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Vaknin A, Grossman A, Durham ND, Lupovitz I, Goren S, Golani G, Roichman Y, Munro JB, Sorkin R. Ebola Virus Glycoprotein Strongly Binds to Membranes in the Absence of Receptor Engagement. ACS Infect Dis 2024; 10:1590-1601. [PMID: 38684073 DOI: 10.1021/acsinfecdis.3c00622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Ebola virus (EBOV) is an enveloped virus that must fuse with the host cell membrane in order to release its genome and initiate infection. This process requires the action of the EBOV envelope glycoprotein (GP), encoded by the virus, which resides in the viral envelope and consists of a receptor binding subunit, GP1, and a membrane fusion subunit, GP2. Despite extensive research, a mechanistic understanding of the viral fusion process is incomplete. To investigate GP-membrane association, a key step in the fusion process, we used two approaches: high-throughput measurements of single-particle diffusion and single-molecule measurements with optical tweezers. Using these methods, we show that the presence of the endosomal Niemann-Pick C1 (NPC1) receptor is not required for primed GP-membrane binding. In addition, we demonstrate this binding is very strong, likely attributed to the interaction between the GP fusion loop and the membrane's hydrophobic core. Our results also align with previously reported findings, emphasizing the significance of acidic pH in the protein-membrane interaction. Beyond Ebola virus research, our approach provides a powerful toolkit for studying other protein-membrane interactions, opening new avenues for a better understanding of protein-mediated membrane fusion events.
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Affiliation(s)
- Alisa Vaknin
- School of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Alon Grossman
- School of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Natasha D Durham
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
| | - Inbal Lupovitz
- School of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Shahar Goren
- School of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Gonen Golani
- Department of Physics and Haifa Research Center for Theoretical Physics and Astrophysics, University of Haifa, Haifa 3498838, Israel
| | - Yael Roichman
- School of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
- Raymond and Beverly Sackler School of Physics & Astronomy, Tel Aviv University, Tel Aviv 6997801, Israel
| | - James B Munro
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
| | - Raya Sorkin
- School of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
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2
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Kabtiyal P, Robbins A, Jergens E, Castro CE, Winter JO, Poirier MG, Johnston-Halperin E. Localized Plasmonic Heating for Single-Molecule DNA Rupture Measurements in Optical Tweezers. Nano Lett 2024; 24:3097-3103. [PMID: 38417053 DOI: 10.1021/acs.nanolett.3c04848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2024]
Abstract
To date, studies on the thermodynamic and kinetic processes that underlie biological function and nanomachine actuation in biological- and biology-inspired molecular constructs have primarily focused on photothermal heating of ensemble systems, highlighting the need for probes that are localized within the molecular construct and capable of resolving single-molecule response. Here we present an experimental demonstration of wavelength-selective, localized heating at the single-molecule level using the surface plasmon resonance of a 15 nm gold nanoparticle (AuNP). Our approach is compatible with force-spectroscopy measurements and can be applied to studies of the single-molecule thermodynamic properties of DNA origami nanomachines as well as biomolecular complexes. We further demonstrate wavelength selectivity and establish the temperature dependence of the reaction coordinate for base-pair disruption in the shear-rupture geometry, demonstrating the utility and flexibility of this approach for both fundamental studies of local (nanometer-scale) temperature gradients and rapid and multiplexed nanomachine actuation.
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Affiliation(s)
- Prerna Kabtiyal
- Department of Physics, The Ohio State University, Columbus, Ohio 43210, United States
| | - Ariel Robbins
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Elizabeth Jergens
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Carlos E Castro
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jessica O Winter
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, United States
| | - Michael G Poirier
- Department of Physics, The Ohio State University, Columbus, Ohio 43210, United States
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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3
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Truong HP, Saleh OA. Magnetic tweezers characterization of the entropic elasticity of intrinsically disordered proteins and peptoids. Methods Enzymol 2024; 694:209-236. [PMID: 38492952 DOI: 10.1016/bs.mie.2023.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2024]
Abstract
Understanding the conformational behavior of biopolymers is essential to unlocking knowledge of their biophysical mechanisms and functional roles. Single-molecule force spectroscopy can provide a unique perspective on this by exploiting entropic elasticity to uncover key biopolymer structural parameters. A particularly powerful approach involves the use of magnetic tweezers, which can easily generate lower stretching forces (0.1-20 pN). For forces at the low end of this range, the elastic response of biopolymers is sensitive to excluded volume effects, and they can be described by Pincus blob elasticity model that allow robust extraction of the Flory polymer scaling exponent. Here, we detail protocols for the use of magnetic tweezers for force-extension measurements of intrinsically disordered proteins and peptoids. We also discuss procedures for fitting low-force elastic curves to the predictions of polymer physics models to extract key conformational parameters.
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Affiliation(s)
- Hoang P Truong
- Materials Department, University of California, Santa Barbara, CA, United States
| | - Omar A Saleh
- Materials Department, University of California, Santa Barbara, CA, United States; Biomolecular Sciences and Engineering Program, University of California, Santa Barbara, CA, United States; Physics Department, University of California, Santa Barbara, CA, United States.
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4
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Bhuiyan FH, Li YS, Kim SH, Martini A. Shear-activation of mechanochemical reactions through molecular deformation. Sci Rep 2024; 14:2992. [PMID: 38316829 PMCID: PMC10844542 DOI: 10.1038/s41598-024-53254-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/30/2024] [Indexed: 02/07/2024] Open
Abstract
Mechanical stress can directly activate chemical reactions by reducing the reaction energy barrier. A possible mechanism of such mechanochemical activation is structural deformation of the reactant species. However, the effect of deformation on the reaction energetics is unclear, especially, for shear stress-driven reactions. Here, we investigated shear stress-driven oligomerization reactions of cyclohexene on silica using a combination of reactive molecular dynamics simulations and ball-on-flat tribometer experiments. Both simulations and experiments captured an exponential increase in reaction yield with shear stress. Elemental analysis of ball-on-flat reaction products revealed the presence of oxygen in the polymers, a trend corroborated by the simulations, highlighting the critical role of surface oxygen atoms in oligomerization reactions. Structural analysis of the reacting molecules in simulations indicated the reactants were deformed just before a reaction occurred. Quantitative evidence of shear-induced deformation was established by comparing bond lengths in cyclohexene molecules in equilibrium and prior to reactions. Nudged elastic band calculations showed that the deformation had a small effect on the transition state energy but notably increased the reactant state energy, ultimately leading to a reduction in the energy barrier. Finally, a quantitative relationship was developed between molecular deformation and energy barrier reduction by mechanical stress.
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Affiliation(s)
- Fakhrul H Bhuiyan
- Department of Mechanical Engineering, University of California Merced, 5200 N. Lake Road, Merced, CA, 95343, USA
| | - Yu-Sheng Li
- Department of Chemical Engineering and Materials Research Institute, Pennsylvania State University, University Park, PA, 16802, USA
| | - Seong H Kim
- Department of Chemical Engineering and Materials Research Institute, Pennsylvania State University, University Park, PA, 16802, USA
| | - Ashlie Martini
- Department of Mechanical Engineering, University of California Merced, 5200 N. Lake Road, Merced, CA, 95343, USA.
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Prüßner T, Meinderink D, Zhu S, Orive AG, Kielar C, Huck M, Steinrück HG, Keller A, Grundmeier G. Molecular Adhesion of a Pilus-Derived Peptide Involved in Pseudomonas aeruginosa Biofilm Formation on Non-Polar ZnO-Surfaces. Chemistry 2024; 30:e202302464. [PMID: 37909474 DOI: 10.1002/chem.202302464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/30/2023] [Accepted: 10/30/2023] [Indexed: 11/03/2023]
Abstract
Bacterial colonization and biofilm formation on abiotic surfaces are initiated by the adhesion of peptides and proteins. Understanding the adhesion of such peptides and proteins at a molecular level thus represents an important step toward controlling and suppressing biofilm formation on technological and medical materials. This study investigates the molecular adhesion of a pilus-derived peptide that facilitates biofilm formation of Pseudomonas aeruginosa, a multidrug-resistant opportunistic pathogen frequently encountered in healthcare settings. Single-molecule force spectroscopy (SMFS) was performed on chemically etched ZnO11 2 ‾ 0 ${\left(11\bar{2}0\right)}$ surfaces to gather insights about peptide adsorption force and its kinetics. Metal-free click chemistry for the fabrication of peptide-terminated SMFS cantilevers was performed on amine-terminated gold cantilevers and verified by X-ray photoelectron spectroscopy (XPS) and polarization-modulated infrared reflection absorption spectroscopy (PM-IRRAS). Atomic force microscopy (AFM) and XPS analyses reveal stable topographies and surface chemistries of the substrates that are not affected by SMFS. Rupture events described by the worm-like chain model (WLC) up to 600 pN were detected for the non-polar ZnO surfaces. The dissociation barrier energy at zero force ΔG(0), the transition state distance xb and bound-unbound dissociation rate at zero force koff (0) for the single crystalline substrate indicate that coordination and hydrogen bonds dominate the peptide/surface interaction.
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Affiliation(s)
- Tim Prüßner
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Dennis Meinderink
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Siqi Zhu
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Alejandro G Orive
- Department of Chemistry, Materials and Nanotechnology Institute, University of La Laguna, Avda. Astrofisico Francisco Sánchez s/n, 38206, San Cristóbal de La Laguna, Spain
| | - Charlotte Kielar
- Insitute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Marten Huck
- Chemistry Department, Paderborn University, 33098, Paderborn, Germany
| | | | - Adrian Keller
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Guido Grundmeier
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
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6
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Vogt M, List J, Langecker M, Santiago I, Simmel FC, Kopperger E. Electrokinetic Torque Generation by DNA Nanorobotic Arms Studied via Single-Molecule Fluctuation Analysis. J Phys Chem B 2023; 127:10710-10722. [PMID: 38060372 DOI: 10.1021/acs.jpcb.3c05959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
DNA nanotechnology has enabled the creation of supramolecular machines, whose shape and function are inspired from traditional mechanical engineering as well as from biological examples. As DNA inherently is a highly charged biopolymer, the external application of electric fields provides a versatile, computer-programmable way to control the movement of DNA-based machines. However, the details of the electrohydrodynamic interactions underlying the electrical manipulation of these machines are complex, as the influence of their intrinsic charge, the surrounding cloud of counterions, and the effect of electrokinetic fluid flow have to be taken into account. In this work, we identify the relevant effects involved in this actuation mechanism by determining the electric response of an established DNA-based nanorobotic arm to varying design and operation parameters. Borrowing an approach from single-molecule biophysics, we determined the electrical torque exerted on the nanorobotic arms by analyzing their thermal fluctuations when oriented in an electric field. We analyze the influence of various experimental and design parameters on the "actuatability" of the nanostructures and optimize the generated torque according to these parameters. Our findings give insight into the physical processes involved in the actuation mechanism and provide general guidelines that aid in designing and efficiently operating electrically driven nanorobotic devices made from DNA.
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Affiliation(s)
- Matthias Vogt
- Physics of Synthetic Biological Systems─E14, Department of Bioscience, TUM School of Natural Science, Technical University of Munich, 85748 Garching, Germany
| | - Jonathan List
- Physics of Synthetic Biological Systems─E14, Department of Bioscience, TUM School of Natural Science, Technical University of Munich, 85748 Garching, Germany
| | - Martin Langecker
- Physics of Synthetic Biological Systems─E14, Department of Bioscience, TUM School of Natural Science, Technical University of Munich, 85748 Garching, Germany
| | - Ibon Santiago
- CIC nanoGUNE BRTA, Donostia-San Sebastián 20018, Spain
| | - Friedrich C Simmel
- Physics of Synthetic Biological Systems─E14, Department of Bioscience, TUM School of Natural Science, Technical University of Munich, 85748 Garching, Germany
| | - Enzo Kopperger
- Physics of Synthetic Biological Systems─E14, Department of Bioscience, TUM School of Natural Science, Technical University of Munich, 85748 Garching, Germany
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7
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Yang H, Shi X. The Free Energy of Nucleosomal DNA Based on the Landau Model and Topology. Biomolecules 2023; 13:1686. [PMID: 38136559 PMCID: PMC10741420 DOI: 10.3390/biom13121686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/30/2023] [Accepted: 11/09/2023] [Indexed: 12/24/2023] Open
Abstract
The free energy of nucleosomal DNA plays a key role in the formation of nucleosomes in eukaryotes. Some work on the free energy of nucleosomal DNA have been carried out in experiments. However, the relationships between the free energy of nucleosomal DNA and its conformation, especially its topology, remain unclear in theory. By combining the Landau theory, the Hopfion model and experimental data, we find that the free energy of nucleosomal DNA is at the lower level. With the help of the energy minimum principle, we conclude that nucleosomal DNA stays in a stable state. Moreover, we discover that small perturbations on nucleosomal DNA have little effect on its free energy. This implies that nucleosomal DNA has a certain redundancy in order to stay stable. This explains why nucleosomal DNA will not change significantly due to small perturbations.
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Affiliation(s)
| | - Xuguang Shi
- College of Science, Beijing Forestry University, Beijing 100083, China;
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8
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Li R, Madhvacharyula AS, Du Y, Adepu HK, Choi JH. Mechanics of dynamic and deformable DNA nanostructures. Chem Sci 2023; 14:8018-8046. [PMID: 37538812 PMCID: PMC10395309 DOI: 10.1039/d3sc01793a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/05/2023] [Indexed: 08/05/2023] Open
Abstract
In DNA nanotechnology, DNA molecules are designed, engineered, and assembled into arbitrary-shaped architectures with predesigned functions. Static DNA assemblies often have delicate designs with structural rigidity to overcome thermal fluctuations. Dynamic structures reconfigure in response to external cues, which have been explored to create functional nanodevices for environmental sensing and other applications. However, the precise control of reconfiguration dynamics has been a challenge due partly to flexible single-stranded DNA connections between moving parts. Deformable structures are special dynamic constructs with deformation on double-stranded parts and single-stranded hinges during transformation. These structures often have better control in programmed deformation. However, related deformability and mechanics including transformation mechanisms are not well understood or documented. In this review, we summarize the development of dynamic and deformable DNA nanostructures from a mechanical perspective. We present deformation mechanisms such as single-stranded DNA hinges with lock-and-release pairs, jack edges, helicity modulation, and external loading. Theoretical and computational models are discussed for understanding their associated deformations and mechanics. We elucidate the pros and cons of each model and recommend design processes based on the models. The design guidelines should be useful for those who have limited knowledge in mechanics as well as expert DNA designers.
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Affiliation(s)
- Ruixin Li
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Anirudh S Madhvacharyula
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Yancheng Du
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Harshith K Adepu
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Jong Hyun Choi
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
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9
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Ruzycki CA, Montoya D, Irshad H, Cox J, Zhou Y, McDonald JD, Kuehl PJ. Inhalation delivery of nucleic acid gene therapies in preclinical drug development. Expert Opin Drug Deliv 2023; 20:1097-1113. [PMID: 37732957 DOI: 10.1080/17425247.2023.2261369] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/18/2023] [Indexed: 09/22/2023]
Abstract
INTRODUCTION Inhaled gene therapy programs targeting diseases of the lung have seen increasing interest in recent years, though as of yet no product has successfully entered the market. Preclinical research to support such programs is critically important in maximizing the chances of developing successful candidates. AREAS COVERED Aspects of inhalation delivery of gene therapies are reviewed, with a focus on preclinical research in animal models. Various barriers to inhalation delivery of gene therapies are discussed, including aerosolization stresses, aerosol behavior in the respiratory tract, and disposition processes post-deposition. Important aspects of animal models are considered, including determinations of biologically relevant determinations of dose and issues related to translatability. EXPERT OPINION Development of clinically-efficacious inhaled gene therapies has proven difficult owing to numerous challenges. Fit-for-purpose experimental and analytical methods are necessary for determinations of biologically relevant doses in preclinical animal models. Further developments in disease-specific animal models may aid in improving the translatability of results in future work, and we expect to see accelerated interests in inhalation gene therapies for various diseases. Sponsors, researchers, and regulators are encouraged to engage in early and frequent discussion regarding candidate therapies, and additional dissemination of preclinical methodologies would be of immense value in avoiding common pitfalls.
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Affiliation(s)
- Conor A Ruzycki
- Lovelace Biomedical Research Institute, Albuquerque, NM, USA
| | - Derek Montoya
- Lovelace Biomedical Research Institute, Albuquerque, NM, USA
| | - Hammad Irshad
- Lovelace Biomedical Research Institute, Albuquerque, NM, USA
| | - Jason Cox
- Lovelace Biomedical Research Institute, Albuquerque, NM, USA
| | - Yue Zhou
- Lovelace Biomedical Research Institute, Albuquerque, NM, USA
| | | | - Philip J Kuehl
- Lovelace Biomedical Research Institute, Albuquerque, NM, USA
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10
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Geyer VF, Diez S. Horizontal Magnetic Tweezers to Directly Measure the Force-Velocity Relationship for Multiple Kinesin Motors. Small 2023:e2300558. [PMID: 37035988 DOI: 10.1002/smll.202300558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/11/2023] [Indexed: 06/19/2023]
Abstract
Transport of intracellular cargo along cytoskeletal filaments is often achieved by the concerted action of multiple motor molecules. While single-molecule studies have provided profound insight into the mechano-chemical principles and force generation of individual motors, studies on multi-motor systems are less advanced. Here, a horizontal magnetic-tweezers setup is applied, capable of producing up to 150 pN of horizontal force onto 2.8 µm superparamagnetic beads, to motor-propelled cytoskeletal filaments. It is found that kinesin-1 driven microtubules decorated with individual beads display frequent transitions in their gliding velocities which we attribute to dynamic changes in the number of engaged motors. Applying defined temporal force-ramps the force-velocity relationship is directly measured for multi-motor transport. It is found that the stall forces of individual motors are approximately additive and collective backward motion of the transport system under super-stall forces is observed. The magnetic-tweezers apparatus is expected to be readily applicable to a wide range of molecular and cellular motility assays.
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Affiliation(s)
- Veikko F Geyer
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
| | - Stefan Diez
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Tatzberg 41, 01307, Dresden, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, Arnoldstraße 18, 01307, Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307, Dresden, Germany
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11
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Wang J, Kouznetsova TB, Xia J, Ángeles FJ, de la Cruz MO, Craig SL. A polyelectrolyte handle for single‐molecule force spectroscopy. Journal of Polymer Science 2023. [DOI: 10.1002/pol.20230051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Affiliation(s)
- Junpeng Wang
- Department of Chemistry Duke University Durham North Carolina USA
| | | | - Jianshe Xia
- Department of Materials Science and Engineering Northwestern University Evanston Illinois USA
| | - Felipe Jiménez Ángeles
- Department of Materials Science and Engineering Northwestern University Evanston Illinois USA
| | | | - Stephen L. Craig
- Department of Chemistry Duke University Durham North Carolina USA
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12
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Legan ER, Liu Y, Arce NA, Parker ET, Lollar P, Zhang XF, Li R. Type 2B von Willebrand disease mutations differentially perturb autoinhibition of the A1 domain. Blood 2023; 141:1221-1232. [PMID: 36580664 PMCID: PMC10023833 DOI: 10.1182/blood.2022017239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 12/05/2022] [Accepted: 12/23/2022] [Indexed: 12/31/2022] Open
Abstract
Type 2B von Willebrand disease (VWD) is an inherited bleeding disorder in which a subset of point mutations in the von Willebrand factor (VWF) A1 domain and recently identified autoinhibitory module (AIM) cause spontaneous binding to glycoprotein Ibα (GPIbα) on the platelet surface. All reported type 2B VWD mutations share this enhanced binding; however, type 2B VWD manifests as variable bleeding complications and platelet levels in patients, depending on the underlying mutation. Understanding how these mutations localizing to a similar region can result in such disparate patient outcomes is essential for detailing our understanding of VWF regulatory and activation mechanisms. In this study, we produced recombinant glycosylated AIM-A1 fragments bearing type 2B VWD mutations and examined how each mutation affects the A1 domain's thermodynamic stability, conformational dynamics, and biomechanical regulation of the AIM. We found that the A1 domain with mutations associated with severe bleeding occupy a higher affinity state correlating with enhanced flexibility in the secondary GPIbα-binding sites. Conversely, mutation P1266L, associated with normal platelet levels, has similar proportions of high-affinity molecules to wild-type (WT) but shares regions of solvent accessibility with both WT and other type 2B VWD mutations. V1316M exhibited exceptional instability and solvent exposure compared with all variants. Lastly, examination of the mechanical stability of each variant revealed variable AIM unfolding. Together, these studies illustrate that the heterogeneity among type 2B VWD mutations is evident in AIM-A1 fragments.
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Affiliation(s)
- Emily R. Legan
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Emory University, Atlanta, GA
| | - Yi Liu
- Department of Bioengineering, Lehigh University, Bethlehem, PA
- Department of Biomedical Engineering, University of Massachusetts Amherst, Amherst, MA
| | - Nicholas A. Arce
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Emory University, Atlanta, GA
| | - Ernest T. Parker
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Emory University, Atlanta, GA
| | - Pete Lollar
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Emory University, Atlanta, GA
| | - X. Frank Zhang
- Department of Biomedical Engineering, University of Massachusetts Amherst, Amherst, MA
| | - Renhao Li
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Emory University, Atlanta, GA
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13
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Magazzù A, Marcuello C. Investigation of Soft Matter Nanomechanics by Atomic Force Microscopy and Optical Tweezers: A Comprehensive Review. Nanomaterials (Basel) 2023; 13:nano13060963. [PMID: 36985857 PMCID: PMC10053849 DOI: 10.3390/nano13060963] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 05/17/2023]
Abstract
Soft matter exhibits a multitude of intrinsic physico-chemical attributes. Their mechanical properties are crucial characteristics to define their performance. In this context, the rigidity of these systems under exerted load forces is covered by the field of biomechanics. Moreover, cellular transduction processes which are involved in health and disease conditions are significantly affected by exogenous biomechanical actions. In this framework, atomic force microscopy (AFM) and optical tweezers (OT) can play an important role to determine the biomechanical parameters of the investigated systems at the single-molecule level. This review aims to fully comprehend the interplay between mechanical forces and soft matter systems. In particular, we outline the capabilities of AFM and OT compared to other classical bulk techniques to determine nanomechanical parameters such as Young's modulus. We also provide some recent examples of nanomechanical measurements performed using AFM and OT in hydrogels, biopolymers and cellular systems, among others. We expect the present manuscript will aid potential readers and stakeholders to fully understand the potential applications of AFM and OT to soft matter systems.
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Affiliation(s)
- Alessandro Magazzù
- CNR-IPCF, Istituto per i Processi Chimico-Fisici, 98158 Mesina, Italy
- NLHT-Lab, Department of Physics, University of Calabria, 87036 Rende, Italy
| | - Carlos Marcuello
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain
- Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, 50018 Zaragoza, Spain
- Correspondence: ; Tel.: +34-876555357
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14
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Li T, Dufresne ER, Kröger M, Heyden S. Siloxane Molecules: Nonlinear Elastic Behavior and Fracture Characteristics. Macromolecules 2023; 56:1303-1310. [PMID: 36874533 PMCID: PMC9979691 DOI: 10.1021/acs.macromol.2c02576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/17/2023] [Indexed: 02/10/2023]
Abstract
Fracture phenomena in soft materials span multiple length and time scales. This poses a major challenge in computational modeling and predictive materials design. To pass quantitatively from molecular to continuum scales, a precise representation of the material response at the molecular level is vital. Here, we derive the nonlinear elastic response and fracture characteristics of individual siloxane molecules using molecular dynamics (MD) studies. For short chains, we find deviations from classical scalings for both the effective stiffness and mean chain rupture times. A simple model of a nonuniform chain of Kuhn segments captures the observed effect and agrees well with MD data. We find that the dominating fracture mechanism depends on the applied force scale in a nonmonotonic fashion. This analysis suggests that common polydimethylsiloxane (PDMS) networks fail at cross-linking points. Our results can be readily lumped into coarse-grained models. Although focusing on PDMS as a model system, our study presents a general procedure to pass beyond the window of accessible rupture times in MD studies employing mean first passage time theory, which can be exploited for arbitrary molecular systems.
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Affiliation(s)
- Tianchi Li
- Soft and Living Materials, Department of Materials, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Eric R Dufresne
- Soft and Living Materials, Department of Materials, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Martin Kröger
- Polymer Physics, Department of Materials, ETH Zurich, CH-8093 Zurich, Switzerland.,Magnetism and Interface Physics, Department of Materials, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Stefanie Heyden
- Soft and Living Materials, Department of Materials, ETH Zurich, CH-8093 Zurich, Switzerland
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15
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Florio G, Puglisi G. A predictive model for the thermomechanical melting transition of double stranded DNA. Acta Biomater 2023; 157:225-235. [PMID: 36450304 DOI: 10.1016/j.actbio.2022.11.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/24/2022] [Accepted: 11/21/2022] [Indexed: 11/30/2022]
Abstract
By extending the classical Peyrard-Bishop model, we are able to obtain a fully analytical description for the mechanical response of DNA under stretching at variable values of temperature, number of base pairs and intrachains and interchains bonds stiffness. In order to compare elasticity and temperature effects, we first analyze the system in the zero temperature mechanical limit, important to describe several experimental effects including possible hysteresis. We then analyze temperature effects in the framework of equilibrium Statistical Mechanics. In particular, we obtain an analytical expression for the temperature-dependent melting force and unzipping assigned displacement in the thermodynamical limit, also depending on the relative stability of intra vs. inter molecular bonds. Such results coincide with the purely mechanical model in the limit of zero temperature and with the denaturation temperature that we obtain with the classical transfer integral method. Based on our analytical results, we obtain explicitly phase diagrams and cooperativity parameters, where also discreteness effect can be accounted for. The obtained results are successfully applied in reproducing the thermomechanical experimental melting of DNA and the response of DNA hairpins. Due to the generality of the model, exemplified in the proposed analysis of both overstretching and unzipping experiments, we argue that the proposed approach can be extended to other thermomechanically induced molecular melting phenomena. STATEMENT OF SIGNIFICANCE: We obtain a fully analytical description of the complex wiggly energy landscape of two stranded macromolecules under unzipping loading. Based on Equilibrium Statistical Mechanics, we describe the combined thermomechanical effects and the melting transition of double stranded molecules such as nucleic acids. This is proved by quantitatively predicting the experimental behavior of both melting of DNA and DNA hairpins opening. While analytical results have been previously attained under special conditions on the relative stiffness of the covalent vs. non-covalent bonds of the base pairs, our model is completely general in this respect, thus representing a tool in the perspective of the design at the molecular scale. We show that the obtained model can be fully inscribed in the theory of phase transitions giving a new interpretation of the thermomechanical behavior of double stranded molecules.
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Affiliation(s)
- Giuseppe Florio
- Politecnico di Bari, Dipartimento di Ing. Civile, Ambientale, del Territorio, Edile e di Chimica, Via Re David 200, Bari 70126, Italy; INFN, Sezione di Bari, I-70126, Italy.
| | - Giuseppe Puglisi
- Politecnico di Bari, Dipartimento di Ing. Civile, Ambientale, del Territorio, Edile e di Chimica, Via Re David 200, Bari 70126, Italy.
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16
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Liu F, Li J, Zhang T, Chen J, Ho CL. Engineered Spore-Forming Bacillus as a Microbial Vessel for Long-Term DNA Data Storage. ACS Synth Biol 2022; 11:3583-3591. [PMID: 36150134 DOI: 10.1021/acssynbio.2c00291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
DNA data storage technology may supersede conventional chip or magnetic data storage medium, providing long-term stability, high density, and sustainable storage. Due to its error-correcting capability, DNA data stored in living organisms exhibits high fidelity in information replication. Here we report the development of a Bacillus chassis integrated with an inducible artificially assembled bacterial chromosome to facilitate random data access. We generated three sets of data in the form of DNA sequences using a rudimentary coding system accessible by the regulatory promoter. Sporulated Bacillus harboring the genes were used for long-term storage, where viability assays of spores were subjected to harsh environmental stresses to evaluate the data storage stability. The data accuracy remained above 99% after high temperature and oxidative stress treatment, whereas UV irradiation treatment provided above 96% accuracy. The developed Bacillus chassis and artificial chromosome facilitate the long-term storage of larger datum volume by using other DNA digital encoding and decoding programs.
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Affiliation(s)
- Feng Liu
- Department of Biomedical Engineering, Southern University of Science and Technology (SUSTech), Shenzhen518055, China
| | - Jiashu Li
- Department of Biomedical Engineering, Southern University of Science and Technology (SUSTech), Shenzhen518055, China
| | - Tongzhou Zhang
- Department of Biomedical Engineering, Southern University of Science and Technology (SUSTech), Shenzhen518055, China
| | - Jun Chen
- Department of Biomedical Engineering, Southern University of Science and Technology (SUSTech), Shenzhen518055, China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology (SIAT), Chinese Academy of Sciences, Shenzhen518055, China
| | - Chun Loong Ho
- Department of Biomedical Engineering, Southern University of Science and Technology (SUSTech), Shenzhen518055, China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology (SIAT), Chinese Academy of Sciences, Shenzhen518055, China
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17
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Zhang CY, Zhang NH. Mechanical Constraint Effect on DNA Persistence Length. Molecules 2022; 27:molecules27227769. [PMID: 36431871 PMCID: PMC9696218 DOI: 10.3390/molecules27227769] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/31/2022] [Accepted: 11/04/2022] [Indexed: 11/16/2022]
Abstract
Persistence length is a significant criterion to characterize the semi-flexibility of DNA molecules. The mechanical constraints applied on DNA chains in new single-molecule experiments play a complex role in measuring DNA persistence length; however, there is a difficulty in quantitatively characterizing the mechanical constraint effects due to their complex interactions with electrostatic repulsions and thermal fluctuations. In this work, the classical buckling theory of Euler beam and Manning's statistical theories of electrostatic force and thermal fluctuation force are combined for an isolated DNA fragment to formulate a quantitative model, which interprets the relationship between DNA persistence length and critical buckling length. Moreover, this relationship is further applied to identify the mechanical constraints in different DNA experiments by fitting the effective length factors of buckled fragments. Then, the mechanical constraint effects on DNA persistence lengths are explored. A good agreement among the results by theoretical models, previous experiments, and present molecular dynamics simulations demonstrates that the new superposition relationship including three constraint-dependent terms can effectively characterize changes in DNA persistence lengths with environmental conditions, and the strong constraint-environment coupling term dominates the significant changes of persistence lengths; via fitting effective length factors, the weakest mechanical constraints on DNAs in bulk experiments and stronger constraints on DNAs in single-molecule experiments are identified, respectively. Moreover, the consideration of DNA buckling provides a new perspective to examine the bendability of short-length DNA.
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Affiliation(s)
- Cheng-Yin Zhang
- Department of Mechanics, School of Mechanics and Engineering Science, Shanghai University, Shanghai 200444, China
| | - Neng-Hui Zhang
- Department of Mechanics, School of Mechanics and Engineering Science, Shanghai University, Shanghai 200444, China
- Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai Institute of Applied Mathematics and Mechanics, Shanghai University, Shanghai 200072, China
- Correspondence:
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18
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Li R, Zheng M, Madhvacharyula AS, Du Y, Mao C, Choi JH. Mechanical deformation behaviors and structural properties of ligated DNA crystals. Biophys J 2022; 121:4078-4090. [PMID: 36181269 PMCID: PMC9675025 DOI: 10.1016/j.bpj.2022.09.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/21/2022] [Accepted: 09/27/2022] [Indexed: 11/02/2022] Open
Abstract
DNA self-assembly has emerged as a powerful strategy for constructing complex nanostructures. While the mechanics of individual DNA strands have been studied extensively, the deformation behaviors and structural properties of self-assembled architectures are not well understood. This is partly due to the small dimensions and limited experimental methods available. DNA crystals are macroscopic crystalline structures assembled from nanoscale motifs via sticky-end association. The large DNA constructs may thus be an ideal platform to study structural mechanics. Here, we investigate the fundamental mechanical properties and behaviors of ligated DNA crystals made of tensegrity triangular motifs. We perform coarse-grained molecular dynamics simulations and confirm the results with nanoindentation experiments using atomic force microscopy. We observe various deformation modes, including untension, linear elasticity, duplex dissociation, and single-stranded component stretch. We find that the mechanical properties of a DNA architecture are correlated with those of its components. However, the structure shows complex behaviors which may not be predicted by components alone and the architectural design must be considered.
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Affiliation(s)
- Ruixin Li
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana
| | - Mengxi Zheng
- Department of Chemistry, Purdue University, West Lafayette, Indiana
| | | | - Yancheng Du
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, Indiana
| | - Jong Hyun Choi
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana.
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19
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Arce NA, Liu Y, Chen W, Zhang XF, Li R. Autoinhibitory module underlies species difference in shear activation of von Willebrand factor. J Thromb Haemost 2022; 20:2686-2696. [PMID: 36031939 PMCID: PMC9588639 DOI: 10.1111/jth.15837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/05/2022] [Accepted: 07/22/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Von Willebrand factor (VWF) is a multimeric plasma protein that bridges the gap between vessel injury and platelet capture at high shear rates. Under high shear or tension, VWF can become activated upon the unfolding of its autoinhibitory module (AIM). AIM unfolding exposes the A1 domain, allowing for binding to platelet glycoprotein (GP)Ibα to initiate primary hemostasis. The characteristics of the AIM and its inhibitory properties within mouse VWF are unknown. OBJECTIVES To determine and characterize the autoinhibitory properties of mouse VWF. METHODS Recombinant mouse VWF A1 fragments containing or lacking the flanking regions around the A1 domain were generated. We tested the ability of these fragments to bind to human or mouse GPIbα and platelets. We compared the unfolding of mouse AIM-A1 to human AIM-A1 by single-molecule force spectroscopy. RESULTS Recombinant mouse AIM-A1 binds with higher affinity to GPIbα than its human counterpart. Recombinant mouse proteins lacking part of the AIM show increased binding to GPIbα. Activated A1 fragments lacking the AIM can effectively agglutinate platelets across the species barrier. Using single-molecule force spectroscopy, we determined that the mouse AIM unfolds under forces similar to the human AIM. Additionally, the human AIM paired with mouse A1 largely recapitulates the behavior of human AIM-A1. CONCLUSIONS Our results suggest that the regulation of VWF-GPIbα binding has been specifically tuned to work optimally in different rheological architectures. Differences in the AIM sequence may contribute to the difference in VWF shear response between human and mice.
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Affiliation(s)
- Nicholas A. Arce
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Yi Liu
- Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Wenchun Chen
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - X. Frank Zhang
- Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Renhao Li
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
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20
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Kaczmarczyk AP, Déclais AC, Newton MD, Boulton SJ, Lilley DMJ, Rueda DS. Search and processing of Holliday junctions within long DNA by junction-resolving enzymes. Nat Commun 2022; 13:5921. [PMID: 36207294 PMCID: PMC9547003 DOI: 10.1038/s41467-022-33503-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 09/21/2022] [Indexed: 12/05/2022] Open
Abstract
Resolution of Holliday junctions is a critical intermediate step of homologous recombination in which junctions are processed by junction-resolving endonucleases. Although binding and cleavage are well understood, the question remains how the enzymes locate their substrate within long duplex DNA. Here we track fluorescent dimers of endonuclease I on DNA, presenting the complete single-molecule reaction trajectory for a junction-resolving enzyme finding and cleaving a Holliday junction. We show that the enzyme binds remotely to dsDNA and then undergoes 1D diffusion. Upon encountering a four-way junction, a catalytically-impaired mutant remains bound at that point. An active enzyme, however, cleaves the junction after a few seconds. Quantitative analysis provides a comprehensive description of the facilitated diffusion mechanism. We show that the eukaryotic junction-resolving enzyme GEN1 also undergoes facilitated diffusion on dsDNA until it becomes located at a junction, so that the general resolution trajectory is probably applicable to many junction resolving enzymes.
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Affiliation(s)
- Artur P Kaczmarczyk
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, W12 0NN, UK
| | | | - Matthew D Newton
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, W12 0NN, UK
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Simon J Boulton
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - David M J Lilley
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.
| | - David S Rueda
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, W12 0NN, UK.
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, W12 0NN, UK.
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21
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Abstract
The presence of athermal noise or biological fluctuations control and maintain crucial life-processes. In this work, we present an exact analytical treatment of the dynamic behavior of a flexible polymer chain that is subjected to both thermal and active forces. Our model for active forces incorporates temporal correlation associated with the characteristic time scale and processivity of enzymatic function (driven by ATP hydrolysis), leading to an active-force time scale that competes with relaxation processes within the polymer chain. We analyze the structure and dynamics of an active-Brownian polymer using our exact results for the dynamic structure factor and the looping time for the chain ends. The spectrum of relaxation times within a polymer chain implies two different behaviors at small and large length scales. Small length-scale relaxation is faster than the active-force time scale, and the dynamic and structural behavior at these scales are oblivious to active forces and, are thus governed by the true thermal temperature. Large length-scale behavior is governed by relaxation times that are much longer than the active-force time scale, resulting in an effective active-Brownian temperature that dramatically alters structural and dynamic behavior. These complex multi-scale effects imply a time-dependent temperature that governs living and non-equilibrium systems, serving as a unifying concept for interpreting and predicting their physical behavior.
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Affiliation(s)
- Ashesh Ghosh
- Department of Chemical Engineering, Stanford University, Stanford, California, USA.
| | - Andrew J Spakowitz
- Department of Chemical Engineering, Stanford University, Stanford, California, USA.
- Biophysics Program, Stanford University, Stanford, California, USA
- Department of Materials Science & Engineering, Stanford University, Stanford, California, USA
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22
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Abstract
Knowledge of the elastic properties, e.g., the persistence length or interphosphate distance, of single-stranded (ss) and double-stranded (ds) DNA under different experimental conditions is critical to characterizing molecular reactions studied with single-molecule techniques. While previous experiments have addressed the dependence of the elastic parameters upon varying ionic strength and contour length, temperature-dependent effects are less studied. Here, we examine the temperature-dependent elasticity of ssDNA and dsDNA in the range 5°C-50°C using a temperature-jump optical trap. We find a temperature softening for dsDNA and a temperature stiffening for ssDNA. Our results highlight the need for a general theory explaining the phenomenology observed.
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Affiliation(s)
- Marc Rico-Pasto
- Small Biosystems Lab, Condensed Matter Physics Department, University of Barcelona, Barcelona, Spain
| | - Felix Ritort
- Small Biosystems Lab, Condensed Matter Physics Department, University of Barcelona, Barcelona, Spain
- Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, Barcelona, Spain
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23
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Huang C, Louis B, Bresolí-obach R, Kudo T, Camacho R, Scheblykin IG, Sugiyama T, Hofkens J, Masuhara H. The primeval optical evolving matter by optical binding inside and outside the photon beam. Nat Commun 2022; 13. [PMID: 36088393 PMCID: PMC9464242 DOI: 10.1038/s41467-022-33070-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 08/25/2022] [Indexed: 11/08/2022] Open
Abstract
AbstractOptical binding has recently gained considerable attention because it enables the light-induced assembly of many-body systems; however, this phenomenon has only been described between directly irradiated particles. Here, we demonstrate that optical binding can occur outside the focal spot of a single tightly focused laser beam. By trapping at an interface, we assemble up to three gold nanoparticles with a linear arrangement which fully-occupies the laser focus. The trapping laser is efficiently scattered by this linear alignment and interacts with particles outside the focus area, generating several discrete arc-shape potential wells with a half-wavelength periodicity. Those external nanoparticles inside the arcs show a correlated motion not only with the linear aligned particles, but also between themselves even both are not directly illuminated. We propose that the particles are optically bound outside the focal spot by the back-scattered light and multi-channel light scattering, forming a dynamic optical binding network.
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24
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Baig MMFA, Gao X, Khan MA, Farid A, Zia AW, Wu H. Nanoscale packing of DNA tiles into DNA macromolecular lattices. Int J Biol Macromol 2022; 220:520-527. [PMID: 35988727 DOI: 10.1016/j.ijbiomac.2022.08.107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 11/05/2022]
Abstract
Nanoscale double-crossovers (DX), antiparallel (A), and even half-turns-perimeter (E) DNA tiles (DAE-tiles) with rectangular shapes can be packed into large arrays of micrometer-scale lattices. But the features and mechanical strength of DNA assembly made from differently shaped large-sized DAE DNA tiles and the effects of various geometries on the final DNA assembly are yet to be explored. Herein, we focused on examining DNA lattices synthesized from DX bi-triangular, DNA tiles (T) with concave and convex regions along the perimeter of the tiles. The bi-triangular DNA tiles "T(A) and T(B)" were synthesized by self-assembling the freshly prepared short circular scaffold (S) strands "S(A) and S(B)", each of 106 nucleotides (NT) lengths. The tiles "T(A) and T(B)" were then coupled together to get assembled via sticky ends. It resulted in the polymerization of DNA tiles into large-sized DNA lattices with giant micrometer-scale dimensions to form the "T(A) + T(B)" assembly. These DNA macro-frameworks were visualized "in the air" under atomic force microscopy (AFM) employing tapping mode. We have characterized how curvature in DNA tiles may undergo transitions and transformations to adjust the overall torque, strain, twists, and the topology of the final self-assembly array of DNA tiles. According to our results, our large-span DX tiles assembly "T(A) + T(B)" despite the complicated curvatures and mechanics, was successfully packed into giant DNA lattices of the width of 30-500 nm and lengths of 500 nm to over 10 μm. Conclusively, the micrometer-scale "T(A) + T(B)" framework assembly was rigid, stable, stiff, and exhibited enough tensile strength to form monocrystalline lattices.
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Affiliation(s)
- Mirza Muhammad Faran Ashraf Baig
- Department of Chemistry, School of Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
| | - Xiuli Gao
- Microbiological and Biochemical Pharmaceutical Engineering Research Center of Guizhou Province, State Key Laboratory of Functions and Applications of Medicinal Plants, School of Pharmacy, Guizhou Medical University, Guiyang 550025, China.
| | - Muhammad Ajmal Khan
- Division of Life Science, Center for Cancer Research, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Awais Farid
- Division of Environment and Sustainability, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Abdul Wasy Zia
- Department of Mechanical and Construction Engineering, Marie Curie Research Unit, Northumbria University, Newcastle, United Kingdom
| | - Hongkai Wu
- Department of Chemistry, School of Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; Department of Chemical and Biological Engineering, Division of Biomedical Engineering, School of Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
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25
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Berryman JT, Taghavi A, Mazur F, Tkatchenko A. Quantum machine learning corrects classical forcefields: Stretching DNA base pairs in explicit solvent. J Chem Phys 2022; 157:064107. [PMID: 35963717 DOI: 10.1063/5.0094727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In order to improve the accuracy of molecular dynamics simulations, classical forcefields are supplemented with a kernel-based machine learning method trained on quantum-mechanical fragment energies. As an example application, a potential-energy surface is generalized for a small DNA duplex, taking into account explicit solvation and long-range electron exchange-correlation effects. A long-standing problem in molecular science is that experimental studies of the structural and thermodynamic behavior of DNA under tension are not well confirmed by simulation; study of the potential energy vs extension taking into account a novel correction shows that leading classical DNA models have excessive stiffness with respect to stretching. This discrepancy is found to be common across multiple forcefields. The quantum correction is in qualitative agreement with the experimental thermodynamics for larger DNA double helices, providing a candidate explanation for the general and long-standing discrepancy between single molecule stretching experiments and classical calculations of DNA stretching. The new dataset of quantum calculations should facilitate multiple types of nucleic acid simulation, and the associated Kernel Modified Molecular Dynamics method (KMMD) is applicable to biomolecular simulations in general. KMMD is made available as part of the AMBER22 simulation software.
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Affiliation(s)
- Joshua T Berryman
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Amirhossein Taghavi
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Florian Mazur
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Alexandre Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
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26
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Leal FCB, Gomes MAF. Unfolding of crumpled thin sheets. Phys Rev E 2022; 106:025002. [PMID: 36110023 DOI: 10.1103/physreve.106.025002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
Crumpled thin sheets are complex fractal structures whose physical properties are influenced by a hierarchy of ridges. In this paper, we report experiments that measure the stress-strain relation and show the coexistence of phases in the stretching of crumpled surfaces. The pull stress showed a change from a linear Hookean regime to a sublinear scaling with an exponent of 0.65±0.03, which is identified with the Hurst exponent of the crumpled sheets. The stress fluctuations are studied. The statistical distribution of force peaks is analyzed. It is shown that the unpacking of crumpled sheets is guided by a hierarchical order of ridges.
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Affiliation(s)
- F C B Leal
- Departamento de Física, Universidade Federal de Pernambuco, Recife, Pernambuco 50670-901, Brazil
| | - M A F Gomes
- Departamento de Física, Universidade Federal de Pernambuco, Recife, Pernambuco 50670-901, Brazil
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27
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Abstract
Quadratic trapping potentials are widely used to experimentally probe biopolymers and molecular machines and drive transitions in steered molecular-dynamics simulations. Approximating energy landscapes as locally quadratic, we design multidimensional trapping protocols that minimize dissipation. The designed protocols are easily solvable and applicable to a wide range of systems. The approximation does not rely on either fast or slow limits and is valid for any duration provided the trapping potential is sufficiently strong. We demonstrate the utility of the designed protocols with a simple model of a periodically driven rotary motor. Our results elucidate principles of effective single-molecule manipulation and efficient nonequilibrium free-energy estimation.
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Affiliation(s)
- Steven Blaber
- Department of Physics, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| | - David A Sivak
- Department of Physics, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
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28
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Rahman M, Islam KR, Islam MR, Islam MJ, Kaysir MR, Akter M, Rahman MA, Alam SMM. A Critical Review on the Sensing, Control, and Manipulation of Single Molecules on Optofluidic Devices. Micromachines (Basel) 2022; 13:968. [PMID: 35744582 PMCID: PMC9229244 DOI: 10.3390/mi13060968] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 02/06/2023]
Abstract
Single-molecule techniques have shifted the paradigm of biological measurements from ensemble measurements to probing individual molecules and propelled a rapid revolution in related fields. Compared to ensemble measurements of biomolecules, single-molecule techniques provide a breadth of information with a high spatial and temporal resolution at the molecular level. Usually, optical and electrical methods are two commonly employed methods for probing single molecules, and some platforms even offer the integration of these two methods such as optofluidics. The recent spark in technological advancement and the tremendous leap in fabrication techniques, microfluidics, and integrated optofluidics are paving the way toward low cost, chip-scale, portable, and point-of-care diagnostic and single-molecule analysis tools. This review provides the fundamentals and overview of commonly employed single-molecule methods including optical methods, electrical methods, force-based methods, combinatorial integrated methods, etc. In most single-molecule experiments, the ability to manipulate and exercise precise control over individual molecules plays a vital role, which sometimes defines the capabilities and limits of the operation. This review discusses different manipulation techniques including sorting and trapping individual particles. An insight into the control of single molecules is provided that mainly discusses the recent development of electrical control over single molecules. Overall, this review is designed to provide the fundamentals and recent advancements in different single-molecule techniques and their applications, with a special focus on the detection, manipulation, and control of single molecules on chip-scale devices.
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Affiliation(s)
- Mahmudur Rahman
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Kazi Rafiqul Islam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Rashedul Islam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Jahirul Islam
- Department of Electrical and Electronic Engineering, Khulna University of Engineering & Technology, Khulna 9203, Bangladesh;
| | - Md. Rejvi Kaysir
- Department of Electrical and Computer Engineering, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada;
- Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada
| | - Masuma Akter
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Arifur Rahman
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - S. M. Mahfuz Alam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
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Afanasyev AY, Onufriev AV. Stretching of Long Double-Stranded DNA and RNA Described by the Same Approach. J Chem Theory Comput 2022; 18:3911-3920. [PMID: 35544776 DOI: 10.1021/acs.jctc.1c01221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We propose an approach to help interpret polymer force-extension curves that exhibit plateau regimes. When coupled to a bead-spring dynamic model, the approach accurately reproduces a variety of experimental force-extension curves of long double-stranded DNA and RNA, including torsionally constrained and unconstrained DNA and negatively supercoiled DNA. A key feature of the model is a specific nonconvex energy function of the spring. We provide an algorithm to obtain the five required parameters of the model from experimental force-extension curves. The applicability of the approach to the force-extension curves of double-stranded (ds) DNA of variable GC content as well as to a DNA/RNA hybrid structure is explored and confirmed. We use the approach to explain counterintuitive sequence-dependent trends and make predictions. In the plateau region of the force-extension curves, our molecular dynamics simulations show that the polymer separates into a mix of weakly and strongly stretched states without forming macroscopically distinct phases. The distribution of these states is predicted to depend on the sequence.
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Affiliation(s)
- Alexander Y Afanasyev
- Department of Biomedical Engineering and Mechanics, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Alexey V Onufriev
- Departments of Computer Science and Physics, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
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30
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Raudsepp A, Williams MA, Jameson GB. Modeling multiple duplex DNA attachments in a force-extension experiment. Biophysical Reports 2022; 2:100045. [PMID: 36425083 PMCID: PMC9680770 DOI: 10.1016/j.bpr.2022.100045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/20/2021] [Accepted: 01/28/2022] [Indexed: 11/30/2022]
Abstract
Optical tweezers-based DNA stretching often relies on tethering a single end-activated DNA molecule between optically manipulated end-binding beads. Measurement success can depend on DNA concentration. At lower DNA concentrations tethering is less common, and many trials may be required to observe a single-molecule stretch. At higher DNA concentrations tethering is more common; however, the resulting force-extensions observed are more complex and may vary from measurement to measurement. Typically these more complex results are attributed to the formation of multiple tethers between the beads; however, to date there does not appear to have been a critical examination of this hypothesis or the potential usefulness of such data. Here we examine stretches at a higher DNA concentration and use analysis and simulation to show how the more complex force-extensions observed can be understood in terms of multiple DNA attachments.
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31
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Wan B, Yu J. Two-phase dynamics of DNA supercoiling based on DNA polymer physics. Biophys J 2022; 121:658-669. [PMID: 35016860 PMCID: PMC8873955 DOI: 10.1016/j.bpj.2022.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 10/11/2021] [Accepted: 01/05/2022] [Indexed: 11/28/2022] Open
Abstract
DNA supercoils are generated in genome regulation processes such as transcription and replication and provide mechanical feedback to such processes. Under tension, a DNA supercoil can present a coexistence state of plectonemic and stretched phases. Experiments have revealed the dynamic behaviors of plectonemes, e.g., diffusion, nucleation, and hopping. To represent these dynamics with conformational changes, we demonstrated first the fast dynamics on the DNA to reach torque equilibrium within the plectonemic and stretched phases, and then identified the two-phase boundaries as collective slow variables to describe the essential dynamics. According to the timescale separation demonstrated here, we developed a two-phase model on the dynamics of DNA supercoiling, which can capture physiologically relevant events across timescales of several orders of magnitudes. In this model, we systematically characterized the slow dynamics between the two phases and compared the numerical results with those from the DNA polymer physics-based worm-like chain model. The supercoiling dynamics, including the nucleation, diffusion, and hopping of plectonemes, have been well represented and reproduced, using the two-phase dynamic model, at trivial computational costs. Our current developments, therefore, can be implemented to explore multiscale physical mechanisms of the DNA supercoiling-dependent physiological processes.
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Affiliation(s)
- Biao Wan
- Complex Systems Division, Beijing Computational Science Research Center, Beijing, China.
| | - Jin Yu
- Department of Physics and Astronomy, Department of Chemistry, NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, California.
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32
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Lee JJ, Kim SH, Lee KA, Chuon K, Jung KH, Kim D. Kinetics of DNA looping by Anabaena sensory rhodopsin transducer (ASRT) by using DNA cyclization assay. Sci Rep 2021; 11:23721. [PMID: 34887464 DOI: 10.1038/s41598-021-03148-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/29/2021] [Indexed: 11/09/2022] Open
Abstract
DNA cyclization assay together with single-molecule FRET was employed to monitor protein-mediated bending of a short dsDNA (~ 100 bp). This method provides a simple and easy way to monitor the structural change of DNA in real-time without necessitating prior knowledge of the molecular structures for the optimal dye-labeling. This assay was applied to study how Anabaena sensory rhodopsin transducer (ASRT) facilitates loop formation of DNA as a possible mechanism for gene regulation. The ASRT-induced DNA looping was maximized at 50 mM of Na+, while Mg2+ also played an essential role in the loop formation.
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33
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Lee C, Kim YJ, Kim KS, Lee JY, Kim DN. Modulating the chemo-mechanical response of structured DNA assemblies through binding molecules. Nucleic Acids Res 2021; 49:12591-12599. [PMID: 34850119 PMCID: PMC8643692 DOI: 10.1093/nar/gkab1119] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/06/2021] [Accepted: 10/26/2021] [Indexed: 11/13/2022] Open
Abstract
Recent advances in DNA nanotechnology led the fabrication and utilization of various DNA assemblies, but the development of a method to control their global shapes and mechanical flexibilities with high efficiency and repeatability is one of the remaining challenges for the realization of the molecular machines with on-demand functionalities. DNA-binding molecules with intercalation and groove binding modes are known to induce the perturbation on the geometrical and mechanical characteristics of DNA at the strand level, which might be effective in structured DNA assemblies as well. Here, we demonstrate that the chemo-mechanical response of DNA strands with binding ligands can change the global shape and stiffness of DNA origami nanostructures, thereby enabling the systematic modulation of them by selecting a proper ligand and its concentration. Multiple DNA-binding drugs and fluorophores were applied to straight and curved DNA origami bundles, which demonstrated a fast, recoverable, and controllable alteration of the bending persistence length and the radius of curvature of DNA nanostructures. This chemo-mechanical modulation of DNA nanostructures would provide a powerful tool for reconfigurable and dynamic actuation of DNA machineries.
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Affiliation(s)
- Chanseok Lee
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Korea
| | - Young-Joo Kim
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Korea
| | - Kyung Soo Kim
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Korea
| | - Jae Young Lee
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Korea
| | - Do-Nyun Kim
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Korea.,Department of Mechanical Engineering, Seoul National University, Seoul 08826, Korea.,Institute of Engineering Research, Seoul National University, Seoul 08826, Korea
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34
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Buzón P, Maity S, Christodoulis P, Wiertsema MJ, Dunkelbarger S, Kim C, Wuite GJ, Zlotnick A, Roos WH. Virus self-assembly proceeds through contact-rich energy minima. Sci Adv 2021; 7:eabg0811. [PMID: 34730996 PMCID: PMC8565845 DOI: 10.1126/sciadv.abg0811] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Self-assembly of supramolecular complexes such as viral capsids occurs prominently in nature. Nonetheless, the mechanisms underlying these processes remain poorly understood. Here, we uncover the assembly pathway of hepatitis B virus (HBV), applying fluorescence optical tweezers and high-speed atomic force microscopy. This allows tracking the assembly process in real time with single-molecule resolution. Our results identify a specific, contact-rich pentameric arrangement of HBV capsid proteins as a key on-path assembly intermediate and reveal the energy balance of the self-assembly process. Real-time nucleic acid packaging experiments show that a free energy change of ~1.4 kBT per condensed nucleotide is used to drive protein oligomerization. The finding that HBV assembly occurs via contact-rich energy minima has implications for our understanding of the assembly of HBV and other viruses and also for the development of new antiviral strategies and the rational design of self-assembling nanomaterials.
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Affiliation(s)
- Pedro Buzón
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, Netherlands
| | - Sourav Maity
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, Netherlands
| | | | - Monique J. Wiertsema
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, Netherlands
| | - Steven Dunkelbarger
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN, USA
| | - Christine Kim
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN, USA
| | - Gijs J.L. Wuite
- Physics of Living Systems, Vrije Universiteit, Amsterdam, Netherlands
| | - Adam Zlotnick
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN, USA
| | - Wouter H. Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, Netherlands
- Corresponding author.
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35
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Abstract
Invention of DNA origami has transformed the fabrication and application of biological nanomaterials. In this review, we discuss DNA origami nanoassemblies according to their four fundamental mechanical properties in response to external forces: elasticity, pliability, plasticity and stability. While elasticity and pliability refer to reversible changes in structures and associated properties, plasticity shows irreversible variation in topologies. The irreversible property is also inherent in the disintegration of DNA nanoassemblies, which is manifested by its mechanical stability. Disparate DNA origami devices in the past decade have exploited the mechanical regimes of pliability, elasticity, and plasticity, among which plasticity has shown its dominating potential in biomechanical and physiochemical applications. On the other hand, the mechanical stability of the DNA origami has been used to understand the mechanics of the assembly and disassembly of DNA nano-devices. At the end of this review, we discuss the challenges and future development of DNA origami nanoassemblies, again, from these fundamental mechanical perspectives.
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Affiliation(s)
- Jiahao Ji
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44240, USA.
| | - Deepak Karna
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44240, USA.
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44240, USA.
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36
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Wang Y, Le JV, Crocker K, Darcy MA, Halley PD, Zhao D, Andrioff N, Croy C, Poirier MG, Bundschuh R, Castro CE. A nanoscale DNA force spectrometer capable of applying tension and compression on biomolecules. Nucleic Acids Res 2021; 49:8987-8999. [PMID: 34358322 PMCID: PMC8421221 DOI: 10.1093/nar/gkab656] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 06/30/2021] [Accepted: 07/27/2021] [Indexed: 02/04/2023] Open
Abstract
Single molecule force spectroscopy is a powerful approach to probe the structure, conformational changes, and kinetic properties of biological and synthetic macromolecules. However, common approaches to apply forces to biomolecules require expensive and cumbersome equipment and relatively large probes such as beads or cantilevers, which limits their use for many environments and makes integrating with other methods challenging. Furthermore, existing methods have key limitations such as an inability to apply compressive forces on single molecules. We report a nanoscale DNA force spectrometer (nDFS), which is based on a DNA origami hinge with tunable mechanical and dynamic properties. The angular free energy landscape of the nDFS can be engineered across a wide range through substitution of less than 5% of the strand components. We further incorporate a removable strut that enables reversible toggling of the nDFS between open and closed states to allow for actuated application of tensile and compressive forces. We demonstrate the ability to apply compressive forces by inducing a large bend in a 249bp DNA molecule, and tensile forces by inducing DNA unwrapping of a nucleosome sample. These results establish a versatile tool for force spectroscopy and robust methods for designing nanoscale mechanical devices with tunable force application.
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Affiliation(s)
- Yuchen Wang
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Jenny V Le
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Kyle Crocker
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Michael A Darcy
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Patrick D Halley
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Dengke Zhao
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Nick Andrioff
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Cassie Croy
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Michael G Poirier
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Ralf Bundschuh
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Carlos E Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
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37
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Higashi TL, Pobegalov G, Tang M, Molodtsov MI, Uhlmann F. A Brownian ratchet model for DNA loop extrusion by the cohesin complex. eLife 2021; 10:e67530. [PMID: 34309513 PMCID: PMC8313234 DOI: 10.7554/elife.67530] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 06/10/2021] [Indexed: 12/12/2022] Open
Abstract
The cohesin complex topologically encircles DNA to promote sister chromatid cohesion. Alternatively, cohesin extrudes DNA loops, thought to reflect chromatin domain formation. Here, we propose a structure-based model explaining both activities. ATP and DNA binding promote cohesin conformational changes that guide DNA through a kleisin N-gate into a DNA gripping state. Two HEAT-repeat DNA binding modules, associated with cohesin's heads and hinge, are now juxtaposed. Gripping state disassembly, following ATP hydrolysis, triggers unidirectional hinge module movement, which completes topological DNA entry by directing DNA through the ATPase head gate. If head gate passage fails, hinge module motion creates a Brownian ratchet that, instead, drives loop extrusion. Molecular-mechanical simulations of gripping state formation and resolution cycles recapitulate experimentally observed DNA loop extrusion characteristics. Our model extends to asymmetric and symmetric loop extrusion, as well as z-loop formation. Loop extrusion by biased Brownian motion has important implications for chromosomal cohesin function.
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Affiliation(s)
- Torahiko L Higashi
- Chromosome Segregation Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Georgii Pobegalov
- Mechanobiology and Biophysics Laboratory, The Francis Crick InstituteLondonUnited Kingdom
- Department of Physics and Astronomy, University College LondonLondonUnited Kingdom
| | - Minzhe Tang
- Chromosome Segregation Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Maxim I Molodtsov
- Mechanobiology and Biophysics Laboratory, The Francis Crick InstituteLondonUnited Kingdom
- Department of Physics and Astronomy, University College LondonLondonUnited Kingdom
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick InstituteLondonUnited Kingdom
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38
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Li X, Song G, Dou L, Yan S, Zhang M, Yuan W, Lai S, Jiang X, Li K, Sun K, Zhao C, Geng J. The structure and unzipping behavior of dumbbell and hairpin DNA revealed by real-time nanopore sensing. Nanoscale 2021; 13:11827-11835. [PMID: 34152351 DOI: 10.1039/d0nr08729g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Hairpin structures play an essential role in DNA replication, transcription, and recombination. Single-molecule studies enable the real-time measurement and observation of the energetics and dynamics of hairpin structures, including folding and DNA-protein interactions. Nanopore sensing is emerging as a powerful tool for DNA sensing and sequencing, and previous research into hairpins using an α-hemolysin (α-HL) nanopore suggested that hairpin DNA enters from its stem side. In this work, the translocation and interaction of hairpin and dumbbell DNA samples with varying stems, loops, and toeholds were investigated systematically using a Mycobacterium smegmatis porin A (MspA) nanopore. It was found that these DNA constructs could translocate through the pore under a bias voltage above +80 mV, and blockage events with two conductance states could be observed. The events of the lower blockage were correlated with the loop size of the hairpin or dumbbell DNA (7 nt to 25 nt), which could be attributed to non-specific collisions with the pore, whereas the dwell time of events with the higher blockage were correlated with the stem length, thus indicating effective translocation. Furthermore, dumbbell DNA with and without a stem opening generated different dwell times when driven through the MspA nanopore. Finally, a new strategy based on the dwell time difference was developed to detect single nucleotide polymorphisms (SNPs). These results demonstrated that the unzipping behaviors and DNA-protein interactions of hairpin and dumbbell DNA could be revealed using nanopore technology, and this could be further developed to create sensors for the secondary structures of nucleic acids.
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Affiliation(s)
- Xinqiong Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China.
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39
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Cerrón F, Ibarra B. Measurements of Real-Time Replication Kinetics of DNA Polymerases on ssDNA Templates Coated with Single-Stranded DNA-Binding Proteins. Methods Mol Biol 2021; 2281:289-301. [PMID: 33847966 DOI: 10.1007/978-1-0716-1290-3_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Optical tweezers can monitor and control the activity of individual DNA polymerase molecules in real time, providing in this way unprecedented insight into the complex dynamics and mechanochemical processes that govern their operation. Here, we describe an optical tweezers-based assay to determine at the single-molecule level the effect of single-stranded DNA-binding proteins (SSB) on the real-time replication kinetics of the human mitochondrial DNA polymerase during the synthesis of the lagging strand.
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40
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Abstract
Accurate chromosome segregation requires the removal of all chromatin bridges, which link chromosomes before cell division. When chromatin bridges fail to be removed, cell cycle progression may halt, or cytokinesis failure and ensuing polyploidization may occur. Conversely, the inappropriate severing of chromatin bridges leads to chromosome fragmentation, excessive genome instability at breakpoints, micronucleus formation, and chromothripsis. In this mini-review, we first describe the origins of chromatin bridges, the toxic processing of chromatin bridges by mechanical force, and the TREX1 exonuclease. We then focus on the abscission checkpoint (NoCut) which can confer a transient delay in cytokinesis progression to facilitate bridge resolution. Finally, we describe a recently identified mechanism uncovered in C. elegans where the conserved midbody associated endonuclease LEM-3/ANKLE1 is able to resolve chromatin bridges generated by various perturbations of DNA metabolism at the final stage of cell division. We also discuss how LEM-3 dependent chromatin bridge resolution may be coordinated with abscission checkpoint (NoCut) to achieve an error-free cleavage, therefore acting as a "last chance saloon" to facilitate genome integrity and organismal survival.
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Affiliation(s)
- Ye Hong
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Hongtao Zhang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Anton Gartner
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, South Korea
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41
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Arce NA, Cao W, Brown AK, Legan ER, Wilson MS, Xu ER, Berndt MC, Emsley J, Zhang XF, Li R. Activation of von Willebrand factor via mechanical unfolding of its discontinuous autoinhibitory module. Nat Commun 2021; 12:2360. [PMID: 33883551 PMCID: PMC8060278 DOI: 10.1038/s41467-021-22634-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 03/16/2021] [Indexed: 01/05/2023] Open
Abstract
Von Willebrand factor (VWF) activates in response to shear flow to initiate hemostasis, while aberrant activation could lead to thrombosis. Above a critical shear force, the A1 domain of VWF becomes activated and captures platelets via the GPIb-IX complex. Here we show that the shear-responsive element controlling VWF activation resides in the discontinuous autoinhibitory module (AIM) flanking A1. Application of tensile force in a single-molecule setting induces cooperative unfolding of the AIM to expose A1. The AIM-unfolding force is lowered by truncating either N- or C-terminal AIM region, type 2B VWD mutations, or binding of a ristocetin-mimicking monoclonal antibody, all of which could activate A1. Furthermore, the AIM is mechanically stabilized by the nanobody that comprises caplacizumab, the only FDA-approved anti-thrombotic drug to-date that targets VWF. Thus, the AIM is a mechano-regulator of VWF activity. Its conformational dynamics may define the extent of VWF autoinhibition and subsequent activation under force. Von Willebrand factor (VWF) is a large glycoprotein in the blood secreted from endothelial cells lining the blood vessel and activation of VWF leads to formation of VWF-platelet complexes or thrombi. Here authors use single-molecule force measurement, X-ray crystallography and functional measurements to monitor the activation of VWF via mechanical unfolding of the autoinhibitory module (AIM).
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Affiliation(s)
- Nicholas A Arce
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Wenpeng Cao
- Department of Bioengineering, Department of Mechanical Engineering & Mechanics, Lehigh University, Bethlehem, PA, USA
| | - Alexander K Brown
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, UK
| | - Emily R Legan
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Moriah S Wilson
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Emma-Ruoqi Xu
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, UK
| | - Michael C Berndt
- Faculty of Health Sciences, Curtin University, Perth, WA, Australia
| | - Jonas Emsley
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, UK
| | - X Frank Zhang
- Department of Bioengineering, Department of Mechanical Engineering & Mechanics, Lehigh University, Bethlehem, PA, USA.
| | - Renhao Li
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.
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Heidarsson PO, Cecconi C. From folding to function: complex macromolecular reactions unraveled one-by-one with optical tweezers. Essays Biochem 2021; 65:129-42. [PMID: 33438724 DOI: 10.1042/EBC20200024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/08/2020] [Accepted: 12/11/2020] [Indexed: 12/13/2022]
Abstract
Single-molecule manipulation with optical tweezers has uncovered macromolecular behaviour hidden to other experimental techniques. Recent instrumental improvements have made it possible to expand the range of systems accessible to optical tweezers. Beyond focusing on the folding and structural changes of isolated single molecules, optical tweezers studies have evolved into unraveling the basic principles of complex molecular processes such as co-translational folding on the ribosome, kinase activation dynamics, ligand-receptor binding, chaperone-assisted protein folding, and even dynamics of intrinsically disordered proteins (IDPs). In this mini-review, we illustrate the methodological principles of optical tweezers before highlighting recent advances in studying complex protein conformational dynamics - from protein synthesis to physiological function - as well as emerging future issues that are beginning to be addressed with novel approaches.
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Mo Y, Fizari M, Koharchik K, Smith DE. Determining Trap Compliances, Microsphere Size Variations, and Response Linearities in Single DNA Molecule Elasticity Measurements with Optical Tweezers. Front Mol Biosci 2021; 8:605102. [PMID: 33829038 PMCID: PMC8019724 DOI: 10.3389/fmolb.2021.605102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 02/05/2021] [Indexed: 11/25/2022] Open
Abstract
We previously introduced the use of DNA molecules for calibration of biophysical force and displacement measurements with optical tweezers. Force and length scale factors can be determined from measurements of DNA stretching. Trap compliance can be determined by fitting the data to a nonlinear DNA elasticity model, however, noise/drift/offsets in the measurement can affect the reliability of this determination. Here we demonstrate a more robust method that uses a linear approximation for DNA elasticity applied to high force range (25-45 pN) data. We show that this method can be used to assess how small variations in microsphere sizes affect DNA length measurements and demonstrate methods for correcting for these errors. We further show that these measurements can be used to check assumed linearities of system responses. Finally, we demonstrate methods combining microsphere imaging and DNA stretching to check the compliance and positioning of individual traps.
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Affiliation(s)
| | | | | | - Douglas E. Smith
- Department of Physics, University of California San Diego, La Jolla, CA, United States
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44
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Ferger M, Ban Ž, Krošl I, Tomić S, Dietrich L, Lorenzen S, Rauch F, Sieh D, Friedrich A, Griesbeck S, Kenđel A, Miljanić S, Piantanida I, Marder TB. Bis(phenylethynyl)arene Linkers in Tetracationic Bis-triarylborane Chromophores Control Fluorimetric and Raman Sensing of Various DNAs and RNAs. Chemistry 2021; 27:5142-5159. [PMID: 33411942 PMCID: PMC8048639 DOI: 10.1002/chem.202005141] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 12/20/2020] [Indexed: 11/24/2022]
Abstract
We report four new luminescent tetracationic bis-triarylborane DNA and RNA sensors that show high binding affinities, in several cases even in the nanomolar range. Three of the compounds contain substituted, highly emissive and structurally flexible bis(2,6-dimethylphenyl-4-ethynyl)arene linkers (3: arene=5,5'-2,2'-bithiophene; 4: arene=1,4-benzene; 5: arene=9,10-anthracene) between the two boryl moieties and serve as efficient dual Raman and fluorescence chromophores. The shorter analogue 6 employs 9,10-anthracene as the linker and demonstrates the importance of an adequate linker length with a certain level of flexibility by exhibiting generally lower binding affinities than 3-5. Pronounced aggregation-deaggregation processes are observed in fluorimetric titration experiments with DNA for compounds 3 and 5. Molecular modelling of complexes of 5 with AT-DNA, suggest the minor groove as the dominant binding site for monomeric 5, but demonstrate that dimers of 5 can also be accommodated. Strong SERS responses for 3-5 versus a very weak response for 6, particularly the strong signals from anthracene itself observed for 5 but not for 6, demonstrate the importance of triple bonds for strong Raman activity in molecules of this compound class. The energy of the characteristic stretching vibration of the C≡C bonds is significantly dependent on the aromatic moiety between the triple bonds. The insertion of aromatic moieties between two C≡C bonds thus offers an alternative design for dual Raman and fluorescence chromophores, applicable in multiplex biological Raman imaging.
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Affiliation(s)
- Matthias Ferger
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Željka Ban
- Division of Organic Chemistry & BiochemistryRuđer Bošković Institute, Bijenička 5410000ZagrebCroatia
| | - Ivona Krošl
- Division of Organic Chemistry & BiochemistryRuđer Bošković Institute, Bijenička 5410000ZagrebCroatia
| | - Sanja Tomić
- Division of Organic Chemistry & BiochemistryRuđer Bošković Institute, Bijenička 5410000ZagrebCroatia
| | - Lena Dietrich
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Sabine Lorenzen
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Florian Rauch
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Daniel Sieh
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Alexandra Friedrich
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Stefanie Griesbeck
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Adriana Kenđel
- Division of Analytical ChemistryDepartment of Chemistry, Faculty of ScienceUniversity of Zagreb, Horvatovac 102a10000ZagrebCroatia
| | - Snežana Miljanić
- Division of Analytical ChemistryDepartment of Chemistry, Faculty of ScienceUniversity of Zagreb, Horvatovac 102a10000ZagrebCroatia
| | - Ivo Piantanida
- Division of Organic Chemistry & BiochemistryRuđer Bošković Institute, Bijenička 5410000ZagrebCroatia
| | - Todd B. Marder
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
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45
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Keenen MM, Brown D, Brennan LD, Renger R, Khoo H, Carlson CR, Huang B, Grill SW, Narlikar GJ, Redding S. HP1 proteins compact DNA into mechanically and positionally stable phase separated domains. eLife 2021; 10:e64563. [PMID: 33661100 PMCID: PMC7932698 DOI: 10.7554/elife.64563] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 02/22/2021] [Indexed: 12/11/2022] Open
Abstract
In mammals, HP1-mediated heterochromatin forms positionally and mechanically stable genomic domains even though the component HP1 paralogs, HP1α, HP1β, and HP1γ, display rapid on-off dynamics. Here, we investigate whether phase-separation by HP1 proteins can explain these biological observations. Using bulk and single-molecule methods, we show that, within phase-separated HP1α-DNA condensates, HP1α acts as a dynamic liquid, while compacted DNA molecules are constrained in local territories. These condensates are resistant to large forces yet can be readily dissolved by HP1β. Finally, we find that differences in each HP1 paralog's DNA compaction and phase-separation properties arise from their respective disordered regions. Our findings suggest a generalizable model for genome organization in which a pool of weakly bound proteins collectively capitalize on the polymer properties of DNA to produce self-organizing domains that are simultaneously resistant to large forces at the mesoscale and susceptible to competition at the molecular scale.
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Affiliation(s)
- Madeline M Keenen
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Tetrad Graduate Program, University of California, San FranciscoSan FranciscoUnited States
| | - David Brown
- Department of Pharmaceutical Chemistry, University of California, San FranciscoSan FranciscoUnited States
| | - Lucy D Brennan
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Roman Renger
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- German Center for Neurodegenerative Diseases (DZNE)BonnGermany
| | - Harrison Khoo
- Department of Mechanical Engineering, Johns Hopkins UniversityBaltimoreUnited States
| | - Christopher R Carlson
- Tetrad Graduate Program, University of California, San FranciscoSan FranciscoUnited States
- Department of Physiology, University of California, San FranciscoSan FranciscoUnited States
| | - Bo Huang
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Department of Pharmaceutical Chemistry, University of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Stephan W Grill
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Cluster of Excellence Physics of Life, Technische Universität DresdenDresdenGermany
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Sy Redding
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Marine Biological LaboratoryWoods HoleUnited States
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46
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Abstract
Using the positional-orientational propagator of a semiflexible filament in the weakly bending regime, we analytically calculate the probability densities associated with the fluctuating tip and the corners of a grafted system of connected quadrilaterals. We calculate closed analytic expressions for the probability densities within the framework of the worm-like chain model, which are valid in the weakly bending regime. The probability densities give the physical quantities related to the elasticity of the system such as the force-extension relation in the fixed extension ensemble, the Poisson's ratio and the average of the force exerted to a confining stiff planar wall by the fluctuating tip of the system. Our analysis reveals that the force-extension relations depend on the contour length of the system (material content), the bending stiffness (chemical nature), the geometrical angle and the number of the quadrilaterals, while the Poisson's ratio depends only on the geometrical angle and the number of the quadrilaterals, and is thus a purely geometric property of the system.
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Affiliation(s)
- Mohammadhosein Razbin
- Department of Energy Engineering and Physics, Amirkabir University of Technology, 14588 Tehran, Iran.
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47
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Affiliation(s)
- Michael Jacobs
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, United States
| | - Andrey V. Dobrynin
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, United States
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48
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Abraham Punnoose J, Hayden A, Zhou L, Halvorsen K. Wi-Fi Live-Streaming Centrifuge Force Microscope for Benchtop Single-Molecule Experiments. Biophys J 2020; 119:2231-2239. [PMID: 33121943 PMCID: PMC7732769 DOI: 10.1016/j.bpj.2020.10.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/02/2020] [Accepted: 10/08/2020] [Indexed: 11/21/2022] Open
Abstract
The ability to apply controlled forces to individual molecules has been revolutionary in shaping our understanding of biophysics in areas as diverse as dynamic bond strength, biological motor operation, and DNA replication. However, the methodology to perform single-molecule experiments remains relatively inaccessible because of cost and complexity. In 2010, we introduced the centrifuge force microscope (CFM) as a platform for accessible and high-throughput single-molecule experimentation. The CFM consists of a rotating microscope with which prescribed centrifugal forces can be applied to microsphere-tethered biomolecules. In this work, we develop and demonstrate a next-generation Wi-Fi CFM that offers unprecedented ease of use and flexibility in design. The modular CFM unit fits within a standard benchtop centrifuge and connects by Wi-Fi to an external computer for live control and streaming at near gigabit speeds. The use of commercial wireless hardware allows for flexibility in programming and provides a streamlined upgrade path as Wi-Fi technology advances. To facilitate ease of use, detailed build and setup instructions, as well as LabVIEW-based control software and MATLAB-based analysis software, are provided. We demonstrate the instrument’s performance by analysis of force-dependent dissociation of short DNA duplexes of 7, 8, and 9 bp. We showcase the sensitivity of the approach by resolving distinct dissociation kinetic rates for a 7 bp duplex in which one G-C basepair is mutated to an A-T basepair.
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Affiliation(s)
| | | | - Lifeng Zhou
- RNA Institute, SUNY at Albany, Albany, New York
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49
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Pang L, Abeysekera G, Hanning K, Premaratne A, Robson B, Abraham P, Sutton R, Hanson C, Hadfield J, Heiligenthal L, Stone D, McBeth K, Billington C. Water tracking in surface water, groundwater and soils using free and alginate-chitosan encapsulated synthetic DNA tracers. Water Res 2020; 184:116192. [PMID: 32731038 DOI: 10.1016/j.watres.2020.116192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/09/2020] [Accepted: 07/15/2020] [Indexed: 06/11/2023]
Abstract
Investigating contamination pathways and hydraulic connections in complex hydrological systems will benefit greatly from multi-tracer approaches. The use of non-toxic synthetic DNA tracers is promising, because unlimited numbers of tracers, each with a unique DNA identifier, could be used concurrently and detected at extremely low concentrations. This study aimed to develop multiple synthetic DNA tracers as free molecules and encapsulated within microparticles of biocompatible and biodegradable alginate and chitosan, and to validate their field utility in different systems. Experiments encompassing a wide range of conditions and flow rates (19 cm/day-39 km/day) were conducted in a stream, an alluvial gravel aquifer, a fine coastal sand aquifer, and in lysimeters containing undisturbed silt loam over gravels. The DNA tracers were identifiable in all field conditions investigated, and they were directly detectable in the stream at a distance of at least 1 km. The DNA tracers showed promise at tracking fast-flowing water in the stream, gravel aquifer and permeable soils, but were unsatisfactory at tracking slow-moving groundwater in the fine sand aquifer. In the surface water experiments, the microencapsulated DNA tracers' concentrations and mass recoveries were 1-3 orders of magnitude greater than those of the free DNA tracers, because encapsulation protected them from environmental stressors and they were more negatively charged. The opposite was observed in the gravel aquifer, probably due to microparticle filtration by the aquifer media. Although these new DNA tracers showed promise in proof-of-concept field validations, further work is needed before they can be used for large-scale investigations.
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Affiliation(s)
- Liping Pang
- Institute of Environmental Science and Research, PO Box 29181, Christchurch 8540, New Zealand.
| | - Gayan Abeysekera
- Institute of Environmental Science and Research, PO Box 29181, Christchurch 8540, New Zealand
| | - Kyrin Hanning
- Institute of Environmental Science and Research, PO Box 29181, Christchurch 8540, New Zealand; School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Aruni Premaratne
- Institute of Environmental Science and Research, PO Box 29181, Christchurch 8540, New Zealand
| | - Beth Robson
- Institute of Environmental Science and Research, PO Box 29181, Christchurch 8540, New Zealand
| | - Phillip Abraham
- Institute of Environmental Science and Research, PO Box 29181, Christchurch 8540, New Zealand
| | - Richard Sutton
- Institute of Environmental Science and Research, PO Box 29181, Christchurch 8540, New Zealand
| | - Carl Hanson
- Environment Canterbury, PO Box 345, Christchurch 8140, New Zealand
| | - John Hadfield
- Waikato Regional Council, Private Bag 3038, Hamilton 3240, New Zealand
| | - Laura Heiligenthal
- Institute of Environmental Science and Research, PO Box 29181, Christchurch 8540, New Zealand
| | - Dana Stone
- Institute of Environmental Science and Research, PO Box 29181, Christchurch 8540, New Zealand
| | - Kurt McBeth
- Institute of Environmental Science and Research, PO Box 29181, Christchurch 8540, New Zealand
| | - Craig Billington
- Institute of Environmental Science and Research, PO Box 29181, Christchurch 8540, New Zealand
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50
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Cao W, Cao W, Zhang W, Zheng XL, Zhang XF. Factor VIII binding affects the mechanical unraveling of the A2 domain of von Willebrand factor. J Thromb Haemost 2020; 18:2169-2176. [PMID: 32544272 PMCID: PMC7789802 DOI: 10.1111/jth.14962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 05/05/2020] [Accepted: 06/05/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND Proteolytic cleavage of von Willebrand factor (VWF) by ADAMTS13 is crucial for normal hemostasis. Our previous studies demonstrate that binding of coagulation factor VIII (or FVIII) to VWF enhances the proteolytic cleavage of VWF by ADAMTS13 under shear. OBJECTIVES Present study aims to determine the mechanism underlying FVIII-mediated enhancing effect on VWF proteolysis by ADAMTS13 under force. METHODS Single molecular force spectroscopy, atomic force microscopy, and surface plasmon resonance are all used. RESULTS Using single molecule force spectroscopy, we show that an addition of FVIII (~5 nmol/L) to D'D3 or D'D3A1 does not significantly alter force-induced unfolding of these fragments; however, an addition of FVIII at the same concentration to D'D3A1A2 eliminates its long unfolding event at ~40 nm, suggesting that binding of FVIII to D'D3 and/or A2 may result in force-induced conformational changes in A2 domain. Atomic force spectroscopy further demonstrates the direct binding between FVIII and D'D3 (or A2) with an intrinsic 2-dimensional off-rate (k0 ) of 0.02 ± 0.01/s (or 0.3 ± 0.1/s). The direct binding interaction between FVIII and A2 is further confirmed with the surface plasmon resonance assay, with a dissociation constant of ~0.2 μmol/L; no binding is detected between FVIII and A1 under the same conditions. CONCLUSIONS Our results suggest that binding of FVIII to D'D3 and/or A2 may alter the mechanical property in the central A2 domain. The findings provide novel insight into the molecular mechanism underlying FVIII-dependent regulation of VWF proteolysis by ADAMTS13 under mechanical force.
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Affiliation(s)
- Wenpeng Cao
- Department of Bioengineering, and Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, PA
| | - Wenjing Cao
- Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Wei Zhang
- Department of Bioengineering, and Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, PA
| | - X. Long Zheng
- Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - X. Frank Zhang
- Department of Bioengineering, and Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, PA
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