1
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Combs JD, Foote AK, Ogasawara H, Velusamy A, Rashid SA, Mancuso JN, Salaita K. Measuring Integrin Force Loading Rates Using a Two-Step DNA Tension Sensor. J Am Chem Soc 2024; 146:23034-23043. [PMID: 39133202 PMCID: PMC11345772 DOI: 10.1021/jacs.4c03629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 07/22/2024] [Accepted: 07/24/2024] [Indexed: 08/13/2024]
Abstract
Cells apply forces to extracellular matrix (ECM) ligands through transmembrane integrin receptors: an interaction which is intimately involved in cell motility, wound healing, cancer invasion and metastasis. These small (piconewton) integrin-ECM forces have been studied by molecular tension fluorescence microscopy (MTFM), which utilizes a force-induced conformational change of a probe to detect mechanical events. MTFM has revealed the force magnitude for integrin receptors in a variety of cell models including primary cells. However, force dynamics and specifically the force loading rate (LR) have important implications in receptor signaling and adhesion formation and remain poorly characterized. Here, we develop an LR probe composed of an engineered DNA structure that undergoes two mechanical transitions at distinct force thresholds: a low force threshold at 4.7 pN (hairpin unfolding) and a high force threshold at 47 pN (duplex shearing). These transitions yield distinct fluorescence signatures observed through single-molecule fluorescence microscopy in live cells. Automated analysis of tens of thousands of events from eight cells showed that the bond lifetime of integrins that engage their ligands and transmit a force >4.7 pN decays exponentially with a τ of 45.6 s. A subset of these events mature in magnitude to >47 pN with a median loading rate of 1.1 pN s-1 and primarily localize at the periphery of the cell-substrate junction. The LR probe design is modular and can be adapted to measure force ramp rates for a broad range of mechanoreceptors and cell models, thus aiding in the study of molecular mechanotransduction in living systems.
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Affiliation(s)
- J. Dale Combs
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Alexander K. Foote
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Hiroaki Ogasawara
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Arventh Velusamy
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Sk Aysha Rashid
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | | | - Khalid Salaita
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
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2
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Hu Y, Rogers J, Duan Y, Velusamy A, Narum S, Al Abdullatif S, Salaita K. Quantifying T cell receptor mechanics at membrane junctions using DNA origami tension sensors. NATURE NANOTECHNOLOGY 2024:10.1038/s41565-024-01723-0. [PMID: 39103452 DOI: 10.1038/s41565-024-01723-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 06/21/2024] [Indexed: 08/07/2024]
Abstract
The T cell receptor (TCR) is thought to be a mechanosensor, meaning that it transmits mechanical force to its antigen and leverages the force to amplify the specificity and magnitude of TCR signalling. Although a variety of molecular probes have been proposed to quantify TCR mechanics, these probes are immobilized on hard substrates, and thus fail to reveal fluid TCR-antigen interactions in the physiological context of cell membranes. Here we developed DNA origami tension sensors (DOTS) which bear force sensors on a DNA origami breadboard and allow mapping of TCR mechanotransduction at dynamic intermembrane junctions. We quantified the mechanical forces at fluid TCR-antigen bonds and observed their dependence on cell state, antigen mobility, antigen potency, antigen height and F-actin activity. The programmability of DOTS allows us to tether these to microparticles to mechanically screen antigens in high throughput using flow cytometry. Additionally, DOTS were anchored onto live B cells, allowing quantification of TCR mechanics at immune cell-cell junctions.
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Affiliation(s)
- Yuesong Hu
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | - Jhordan Rogers
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | - Yuxin Duan
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | | | - Steven Narum
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | | | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, GA, USA.
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
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3
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Kim SH, Li ITS. Altering Cell Junctional Tension in Spheroids through E-Cadherin Engagement Modulation. ACS APPLIED BIO MATERIALS 2024; 7:3766-3776. [PMID: 38729097 DOI: 10.1021/acsabm.4c00142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
Cadherin-mediated tension at adherens junctions (AJs) is fundamental for cell-cell adhesion and maintaining epithelial integrity. Despite the importance of manipulating AJs to dissect cell-cell interactions, existing three-dimensional (3D) multicellular models have not adequately addressed the precise manipulation of these junctions. To fill this gap, we introduce E-cadherin-modified tension gauge tethers (TGTs) at the junctions within spheroids. The system enables both quantification and modulation of junctional tension with specific DNA triggers. Using rupture-induced fluorescence, we successfully measure mechanical forces in 3D spheroids. Furthermore, mechanically strong TGTs can maintain normal E-cadherin-mediated adhesion. Employing toehold-mediated strand displacement allowed us to disrupt E-cadherin-specific cell-cell adhesion, consequently altering intracellular tension within the spheroids. Our methodology offers a robust and precise way to manipulate cell-cell adhesion and intracellular mechanics in spheroid models.
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Affiliation(s)
- Seong Ho Kim
- Department of Chemistry, The University of British Columbia, Kelowna, British Columbia V1 V 1 V7, Canada
| | - Isaac T S Li
- Department of Chemistry, The University of British Columbia, Kelowna, British Columbia V1 V 1 V7, Canada
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4
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Chen H, Wang S, Cao Y, Lei H. Molecular Force Sensors for Biological Application. Int J Mol Sci 2024; 25:6198. [PMID: 38892386 PMCID: PMC11173168 DOI: 10.3390/ijms25116198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/29/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
The mechanical forces exerted by cells on their surrounding microenvironment are known as cellular traction forces. These forces play crucial roles in various biological processes, such as tissue development, wound healing and cell functions. However, it is hard for traditional techniques to measure cellular traction forces accurately because their magnitude (from pN to nN) and the length scales over which they occur (from nm to μm) are extremely small. In order to fully understand mechanotransduction, highly sensitive tools for measuring cellular forces are needed. Current powerful techniques for measuring traction forces include traction force microscopy (TFM) and fluorescent molecular force sensors (FMFS). In this review, we elucidate the force imaging principles of TFM and FMFS. Then we highlight the application of FMFS in a variety of biological processes and offer our perspectives and insights into the potential applications of FMFS.
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Affiliation(s)
- Huiyan Chen
- National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China; (H.C.); (S.W.)
| | - Shouhan Wang
- National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China; (H.C.); (S.W.)
| | - Yi Cao
- National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China; (H.C.); (S.W.)
| | - Hai Lei
- School of Physics, Zhejiang University, Hangzhou 310027, China
- Institute for Advanced Study in Physics, Zhejiang University, Hangzhou 310027, China
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5
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Qiu Y, Xiao Q, Wang Y, Cao Y, Wang J, Wan Z, Chen X, Liu W, Ma L, Xu C. Mechanical force determines chimeric antigen receptor microclustering and signaling. Mol Ther 2024; 32:1016-1032. [PMID: 38327049 PMCID: PMC11163199 DOI: 10.1016/j.ymthe.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 01/03/2024] [Accepted: 02/02/2024] [Indexed: 02/09/2024] Open
Abstract
Chimeric antigen receptor (CAR) T cells are activated to trigger the lytic machinery after antigen engagement, and this has been successfully applied clinically as therapy. The mechanism by which antigen binding leads to the initiation of CAR signaling remains poorly understood. Here, we used a set of short double-stranded DNA (dsDNA) tethers with mechanical forces ranging from ∼12 to ∼51 pN to manipulate the mechanical force of antigen tether and decouple the microclustering and signaling events. Our results revealed that antigen-binding-induced CAR microclustering and signaling are mechanical force dependent. Additionally, the mechanical force delivered to the antigen tether by the CAR for microclustering is generated by autonomous cell contractility. Mechanistically, the mechanical-force-induced strong adhesion and CAR diffusion confinement led to CAR microclustering. Moreover, cytotoxicity may have a lower mechanical force threshold than cytokine generation. Collectively, these results support a model of mechanical-force-induced CAR microclustering for signaling.
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Affiliation(s)
- Yue Qiu
- Institute of Molecular Immunology, Department of Biotechnology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China
| | - Qingyue Xiao
- Institute of Molecular Immunology, Department of Biotechnology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China
| | - Yucai Wang
- Institute of Molecular Immunology, Department of Biotechnology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China
| | - Yichen Cao
- Institute of Molecular Immunology, Department of Biotechnology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China
| | - Jing Wang
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Zhengpeng Wan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Xiangjun Chen
- Center for Infectious Disease Research, School of Medicine, Westlake University, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Wanli Liu
- MOE Key Laboratory of Protein Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Li Ma
- Institute of Molecular Immunology, Department of Biotechnology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China.
| | - Chenguang Xu
- Institute of Molecular Immunology, Department of Biotechnology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, China.
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6
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Liu J, Yan J. Unraveling the Dual-Stretch-Mode Impact on Tension Gauge Tethers' Mechanical Stability. J Am Chem Soc 2024; 146:7266-7273. [PMID: 38451494 PMCID: PMC10959107 DOI: 10.1021/jacs.3c10923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/29/2024] [Accepted: 02/23/2024] [Indexed: 03/08/2024]
Abstract
Tension gauge tethers (TGTs), short DNA segments serving as extracellular tension sensors, are instrumental in assessing the tension dynamics in mechanotransduction. These TGTs feature an initial shear-stretch region and an unzip-stretch region. Despite their utility, no theoretical model has been available to estimate their tension-dependent lifetimes [τ(f)], restricting insights from cellular mechanotransduction experiments. We have now formulated a concise expression for τ(f) of TGTs, accommodating contributions from both stretch regions. Our model uncovers a tension-dependent energy barrier shift occurring when tension surpasses a switching force of approximately 13 pN for the recently developed TGTs, greatly influencing τ(f) profiles. Experimental data from several TGTs validated our model. The calibrated expression can predict τ(f) of TGTs at 37 °C based on their sequences with minor fold changes, supporting future applications of TGTs.
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Affiliation(s)
- Jingzhun Liu
- Department
of Physics, National University of Singapore, Singapore 117542, Singapore
| | - Jie Yan
- Mechanobiology
Institute, National University of Singapore, Singapore 117411, Singapore
- Department
of Physics, National University of Singapore, Singapore 117542, Singapore
- Joint
School of National University of Singapore and Tianjin University,
International Campus of Tianjin University, Binhai New City, Fuzhou 350207, China
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7
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Combs JD, Foote AK, Ogasawara H, Velusamy A, Rashid SA, Mancuso JN, Salaita K. Measuring integrin force loading rates using a two-step DNA tension sensor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.585042. [PMID: 38558970 PMCID: PMC10980004 DOI: 10.1101/2024.03.15.585042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Cells apply forces to extracellular matrix (ECM) ligands through transmembrane integrin receptors: an interaction which is intimately involved in cell motility, wound healing, cancer invasion and metastasis. These small (pN) forces exerted by cells have been studied by molecular tension fluorescence microscopy (MTFM), which utilizes a force-induced conformational change of a probe to detect mechanical events. MTFM has revealed the force magnitude for integrins receptors in a variety of cell models including primary cells. However, force dynamics and specifically the force loading rate (LR) have important implications in receptor signaling and adhesion formation and remain poorly characterized. Here, we develop a LR probe which is comprised of an engineered DNA structures that undergoes two mechanical transitions at distinct force thresholds: a low force threshold at 4.7 pN corresponding to hairpin unfolding and a high force threshold at 56 pN triggered through duplex shearing. These transitions yield distinct fluorescence signatures observed through single-molecule fluorescence microscopy in live-cells. Automated analysis of tens of thousands of events from 8 cells showed that the bond lifetime of integrins that engage their ligands and transmit a force >4.7 pN decays exponentially with a τ of 45.6 sec. A small subset of these events (<10%) mature in magnitude to >56pN with a median loading rate of 1.3 pNs-1 with these mechanical ramp events localizing at the periphery of the cell-substrate junction. Importantly, the LR probe design is modular and can be adapted to measure force ramp rates for a broad range of mechanoreceptors and cell models, thus aiding in the study of mechanotransduction.
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Affiliation(s)
- J. Dale Combs
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | | | | | - Arventh Velusamy
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Sk Aysha Rashid
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | | | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, GA 30322, USA
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8
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Rajasooriya T, Ogasawara H, Dong Y, Mancuso JN, Salaita K. Force-Triggered Self-Destructive Hydrogels. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2305544. [PMID: 37724392 PMCID: PMC10764057 DOI: 10.1002/adma.202305544] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/22/2023] [Indexed: 09/20/2023]
Abstract
Self-destructive polymers (SDPs) are defined as a class of smart polymers that autonomously degrade upon experiencing an external trigger, such as a chemical cue or optical excitation. Because SDPs release the materials trapped inside the network upon degradation, they have potential applications in drug delivery and analytical sensing. However, no known SDPs that respond to external mechanical forces have been reported, as it is fundamentally challenging to create mechano-sensitivity in general and especially so for force levels below those required for classical force-induced bond scission. To address this challenge, the development of force-triggered SDPs composed of DNA crosslinked hydrogels doped with nucleases is described here. Externally applied piconewton forces selectively expose enzymatic cleavage sites within the DNA crosslinks, resulting in rapid polymer self-degradation. The synthesis and the chemical and mechanical characterization of DNA crosslinked hydrogels, as well as the kinetics of force-triggered hydrolysis, are described. As a proof-of-concept, force-triggered and time-dependent rheological changes in the polymer as well as encapsulated nanoparticle release are demonstrated. Finally, that the kinetics of self-destruction are shown to be tuned as a function of nuclease concentration, incubation time, and thermodynamic stability of DNA crosslinkers.
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Affiliation(s)
| | | | - Yixiao Dong
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | | | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30322, USA
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9
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Peng YH, Hsiao SK, Gupta K, Ruland A, Auernhammer GK, Maitz MF, Boye S, Lattner J, Gerri C, Honigmann A, Werner C, Krieg E. Dynamic matrices with DNA-encoded viscoelasticity for cell and organoid culture. NATURE NANOTECHNOLOGY 2023; 18:1463-1473. [PMID: 37550574 PMCID: PMC10716043 DOI: 10.1038/s41565-023-01483-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 07/10/2023] [Indexed: 08/09/2023]
Abstract
Three-dimensional cell and organoid cultures rely on the mechanical support of viscoelastic matrices. However, commonly used matrix materials lack control over key cell-instructive properties. Here we report on fully synthetic hydrogels based on DNA libraries that self-assemble with ultrahigh-molecular-weight polymers, forming a dynamic DNA-crosslinked matrix (DyNAtrix). DyNAtrix enables computationally predictable and systematic control over its viscoelasticity, thermodynamic and kinetic parameters by changing DNA sequence information. Adjustable heat activation allows homogeneous embedding of mammalian cells. Intriguingly, stress-relaxation times can be tuned over four orders of magnitude, recapitulating mechanical characteristics of living tissues. DyNAtrix is self-healing, printable, exhibits high stability, cyto- and haemocompatibility, and controllable degradation. DyNAtrix-based cultures of human mesenchymal stromal cells, pluripotent stem cells, canine kidney cysts and human trophoblast organoids show high viability, proliferation and morphogenesis. DyNAtrix thus represents a programmable and versatile precision matrix for advanced approaches to biomechanics, biophysics and tissue engineering.
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Affiliation(s)
- Yu-Hsuan Peng
- Institute for Biofunctional Polymer Materials, Leibniz Institute of Polymer Research Dresden, Dresden, Germany
- Center for Regenerative Therapies Dresden, Cluster of Excellence Physics of Life and Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Dresden, Germany
| | - Syuan-Ku Hsiao
- Institute for Biofunctional Polymer Materials, Leibniz Institute of Polymer Research Dresden, Dresden, Germany
- Center for Regenerative Therapies Dresden, Cluster of Excellence Physics of Life and Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Dresden, Germany
| | - Krishna Gupta
- Institute for Biofunctional Polymer Materials, Leibniz Institute of Polymer Research Dresden, Dresden, Germany
- Center for Regenerative Therapies Dresden, Cluster of Excellence Physics of Life and Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Dresden, Germany
| | - André Ruland
- Institute for Biofunctional Polymer Materials, Leibniz Institute of Polymer Research Dresden, Dresden, Germany
| | - Günter K Auernhammer
- Institute for Physical Chemistry and Polymer Physics, Polymer Interfaces, Leibniz Institute of Polymer Research Dresden, Dresden, Germany
| | - Manfred F Maitz
- Institute for Biofunctional Polymer Materials, Leibniz Institute of Polymer Research Dresden, Dresden, Germany
| | - Susanne Boye
- Institute for Macromolecular Chemistry, Leibniz Institute of Polymer Research Dresden, Dresden, Germany
| | - Johanna Lattner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | - Claudia Gerri
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | - Alf Honigmann
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | - Carsten Werner
- Institute for Biofunctional Polymer Materials, Leibniz Institute of Polymer Research Dresden, Dresden, Germany
- Center for Regenerative Therapies Dresden, Cluster of Excellence Physics of Life and Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Dresden, Germany
| | - Elisha Krieg
- Institute for Biofunctional Polymer Materials, Leibniz Institute of Polymer Research Dresden, Dresden, Germany.
- Center for Regenerative Therapies Dresden, Cluster of Excellence Physics of Life and Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Dresden, Germany.
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10
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Kim Y, Tram LTH, Kim KA, Kim BC. Defining Integrin Tension Required for Chemotaxis of Metastatic Breast Cancer Cells in Confinement. Adv Healthc Mater 2023; 12:e2202747. [PMID: 37256848 DOI: 10.1002/adhm.202202747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 05/21/2023] [Indexed: 06/02/2023]
Abstract
Cancer metastasis is affected by chemical factors and physical cues. From cell adhesion to migration, mechanical tension applied to integrin expresses on the cell membrane and physical confinement significantly regulates cancer cell behaviors. Despite the physical interplay between integrins in cells and ligands in the tumor microenvironment, quantitative analysis of integrin tension during cancer cell migration in microconfined spaces remains elusive owing to the limited experimental tools. Herein, a platform termed microconfinement tension gauge tether to monitor spatial integrin tension with single-molecule precision by analyzing the epithelial-growth-factor-induced chemotaxis of metastatic human breast cancer cells in microfluidic channels is developed. The results reveal that the metastatic cancer cells exert the strongest integrin tension in the range of 54-100 pN at the leading edges of cells during chemokinetic migration on a planar surface, while the cells exert the strongest integrin tension exceeding 100 pN at the cell rear when entering microconfinement. Further analysis demonstrates that cells undergo mesenchymal migration under high integrin tension and less confinement, which is converted to amoeboid migration under low integrin tension or high confinement. In summary, the results identify a basic mechanism underlying the mechanical interactions between integrin tension and microenvironment that determines cancer invasion and metastasis.
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Affiliation(s)
- Young Kim
- Department of Nano-bioengineering, Incheon National University, Incheon, 22012, Republic of Korea
| | - Le Thi Hong Tram
- Department of Nano-bioengineering, Incheon National University, Incheon, 22012, Republic of Korea
| | - Kyung Ah Kim
- Department of Nano-bioengineering, Incheon National University, Incheon, 22012, Republic of Korea
| | - Byoung Choul Kim
- Department of Nano-bioengineering, Incheon National University, Incheon, 22012, Republic of Korea
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11
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Hu Y, Duan Y, Salaita K. DNA Nanotechnology for Investigating Mechanical Signaling in the Immune System. Angew Chem Int Ed Engl 2023; 62:e202302967. [PMID: 37186502 PMCID: PMC11336604 DOI: 10.1002/anie.202302967] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Indexed: 05/17/2023]
Abstract
Immune recognition occurs at specialized cell-cell junctions when immune cells and target cells physically touch. In this junction, groups of receptor-ligand complexes assemble and experience molecular forces that are ultimately generated by the cellular cytoskeleton. These forces are in the range of piconewton (pN) but play crucial roles in immune cell activation and subsequent effector responses. In this minireview, we will review the development of DNA based molecular tension sensors and their applications in mapping and quantifying mechanical forces experienced by immunoreceptors including T-cell receptor (TCR), Lymphocyte function-associated antigen (LFA-1), and the B-cell receptor (BCR) among others. In addition, we will highlight the use of DNA as a mechanical gate to manipulate mechanotransduction and decipher how mechanical forces regulate antigen discrimination and receptor signaling.
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Affiliation(s)
- Yuesong Hu
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Yuxin Duan
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
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12
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Matsubara H, Fukunaga H, Saito T, Ikezaki K, Iwaki M. A Programmable DNA Origami Nanospring That Reports Dynamics of Single Integrin Motion, Force Magnitude and Force Orientation in Living Cells. ACS NANO 2023. [PMID: 37394270 PMCID: PMC10373515 DOI: 10.1021/acsnano.2c12545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Mechanical forces are critical for regulating many biological processes such as cell differentiation, proliferation, and death. Probing the continuously changing molecular force through integrin receptors provides insights into the molecular mechanism of rigidity sensing in cells; however, the force information is still limited. Here, we built a coil-shaped DNA origami (DNA nanospring, NS) as a force sensor that reports the dynamic motion of single integrins as well as the magnitude and orientation of the force through integrins in living cells. We monitored the extension with nanometer accuracy and the orientation of the NS linked with a single integrin by the shape of the fluorescence spots. We used acoustic force spectroscopy to estimate the force-extension curve of the NS and determined the force with an ∼10% force error at a broad detectable range from subpicoNewtons (pN) to ∼50 pN. We found single integrins tethered with the NS moved several tens of nanometers, and the contraction and relaxation speeds were load dependent at less than ∼20 pN but robust over ∼20 pN. Fluctuations of the traction force orientation were suppressed with increasing load. Our assay system is a potentially powerful tool for studying mechanosensing at the molecular level.
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Affiliation(s)
- Hitomi Matsubara
- RIKEN Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka 5650874, Japan
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 5650871, Japan
| | - Hiroki Fukunaga
- RIKEN Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka 5650874, Japan
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 5650871, Japan
| | - Takahiro Saito
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 5650871, Japan
| | - Keigo Ikezaki
- Department of Physics, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 1130033, Japan
| | - Mitsuhiro Iwaki
- RIKEN Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka 5650874, Japan
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 5650871, Japan
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe, Hyogo 6512492, Japan
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13
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Zhou P, Ding L, Yan Y, Wang Y, Su B. Recent advances in label-free imaging of cell-matrix adhesions. Chem Commun (Camb) 2023; 59:2341-2351. [PMID: 36744880 DOI: 10.1039/d2cc06499e] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Cell-matrix adhesions play an essential role in mediating and regulating many biological processes. The adhesion receptors, typically transmembrane integrins, provide dynamic correlations between intracellular environments and extracellular matrixes (ECMs) by bi-directional signaling. In-depth investigations of cell-matrix adhesion and integrin-mediated cell adhesive force are of great significance in biology and medicine. The emergence of advanced imaging techniques and principles has facilitated the understanding of the molecular composition and structure dynamics of cell-matrix adhesions, especially the label-free imaging methods that can be used to study living cell dynamics without immunofluorescence staining. This highlight article aims to give an overview of recent developments in imaging cell-matrix adhesions in a label-free manner. Electrochemiluminescence microscopy (ECLM) and surface plasmon resonance microscopy (SPRM) are briefly introduced and their applications in imaging analysis of cell-matrix adhesions are summarized. Then we highlight the advances in mapping cell-matrix adhesion force based on molecular tension probes and fluorescence microscopy (collectively termed as MTFM). The biomaterials including polyethylene glycol (PEG), peptides and DNA for constructing tension probes in MTFM are summarized. Finally, the outlook and perspectives on the further developments of cell-matrix adhesion imaging are presented.
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Affiliation(s)
- Ping Zhou
- Key Laboratory of Excited-State Materials of Zhejiang Province, Institute of Analytical Chemistry, Department of Chemistry, Zhejiang University, Hangzhou 310058, China.
| | - Lurong Ding
- Key Laboratory of Excited-State Materials of Zhejiang Province, Institute of Analytical Chemistry, Department of Chemistry, Zhejiang University, Hangzhou 310058, China.
| | - Yajuan Yan
- Key Laboratory of Excited-State Materials of Zhejiang Province, Institute of Analytical Chemistry, Department of Chemistry, Zhejiang University, Hangzhou 310058, China.
| | - Yafeng Wang
- Key Laboratory of Excited-State Materials of Zhejiang Province, Institute of Analytical Chemistry, Department of Chemistry, Zhejiang University, Hangzhou 310058, China.
| | - Bin Su
- Key Laboratory of Excited-State Materials of Zhejiang Province, Institute of Analytical Chemistry, Department of Chemistry, Zhejiang University, Hangzhou 310058, China.
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14
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Abraham Punnoose J, Thomas KJ, Chandrasekaran AR, Vilcapoma J, Hayden A, Kilpatrick K, Vangaveti S, Chen A, Banco T, Halvorsen K. High-throughput single-molecule quantification of individual base stacking energies in nucleic acids. Nat Commun 2023; 14:631. [PMID: 36746949 PMCID: PMC9902561 DOI: 10.1038/s41467-023-36373-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 01/26/2023] [Indexed: 02/08/2023] Open
Abstract
Base stacking interactions between adjacent bases in DNA and RNA are important for many biological processes and in biotechnology applications. Previous work has estimated stacking energies between pairs of bases, but contributions of individual bases has remained unknown. Here, we use a Centrifuge Force Microscope for high-throughput single molecule experiments to measure stacking energies between adjacent bases. We found stacking energies strongest between purines (G|A at -2.3 ± 0.2 kcal/mol) and weakest between pyrimidines (C|T at -0.5 ± 0.1 kcal/mol). Hybrid stacking with phosphorylated, methylated, and RNA nucleotides had no measurable effect, but a fluorophore modification reduced stacking energy. We experimentally show that base stacking can influence stability of a DNA nanostructure, modulate kinetics of enzymatic ligation, and assess accuracy of force fields in molecular dynamics simulations. Our results provide insights into fundamental DNA interactions that are critical in biology and can inform design in biotechnology applications.
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Affiliation(s)
- Jibin Abraham Punnoose
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Kevin J Thomas
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | | | - Javier Vilcapoma
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Andrew Hayden
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Kacey Kilpatrick
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA.,Department of Chemistry, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Sweta Vangaveti
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Alan Chen
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA.,Department of Chemistry, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Thomas Banco
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA.
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15
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Mishra RK, Mukherjee S, Bhattacharyya D. Maturation of siRNA by strand separation: Steered molecular dynamics study. J Biomol Struct Dyn 2022; 40:13682-13692. [PMID: 34726123 DOI: 10.1080/07391102.2021.1994468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
RNA interference, particularly siRNA induced gene silencing is becoming an important avenue of modern therapeutics. The siRNA is delivered to the cells as short double helical RNA which becomes single stranded for forming the RISC complex. Significant experimental evidence is available for most of the steps except the process of the separation of the two strands. We have attempted to understand the pathway for double stranded siRNA (dsRNA) to single stranded (ssRNA) molecules using steered molecular dynamics simulations. As the process is completely unexplored we have applied force from all possible directions restraining all possible residues to convert dsRNA to ssRNA. We found pulling one strand along the helical axis direction restraining the far end of the other strand demands excessive force for ssRNA formation. Pulling a central residue of one strand, in a direction perpendicular to the helix axis, while keeping the base paired residue fixed requires intermediate force for strand separation. Moreover, we found that in this process the force requirement is quite high for the first bubble formation (nucleation energy) and the bubble propagation energies are quite small. We believe the success rate of the design of siRNA sequences for gene silencing may increase if this mechanistic knowledge is utilized for such a design process.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rakesh Kumar Mishra
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sanchita Mukherjee
- Department of Biological Sciences, Indian Institute of Science Education and Research, Kolkata, India
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16
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Mishra RK, Maganti L. Antitumor drugs effect on the stability of double-stranded DNA: steered molecular dynamics analysis. J Biomol Struct Dyn 2022; 40:11373-11382. [PMID: 34355668 DOI: 10.1080/07391102.2021.1960193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Denaturation of the DNA double helix inside the cell is essential for cellular processes such as replication and transcription for the growth of the cells. However, the growth of unwanted cells, which are responsible for cancerous kind of disease, is one of the biggest challenges of modern therapeutics. DNA cross-linking agents may kill cancer cells by damaging their DNA and stopping them from dividing. In the present study, we have carried out steered molecular dynamics simulations to study the effects of rupture and unzipping forces on the stability of dsDNA in the absence and presence of covalently bonded drugs. We have found that the stability of dsDNA increases strongly in the presence of covalently bonded drugs. The microscopic study of disruption of hydrogen-bonds associated with base-pairs of the dsDNA and the study of the variation of stacking overlap parameters gives evidence of symmetry during the rupture and asymmetry in the unzip event. The significance of the mechanism of force-induced melting study of the dsDNA in the absence and presence of antitumor drugs might have a biological relevance as it provides a pathway to open the double helix in a specific position and may help for the pharmaceutical design of drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rakesh Kumar Mishra
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Lakshmi Maganti
- Computational Science Division, Saha Institute of Nuclear Physics, Kolkata, West Bengal, India
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17
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Single-molecule characterization of subtype-specific β1 integrin mechanics. Nat Commun 2022; 13:7471. [PMID: 36463259 PMCID: PMC9719539 DOI: 10.1038/s41467-022-35173-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 11/17/2022] [Indexed: 12/05/2022] Open
Abstract
Although integrins are known to be mechanosensitive and to possess many subtypes that have distinct physiological roles, single molecule studies of force exertion have thus far been limited to RGD-binding integrins. Here, we show that integrin α4β1 and RGD-binding integrins (αVβ1 and α5β1) require markedly different tension thresholds to support cell spreading. Furthermore, actin assembled downstream of α4β1 forms cross-linked networks in circularly spread cells, is in rapid retrograde flow, and exerts low forces from actin polymerization. In contrast, actin assembled downstream of αVβ1 forms stress fibers linking focal adhesions in elongated cells, is in slow retrograde flow, and matures to exert high forces (>54-pN) via myosin II. Conformational activation of both integrins occurs below 12-pN, suggesting that post-activation subtype-specific cytoskeletal remodeling imposes the higher threshold for spreading on RGD substrates. Multiple layers of single integrin mechanics for activation, mechanotransduction and cytoskeleton remodeling revealed here may underlie subtype-dependence of diverse processes such as somite formation and durotaxis.
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18
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Akbari E, Shahhosseini M, Robbins A, Poirier MG, Song JW, Castro CE. Low cost and massively parallel force spectroscopy with fluid loading on a chip. Nat Commun 2022; 13:6800. [PMID: 36357383 PMCID: PMC9649742 DOI: 10.1038/s41467-022-34212-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 10/18/2022] [Indexed: 11/12/2022] Open
Abstract
Current approaches for single molecule force spectroscopy are typically constrained by low throughput and high instrumentation cost. Herein, a low-cost, high throughput technique is demonstrated using microfluidics for multiplexed mechanical manipulation of up to ~4000 individual molecules via molecular fluid loading on-a-chip (FLO-Chip). The FLO-Chip consists of serially connected microchannels with varying width, allowing for simultaneous testing at multiple loading rates. Molecular force measurements are demonstrated by dissociating Biotin-Streptavidin and Digoxigenin-AntiDigoxigenin interactions along with unzipping of double stranded DNA of varying sequence under different dynamic loading rates and solution conditions. Rupture force results under varying loading rates and solution conditions are in good agreement with prior studies, verifying a versatile approach for single molecule biophysics and molecular mechanobiology. FLO-Chip enables straightforward, rapid, low-cost, and portable mechanical testing of single molecules that can be implemented on a wide range of microscopes to broaden access and may enable new applications of molecular force spectroscopy.
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Affiliation(s)
- Ehsan Akbari
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
| | - Melika Shahhosseini
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Ariel Robbins
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
| | - Michael G Poirier
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
| | - Jonathan W Song
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
- Comprehensive Cancer Center, 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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19
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Ruiz-Gutierrez N, Rieu M, Ouellet J, Allemand JF, Croquette V, Le Hir H. Novel approaches to study helicases using magnetic tweezers. Methods Enzymol 2022; 673:359-403. [PMID: 35965012 DOI: 10.1016/bs.mie.2022.03.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Helicases form a universal family of molecular motors that bind and translocate onto nucleic acids. They are involved in essentially every aspect of nucleic acid metabolism: from DNA replication to RNA decay, and thus ensure a large spectrum of functions in the cell, making their study essential. The development of micromanipulation techniques such as magnetic tweezers for the mechanistic study of these enzymes has provided new insights into their behavior and their regulation that were previously unrevealed by bulk assays. These experiments allowed very precise measures of their translocation speed, processivity and polarity. Here, we detail our newest technological advances in magnetic tweezers protocols for high-quality measurements and we describe the new procedures we developed to get a more profound understanding of helicase dynamics, such as their translocation in a force independent manner, their nucleic acid binding kinetics and their interaction with roadblocks.
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Affiliation(s)
- Nadia Ruiz-Gutierrez
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Martin Rieu
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Research University, Paris, France; Laboratoire de Physique de L'Ecole Normale Supérieure de Paris, CNRS, ENS, Université PSL, Sorbonne Université, Université de Paris, Paris, France
| | | | - Jean-François Allemand
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Research University, Paris, France; Laboratoire de Physique de L'Ecole Normale Supérieure de Paris, CNRS, ENS, Université PSL, Sorbonne Université, Université de Paris, Paris, France
| | - Vincent Croquette
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Research University, Paris, France; Laboratoire de Physique de L'Ecole Normale Supérieure de Paris, CNRS, ENS, Université PSL, Sorbonne Université, Université de Paris, Paris, France; ESPCI Paris, Université PSL, Paris, France.
| | - Hervé Le Hir
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Research University, Paris, France.
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20
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Kim KA, Vellampatti S, Kim BC. Characterization of Integrin Molecular Tension of Human Breast Cancer Cells on Anisotropic Nanopatterns. Front Mol Biosci 2022; 9:825970. [PMID: 35755806 PMCID: PMC9218603 DOI: 10.3389/fmolb.2022.825970] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 04/26/2022] [Indexed: 11/13/2022] Open
Abstract
Physical interactions between cells and micro/nanometer-sized architecture presented in an extracellular matrix (ECM) environment significantly influence cell adhesion and morphology, often facilitating the incidence of diseases, such as cancer invasion and metastasis. Sensing and responding to the topographical cues are deeply associated with a physical interplay between integrins, ligands, and mechanical force transmission, ultimately determining diverse cell behavior. Thus, how the tension applied to the integrin-ligand bonds controls cells' response to the topographical cues needs to be elucidated through quantitative analysis. Here, in this brief research report, we reported a novel platform, termed "topo-tension gauge tether (TGT)," to visualize single-molecule force applied to the integrin-ligand on the aligned anisotropic nanopatterns. Using the topo-TGT assay, first, topography-induced adhesion and morphology of cancerous and normal cells were compared with the pre-defined peak integrin tension. Next, spatial integrin tensions underneath cells were identified using reconstructed integrin tension maps. As a result, we characterized each cell's capability to comply with nanotopographies and the magnitude of the spatial integrin tension. Altogether, the quantitative information on integrin tension will be a valuable basis for understanding the biophysical mechanisms underlying the force balance influencing adhesion to the topographical cues.
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Affiliation(s)
- Kyung Ah Kim
- Department of Nano-Bioengineering, Incheon National University, Incheon, South Korea
| | - Srivithya Vellampatti
- Department of Nano-Bioengineering, Incheon National University, Incheon, South Korea
| | - Byoung Choul Kim
- Department of Nano-Bioengineering, Incheon National University, Incheon, South Korea
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21
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Kuo YW, Mahamdeh M, Tuna Y, Howard J. The force required to remove tubulin from the microtubule lattice by pulling on its α-tubulin C-terminal tail. Nat Commun 2022; 13:3651. [PMID: 35752623 PMCID: PMC9233703 DOI: 10.1038/s41467-022-31069-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/01/2022] [Indexed: 11/18/2022] Open
Abstract
Severing enzymes and molecular motors extract tubulin from the walls of microtubules by exerting mechanical force on subunits buried in the lattice. However, how much force is needed to remove tubulin from microtubules is not known, nor is the pathway by which subunits are removed. Using a site-specific functionalization method, we applied forces to the C-terminus of α-tubulin with an optical tweezer and found that a force of ~30 pN is required to extract tubulin from the microtubule wall. Additionally, we discovered that partial unfolding is an intermediate step in tubulin removal. The unfolding and extraction forces are similar to those generated by AAA-unfoldases. Lastly, we show that three kinesin-1 motor proteins can also extract tubulin from the microtubule lattice. Our results provide the first experimental investigation of how tubulin responds to mechanical forces exerted on its α-tubulin C-terminal tail and have implications for the mechanisms of severing enzymes and microtubule stability. Tubulin, the building blocks of microtubules, can be removed from the microtubule wall by mechanical forces. Using single-molecule methods, the authors show that tubulin partially unfolds prior to its removal and determined the tubulin-extraction force.
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Affiliation(s)
- Yin-Wei Kuo
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Mohammed Mahamdeh
- Harvard Medical School, Boston, MA, USA.,Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Yazgan Tuna
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jonathon Howard
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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22
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Darcy M, Crocker K, Wang Y, Le JV, Mohammadiroozbahani G, Abdelhamid MAS, Craggs TD, Castro CE, Bundschuh R, Poirier MG. High-Force Application by a Nanoscale DNA Force Spectrometer. ACS NANO 2022; 16:5682-5695. [PMID: 35385658 PMCID: PMC9048690 DOI: 10.1021/acsnano.1c10698] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/28/2022] [Indexed: 05/06/2023]
Abstract
The ability to apply and measure high forces (>10 pN) on the nanometer scale is critical to the development of nanomedicine, molecular robotics, and the understanding of biological processes such as chromatin condensation, membrane deformation, and viral packaging. Established force spectroscopy techniques including optical traps, magnetic tweezers, and atomic force microscopy rely on micron-sized or larger handles to apply forces, limiting their applications within constrained geometries including cellular environments and nanofluidic devices. A promising alternative to these approaches is DNA-based molecular calipers. However, this approach is currently limited to forces on the scale of a few piconewtons. To study the force application capabilities of DNA devices, we implemented DNA origami nanocalipers with tunable mechanical properties in a geometry that allows application of force to rupture a DNA duplex. We integrated static and dynamic single-molecule characterization methods and statistical mechanical modeling to quantify the device properties including force output and dynamic range. We found that the thermally driven dynamics of the device are capable of applying forces of at least 20 piconewtons with a nanometer-scale dynamic range. These characteristics could eventually be used to study other biomolecular processes such as protein unfolding or to control high-affinity interactions in nanomechanical devices or molecular robots.
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Affiliation(s)
- Michael Darcy
- Department
of Physics, Department of Mechanical and Aerospace Engineering, Biophysics Graduate
Program, Department of Chemistry and Biochemistry, and Division of Hematology, Department
of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Kyle Crocker
- Department
of Physics, Department of Mechanical and Aerospace Engineering, Biophysics Graduate
Program, Department of Chemistry and Biochemistry, and Division of Hematology, Department
of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yuchen Wang
- Department
of Physics, Department of Mechanical and Aerospace Engineering, Biophysics Graduate
Program, Department of Chemistry and Biochemistry, and Division of Hematology, Department
of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jenny V. Le
- Department
of Physics, Department of Mechanical and Aerospace Engineering, Biophysics Graduate
Program, Department of Chemistry and Biochemistry, and Division of Hematology, Department
of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Golbarg Mohammadiroozbahani
- Department
of Physics, Department of Mechanical and Aerospace Engineering, Biophysics Graduate
Program, Department of Chemistry and Biochemistry, and Division of Hematology, Department
of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | | | - Timothy D. Craggs
- Department
of Chemistry, University of Sheffield, Sheffield S3 7HF, U.K.
| | - Carlos E. Castro
- Department
of Physics, Department of Mechanical and Aerospace Engineering, Biophysics Graduate
Program, Department of Chemistry and Biochemistry, and Division of Hematology, Department
of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Ralf Bundschuh
- Department
of Physics, Department of Mechanical and Aerospace Engineering, Biophysics Graduate
Program, Department of Chemistry and Biochemistry, and Division of Hematology, Department
of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Michael G. Poirier
- Department
of Physics, Department of Mechanical and Aerospace Engineering, Biophysics Graduate
Program, Department of Chemistry and Biochemistry, and Division of Hematology, Department
of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, United States
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23
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Shrestha P, Yang D, Tomov TE, MacDonald JI, Ward A, Bergal HT, Krieg E, Cabi S, Luo Y, Nathwani B, Johnson-Buck A, Shih WM, Wong WP. Single-molecule mechanical fingerprinting with DNA nanoswitch calipers. NATURE NANOTECHNOLOGY 2021; 16:1362-1370. [PMID: 34675411 PMCID: PMC8678201 DOI: 10.1038/s41565-021-00979-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 08/16/2021] [Indexed: 05/31/2023]
Abstract
Decoding the identity of biomolecules from trace samples is a longstanding goal in the field of biotechnology. Advances in DNA analysis have substantially affected clinical practice and basic research, but corresponding developments for proteins face challenges due to their relative complexity and our inability to amplify them. Despite progress in methods such as mass spectrometry and mass cytometry, single-molecule protein identification remains a highly challenging objective. Towards this end, we combine DNA nanotechnology with single-molecule force spectroscopy to create a mechanically reconfigurable DNA nanoswitch caliper capable of measuring multiple coordinates on single biomolecules with atomic resolution. Using optical tweezers, we demonstrate absolute distance measurements with ångström-level precision for both DNA and peptides, and using multiplexed magnetic tweezers, we demonstrate quantification of relative abundance in mixed samples. Measuring distances between DNA-labelled residues, we perform single-molecule fingerprinting of synthetic and natural peptides, and show discrimination, within a heterogeneous population, between different posttranslational modifications. DNA nanoswitch calipers are a powerful and accessible tool for characterizing distances within nanoscale complexes that will enable new applications in fields such as single-molecule proteomics.
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Affiliation(s)
- Prakash Shrestha
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Darren Yang
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Toma E Tomov
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - James I MacDonald
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Andrew Ward
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Hans T Bergal
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Biophysics Program, Harvard University, Cambridge, MA, USA
| | - Elisha Krieg
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Serkan Cabi
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yi Luo
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Bhavik Nathwani
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alexander Johnson-Buck
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Biophysics Program, Harvard University, Cambridge, MA, USA
| | - William M Shih
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Wesley P Wong
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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24
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Sung CY, Huang CC, Chen YS, Hsu KF, Lee GB. Isolation and quantification of extracellular vesicle-encapsulated microRNA on an integrated microfluidic platform. LAB ON A CHIP 2021; 21:4660-4671. [PMID: 34739016 DOI: 10.1039/d1lc00663k] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Ovarian cancer (OvCa) is the most fatal among gynecological cancers and affects many women worldwide. Since OvCa is prone to metastasis, which significantly increases chances of death, biomarkers for early-stage OvCa are greatly needed. This study develops an integrated microfluidic platform for isolating and quantifying one of the OvCa blood biomarkers. As a demonstration, microRNA-21 (miRNA-21), which is one of the important biomarkers for cancers, was isolated and measured in this study. Extracellular vesicles (EVs) in blood were first captured and isolated by anti-CD63-coated magnetic beads. Then, EV-encapsulated miRNA-21 was isolated by complementary DNA-coated magnetic beads, and finally the isolated miRNA-21 was quantified by digital polymerase chain reaction (digital PCR, dPCR). The integrated chip featured a sample treatment module and a miRNA quantification module that automated the entire process, and the limit of detection (LOD) was 11 copies per mL. The inaccuracy of the miRNA quantification module (i.e. dPCR) was found to be <12%. Additionally, spiked samples and clinical samples were used to test the performance of the developed platform. It is envisioned that the developed system can serve as a valuable and promising tool for OvCa biomarker measurements.
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Affiliation(s)
- Chia-Yu Sung
- Department of Life Science, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chi-Chien Huang
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan.
| | - Yi-Sin Chen
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan.
| | - Keng-Fu Hsu
- Department of Obstetrics and Gynecology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 70403 Taiwan.
| | - Gwo-Bin Lee
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan.
- Institute of NanoEngineering and Microsystems, National Tsing Hua University, Hsinchu 30013, Taiwan
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25
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Su H, Brockman JM, Duan Y, Sen N, Chhabra H, Bazrafshan A, Blanchard AT, Meyer T, Andrews B, Doye JPK, Ke Y, Dyer RB, Salaita K. Massively Parallelized Molecular Force Manipulation with On-Demand Thermal and Optical Control. J Am Chem Soc 2021; 143:19466-19473. [PMID: 34762807 DOI: 10.1021/jacs.1c08796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In single-molecule force spectroscopy (SMFS), a tethered molecule is stretched using a specialized instrument to study how macromolecules extend under force. One problem in SMFS is the serial and slow nature of the measurements, performed one molecule at a time. To address this long-standing challenge, we report on the origami polymer force clamp (OPFC) which enables parallelized manipulation of the mechanical forces experienced by molecules without the need for dedicated SMFS instruments or surface tethering. The OPFC positions target molecules between a rigid nanoscale DNA origami beam and a responsive polymer particle that shrinks on demand. As a proof-of-concept, we record the steady state and time-resolved mechanical unfolding dynamics of DNA hairpins using the fluorescence signal from ensembles of molecules and confirm our conclusion using modeling.
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Affiliation(s)
- Hanquan Su
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Joshua M Brockman
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Yuxin Duan
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Navoneel Sen
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Hemani Chhabra
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Alisina Bazrafshan
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Aaron T Blanchard
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Travis Meyer
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Brooke Andrews
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Yonggang Ke
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States.,Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - R Brian Dyer
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States.,Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
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26
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Duan Y, Glazier R, Bazrafshan A, Hu Y, Rashid SA, Petrich BG, Ke Y, Salaita K. Mechanically Triggered Hybridization Chain Reaction. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107660] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Yuxin Duan
- Department of Chemistry Emory University Atlanta GA 30322 USA
| | - Roxanne Glazier
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta GA 30322 USA
| | | | - Yuesong Hu
- Department of Chemistry Emory University Atlanta GA 30322 USA
| | - Sk Aysha Rashid
- Department of Chemistry Emory University Atlanta GA 30322 USA
| | | | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta GA 30322 USA
| | - Khalid Salaita
- Department of Chemistry Emory University Atlanta GA 30322 USA
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta GA 30322 USA
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27
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Duan Y, Glazier R, Bazrafshan A, Hu Y, Rashid SA, Petrich BG, Ke Y, Salaita K. Mechanically Triggered Hybridization Chain Reaction. Angew Chem Int Ed Engl 2021; 60:19974-19981. [PMID: 34242462 PMCID: PMC8390435 DOI: 10.1002/anie.202107660] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Indexed: 01/16/2023]
Abstract
Cells transmit piconewton forces to receptors to mediate processes such as migration and immune recognition. A major challenge in quantifying such forces is the sparsity of cell mechanical events. Accordingly, molecular tension is typically quantified with high resolution fluorescence microscopy, which hinders widespread adoption and application. Here, we report a mechanically triggered hybridization chain reaction (mechano-HCR) that allows chemical amplification of mechanical events. The amplification is triggered when a cell receptor mechanically denatures a duplex revealing a cryptic initiator to activate the HCR reaction in situ. Importantly, mechano-HCR enables direct readout of pN forces using a plate reader. We leverage this capability and measured mechano-IC50 for aspirin, Y-27632, and eptifibatide. Given that cell mechanical phenotypes are of clinical importance, mechano-HCR may offer a convenient route for drug discovery, personalized medicine, and disease diagnosis.
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Affiliation(s)
- Yuxin Duan
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Roxanne Glazier
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30322, USA
| | | | - Yuesong Hu
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Sk Aysha Rashid
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Brian G Petrich
- Department of Pediatrics, Emory University, Atlanta, GA, 30322, USA
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30322, USA
| | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30322, USA
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28
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Jo MH, Kim BC, Sung K, Panettieri RA, An SS, Liu J, Ha T. Molecular Nanomechanical Mapping of Histamine-Induced Smooth Muscle Cell Contraction and Shortening. ACS NANO 2021; 15:11585-11596. [PMID: 34197709 PMCID: PMC10144385 DOI: 10.1021/acsnano.1c01782] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Mechanical response to external stimuli is a conserved feature of many cell types. For example, neurotransmitters (e.g., histamine) trigger calcium signals that induce actomyosin-regulated contraction of airway smooth muscle (ASM); the resulting cell shortening causes airway narrowing, the excess of which can cause asthma. Despite intensive studies, however, it remains unclear how physical forces are propagated through focal adhesion (FA)-the major force-transmission machinery of the cell-during ASM shortening. We provide a nanomechanical platform to directly image single molecule forces during ASM cell shortening by repurposing DNA tension sensors. Surprisingly, cell shortening and FA disassembly that immediately precedes it occurred long after histamine-evoked increases in intracellular calcium levels ([Ca2+]i). Our mathematical model that fully integrates cell edge protrusion and retraction with contractile forces acting on FA predicted that (1) stabilization of FA impedes cell shortening and (2) the disruption of FAs is preceded by their strengthening through actomyosin-activated molecular tension. We confirmed these predictions via real-time imaging and molecular force measurements. Together, our work highlights a key role of FA dynamics in regulating ASM contraction induced by an allergen with potential therapeutic implications.
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Affiliation(s)
- Myung Hyun Jo
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Byoung Choul Kim
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Division of Nano-Bioengineering, Incheon National University, Incheon 22012, South Korea
| | - Keewon Sung
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
| | - Reynold A. Panettieri
- Rutgers Institute for Translational Medicine and Science, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Steven S. An
- Rutgers Institute for Translational Medicine and Science, The State University of New Jersey, New Brunswick, NJ 08901, USA
- Department of Pharmacology, Rutgers-Robert Wood Johnson Medical School, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jian Liu
- Department of Cell Biology and Center for Cell Dynamics, Johns Hopkins School of Medicine, Baltimore, MD 20205, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Howard Hughes Medical Institute, Baltimore, MD 21205, USA
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29
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Abstract
Cytoskeletal active nematics exhibit striking nonequilibrium dynamics that are powered by energy-consuming molecular motors. To gain insight into the structure and mechanics of these materials, we design programmable clusters in which kinesin motors are linked by a double-stranded DNA linker. The efficiency by which DNA-based clusters power active nematics depends on both the stepping dynamics of the kinesin motors and the chemical structure of the polymeric linker. Fluorescence anisotropy measurements reveal that the motor clusters, like filamentous microtubules, exhibit local nematic order. The properties of the DNA linker enable the design of force-sensing clusters. When the load across the linker exceeds a critical threshold, the clusters fall apart, ceasing to generate active stresses and slowing the system dynamics. Fluorescence readout reveals the fraction of bound clusters that generate interfilament sliding. In turn, this yields the average load experienced by the kinesin motors as they step along the microtubules. DNA-motor clusters provide a foundation for understanding the molecular mechanism by which nanoscale molecular motors collectively generate mesoscopic active stresses, which in turn power macroscale nonequilibrium dynamics of active nematics.
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30
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Upadhyaya A, Kumar S. Effect of loop sequence on unzipping of short DNA hairpins. Phys Rev E 2021; 103:062411. [PMID: 34271739 DOI: 10.1103/physreve.103.062411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 05/27/2021] [Indexed: 11/07/2022]
Abstract
The dependence of stability on the sequence of a DNA hairpin has been investigated through atomistic simulations. For this, a sequence of 16 bases of a hairpin, which consists of a loop of four bases and a stem of six base pairs, has been considered. We have taken eight different sequences, where the first five base pairs were kept fixed in all sequences, whereas the loop sequence and the identity of the duplex base pair closing the loop have been varied. For these hairpin structures, force-induced melting (unzipping) studies were carried out to investigate the effect of the variables on the stability of hairpin. The temperature at which half of the base pairs are open is termed the melting temperature. We defined the unzipping force F_{h} (half of the base pairs are open) and showed that it may not provide the effect of closing the base pair or loop sequence on the stability of the DNA hairpin. In order to have a better understanding of the stability of a DNA hairpin, the closing base pair or hairpin loop must be open. This requires complete opening of the stem. We defined a force F_{c} at which all base pairs of the stem are open, and we showed that the F_{c} gives better understanding of DNA hairpin stability.
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Affiliation(s)
- Anurag Upadhyaya
- Department of Physics, Banaras Hindu University, Varanasi, 221 005, India
| | - Sanjay Kumar
- Department of Physics, Banaras Hindu University, Varanasi, 221 005, India
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31
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Sengar A, Ouldridge TE, Henrich O, Rovigatti L, Šulc P. A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results. Front Mol Biosci 2021; 8:693710. [PMID: 34235181 PMCID: PMC8256390 DOI: 10.3389/fmolb.2021.693710] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022] Open
Abstract
The oxDNA model of Deoxyribonucleic acid has been applied widely to systems in biology, biophysics and nanotechnology. It is currently available via two independent open source packages. Here we present a set of clearly documented exemplar simulations that simultaneously provide both an introduction to simulating the model, and a review of the model's fundamental properties. We outline how simulation results can be interpreted in terms of-and feed into our understanding of-less detailed models that operate at larger length scales, and provide guidance on whether simulating a system with oxDNA is worthwhile.
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Affiliation(s)
- A. Sengar
- Centre for Synthetic Biology, Department of Bioengineering, Imperial College London, London, United Kingdom
| | - T. E. Ouldridge
- Centre for Synthetic Biology, Department of Bioengineering, Imperial College London, London, United Kingdom
| | - O. Henrich
- Department of Physics, SUPA, University of Strathclyde, Glasgow, United Kingdom
| | - L. Rovigatti
- Department of Physics, Sapienza University of Rome, Rome, Italy
- CNR Institute of Complex Systems, Sapienza University of Rome, Rome, Italy
| | - P. Šulc
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States
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32
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Li H, Zhang C, Hu Y, Liu P, Sun F, Chen W, Zhang X, Ma J, Wang W, Wang L, Wu P, Liu Z. A reversible shearing DNA probe for visualizing mechanically strong receptors in living cells. Nat Cell Biol 2021; 23:642-651. [PMID: 34059812 DOI: 10.1038/s41556-021-00691-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 04/28/2021] [Indexed: 02/05/2023]
Abstract
In the last decade, DNA-based tension sensors have made significant contributions to the study of the importance of mechanical forces in many biological systems. Albeit successful, one shortcoming of these techniques is their inability to reversibly measure receptor forces in a higher regime (that is, >20 pN), which limits our understanding of the molecular details of mechanochemical transduction in living cells. Here, we developed a reversible shearing DNA-based tension probe (RSDTP) for probing molecular piconewton-scale forces between 4 and 60 pN transmitted by cells. Using these probes, we can easily distinguish the differences in force-bearing integrins without perturbing adhesion biology and reveal that a strong force-bearing integrin cluster can serve as a 'mechanical pivot' to maintain focal adhesion architecture and facilitate its maturation. The benefits of the RSDTP include a high dynamic range, reversibility and single-molecule sensitivity, all of which will facilitate a better understanding of the molecular mechanisms of mechanobiology.
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Affiliation(s)
- Hongyun Li
- The Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Chen Zhang
- College of Life Sciences, State Key Laboratory of Virology, Wuhan University, Wuhan, China
| | - Yuru Hu
- The Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Pengxiang Liu
- The Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Feng Sun
- The Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Wei Chen
- The Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Xinghua Zhang
- The Institute for Advanced Studies, Wuhan University, Wuhan, China.,College of Life Sciences, State Key Laboratory of Virology, Wuhan University, Wuhan, China
| | - Jie Ma
- School of Physics, Sun Yat-sen University, Guangzhou, China
| | - Wenxu Wang
- The Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Liang Wang
- The Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Piyu Wu
- The Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Zheng Liu
- The Institute for Advanced Studies, Wuhan University, Wuhan, China.
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33
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Mulhall EM, Ward A, Yang D, Koussa MA, Corey DP, Wong WP. Single-molecule force spectroscopy reveals the dynamic strength of the hair-cell tip-link connection. Nat Commun 2021; 12:849. [PMID: 33558532 PMCID: PMC7870652 DOI: 10.1038/s41467-021-21033-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 01/08/2021] [Indexed: 01/11/2023] Open
Abstract
The conversion of auditory and vestibular stimuli into electrical signals is initiated by force transmitted to a mechanotransduction channel through the tip link, a double stranded protein filament held together by two adhesion bonds in the middle. Although thought to form a relatively static structure, the dynamics of the tip-link connection has not been measured. Here, we biophysically characterize the strength of the tip-link connection at single-molecule resolution. We show that a single tip-link bond is more mechanically stable relative to classic cadherins, and our data indicate that the double stranded tip-link connection is stabilized by single strand rebinding facilitated by strong cis-dimerization domains. The measured lifetime of seconds suggests the tip-link is far more dynamic than previously thought. We also show how Ca2+ alters tip-link lifetime through elastic modulation and reveal the mechanical phenotype of a hereditary deafness mutation. Together, these data show how the tip link is likely to function during mechanical stimuli.
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Affiliation(s)
- Eric M Mulhall
- Department of Neurobiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Program in Neuroscience, Harvard University, Cambridge, MA, USA
| | - Andrew Ward
- Department of Neurobiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Darren Yang
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Mounir A Koussa
- Department of Neurobiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Program in Neuroscience, Harvard University, Cambridge, MA, USA
| | - David P Corey
- Department of Neurobiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
| | - Wesley P Wong
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
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34
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Zhao Y, Sarkar A, Wang X. Peptide nucleic acid based tension sensor for cellular force imaging with strong DNase resistance. Biosens Bioelectron 2020; 150:111959. [PMID: 31929090 PMCID: PMC6961813 DOI: 10.1016/j.bios.2019.111959] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/06/2019] [Accepted: 12/08/2019] [Indexed: 11/17/2022]
Abstract
DNA is a versatile biomaterial with well-defined mechanical and biochemical properties. It has been broadly adopted to synthesize tension sensors that calibrate and visualize cellular forces at the cell-matrix interface. Here we showed that DNA-based tension sensors are vulnerable to deoxyribonucleases (DNases) which cells may express on cell membrane or secret to the culture environment. These DNases can damage the sensors, lower signal-to-noise ratio or even produce false signal in cellular force imaging. To address this issue, we tested peptide nucleic acid (PNA), chemically modified RNA and their hybrids with DNA as alternative biomaterials for constructing tension sensors. Four duplexes: double-stranded DNA (dsDNA), PNA/DNA, dsRNA (modified RNA) and PNA/RNA, were tested and evaluated in terms of DNase resistance, cellular force imaging ability and material robustness. The results showed that all PNA/DNA, dsRNA and PNA/RNA exhibited strong resistance to both soluble DNase I and membrane-bound DNase on cells. However, PNA/RNA-based tension sensor had low signal-to-noise ratio in cellular force imaging, and dsRNA-based tension sensor exhibited strong non-specific signal unrelated to cellular forces. Only PNA/DNA-based tension sensor reported cellular forces with highest signal-to-noise ratio and specificity. Collectively, we confirmed that PNA/DNA hybrid is an accessible material for the synthesis of DNase-resistant tension sensor that retains the force-reporting capability and remains stable in DNase-expressing cells. This new class of tension sensors will broaden the application of tension sensors in the study of cell mechanobiology.
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Affiliation(s)
- Yuanchang Zhao
- Department of Physics and Astronomy, Iowa State University, Ames, IA, 50011, USA
| | - Anwesha Sarkar
- Department of Physics and Astronomy, Iowa State University, Ames, IA, 50011, USA
| | - Xuefeng Wang
- Department of Physics and Astronomy, Iowa State University, Ames, IA, 50011, USA; Molecular, Cellular, and Developmental Biology interdepartmental program, Iowa State University, Ames, IA, 50011, USA.
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35
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Simultaneous sensing and imaging of individual biomolecular complexes enabled by modular DNA-protein coupling. Commun Chem 2020; 3:20. [PMID: 36703465 PMCID: PMC9814868 DOI: 10.1038/s42004-020-0267-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 01/17/2020] [Indexed: 01/29/2023] Open
Abstract
Many proteins form dynamic complexes with DNA, RNA, and other proteins, which often involves protein conformational changes that are key to function. Yet, methods to probe these critical dynamics are scarce. Here we combine optical tweezers with fluorescence imaging to simultaneously monitor the conformation of individual proteins and their binding to partner proteins. Central is a protein-DNA coupling strategy, which uses exonuclease digestion and partial re-synthesis to generate DNA overhangs of different lengths, and ligation to oligo-labeled proteins. It provides up to 40 times higher coupling yields than existing protocols and enables new fluorescence-tweezers assays, which require particularly long and strong DNA handles. We demonstrate the approach by detecting the emission of a tethered fluorescent protein and of a molecular chaperone (trigger factor) complexed with its client. We conjecture that our strategy will be an important tool to study conformational dynamics within larger biomolecular complexes.
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36
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Molecular scaffolds: when DNA becomes the hardware for single-molecule investigations. Curr Opin Chem Biol 2019; 53:192-203. [DOI: 10.1016/j.cbpa.2019.09.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 09/21/2019] [Accepted: 09/24/2019] [Indexed: 01/14/2023]
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37
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Yin H, Gavriliuc M, Lin R, Xu S, Wang Y. Modulation and Visualization of EF-G Power Stroke During Ribosomal Translocation. Chembiochem 2019; 20:2927-2935. [PMID: 31194278 PMCID: PMC6888950 DOI: 10.1002/cbic.201900276] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Indexed: 11/30/2022]
Abstract
During ribosome translocation, the elongation factor EF‐G undergoes large conformational change while maintaining its contact with the moving tRNA. We previously measured a power stroke accompanying EF‐G catalysis, which was consistent with structural studies. However, the role of power stroke in translocation fidelity remains unclear. Here, we report quantitative measurements of the power strokes of structurally modified EF‐Gs by using two different techniques and reveal the correlation between power stroke and translocation efficiency and fidelity. We discovered that the reduced power stroke only lowered the percentage of translocation but did not introduce translocation error. The established force ‐structure–function correlation for EF‐G indicates that power stroke drives ribosomal translocation, but the mRNA reading frame is probably maintained by ribosome itself. Furthermore, the microscope detection method reported here can be simply implemented for other biochemical applications.
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Affiliation(s)
- Heng Yin
- Department of Chemistry, University of Houston, Houston, TX, 77204, USA
| | - Miriam Gavriliuc
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204, USA
| | - Ran Lin
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204, USA
| | - Shoujun Xu
- Department of Chemistry, University of Houston, Houston, TX, 77204, USA
| | - Yuhong Wang
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204, USA
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38
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Harrison RM, Romano F, Ouldridge TE, Louis AA, Doye JPK. Identifying Physical Causes of Apparent Enhanced Cyclization of Short DNA Molecules with a Coarse-Grained Model. J Chem Theory Comput 2019; 15:4660-4672. [PMID: 31282669 PMCID: PMC6694408 DOI: 10.1021/acs.jctc.9b00112] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
![]()
DNA
cyclization is a powerful technique to gain insight into the nature
of DNA bending. While the wormlike chain model provides a good description
of small to moderate bending fluctuations, it is expected to break
down for large bending. Recent cyclization experiments on strongly
bent shorter molecules indeed suggest enhanced flexibility over and
above that expected from the wormlike chain. Here, we use a coarse-grained
model of DNA to investigate the subtle thermodynamics of DNA cyclization
for molecules ranging from 30 to 210 base pairs. As the molecules
get shorter, we find increasing deviations between our computed equilibrium j-factor and the classic wormlike chain predictions of Shimada
and Yamakawa for a torsionally aligned looped molecule. These deviations
are due to sharp kinking, first at nicks, and only subsequently in
the body of the duplex. At the shortest lengths, substantial fraying
at the ends of duplex domains is the dominant method of relaxation.
We also estimate the dynamic j-factor measured in
recent FRET experiments. We find that the dynamic j-factor is systematically larger than its equilibrium counterpart—with
the deviation larger for shorter molecules—because not all
the stress present in the fully cyclized state is present in the transition
state. These observations are important for the interpretation of
recent cyclization experiments, suggesting that measured anomalously
high j-factors may not necessarily indicate non-WLC
behavior in the body of duplexes.
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Affiliation(s)
- Ryan M Harrison
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry , University of Oxford , South Parks Road , Oxford OX1 3QZ , United Kingdom
| | - Flavio Romano
- Dipartimento di Scienze Molecolari e Nanosistemi , Universitá Ca' Foscari Venezia , I-30123 Venezia , Italy
| | - Thomas E Ouldridge
- Imperial College Centre for Synthetic Biology and Department of Bioengineering , Imperial College London , 180 Queen's Road , London SW7 2AZ , United Kingdom
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, Department of Physics , University of Oxford , 1 Keble Road , Oxford OX1 3NP , United Kingdom
| | - Jonathan P K Doye
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry , University of Oxford , South Parks Road , Oxford OX1 3QZ , United Kingdom
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39
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Ma VPY, Salaita K. DNA Nanotechnology as an Emerging Tool to Study Mechanotransduction in Living Systems. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1900961. [PMID: 31069945 PMCID: PMC6663650 DOI: 10.1002/smll.201900961] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 04/18/2019] [Indexed: 05/24/2023]
Abstract
The ease of tailoring DNA nanostructures with sub-nanometer precision has enabled new and exciting in vivo applications in the areas of chemical sensing, imaging, and gene regulation. A new emerging paradigm in the field is that DNA nanostructures can be engineered to study molecular mechanics. This new development has transformed the repertoire of capabilities enabled by DNA to include detection of molecular forces in living cells and elucidating the fundamental mechanisms of mechanotransduction. This Review first describes fundamental aspects of force-induced melting of DNA hairpins and duplexes. This is then followed by a survey of the currently available force sensing DNA probes and different fluorescence-based force readout modes. Throughout the Review, applications of these probes in studying immune receptor signaling, including the T cell receptor and B cell receptor, as well as Notch and integrin signaling, are discussed.
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Affiliation(s)
| | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, 30322, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, 30322, USA
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40
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Zhao Y, Wetter NM, Wang X. Imaging Integrin Tension and Cellular Force at Submicron Resolution with an Integrative Tension Sensor. J Vis Exp 2019. [PMID: 31081814 DOI: 10.3791/59476] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Molecular tension transmitted by integrin-ligand bonds is the fundamental mechanical signal in the integrin pathway that plays significant roles in many cell functions and behaviors. To calibrate and image integrin tension with high force sensitivity and spatial resolution, we developed an integrative tension sensor (ITS), a DNA-based fluorescent tension sensor. The ITS is activated to fluoresce if sustaining a molecular tension, thus converting force to fluorescent signal at the molecular level. The tension threshold for ITS activation is tunable in the range of 10-60 pN that well covers the dynamic range of integrin tension in cells. On a substrate grafted with an ITS, the integrin tension of adherent cells is visualized by fluorescence and imaged at submicron resolution. The ITS is also compatible with cell structural imaging in both live cells and fixed cells. The ITS has been successfully applied to the study of platelet contraction and cell migration. This paper details the procedure for the synthesis and application of the ITS in the study of integrin-transmitted cellular force.
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Affiliation(s)
- Yuanchang Zhao
- Department of Physics and Astronomy, Iowa State University
| | | | - Xuefeng Wang
- Department of Physics and Astronomy, Molecular, Cellular, and Developmental Biology Interdepartmental Program, Iowa State University;
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41
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Jo MH, Cottle WT, Ha T. Real-Time Measurement of Molecular Tension during Cell Adhesion and Migration Using Multiplexed Differential Analysis of Tension Gauge Tethers. ACS Biomater Sci Eng 2018; 5:3856-3863. [DOI: 10.1021/acsbiomaterials.8b01216] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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42
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Zhao Y, Wang Y, Sarkar A, Wang X. Keratocytes Generate High Integrin Tension at the Trailing Edge to Mediate Rear De-adhesion during Rapid Cell Migration. iScience 2018; 9:502-512. [PMID: 30472533 PMCID: PMC6257914 DOI: 10.1016/j.isci.2018.11.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/30/2018] [Accepted: 11/07/2018] [Indexed: 01/24/2023] Open
Abstract
Rapid cell migration requires efficient rear de-adhesion. It remains undetermined whether cells mechanically detach or biochemically disassemble integrin-mediated rear adhesion sites in highly motile cells such as keratocytes. Using molecular tension sensor, we calibrated and mapped integrin tension in migrating keratocytes. Our experiments revealed that high-level integrin tension abbreviated as HIT, in the range of 50–100 pN (piconewton) and capable of rupturing integrin-ligand bonds, is exclusively and narrowly generated at cell rear margin during cell migration. Co-imaging of HIT and focal adhesions (FAs) shows that HIT is produced to mechanically peel off FAs that lag behind, and HIT intensity is correlated with the local cell retraction rate. High-level molecular tension was also consistently generated at the cell margin during artificially induced cell front retraction and during keratocyte migration mediated by biotin-streptavidin bonds. Collectively, these experiments provide direct evidence showing that migrating keratocytes concentrate force at the cell rear margin to mediate rear de-adhesion. Tension sensor (ITS) mapped and calibrated integrin tension in migratory cells High-level integrin tension (HIT) above 54 pN was observed in migrating keratocytes HIT is exclusively and narrowly localized at the cell rear margin HIT peels off focal adhesions at cell rear and facilitates keratocyte retraction
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Affiliation(s)
- Yuanchang Zhao
- Department of Physics and Astronomy, Iowa State University, 12 Physics Hall, Ames, IA 50011, USA
| | - Yongliang Wang
- Department of Physics and Astronomy, Iowa State University, 12 Physics Hall, Ames, IA 50011, USA
| | - Anwesha Sarkar
- Department of Physics and Astronomy, Iowa State University, 12 Physics Hall, Ames, IA 50011, USA
| | - Xuefeng Wang
- Department of Physics and Astronomy, Iowa State University, 12 Physics Hall, Ames, IA 50011, USA; Molecular, Cellular, and Developmental Biology Interdepartmental Program, Molecular Biology Building, Ames, IA 50011, USA.
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43
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Krupa P, Wales DJ, Sieradzan AK. Computational Studies of the Mechanical Stability for Single-Strand Break DNA. J Phys Chem B 2018; 122:8166-8173. [DOI: 10.1021/acs.jpcb.8b05417] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Paweł Krupa
- Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668 Warsaw, Poland
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - David J. Wales
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Adam K. Sieradzan
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
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44
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Engel MC, Smith DM, Jobst MA, Sajfutdinow M, Liedl T, Romano F, Rovigatti L, Louis AA, Doye JPK. Force-Induced Unravelling of DNA Origami. ACS NANO 2018; 12:6734-6747. [PMID: 29851456 DOI: 10.1021/acsnano.8b01844] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The mechanical properties of DNA nanostructures are of widespread interest as applications that exploit their stability under constant or intermittent external forces become increasingly common. We explore the force response of DNA origami in comprehensive detail by combining AFM single molecule force spectroscopy experiments with simulations using oxDNA, a coarse-grained model of DNA at the nucleotide level, to study the unravelling of an iconic origami system: the Rothemund tile. We contrast the force-induced melting of the tile with simulations of an origami 10-helix bundle. Finally, we simulate a recently proposed origami biosensor, whose function takes advantage of origami behavior under tension. We observe characteristic stick-slip unfolding dynamics in our force-extension curves for both the Rothemund tile and the helix bundle and reasonable agreement with experimentally observed rupture forces for these systems. Our results highlight the effect of design on force response: we observe regular, modular unfolding for the Rothemund tile that contrasts with strain-softening of the 10-helix bundle which leads to catastropic failure under monotonically increasing force. Further, unravelling occurs straightforwardly from the scaffold ends inward for the Rothemund tile, while the helix bundle unfolds more nonlinearly. The detailed visualization of the yielding events provided by simulation allows preferred pathways through the complex unfolding free-energy landscape to be mapped, as a key factor in determining relative barrier heights is the extensional release per base pair broken. We shed light on two important questions: how stable DNA nanostructures are under external forces and what design principles can be applied to enhance stability.
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Affiliation(s)
- Megan C Engel
- Rudolf Peierls Centre for Theoretical Physics , University of Oxford , 1 Keble Road , Oxford OX1 3NP , United Kingdom
| | - David M Smith
- Fraunhofer Institute for Cell Therapy and Immunology IZI , Perlickstraβe 1 , 04103 Leipzig , Germany
| | - Markus A Jobst
- Department für Physik , Ludwig-Maximilians-Universität Amalienstrasse 54 80799 München , Germany
| | - Martin Sajfutdinow
- Fraunhofer Institute for Cell Therapy and Immunology IZI , Perlickstraβe 1 , 04103 Leipzig , Germany
| | - Tim Liedl
- Department für Physik , Ludwig-Maximilians-Universität Amalienstrasse 54 80799 München , Germany
| | - Flavio Romano
- Dipartimento di Scienze Molecolari e Nanosistemi , Università Ca' Foscari di Venezia , Via Torino 155 , 30172 Venezia Mestre , Italy
| | - Lorenzo Rovigatti
- Rudolf Peierls Centre for Theoretical Physics , University of Oxford , 1 Keble Road , Oxford OX1 3NP , United Kingdom
- CNR-ISC , Uos Sapienza, Piazzale A. Moro 2 , 00185 Roma , Italy
- Dipartimento di Fisica , Sapienza Università di Roma , Piazzale A. Moro 2 , 00185 Roma , Italy
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics , University of Oxford , 1 Keble Road , Oxford OX1 3NP , United Kingdom
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry , University of Oxford , South Parks Road , Oxford OX1 3QZ , United Kingdom
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45
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Upadhyaya A, Nath S, Kumar S. Force-induced rupture of double-stranded DNA in the absence and presence of covalently bonded anti-tumor drugs: Insights from molecular dynamics simulations. J Chem Phys 2018; 148:215105. [DOI: 10.1063/1.5024975] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- Anurag Upadhyaya
- Department of Physics, Banaras Hindu University, Varanasi 221 005, India
| | - Shesh Nath
- Department of Physics, Banaras Hindu University, Varanasi 221 005, India
| | - Sanjay Kumar
- Department of Physics, Banaras Hindu University, Varanasi 221 005, India
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46
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Su H, Liu Z, Liu Y, Ma VPY, Blanchard A, Zhao J, Galior K, Dyer RB, Salaita K. Light-Responsive Polymer Particles as Force Clamps for the Mechanical Unfolding of Target Molecules. NANO LETTERS 2018; 18:2630-2636. [PMID: 29589759 PMCID: PMC6110664 DOI: 10.1021/acs.nanolett.8b00459] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Single-molecule force spectroscopy techniques are powerful tools for investigating the mechanical unfolding of biomolecules. However, they are limited in throughput and require dedicated instrumentation. Here, we report a force-generating particle that can unfold target molecules on-demand. The particle consists of a plasmonic nanorod core encapsulated with a thermoresponsive polymer shell. Optical heating of the nanorod leads to rapid collapse of the polymer, thus transducing light into mechanical work to unfold target molecules. The illumination tunes the duration and degree of particle collapse, thus controlling the lifetime and magnitude of applied forces. Single-molecule fluorescence imaging showed reproducible mechanical unfolding of DNA hairpins. We also demonstrate the triggering of 50 different particles in <1 min, exceeding the speed of conventional atomic force microscopy. The polymer force clamp represents a facile and bottom-up approach to force manipulation.
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Affiliation(s)
- Hanquan Su
- Department of Chemistry, Emory University, Atlanta, Georgia, United States
| | - Zheng Liu
- Department of Chemistry, Emory University, Atlanta, Georgia, United States
| | - Yang Liu
- Department of Chemistry, Emory University, Atlanta, Georgia, United States
| | - Victor Pui-Yan Ma
- Department of Chemistry, Emory University, Atlanta, Georgia, United States
| | - Aaron Blanchard
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, United States
| | - Jing Zhao
- Department of Chemistry, Emory University, Atlanta, Georgia, United States
| | - Kornelia Galior
- Department of Chemistry, Emory University, Atlanta, Georgia, United States
| | - R. Brian Dyer
- Department of Chemistry, Emory University, Atlanta, Georgia, United States
| | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, Georgia, United States
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, United States
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47
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Whitley KD, Comstock MJ, Chemla YR. Ultrashort Nucleic Acid Duplexes Exhibit Long Wormlike Chain Behavior with Force-Dependent Edge Effects. PHYSICAL REVIEW LETTERS 2018; 120:068102. [PMID: 29481284 DOI: 10.1103/physrevlett.120.068102] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 10/23/2017] [Indexed: 05/22/2023]
Abstract
Despite their importance in biology and use in nanotechnology, the elastic behavior of nucleic acids on "ultrashort" (<15 nt) length scales remains poorly understood. Here, we use optical tweezers combined with fluorescence imaging to observe directly the hybridization of oligonucleotides (7-12 nt) to a complementary strand under tension and to measure the difference in end-to-end extension between the single-stranded and duplex states. Data are consistent with long-polymer models at low forces (<8 pN) but smaller than predicted at higher forces (>8 pN), the result of the sequence-dependent duplex edge effects.
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Affiliation(s)
- Kevin D Whitley
- Center for Biophysics and Quantitative Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Matthew J Comstock
- Department of Physics, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Yann R Chemla
- Center for Biophysics and Quantitative Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Physics, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Urbana, Illinois 61801, USA
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48
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Tee S, Wang Z. How Well Can DNA Rupture DNA? Shearing and Unzipping Forces inside DNA Nanostructures. ACS OMEGA 2018; 3:292-301. [PMID: 30023776 PMCID: PMC6044922 DOI: 10.1021/acsomega.7b01692] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 12/26/2017] [Indexed: 05/26/2023]
Abstract
A purely DNA nanomachine must support internal stresses across short DNA segments with finite rigidity, producing effects that can be qualitatively very different from experimental observations of isolated DNA in fixed-force ensembles. In this article, computational simulations are used to study how well the rigidity of a driving DNA duplex can rupture a double-stranded DNA target into single-stranded segments and how well this stress can discriminate between unzipping or shearing geometries. This discrimination is found to be maximized at an optimal length but deteriorates as the driving duplex is either lengthened or shortened. This differs markedly from a fixed-force ensemble and has implications for the design parameters and limitations of dynamic DNA nanomachines.
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49
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Garai A, Mogurampelly S, Bag S, Maiti PK. Overstretching of B-DNA with various pulling protocols: Appearance of structural polymorphism and S-DNA. J Chem Phys 2017; 147:225102. [DOI: 10.1063/1.4991862] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Ashok Garai
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
- Department of Physics, The LNM Institute of Information Technology, Jamdoli, Jaipur 302031, India
| | - Santosh Mogurampelly
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Saientan Bag
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Prabal K. Maiti
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
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50
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Singh AR, Granek R. Manipulation of double-stranded DNA melting by force. Phys Rev E 2017; 96:032417. [PMID: 29347050 DOI: 10.1103/physreve.96.032417] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Indexed: 01/03/2023]
Abstract
By integrating elasticity-as described by the Gaussian network model-with bond binding energies that distinguish between different base-pair identities and stacking configurations, we study the force induced melting of a double-stranded DNA (dsDNA). Our approach is a generalization of our previous study of thermal dsDNA denaturation [J. Chem. Phys. 145, 144101 (2016)JCPSA60021-960610.1063/1.4964285] to that induced by force at finite temperatures. It allows us to obtain semimicroscopic information about the opening of the chain, such as whether the dsDNA opens from one of the ends or from the interior, forming an internal bubble. We study different types of force manipulation: (i) "end unzipping," with force acting at a single end base pair perpendicular to the helix, (ii) "midunzipping," with force acting at a middle base pair perpendicular to the helix, and (iii) "end shearing," where the force acts at opposite ends along the helix. By monitoring the free-energy landscape and probability distribution of intermediate denaturation states, we show that different dominant intermediate states are stabilized depending on the type of force manipulation used. In particular, the bubble state of the sequence L60B36, which we have previously found to be a stable state during thermal denaturation, is absent for end unzipping and end shearing, whereas very similar bubbles are stabilized by midunzipping, or when the force location is near the middle of the chain. Ours results offer a simple tool for stabilizing bubbles and loops using force manipulations at different temperatures, and may implicate on the mechanism in which DNA enzymes or motors open regions of the chain.
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Affiliation(s)
- Amit Raj Singh
- The Stella and Avram Goren-Goldstein Department of Biotechnology Engineering, Ben-Gurion University of The Negev, Beer Sheva 84105, Israel
| | - Rony Granek
- The Stella and Avram Goren-Goldstein Department of Biotechnology Engineering, Ben-Gurion University of The Negev, Beer Sheva 84105, Israel.,The Ilse Katz Institute for Meso and Nanoscale Science and Technology, Ben-Gurion University of The Negev, Beer Sheva 84105, Israel
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