinzhou Ma
- Chemical Biology and Medicinal Chemistry Unit, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany.
- Department of Mechanics and Engineering Science, College of Engineering, Peking University, Beijing, China.
- Beijing Innovation Center for Engineering Science and Advanced Technology, Peking University, Beijing, China.
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9
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Guan Y, Wang X, Liu G, Li W, Zhang K, Sun B, Shi F, Hui Y, Yan B, Xu J, Wu Z, Duan Z, Wei R. Microparticle Manipulation Based on the Bulk Acoustic Wave Combined with the Liquid Crystal Backflow Effect Driving in 2D/3D Platforms. ACS OMEGA 2022; 7:25140-25151. [PMID: 35910182 PMCID: PMC9330138 DOI: 10.1021/acsomega.2c01783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Microparticle manipulation has been widely used in clinical diagnosis, cell separation, and biochemical analysis via optics, electronics, magnetics, or acoustic wave driving. Among them, the bulk acoustic wave (BAW) driving method has been increasingly adopted because of non-contact, easy control, and precise manipulation. However, its low manipulation efficiency limits the usage of the BAW driving in high viscosity solutions. Therefore, in order to obtain larger driving force and more flexible manipulation of microparticles, both two-dimensional (2D) and three-dimensional (3D) platforms based on the BAW and liquid crystal backflow effect (LCBE) driving in liquid crystal (LC) solutions are proposed. The driving forces applied on the microparticles allow for the change of microparticle moving direction, which is also ascertained through theory analysis combined with various driving methods. Specifically, the maximum moving speed (68.78 μm/s) of the polystyrene particles is obtained by the BAW (13 Vpp) combined with LCBE (30 V) at a low frequency of 7.2 kHz in the 2D platform. Precise position manipulation in 3D is also fulfilled through a programmable logic control model using polystyrene particles as a demonstration. In addition, red blood cells mixed with LC solutions are arranged in a line or gathered in the pressure nodes of the BAW forces along with sinusoid signals generated by various transducer combinations. Therefore, it is approved that the LC solution that induces the LCBE force could increase the microparticle manipulation efficiency in both 2D and 3D platforms. The proposed method will open up new avenues in particle manipulation and benefit a variety of applications in cell separation, drug synthesis, analytical chemistry, and others.
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Affiliation(s)
- Yanfang Guan
- School
of Electromechanical Engineering, Henan
University of Technology, Zhengzhou 450001, China
- National
Engineering Laboratory/Key Laboratory of Henan Province, Henan University of Technology, Zhengzhou 450001, China
| | - Xiaoliang Wang
- School
of Electromechanical Engineering, Henan
University of Technology, Zhengzhou 450001, China
| | - Guangyu Liu
- School
of Electromechanical Engineering, Henan
University of Technology, Zhengzhou 450001, China
| | - Wujie Li
- School
of Electromechanical Engineering, Henan
University of Technology, Zhengzhou 450001, China
| | - Kun Zhang
- School
of Electromechanical Engineering, Henan
University of Technology, Zhengzhou 450001, China
| | - Baoshuo Sun
- School
of Electromechanical Engineering, Henan
University of Technology, Zhengzhou 450001, China
| | - Feifan Shi
- School
of Electromechanical Engineering, Henan
University of Technology, Zhengzhou 450001, China
| | - Yanbo Hui
- School
of Electromechanical Engineering, Henan
University of Technology, Zhengzhou 450001, China
| | - Bingsheng Yan
- School
of Electromechanical Engineering, Henan
University of Technology, Zhengzhou 450001, China
| | - Jie Xu
- Mechanical
and Industrial Engineering, University of
Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Zaihui Wu
- Zhengzhou
Institute of Biomedical Engineering and Technology, Zhengzhou 450001, China
| | - Zhiyong Duan
- Nano
Opto-mechatronics & Biomedical Engineering Lab, Zhengzhou University, Zhengzhou 450001, China
| | - Ronghan Wei
- Nano
Opto-mechatronics & Biomedical Engineering Lab, Zhengzhou University, Zhengzhou 450001, China
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10
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Lokesh M, Vaippully R, Nalupurackal G, Roy S, Bhallamudi VP, Prabhakar A, Roy B. Estimation of rolling work of adhesion at the nanoscale with soft probing using optical tweezers. RSC Adv 2021; 11:34636-34642. [PMID: 34737851 PMCID: PMC8546490 DOI: 10.1039/d1ra06960h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 10/19/2021] [Indexed: 12/23/2022] Open
Abstract
Conventionally, the work of adhesion at the nanoscale is estimated using an atomic force microscope with a tip of the size of 10 nm. It is pressed into a surface with nano-Newton forces and then retracted to ascertain when the tip breaks away from the surface. Thus this ensures "hard probing" of a surface. However there can be another configuration where the particle is barely placed into the surface when the work of adhesion attaches the particle to the surface and this can be called "soft probing". In this configuration, if a birefringent particle is confined in linearly polarized optical tweezers, and then the surface is moved in the direction tangential to the plane, a rolling motion can be induced. Study of this rolling motion can also show the work of adhesion. We use this configuration to find the rolling work of adhesion of a 3 μm diameter birefringent particle on a glass surface. We go on to study the effects of changing the surface to a hydrophobic slippery surface like polydimethyl siloxane (PDMS). Then we go on to show that even 500 nm diameter diamonds bearing nitrogen vacancy (NV) centers which are birefringent due to the stresses on the crystal could also be trapped and rolled to generate pitch (out-of-plane rotation) motion with 50 nm contact diameters. We find that this mode of soft probing yields a work of adhesion of about 1 mJ m-2 while the conventional nanoscale probing with atomic force microscopes (AFM) yields about 50 mJ m-2.
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Affiliation(s)
- Muruga Lokesh
- Department of Physics, Indian Institute of Technology MadrasChennai600036India
| | - Rahul Vaippully
- Department of Physics, Indian Institute of Technology MadrasChennai600036India
| | - Gokul Nalupurackal
- Department of Physics, Indian Institute of Technology MadrasChennai600036India
| | - Srestha Roy
- Department of Physics, Indian Institute of Technology MadrasChennai600036India
| | - Vidya P. Bhallamudi
- Department of Physics, Indian Institute of Technology MadrasChennai600036India
| | - Anil Prabhakar
- Department of Electrical Engineering, Indian Institute of Technology MadrasChennai600036India
| | - Basudev Roy
- Department of Physics, Indian Institute of Technology MadrasChennai600036India
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11
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Loop-seq: A high-throughput technique to measure the mesoscale mechanical properties of DNA. Methods Enzymol 2021; 661:305-326. [PMID: 34776217 DOI: 10.1016/bs.mie.2021.08.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The local mechanical properties of the DNA polymer influence molecular processes in biology that require mechanical deformations of DNA. Lack of suitable high-throughput experimental techniques had precluded measuring how these properties might vary with sequence along the vast lengths of genomes. Here, we present a detailed protocol for a recently developed experimental technique called loop-seq, which measures at least one local mechanical property of DNA-its propensity to cyclize-in genome-scale throughput. Loop-seq has been used to obtain experimentally derived genome-wide maps of a physical property of DNA. Such measurements have revealed that diverse DNA-deforming processes involved in chromatin organization at various genomic loci are regulated by the genetically encoded, sequence-dependent variations in the mechanical properties of DNA.
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12
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Fujiwara H, Sudo K, Sunaba Y, Pin C, Ishida S, Sasaki K. Spin-Orbit Angular-Momentum Transfer from a Nanogap Surface Plasmon to a Trapped Nanodiamond. NANO LETTERS 2021; 21:6268-6273. [PMID: 34270262 DOI: 10.1021/acs.nanolett.1c02083] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The ability to control the motion of single nanoparticles or molecules is currently one of the major scientific and technological challenges. Despite tremendous progress in the field of plasmonic nanotweezers, controlled nanoscale manipulation of nanoparticles trapped by a plasmonic nanogap antenna has not been reported yet. Here, we demonstrate the controlled orbital rotation of a single fluorescent nanodiamond trapped by a gold trimer nanoantenna irradiated by a rotating linearly polarized light or circularly polarized light. Remarkably, the rotation direction is opposite to the light's polarization rotation. We numerically show that this inversion comes from sequential excitation of individual nanotriangles in the reverse order when the linear polarization is rotated, whereas using a circular polarization, light-nanoparticle angular momentum transfer occurs via the generation of a Poynting vector vortex of reversed handedness. This work provides a new path for the control of light-matter angular momentum transfer using plasmonic nanogap antennas.
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Affiliation(s)
- Hideki Fujiwara
- Research Institute for Electronic Science, Hokkaido University, N20W10, Kita-ku, Sapporo 001-0020, Japan
- Faculty of Engineering, Hokkai-Gakuen University, 1-1, W11S26, Chuo-ku, Sapporo 064-0926, Japan
| | - Kota Sudo
- Research Institute for Electronic Science, Hokkaido University, N20W10, Kita-ku, Sapporo 001-0020, Japan
| | - Yuji Sunaba
- Research Institute for Electronic Science, Hokkaido University, N20W10, Kita-ku, Sapporo 001-0020, Japan
| | - Christophe Pin
- Research Institute for Electronic Science, Hokkaido University, N20W10, Kita-ku, Sapporo 001-0020, Japan
| | - Shutaro Ishida
- Research Institute for Electronic Science, Hokkaido University, N20W10, Kita-ku, Sapporo 001-0020, Japan
| | - Keiji Sasaki
- Research Institute for Electronic Science, Hokkaido University, N20W10, Kita-ku, Sapporo 001-0020, Japan
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13
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Abstract
DNA dynamics can only be understood by taking into account its complex mechanical behavior at different length scales. At the micrometer level, the mechanical properties of single DNA molecules have been well-characterized by polymer models and are commonly quantified by a persistence length of 50 nm (~150 bp). However, at the base pair level (~3.4 Å), the dynamics of DNA involves complex molecular mechanisms that are still being deciphered. Here, we review recent single-molecule experiments and molecular dynamics simulations that are providing novel insights into DNA mechanics from such a molecular perspective. We first discuss recent findings on sequence-dependent DNA mechanical properties, including sequences that resist mechanical stress and sequences that can accommodate strong deformations. We then comment on the intricate effects of cytosine methylation and DNA mismatches on DNA mechanics. Finally, we review recently reported differences in the mechanical properties of DNA and double-stranded RNA, the other double-helical carrier of genetic information. A thorough examination of the recent single-molecule literature permits establishing a set of general 'rules' that reasonably explain the mechanics of nucleic acids at the base pair level. These simple rules offer an improved description of certain biological systems and might serve as valuable guidelines for future design of DNA and RNA nanostructures.
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14
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Ruijgrok PV, Ghosh RP, Zemsky S, Nakamura M, Gong R, Ning L, Chen R, Vachharajani VT, Chu AE, Anand N, Eguchi RR, Huang PS, Lin MZ, Alushin GM, Liphardt JT, Bryant Z. Optical control of fast and processive engineered myosins in vitro and in living cells. Nat Chem Biol 2021; 17:540-548. [PMID: 33603247 PMCID: PMC10807509 DOI: 10.1038/s41589-021-00740-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 01/15/2021] [Indexed: 02/06/2023]
Abstract
Precision tools for spatiotemporal control of cytoskeletal motor function are needed to dissect fundamental biological processes ranging from intracellular transport to cell migration and division. Direct optical control of motor speed and direction is one promising approach, but it remains a challenge to engineer controllable motors with desirable properties such as the speed and processivity required for transport applications in living cells. Here, we develop engineered myosin motors that combine large optical modulation depths with high velocities, and create processive myosin motors with optically controllable directionality. We characterize the performance of the motors using in vitro motility assays, single-molecule tracking and live-cell imaging. Bidirectional processive motors move efficiently toward the tips of cellular protrusions in the presence of blue light, and can transport molecular cargo in cells. Robust gearshifting myosins will further enable programmable transport in contexts ranging from in vitro active matter reconstitutions to microfabricated systems that harness molecular propulsion.
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Affiliation(s)
- Paul V Ruijgrok
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Rajarshi P Ghosh
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
- Bio-X Institute, Stanford University, Stanford, CA, USA
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, USA
- Howard Hughes Medical Institute, and Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Sasha Zemsky
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Program in Biophysics, Stanford University, Stanford, CA, USA
| | - Muneaki Nakamura
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Rui Gong
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, NY, USA
| | - Lin Ning
- Department of Neurobiology, Stanford University, Stanford, CA, USA
| | - Robert Chen
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Vipul T Vachharajani
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Program in Biophysics, Stanford University, Stanford, CA, USA
| | - Alexander E Chu
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Program in Biophysics, Stanford University, Stanford, CA, USA
| | - Namrata Anand
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Raphael R Eguchi
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Po-Ssu Huang
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
- Bio-X Institute, Stanford University, Stanford, CA, USA
| | - Michael Z Lin
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Bio-X Institute, Stanford University, Stanford, CA, USA
- Department of Neurobiology, Stanford University, Stanford, CA, USA
| | - Gregory M Alushin
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, NY, USA
| | - Jan T Liphardt
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
- Bio-X Institute, Stanford University, Stanford, CA, USA
- Cell Biology Division, Stanford Cancer Institute, Stanford, CA, USA
| | - Zev Bryant
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Bio-X Institute, Stanford University, Stanford, CA, USA.
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
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15
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Bustamante CJ, Chemla YR, Liu S, Wang MD. Optical tweezers in single-molecule biophysics. NATURE REVIEWS. METHODS PRIMERS 2021; 1:25. [PMID: 34849486 PMCID: PMC8629167 DOI: 10.1038/s43586-021-00021-6] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/12/2021] [Indexed: 12/15/2022]
Abstract
Optical tweezers have become the method of choice in single-molecule manipulation studies. In this Primer, we first review the physical principles of optical tweezers and the characteristics that make them a powerful tool to investigate single molecules. We then introduce the modifications of the method to extend the measurement of forces and displacements to torques and angles, and to develop optical tweezers with single-molecule fluorescence detection capabilities. We discuss force and torque calibration of these instruments, their various modes of operation and most common experimental geometries. We describe the type of data obtained in each experimental design and their analyses. This description is followed by a survey of applications of these methods to the studies of protein-nucleic acid interactions, protein/RNA folding and molecular motors. We also discuss data reproducibility, the factors that lead to the data variability among different laboratories and the need to develop field standards. We cover the current limitations of the methods and possible ways to optimize instrument operation, data extraction and analysis, before suggesting likely areas of future growth.
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Affiliation(s)
- Carlos J. Bustamante
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Physics, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- Kavli Energy NanoScience Institute, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Yann R. Chemla
- Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
| | - Michelle D. Wang
- Department of Physics, Laboratory of Atomic and Solid State Physics, Howard Hughes Medical Institute, Cornell University, Ithaca, NY, USA
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16
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Basu A, Bobrovnikov DG, Ha T. DNA mechanics and its biological impact. J Mol Biol 2021; 433:166861. [PMID: 33539885 DOI: 10.1016/j.jmb.2021.166861] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 02/06/2023]
Abstract
Almost all nucleoprotein interactions and DNA manipulation events involve mechanical deformations of DNA. Extraordinary progresses in single-molecule, structural, and computational methods have characterized the average mechanical properties of DNA, such as bendability and torsional rigidity, in high resolution. Further, the advent of sequencing technology has permitted measuring, in high-throughput, how such mechanical properties vary with sequence and epigenetic modifications along genomes. We review these recent technological advancements, and discuss how they have contributed to the emerging idea that variations in the mechanical properties of DNA play a fundamental role in regulating, genome-wide, diverse processes involved in chromatin organization.
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Affiliation(s)
- Aakash Basu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Dmitriy G Bobrovnikov
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA
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17
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Zhang P, Bachman H, Ozcelik A, Huang TJ. Acoustic Microfluidics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2020; 13:17-43. [PMID: 32531185 PMCID: PMC7415005 DOI: 10.1146/annurev-anchem-090919-102205] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Acoustic microfluidic devices are powerful tools that use sound waves to manipulate micro- or nanoscale objects or fluids in analytical chemistry and biomedicine. Their simple device designs, biocompatible and contactless operation, and label-free nature are all characteristics that make acoustic microfluidic devices ideal platforms for fundamental research, diagnostics, and therapeutics. Herein, we summarize the physical principles underlying acoustic microfluidics and review their applications, with particular emphasis on the manipulation of macromolecules, cells, particles, model organisms, and fluidic flows. We also present future goals of this technology in analytical chemistry and biomedical research, as well as challenges and opportunities.
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Affiliation(s)
- Peiran Zhang
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA;
| | - Hunter Bachman
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA;
| | - Adem Ozcelik
- Department of Mechanical Engineering, Aydın Adnan Menderes University, Aydın 09010, Turkey;
| | - Tony Jun Huang
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA;
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18
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Chen YT, Yang H, Chu JW. Structure-mechanics statistical learning unravels the linkage between local rigidity and global flexibility in nucleic acids. Chem Sci 2020; 11:4969-4979. [PMID: 34122953 PMCID: PMC8159235 DOI: 10.1039/d0sc00480d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The mechanical properties of nucleic acids underlie biological processes ranging from genome packaging to gene expression, but tracing their molecular origin has been difficult due to the structural and chemical complexity. We posit that concepts from machine learning can help to tackle this long-standing challenge. Here, we demonstrate the feasibility and advantage of this strategy through developing a structure-mechanics statistical learning scheme to elucidate how local rigidity in double-stranded (ds)DNA and dsRNA may lead to their global flexibility in bend, stretch, and twist. Specifically, the mechanical parameters in a heavy-atom elastic network model are computed from the trajectory data of all-atom molecular dynamics simulation. The results show that the inter-atomic springs for backbone and ribose puckering in dsRNA are stronger than those in dsDNA, but are similar in strengths for base-stacking and base-pairing. Our analysis shows that the experimental observation of dsDNA being easier to bend but harder to stretch than dsRNA comes mostly from the respective B- and A-form topologies. The computationally resolved composition of local rigidity indicates that the flexibility of both nucleic acids is mostly due to base-stacking. But for properties like twist-stretch coupling, backbone springs are shown to play a major role instead. The quantitative connection between local rigidity and global flexibility sets foundation for understanding how local binding and chemical modification of genetic materials effectuate longer-ranged regulatory signals. The mechanical properties of nucleic acids underlie biological processes ranging from genome packaging to gene expression. We devise structural mechanics statistical learning method to reveal their molecular origin in terms of chemical interactions.![]()
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Affiliation(s)
- Yi-Tsao Chen
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University Hsinchu Taiwan 30068 Republic of China
| | - Haw Yang
- Department of Chemistry, Princeton University Princeton NJ 08544 USA
| | - Jhih-Wei Chu
- Institute of Bioinformatics and Systems Biology, Department of Biological Science and Technology, Institute of Molecular Medicine and Bioengineering, National Chiao Tung University Hsinchu Taiwan 30068 Republic of China +886 3 5712121 ext. 56996
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19
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Vanderlinden W, Kolbeck PJ, Kriegel F, Walker PU, Lipfert J. A benchmark data set for the mechanical properties of double-stranded DNA and RNA under torsional constraint. Data Brief 2020; 30:105404. [PMID: 32309523 PMCID: PMC7154992 DOI: 10.1016/j.dib.2020.105404] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/02/2020] [Accepted: 03/03/2020] [Indexed: 11/17/2022] Open
Abstract
Nucleic acids are central to the storage and transmission of genetic information and play essential roles in many cellular processes. Quantitative understanding and modeling of their functions and properties requires quantitative experimental characterization. We use magnetic tweezers (MT) to apply precisely calibrated stretching forces and linking number changes to DNA and RNA molecules tethered between a surface and superparamagnetic beads. Magnetic torque tweezers (MTT) allow to control the linking number of double-stranded DNA or RNA tethers, while directly measuring molecular torque by monitoring changes in the equilibrium rotation angle upon over- or underwinding of the helical molecules. Here, we provide a comprehensive data set of double-stranded DNA and RNA under controlled stretching as a function of the linking number. We present data for extension and torque as a function of linking number in equilibrium. We report data for the critical torque of buckling and of the torsional stiffness of DNA and RNA as a function of applied force. Finally, we provide dynamic data for the hopping behavior at the DNA buckling point.
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20
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Ivanov IE, Wright AV, Cofsky JC, Aris KDP, Doudna JA, Bryant Z. Cas9 interrogates DNA in discrete steps modulated by mismatches and supercoiling. Proc Natl Acad Sci U S A 2020; 117:5853-5860. [PMID: 32123105 PMCID: PMC7084090 DOI: 10.1073/pnas.1913445117] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The CRISPR-Cas9 nuclease has been widely repurposed as a molecular and cell biology tool for its ability to programmably target and cleave DNA. Cas9 recognizes its target site by unwinding the DNA double helix and hybridizing a 20-nucleotide section of its associated guide RNA to one DNA strand, forming an R-loop structure. A dynamic and mechanical description of R-loop formation is needed to understand the biophysics of target searching and develop rational approaches for mitigating off-target activity while accounting for the influence of torsional strain in the genome. Here we investigate the dynamics of Cas9 R-loop formation and collapse using rotor bead tracking (RBT), a single-molecule technique that can simultaneously monitor DNA unwinding with base-pair resolution and binding of fluorescently labeled macromolecules in real time. By measuring changes in torque upon unwinding of the double helix, we find that R-loop formation and collapse proceed via a transient discrete intermediate, consistent with DNA:RNA hybridization within an initial seed region. Using systematic measurements of target and off-target sequences under controlled mechanical perturbations, we characterize position-dependent effects of sequence mismatches and show how DNA supercoiling modulates the energy landscape of R-loop formation and dictates access to states competent for stable binding and cleavage. Consistent with this energy landscape model, in bulk experiments we observe promiscuous cleavage under physiological negative supercoiling. The detailed description of DNA interrogation presented here suggests strategies for improving the specificity and kinetics of Cas9 as a genome engineering tool and may inspire expanded applications that exploit sensitivity to DNA supercoiling.
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Affiliation(s)
- Ivan E Ivanov
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305
- Department of Bioengineering, Stanford University, Stanford, CA 94305
| | - Addison V Wright
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Joshua C Cofsky
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | | | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
| | - Zev Bryant
- Department of Bioengineering, Stanford University, Stanford, CA 94305;
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305
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21
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Fujita K, Ohmachi M, Ikezaki K, Yanagida T, Iwaki M. Direct visualization of human myosin II force generation using DNA origami-based thick filaments. Commun Biol 2019; 2:437. [PMID: 31799438 PMCID: PMC6881340 DOI: 10.1038/s42003-019-0683-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 11/07/2019] [Indexed: 11/08/2022] Open
Abstract
The sarcomere, the minimal mechanical unit of muscle, is composed of myosins, which self-assemble into thick filaments that interact with actin-based thin filaments in a highly-structured lattice. This complex imposes a geometric restriction on myosin in force generation. However, how single myosins generate force within the restriction remains elusive and conventional synthetic filaments do not recapitulate the symmetric bipolar filaments in sarcomeres. Here we engineered thick filaments using DNA origami that incorporate human muscle myosin to directly visualize the motion of the heads during force generation in a restricted space. We found that when the head diffuses, it weakly interacts with actin filaments and then strongly binds preferentially to the forward region as a Brownian ratchet. Upon strong binding, the two-step lever-arm swing dominantly halts at the first step and occasionally reverses direction. Our results illustrate the usefulness of our DNA origami-based assay system to dissect the mechanistic details of motor proteins.
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Affiliation(s)
- Keisuke Fujita
- RIKEN Center for Biosystems Dynamics Research, RIKEN, Osaka, Japan
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Masashi Ohmachi
- RIKEN Center for Biosystems Dynamics Research, RIKEN, Osaka, Japan
| | | | - Toshio Yanagida
- RIKEN Center for Biosystems Dynamics Research, RIKEN, Osaka, Japan
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
- Center for Information and Neural Networks, NICT, Osaka, Japan
| | - Mitsuhiro Iwaki
- RIKEN Center for Biosystems Dynamics Research, RIKEN, Osaka, Japan
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
- AMED-PRIME, Japan Agency for Medical Research and Development, Tokyo, Japan
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22
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Mohapatra S, Lin CT, Feng XA, Basu A, Ha T. Single-Molecule Analysis and Engineering of DNA Motors. Chem Rev 2019; 120:36-78. [DOI: 10.1021/acs.chemrev.9b00361] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
| | | | | | | | - Taekjip Ha
- Howard Hughes Medical Institute, Baltimore, Maryland 21205, United States
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23
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Multi-parameter measurements of conformational dynamics in nucleic acids and nucleoprotein complexes. Methods 2019; 169:69-77. [PMID: 31228549 DOI: 10.1016/j.ymeth.2019.06.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 06/15/2019] [Accepted: 06/18/2019] [Indexed: 11/20/2022] Open
Abstract
Biological macromolecules undergo dynamic conformational changes. Single-molecule methods can track such structural rearrangements in real time. However, while the structure of large macromolecules may change along many degrees of freedom, single-molecule techniques only monitor a limited number of these axes of motion. Advanced single-molecule methods are being developed to track multiple degrees of freedom in nucleic acids and nucleoprotein complexes at high resolution, to enable better manipulation and control of the system under investigation, and to collect measurements in massively parallel fashion. Combining complementary single-molecule methods within the same assay also provides unique measurement opportunities. Implementations of magnetic and optical tweezers combined with fluorescence and FRET have demonstrated results unattainable by either technique alone. Augmenting other advanced single-molecule methods with fluorescence detection will allow us to better capture the multidimensional dynamics of nucleic acids and nucleoprotein complexes central to biology.
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24
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Yang YJ, Song L, Zhao XC, Zhang C, Wu WQ, You HJ, Fu H, Zhou EC, Zhang XH. A Universal Assay for Making DNA, RNA, and RNA-DNA Hybrid Configurations for Single-Molecule Manipulation in Two or Three Steps without Ligation. ACS Synth Biol 2019; 8:1663-1672. [PMID: 31264849 DOI: 10.1021/acssynbio.9b00241] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Despite having a great variety of topologies, most DNA, RNA, and RNA-DNA hybrid (RDH) configurations for single-molecule manipulation are composed of several single-stranded (ss) DNA and ssRNA strands, with functional labels at the two ends for surface tethering. On this basis, we developed a simple, robust, and universal amplification-annealing (AA) assay for making all these configurations in two or three steps without inefficient digestion and ligation reactions. As examples, we made ssDNA, short ssDNA with double-stranded (ds) DNA handles, dsDNA with ssDNA handles, replication-fork shaped DNA/RDH/RNA, DNA holiday junction, three-site multiple-labeled and nicked DNA, torsion-constrained RNA/RDH, and short ssRNA with RDH handles. In addition to single-molecule manipulation techniques including optical tweezers, magnetic tweezers, and atomic force microscopy, these configurations can be applied in other surface-tethering techniques as well.
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Affiliation(s)
- Ya-Jun Yang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Lun Song
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Xiao-Cong Zhao
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Chen Zhang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Wen-Qiang Wu
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475001, China
| | - Hui-Juan You
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hang Fu
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Er-Chi Zhou
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
| | - Xing-Hua Zhang
- College of Life Sciences, the Institute for Advanced Studies, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan 430072, China
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25
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Kosuri P, Altheimer BD, Dai M, Yin P, Zhuang X. Rotation tracking of genome-processing enzymes using DNA origami rotors. Nature 2019; 572:136-140. [PMID: 31316204 PMCID: PMC7036295 DOI: 10.1038/s41586-019-1397-7] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 06/17/2019] [Indexed: 11/24/2022]
Abstract
Many genome-processing reactions, such as transcription, replication and repair, generate DNA rotation. Methods that directly measure DNA rotation, including rotor bead tracking1–3, angular optical trap4, and magnetic tweezers5 have helped unravel the action mechanisms of a range of genome-processing enzymes, such as RNA polymerase (RNAP)6, gyrase2, viral DNA packaging motor7, and DNA recombination enzymes8. However, despite the potential of rotation measurements to transform our understanding of genome-processing reactions, measuring DNA rotation remains a difficult task. The time resolution of existing methods is insufficient to track rotation induced by many enzymes under physiological conditions, and the measurement throughput is typically low. Here we introduce Origami-Rotor-Based Imaging and Tracking (ORBIT), a method that uses fluorescently labeled DNA origami rotors to track DNA rotation at the single-molecule level with millisecond time resolution. We used ORBIT to track DNA rotation resulted from unwinding by RecBCD, a helicase involved in DNA repair9, and transcription by RNAP. We characterized a series of events during RecBCD-induced DNA unwinding, including initiation, processive translocation, pausing and backtracking, and revealed an initiation mechanism that involves reversible, ATP-independent DNA unwinding and engagement of the RecB motor. During transcription by RNAP, we directly observed rotational steps corresponding to single-base-pair unwinding. We envision ORBIT will enable studies of a wide range of protein-DNA interactions.
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Affiliation(s)
- Pallav Kosuri
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Department of Physics, Harvard University, Cambridge, MA, USA
| | - Benjamin D Altheimer
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Department of Physics, Harvard University, Cambridge, MA, USA.,Graduate Program in Biophysics, Harvard University, Cambridge, MA, USA
| | - Mingjie Dai
- Graduate Program in Biophysics, Harvard University, Cambridge, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, MA, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, MA, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA. .,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA. .,Department of Physics, Harvard University, Cambridge, MA, USA.
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26
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Mickolajczyk KJ, Cook ASI, Jevtha JP, Fricks J, Hancock WO. Insights into Kinesin-1 Stepping from Simulations and Tracking of Gold Nanoparticle-Labeled Motors. Biophys J 2019; 117:331-345. [PMID: 31301807 DOI: 10.1016/j.bpj.2019.06.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 06/04/2019] [Accepted: 06/10/2019] [Indexed: 02/02/2023] Open
Abstract
High-resolution tracking of gold nanoparticle-labeled proteins has emerged as a powerful technique for measuring the structural kinetics of processive enzymes and other biomacromolecules. These techniques use point spread function (PSF) fitting methods borrowed from single-molecule fluorescence imaging to determine molecular positions below the diffraction limit. However, compared to fluorescence, gold nanoparticle tracking experiments are performed at significantly higher frame rates and utilize much larger probes. In the current work, we use Brownian dynamics simulations of nanoparticle-labeled proteins to investigate the regimes in which the fundamental assumptions of PSF fitting hold and where they begin to break down. We find that because gold nanoparticles undergo tethered diffusion around their anchor point, PSF fitting cannot be extended to arbitrarily fast frame rates. Instead, camera exposure times that allow the nanoparticle to fully populate its stationary positional distribution achieve a spatial averaging that increases fitting precision. We furthermore find that changes in the rotational freedom of the tagged protein can lead to artifactual translations in the fitted particle position. Finally, we apply these lessons to dissect a standing controversy in the kinesin field over the structure of a dimer in the ATP waiting state. Combining new experiments with simulations, we determine that the rear kinesin head in the ATP waiting state is unbound but not displaced from its previous microtubule binding site and that apparent differences in separately published reports were simply due to differences in the gold nanoparticle attachment position. Our results highlight the importance of gold conjugation decisions and imaging parameters to high-resolution tracking results and will serve as a useful guide for the design of future gold nanoparticle tracking experiments.
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Affiliation(s)
- Keith J Mickolajczyk
- Department of Biomedical Engineering; Intercollege Graduate Degree Program in Bioengineering
| | - Annan S I Cook
- Department of Biomedical Engineering; Department of Physics, Pennsylvania State University, University Park, Pennsylvania
| | | | - John Fricks
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, Arizona
| | - William O Hancock
- Department of Biomedical Engineering; Intercollege Graduate Degree Program in Bioengineering.
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27
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Tracking the rotation of single CdS nanorods during photocatalysis with surface plasmon resonance microscopy. Proc Natl Acad Sci U S A 2019; 116:6630-6634. [PMID: 30872472 PMCID: PMC6452698 DOI: 10.1073/pnas.1820114116] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Rotational dynamics of anisotropic nanomaterials reveals and regulates their behaviors and functions in diverse fields ranging from nanomotors, biomechanics, and enzymatic catalysis to microrheology. An optical imaging technique that is suitable for all kinds of anisotropic nanoobjects, regardless of its inherent optical property, is thus highly desirable and it is yet to be demonstrated. In the present work, by taking a nonfluorescent and nonplasmonic CdS nanorod as an example, we demonstrate the capability of a recently developed surface plasmon resonance microscopy for determining the orientation of single anisotropic nanomaterials with arbitrary chemical composition and morphology. While rotational dynamics of anisotropic nanoobjects has often been limited in plasmonic and fluorescent nanomaterials, here we demonstrate the capability of a surface plasmon resonance microscopy (SPRM) to determine the orientation of all kinds of anisotropic nanomaterials. By taking CdS nanorods as an example, it was found that two-dimensional Fourier transform of the asymmetrical wave-like SPRM image resulted in a peak in its angular spectrum in k space. Consistency between the peak angle and the geometrical orientation of the nanorod was validated by both in situ scanning electron microscope characterizations and theoretical calculations. Real-time monitoring of the rotational dynamics of single CdS nanorods further revealed the accelerated rotation under appropriate reaction conditions for photocatalyzed hydrogen generation. The driving force was attributed to the asymmetric production of hydrogen molecules as a result of inhomogeneous distribution of reactive sites within the nanorod. The present work not only builds the experimental and theoretical connections between the orientation of anisotropic nanomaterials and its SPRM images; the general suitability of SPRM also sheds light on broad types of nonfluorescent and nonplasmonic anisotropic nanoobjects from semiconductors to bacteria and viruses.
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28
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Wang M, Chen M, Zhanghao K, Zhang X, Jing Z, Gao J, Zhang MQ, Jin D, Dai Z, Xi P, Dai Q. Polarization-based super-resolution imaging of surface-enhanced Raman scattering nanoparticles with orientational information. NANOSCALE 2018; 10:19757-19765. [PMID: 30211422 DOI: 10.1039/c8nr04808h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Raman scattering provides key information of the biological environment through light-molecule interaction; yet, it is generally very weak to detect. Surface-enhanced Raman scattering (SERS) can boost the Raman signal by several orders-of-magnitude, and thus is highly attractive for biochemical sensing. However, conventional super-resolution imaging of SERS is challenging as the Raman signal is generated from the virtual state which cannot be easily modulated as fluorescence. Here, we demonstrate super-resolution microscopy with a surface-enhanced Raman scattering (SERS) signal, with a resolution of approximately 50 nm. By modulating the polarization angle of the excitation laser, the SERS nanorods display a dramatic anisotropy effect, allowing nanoscale orientation determination of multiple dipoles with dense concentration. Furthermore, a well-established defocused analysis was performed to reconfirm the orientation accuracy of super-resolved SERS nanorods. Sub-diffraction resolution was achieved in the imaging of SERS nanorod labeled vesicles in fixed macrophages. Finally, we demonstrate dynamic SERS nanorod tracking in living macrophages, which provides not only the particle trajectory with high spatial resolution but also the rotational changes at the nanometer scale. This pioneering study paves a new way for subcellular super-resolution imaging with the SERS effect, shedding light on wider biological applications.
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Affiliation(s)
- Miaoyan Wang
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China.
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29
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Länk NO, Johansson P, Käll M. Directional scattering and multipolar contributions to optical forces on silicon nanoparticles in focused laser beams. OPTICS EXPRESS 2018; 26:29074-29085. [PMID: 30470074 DOI: 10.1364/oe.26.029074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 09/24/2018] [Indexed: 06/09/2023]
Abstract
Nanoparticles made of high index dielectric materials have seen a surge of interest and have been proposed for various applications, such as metalenses, light harvesting and directional scattering. With the advent of fabrication techniques enabling colloidal suspensions, the prospects of optical manipulation of such nanoparticles becomes paramount. High index nanoparticles support electric and magnetic multipolar responses in the visible regime and interference between such modes can give rise to highly directional scattering, in particular a cancellation of back-scattered radiation at the first Kerker condition. Here we present a study of the optical forces on silicon nanoparticles in the visible and near infrared calculated using the transfer matrix method. The zero-backscattering Kerker condition is investigated as an avenue to reduce radiation pressure in an optical trap. We find that while asymmetric scattering does reduce the radiation pressure, the main determining factor of trap stability is the increased particle response near the geometric resonances. The trap stability for non-spherical silicon nanoparticles is also investigated and we find that ellipsoidal deformation of spheres enables trapping of slightly larger particles.
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30
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Hu X, Lim B, Torati SR, Ding J, Novosad V, Im MY, Reddy V, Kim K, Jung E, Shawl AI, Kim E, Kim C. Autonomous Magnetic Microrobots by Navigating Gates for Multiple Biomolecules Delivery. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1800504. [PMID: 29740954 DOI: 10.1002/smll.201800504] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 03/17/2018] [Indexed: 06/08/2023]
Abstract
The precise delivery of biofunctionalized matters is of great interest from the fundamental and applied viewpoints. In spite of significant progress achieved during the last decade, a parallel and automated isolation and manipulation of rare analyte, and their simultaneous on-chip separation and trapping, still remain challenging. Here, a universal micromagnet junction for self-navigating gates of microrobotic particles to deliver the biomolecules to specific sites using a remote magnetic field is described. In the proposed concept, the nonmagnetic gap between the lithographically defined donor and acceptor micromagnets creates a crucial energy barrier to restrict particle gating. It is shown that by carefully designing the geometry of the junctions, it becomes possible to deliver multiple protein-functionalized carriers in high resolution, as well as MCF-7 and THP-1 cells from the mixture, with high fidelity and trap them in individual apartments. Integration of such junctions with magnetophoretic circuitry elements could lead to novel platforms without retrieving for the synchronous digital manipulation of particles/biomolecules in microfluidic multiplex arrays for next-generation biochips.
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Affiliation(s)
- Xinghao Hu
- Department of Emerging Materials Science, DGIST, Daegu, 42988, Republic of Korea
| | - Byeonghwa Lim
- Department of Emerging Materials Science, DGIST, Daegu, 42988, Republic of Korea
| | - Sri Ramulu Torati
- Department of Emerging Materials Science, DGIST, Daegu, 42988, Republic of Korea
| | - Junjia Ding
- Materials Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Valentine Novosad
- Materials Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Mi-Young Im
- Department of Emerging Materials Science, DGIST, Daegu, 42988, Republic of Korea
- Center for X-ray Optics, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Venu Reddy
- Department of Emerging Materials Science, DGIST, Daegu, 42988, Republic of Korea
| | - Kunwoo Kim
- Department of Emerging Materials Science, DGIST, Daegu, 42988, Republic of Korea
| | - Eunjoo Jung
- Department of Emerging Materials Science, DGIST, Daegu, 42988, Republic of Korea
| | - Asif Iqbal Shawl
- Department of Emerging Materials Science, DGIST, Daegu, 42988, Republic of Korea
| | - Eunjoo Kim
- Nano-Bio-materials Division, DGIST, Daegu, 42988, Republic of Korea
| | - CheolGi Kim
- Department of Emerging Materials Science, DGIST, Daegu, 42988, Republic of Korea
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31
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van Oene MM, Ha S, Jager T, Lee M, Pedaci F, Lipfert J, Dekker NH. Quantifying the Precision of Single-Molecule Torque and Twist Measurements Using Allan Variance. Biophys J 2018; 114:1970-1979. [PMID: 29694873 DOI: 10.1016/j.bpj.2018.02.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 02/12/2018] [Accepted: 02/27/2018] [Indexed: 01/06/2023] Open
Abstract
Single-molecule manipulation techniques have provided unprecedented insights into the structure, function, interactions, and mechanical properties of biological macromolecules. Recently, the single-molecule toolbox has been expanded by techniques that enable measurements of rotation and torque, such as the optical torque wrench (OTW) and several different implementations of magnetic (torque) tweezers. Although systematic analyses of the position and force precision of single-molecule techniques have attracted considerable attention, their angle and torque precision have been treated in much less detail. Here, we propose Allan deviation as a tool to systematically quantitate angle and torque precision in single-molecule measurements. We apply the Allan variance method to experimental data from our implementations of (electro)magnetic torque tweezers and an OTW and find that both approaches can achieve a torque precision better than 1 pN · nm. The OTW, capable of measuring torque on (sub)millisecond timescales, provides the best torque precision for measurement times ≲10 s, after which drift becomes a limiting factor. For longer measurement times, magnetic torque tweezers with their superior stability provide the best torque precision. Use of the Allan deviation enables critical assessments of the torque precision as a function of measurement time across different measurement modalities and provides a tool to optimize measurement protocols for a given instrument and application.
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Affiliation(s)
- Maarten M van Oene
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Seungkyu Ha
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Tessa Jager
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Mina Lee
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Francesco Pedaci
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Jan Lipfert
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands; Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, Munich, Germany.
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
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32
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Basu A, Hobson M, Lebel P, Fernandes LE, Tretter EM, Berger JM, Bryant Z. Dynamic coupling between conformations and nucleotide states in DNA gyrase. Nat Chem Biol 2018; 14:565-574. [PMID: 29662209 PMCID: PMC10121156 DOI: 10.1038/s41589-018-0037-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 02/21/2018] [Indexed: 11/09/2022]
Abstract
Gyrase is an essential bacterial molecular motor that supercoils DNA using a conformational cycle in which chiral wrapping of > 100 base pairs confers directionality on topoisomerization. To understand the mechanism of this nucleoprotein machine, global structural transitions must be mapped onto the nucleotide cycle of ATP binding, hydrolysis and product release. Here we investigate coupling mechanisms using single-molecule tracking of DNA rotation and contraction during Escherichia coli gyrase activity under varying nucleotide conditions. We find that ADP must be exchanged for ATP to drive the rate-limiting remodeling transition that generates the chiral wrap. ATP hydrolysis accelerates subsequent duplex strand passage and is required for resetting the enzyme and recapturing transiently released DNA. Our measurements suggest how gyrase coordinates DNA rearrangements with the dynamics of its ATP-driven protein gate, how the motor minimizes futile cycles of ATP hydrolysis and how gyrase may respond to changing cellular energy levels to link gene expression with metabolism.
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Affiliation(s)
- Aakash Basu
- Department of Applied Physics, Stanford University, Stanford, CA, USA.,Department of Bioengineering, Stanford University, Stanford, CA, USA.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Matthew Hobson
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Paul Lebel
- Department of Applied Physics, Stanford University, Stanford, CA, USA.,Department of Bioengineering, Stanford University, Stanford, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Louis E Fernandes
- Department of Bioengineering, Stanford University, Stanford, CA, USA.,Program in Biophysics, Stanford University, Stanford, CA, USA.,Tempus, Inc., Chicago, IL, USA
| | - Elsa M Tretter
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,Nurix Inc., San Francisco, CA, USA
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Zev Bryant
- Department of Bioengineering, Stanford University, Stanford, CA, USA. .,Department of Structural Biology, Stanford University Medical Center, Stanford, CA, USA.
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33
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Martínez-Santiago CJ, Quiñones E. Magnetic modulation of the unbraiding dynamics of pairs of DNA molecules to model the system as an intermittent oscillator. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2017.12.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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34
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Ivanov IE, Lebel P, Oberstrass FC, Starr CH, Parente AC, Ierokomos A, Bryant Z. Multimodal Measurements of Single-Molecule Dynamics Using FluoRBT. Biophys J 2018; 114:278-282. [PMID: 29248150 PMCID: PMC5984952 DOI: 10.1016/j.bpj.2017.11.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 10/15/2017] [Accepted: 11/08/2017] [Indexed: 11/21/2022] Open
Abstract
Single-molecule methods provide direct measurements of macromolecular dynamics, but are limited by the number of degrees of freedom that can be followed at one time. High-resolution rotor bead tracking (RBT) measures DNA torque, twist, and extension, and can be used to characterize the structural dynamics of DNA and diverse nucleoprotein complexes. Here, we extend RBT to enable simultaneous monitoring of additional degrees of freedom. Fluorescence-RBT (FluoRBT) combines magnetic tweezers, infrared evanescent scattering, and single-molecule FRET imaging, providing real-time multiparameter measurements of complex molecular processes. We demonstrate the capabilities of FluoRBT by conducting simultaneous measurements of extension and FRET during opening and closing of a DNA hairpin under tension, and by observing simultaneous changes in FRET and torque during a transition between right-handed B-form and left-handed Z-form DNA under controlled supercoiling. We discover unanticipated continuous changes in FRET with applied torque, and also show how FluoRBT can facilitate high-resolution FRET measurements of molecular states, by using a mechanical signal as an independent temporal reference for aligning and averaging noisy fluorescence data. By combining mechanical measurements of global DNA deformations with FRET measurements of local conformational changes, FluoRBT will enable multidimensional investigations of systems ranging from DNA structures to large macromolecular machines.
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Affiliation(s)
- Ivan E Ivanov
- Department of Chemical Engineering, Stanford University, Stanford, California; Department of Bioengineering, Stanford University, Stanford, California
| | - Paul Lebel
- Department of Bioengineering, Stanford University, Stanford, California; Department of Applied Physics, Stanford University, Stanford, California
| | | | - Charles H Starr
- Department of Bioengineering, Stanford University, Stanford, California; Program in Biophysics, Stanford University, Stanford, California
| | - Angelica C Parente
- Department of Bioengineering, Stanford University, Stanford, California; Program in Biophysics, Stanford University, Stanford, California
| | - Athena Ierokomos
- Department of Bioengineering, Stanford University, Stanford, California; Program in Biophysics, Stanford University, Stanford, California
| | - Zev Bryant
- Department of Bioengineering, Stanford University, Stanford, California; Department of Structural Biology, Stanford University, Stanford, California.
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35
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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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36
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Omabegho T, Gurel PS, Cheng CY, Kim LY, Ruijgrok PV, Das R, Alushin GM, Bryant Z. Controllable molecular motors engineered from myosin and RNA. NATURE NANOTECHNOLOGY 2018; 13:34-40. [PMID: 29109539 PMCID: PMC5762270 DOI: 10.1038/s41565-017-0005-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 09/19/2017] [Indexed: 05/12/2023]
Abstract
Engineering biomolecular motors can provide direct tests of structure-function relationships and customized components for controlling molecular transport in artificial systems 1 or in living cells 2 . Previously, synthetic nucleic acid motors 3-5 and modified natural protein motors 6-10 have been developed in separate complementary strategies to achieve tunable and controllable motor function. Integrating protein and nucleic-acid components to form engineered nucleoprotein motors may enable additional sophisticated functionalities. However, this potential has only begun to be explored in pioneering work harnessing DNA scaffolds to dictate the spacing, number and composition of tethered protein motors 11-15 . Here, we describe myosin motors that incorporate RNA lever arms, forming hybrid assemblies in which conformational changes in the protein motor domain are amplified and redirected by nucleic acid structures. The RNA lever arm geometry determines the speed and direction of motor transport and can be dynamically controlled using programmed transitions in the lever arm structure 7,9 . We have characterized the hybrid motors using in vitro motility assays, single-molecule tracking, cryo-electron microscopy and structural probing 16 . Our designs include nucleoprotein motors that reversibly change direction in response to oligonucleotides that drive strand-displacement 17 reactions. In multimeric assemblies, the controllable motors walk processively along actin filaments at speeds of 10-20 nm s-1. Finally, to illustrate the potential for multiplexed addressable control, we demonstrate sequence-specific responses of RNA variants to oligonucleotide signals.
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Affiliation(s)
- Tosan Omabegho
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Pinar S Gurel
- Cell Biology and Physiology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, NY, USA
| | - Clarence Y Cheng
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Laura Y Kim
- Cell Biology and Physiology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Paul V Ruijgrok
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Rhiju Das
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Gregory M Alushin
- Cell Biology and Physiology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, NY, USA
| | - Zev Bryant
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
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37
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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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38
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Zhao X, Zeng X, Lu C, Yan J. Studying the mechanical responses of proteins using magnetic tweezers. NANOTECHNOLOGY 2017; 28:414002. [PMID: 28766506 DOI: 10.1088/1361-6528/aa837e] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The mechanical stability of proteins has been extensively studied using AFM as a single-molecule force spectroscopy method. While this has led to many important results, these studies have been mainly limited to fast unfolding at a high-force regime due to the rapid mechanical drift in most AFM stretching experiments. Therefore, there is a gap between the knowledge obtained at a high-force regime and the mechanical properties of proteins at a lower force regime which is often more physiologically relevant. Recent studies have demonstrated that this gap can be addressed by stretching single protein molecules using magnetic tweezers, due to the excellent mechanical stability this technology offers. Here we review magnetic tweezers technology and its current application in studies of the force-dependent stability and interactions of proteins.
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Affiliation(s)
- Xiaodan Zhao
- Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1, 117411, Singapore
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39
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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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40
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Meiri A, Ebeling CG, Martineau J, Zalevsky Z, Gerton JM, Menon R. Interference based localization of single emitters. OPTICS EXPRESS 2017; 25:17174-17191. [PMID: 28789212 PMCID: PMC5557332 DOI: 10.1364/oe.25.017174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 03/26/2017] [Accepted: 03/27/2017] [Indexed: 06/07/2023]
Abstract
The ability to localize precisely a single optical emitter is important for particle tracking applications and super resolution microscopy. It is known that for a traditional microscope the ability to localize such an emitter is limited by the photon count. Here we analyze the ability to improve such localization by imposing interference fringes. We show here that a simple grating interferometer can introduce such improvement in certain circumstances and analyze what is required to increase the localization precision further.
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Affiliation(s)
- Amihai Meiri
- Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Carl G. Ebeling
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112, USA
| | - Jason Martineau
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112, USA
| | - Zeev Zalevsky
- Faculty of Engineering, Bar-Ilan University, Ramat-Gan, Israel
| | - Jordan M. Gerton
- Department of Physics and Astronomy, University of Utah, Salt Lake City, UT 84112, USA
| | - Rajesh Menon
- Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, UT 84112, USA
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41
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Martínez-Santiago CJ, Quiñones E. Torque measurements during the spontaneous unbraiding of DNA molecules in the absence of pulling forces. Chem Phys 2017. [DOI: 10.1016/j.chemphys.2017.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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42
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Understanding the mechanical response of double-stranded DNA and RNA under constant stretching forces using all-atom molecular dynamics. Proc Natl Acad Sci U S A 2017. [PMID: 28634300 DOI: 10.1073/pnas.1705642114] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Multiple biological processes involve the stretching of nucleic acids (NAs). Stretching forces induce local changes in the molecule structure, inhibiting or promoting the binding of proteins, which ultimately affects their functionality. Understanding how a force induces changes in the structure of NAs at the atomic level is a challenge. Here, we use all-atom, microsecond-long molecular dynamics to simulate the structure of dsDNA and dsRNA subjected to stretching forces up to 20 pN. We determine all of the elastic constants of dsDNA and dsRNA and provide an explanation for three striking differences in the mechanical response of these two molecules: the threefold softer stretching constant obtained for dsRNA, the opposite twist-stretch coupling, and its nontrivial force dependence. The lower dsRNA stretching resistance is linked to its more open structure, whereas the opposite twist-stretch coupling of both molecules is due to the very different evolution of molecules' interstrand distance with the stretching force. A reduction of this distance leads to overwinding in dsDNA. In contrast, dsRNA is not able to reduce its interstrand distance and can only elongate by unwinding. Interstrand distance is directly correlated with the slide base-pair parameter and its different behavior in dsDNA and dsRNA traced down to changes in the sugar pucker angle of these NAs.
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43
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Abstract
F1- and V1-ATPase are rotary molecular motors that convert chemical energy released upon ATP hydrolysis into torque to rotate a central rotor axle against the surrounding catalytic stator cylinder with high efficiency. How conformational change occurring in the stator is coupled to the rotary motion of the axle is the key unknown in the mechanism of rotary motors. Here, we generated chimeric motor proteins by inserting an exogenous rod protein, FliJ, into the stator ring of F1 or of V1 and tested the rotation properties of these chimeric motors. Both motors showed unidirectional and continuous rotation, despite no obvious homology in amino acid sequence between FliJ and the intrinsic rotor subunit of F1 or V1 These results showed that any residue-specific interactions between the stator and rotor are not a prerequisite for unidirectional rotation of both F1 and V1 The torque of chimeric motors estimated from viscous friction of the rotation probe against medium revealed that whereas the F1-FliJ chimera generates only 10% of WT F1, the V1-FliJ chimera generates torque comparable to that of V1 with the native axle protein that is structurally more similar to FliJ than the native rotor of F1 This suggests that the gross structural mismatch hinders smooth rotation of FliJ accompanied with the stator ring of F1.
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44
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Jiang C, Lionberger TA, Wiener DM, Meyhofer E. Electromagnetic tweezers with independent force and torque control. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2016; 87:084304. [PMID: 27587135 DOI: 10.1063/1.4960811] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Magnetic tweezers are powerful tools to manipulate and study the mechanical properties of biological molecules and living cells. In this paper we present a novel, bona fide electromagnetic tweezer (EMT) setup that allows independent control of the force and torque applied via micrometer-sized magnetic beads to a molecule under study. We implemented this EMT by combining a single solenoid that generates force (f-EMT) with a set of four solenoids arranged into a symmetric quadrupole to generate torque (τ-EMT). To demonstrate the capability of the tweezers, we attached optically asymmetric Janus beads to single, tethered DNA molecules. We show that tension in the piconewton force range can be applied to single DNA molecules and the molecule can simultaneously be twisted with torques in the piconewton-nanometer range. Furthermore, the EMT allows the two components to be independently controlled. At various force levels applied to the Janus bead, the trap torsional stiffness can be continuously changed simply by varying the current magnitude applied to the τ-EMT. The flexible and independent control of force and torque by the EMT makes it an ideal tool for a range of measurements where tensional and torsional properties need to be studied simultaneously on a molecular or cellular level.
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Affiliation(s)
- Chang Jiang
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Troy A Lionberger
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Diane M Wiener
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Edgar Meyhofer
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
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45
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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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46
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Chen GY, Mickolajczyk KJ, Hancock WO. The Kinesin-5 Chemomechanical Cycle Is Dominated by a Two-heads-bound State. J Biol Chem 2016; 291:20283-20294. [PMID: 27402829 DOI: 10.1074/jbc.m116.730697] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Indexed: 12/29/2022] Open
Abstract
Single-molecule microscopy and stopped-flow kinetics assays were carried out to understand the microtubule polymerase activity of kinesin-5 (Eg5). Four lines of evidence argue that the motor primarily resides in a two-heads-bound (2HB) state. First, upon microtubule binding, dimeric Eg5 releases both bound ADPs. Second, microtubule dissociation in saturating ADP is 20-fold slower for the dimer than for the monomer. Third, ATP-triggered mant-ADP release is 5-fold faster than the stepping rate. Fourth, ATP binding is relatively fast when the motor is locked in a 2HB state. Shortening the neck-linker does not facilitate rear-head detachment, suggesting a minimal role for rear-head-gating. This 2HB state may enable Eg5 to stabilize incoming tubulin at the growing microtubule plus-end. The finding that slowly hydrolyzable ATP analogs trigger slower nucleotide release than ATP suggests that ATP hydrolysis in the bound head precedes stepping by the tethered head, leading to a mechanochemical cycle in which processivity is determined by the race between unbinding of the bound head and attachment of the tethered head.
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Affiliation(s)
- Geng-Yuan Chen
- From the Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Keith J Mickolajczyk
- From the Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802
| | - William O Hancock
- From the Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802
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47
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Probing the mechanical properties, conformational changes, and interactions of nucleic acids with magnetic tweezers. J Struct Biol 2016; 197:26-36. [PMID: 27368129 DOI: 10.1016/j.jsb.2016.06.022] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 05/06/2016] [Accepted: 06/28/2016] [Indexed: 11/21/2022]
Abstract
Nucleic acids are central to the storage and transmission of genetic information. Mechanical properties, along with their sequence, both enable and fundamentally constrain the biological functions of DNA and RNA. For small deformations from the equilibrium conformations, nucleic acids are well described by an isotropic elastic rod model. However, external forces and torsional strains can induce conformational changes, giving rise to a complex force-torque phase diagram. This review focuses on magnetic tweezers as a powerful tool to precisely determine both the elastic parameters and conformational transitions of nucleic acids under external forces and torques at the single-molecule level. We review several variations of magnetic tweezers, in particular conventional magnetic tweezers, freely orbiting magnetic tweezers and magnetic torque tweezers, and discuss their characteristic capabilities. We then describe the elastic rod model for DNA and RNA and discuss conformational changes induced by mechanical stress. The focus lies on the responses to torque and twist, which are crucial in the mechanics and interactions of nucleic acids and can directly be measured using magnetic tweezers. We conclude by highlighting several recent studies of nucleic acid-protein and nucleic acid-small-molecule interactions as further applications of magnetic tweezers and give an outlook of some exciting developments to come.
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48
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Structural Dynamics and Mechanochemical Coupling in DNA Gyrase. J Mol Biol 2016; 428:1833-45. [PMID: 27016205 DOI: 10.1016/j.jmb.2016.03.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 02/16/2016] [Accepted: 03/15/2016] [Indexed: 11/22/2022]
Abstract
Gyrase is a molecular motor that harnesses the free energy of ATP hydrolysis to perform mechanical work on DNA. The enzyme specifically introduces negative supercoiling in a process that must coordinate fuel consumption with DNA cleavage and religation and with numerous conformational changes in both the protein and DNA components of a large nucleoprotein complex. Here we present a current understanding of mechanochemical coupling in this essential molecular machine, with a focus on recent diverse biophysical approaches that have revealed details of molecular architectures, new conformational intermediates, structural transitions modulated by ATP binding, and the influence of mechanics on motor function. Recent single-molecule assays have also illuminated the reciprocal relationships between supercoiling and transcription, an illustration of mechanical interactions between gyrase and other molecular machines at the heart of chromosomal biology.
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49
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Kwon AY, Lee NK, Hong SC, Fierling J, Johner A. Annealed random copolymer model of the B-Z transition in DNA: torsional responses. Biophys J 2016; 108:2562-2572. [PMID: 25992734 DOI: 10.1016/j.bpj.2015.03.060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 03/10/2015] [Accepted: 03/17/2015] [Indexed: 11/26/2022] Open
Abstract
Both in vivo and in vitro, specific sequences in double-stranded DNA can adopt the left-handed Z-form when underwound. Recently, the B-Z transition of DNA has been studied in detail in magnetic tweezers experiments by several groups. We present a theoretical description of this transition, based on an annealed random copolymer model. The transition of a switchable sequence is discussed as a function of energetic and geometric parameters of the B- and Z-forms, of the applied boundary conditions, and of the characteristics of the B-Z interface. We address a possible torsional softening upon the B-Z transition. The model can be also applied to other biofilaments with annealed torsional/flexural degrees of freedom.
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Affiliation(s)
- Ah-Young Kwon
- Department of Physics, Sejong University, Seoul, South Korea
| | - Nam-Kyung Lee
- Department of Physics, Sejong University, Seoul, South Korea; Institute Charles Sadron, Centre National de la Recherche Scientifique, Strasbourg, France.
| | | | - Julien Fierling
- Institute Charles Sadron, Centre National de la Recherche Scientifique, Strasbourg, France
| | - Albert Johner
- Department of Physics, Sejong University, Seoul, South Korea; Institute Charles Sadron, Centre National de la Recherche Scientifique, Strasbourg, France
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50
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Kwon AY, Nam GM, Johner A, Kim S, Hong SC, Lee NK. Competition between B-Z and B-L transitions in a single DNA molecule: Computational studies. Phys Rev E 2016; 93:022411. [PMID: 26986366 DOI: 10.1103/physreve.93.022411] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Indexed: 11/07/2022]
Abstract
Under negative torsion, DNA adopts left-handed helical forms, such as Z-DNA and L-DNA. Using the random copolymer model developed for a wormlike chain, we represent a single DNA molecule with structural heterogeneity as a helical chain consisting of monomers which can be characterized by different helical senses and pitches. By Monte Carlo simulation, where we take into account bending and twist fluctuations explicitly, we study sequence dependence of B-Z transitions under torsional stress and tension focusing on the interaction with B-L transitions. We consider core sequences, (GC)_{n} repeats or (TG)_{n} repeats, which can interconvert between the right-handed B form and the left-handed Z form, imbedded in a random sequence, which can convert to left-handed L form with different (tension dependent) helical pitch. We show that Z-DNA formation from the (GC)_{n} sequence is always supported by unwinding torsional stress but Z-DNA formation from the (TG)_{n} sequence, which are more costly to convert but numerous, can be strongly influenced by the quenched disorder in the surrounding random sequence.
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Affiliation(s)
- Ah-Young Kwon
- Institute of Fundamental Physics, Department of Physics, Sejong University, Seoul 143-743, Korea
| | - Gi-Moon Nam
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, USA
| | - Albert Johner
- Institute of Fundamental Physics, Department of Physics, Sejong University, Seoul 143-743, Korea.,Institute Charles Sadron, Université de Strasbourg, CNRS UPR22, 23 rue du Loess 67034, Strasbourg cedex 2, France
| | - Seyong Kim
- Institute of Fundamental Physics, Department of Physics, Sejong University, Seoul 143-743, Korea
| | - Seok-Cheol Hong
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea.,Department of Physics, Korea University, Seoul 02841, Korea
| | - Nam-Kyung Lee
- Institute of Fundamental Physics, Department of Physics, Sejong University, Seoul 143-743, Korea.,Institute Charles Sadron, Université de Strasbourg, CNRS UPR22, 23 rue du Loess 67034, Strasbourg cedex 2, France
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