1
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Niraula G, Pyne A, Wang X. Develop Tandem Tension Sensor to Gauge Integrin-Transmitted Molecular Forces. ACS Sens 2024; 9:3660-3670. [PMID: 38968930 PMCID: PMC11287754 DOI: 10.1021/acssensors.4c00756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/11/2024] [Accepted: 06/27/2024] [Indexed: 07/07/2024]
Abstract
DNA-based tension sensors have innovated the imaging and calibration of mechanosensitive receptor-transmitted molecular forces, such as integrin tensions. However, these sensors mainly serve as binary reporters, only indicating if molecular forces exceed one predefined threshold. Here, we have developed tandem tension sensor (TTS), which comprises two consecutive force-sensing units, each with unique force detection thresholds and distinct fluorescence spectra, thereby enabling the quantification of molecular forces with dual reference levels. With TTS, we revealed that vinculin is not required for transmitting integrin tensions at approximately 10 pN (piconewtons) but is essential for elevating integrin tensions beyond 20 pN in focal adhesions (FAs). Such high tensions have emerged during the early stage of FA formation. TTS also successfully detected changes in integrin tensions in response to disrupted actin formation, inhibited myosin activity, and tuned substrate elasticity. We also applied TTS to examine integrin tensions in platelets and revealed two force regimes, with integrin tensions surpassing 20 pN at cell central regions and 13-20 pN integrin tensions at the cell edge. Overall, TTS, especially the construct consisting of a hairpin DNA (13 pN opening force) and a shearing DNA (20 pN opening force), stands as a valuable tool for the quantification of receptor-transmitted molecular forces within living cells.
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Affiliation(s)
- Gopal Niraula
- Department
of Physics and Astronomy, Iowa State University, Ames, Iowa 50011, United States
| | - Arghajit Pyne
- Research
Division in Hoxworth Center, College of Medicine, University of Cincinnati, Cincinnati, Ohio 45219, United States
| | - Xuefeng Wang
- Research
Division in Hoxworth Center, College of Medicine, University of Cincinnati, Cincinnati, Ohio 45219, United States
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2
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van Galen M, Bok A, Peshkovsky T, van der Gucht J, Albada B, Sprakel J. De novo DNA-based catch bonds. Nat Chem 2024:10.1038/s41557-024-01571-4. [PMID: 38914727 DOI: 10.1038/s41557-024-01571-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 06/06/2024] [Indexed: 06/26/2024]
Abstract
All primary chemical interactions weaken under mechanical stress, which imposes fundamental mechanical limits on the materials constructed from them. Biological materials combine plasticity with strength, for which nature has evolved a unique solution-catch bonds, supramolecular interactions that strengthen under tension. Biological catch bonds use force-gated conformational switches to convert weak bonds into strong ones. So far, catch bonds remain exclusive to nature, leaving their potential as mechanoadaptive elements in synthetic systems untapped. Here we report the design and realization of artificial catch bonds. Starting from a minimal set of thermodynamic design requirements, we created a molecular motif capable of catch bonding. It consists of a DNA duplex featuring a cryptic domain that unfolds under tension to strengthen the interaction. We show that these catch bonds recreate force-enhanced rolling adhesion, a hallmark feature of biological catch bonds in bacteria and leukocytes. This Article introduces catch bonds into the synthetic domain, and could lead to the creation of artificial catch-bonded materials.
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Affiliation(s)
- Martijn van Galen
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, Netherlands
- Physical Chemistry and Soft Matter, Wageningen University & Research, Wageningen, Netherlands
| | - Annemarie Bok
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, Netherlands
| | - Taieesa Peshkovsky
- Physical Chemistry and Soft Matter, Wageningen University & Research, Wageningen, Netherlands
| | - Jasper van der Gucht
- Physical Chemistry and Soft Matter, Wageningen University & Research, Wageningen, Netherlands
| | - Bauke Albada
- Laboratory of Organic Chemistry, Wageningen University & Research, Wageningen, Netherlands.
| | - Joris Sprakel
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, Netherlands.
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3
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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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4
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Huang Y, Chen T, Chen X, Chen X, Zhang J, Liu S, Lu M, Chen C, Ding X, Yang C, Huang R, Song Y. Decoding Biomechanical Cues Based on DNA Sensors. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2310330. [PMID: 38185740 DOI: 10.1002/smll.202310330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/18/2023] [Indexed: 01/09/2024]
Abstract
Biological systems perceive and respond to mechanical forces, generating mechanical cues to regulate life processes. Analyzing biomechanical forces has profound significance for understanding biological functions. Therefore, a series of molecular mechanical techniques have been developed, mainly including single-molecule force spectroscopy, traction force microscopy, and molecular tension sensor systems, which provide indispensable tools for advancing the field of mechanobiology. DNA molecules with a programmable structure and well-defined mechanical characteristics have attached much attention to molecular tension sensors as sensing elements, and are designed for the study of biomechanical forces to present biomechanical information with high sensitivity and resolution. In this work, a comprehensive overview of molecular mechanical technology is presented, with a particular focus on molecular tension sensor systems, specifically those based on DNA. Finally, the future development and challenges of DNA-based molecular tension sensor systems are looked upon.
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Affiliation(s)
- Yihao Huang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Ting Chen
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Xiaodie Chen
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Ximing Chen
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Jialu Zhang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Sinong Liu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Menghao Lu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Chong Chen
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Xiangyu Ding
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
- Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Ruiyun Huang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Yanling Song
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, 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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Bauer MS, Gruber S, Hausch A, Melo MCR, Gomes PSFC, Nicolaus T, Milles LF, Gaub HE, Bernardi RC, Lipfert J. Single-molecule force stability of the SARS-CoV-2-ACE2 interface in variants-of-concern. NATURE NANOTECHNOLOGY 2024; 19:399-405. [PMID: 38012274 DOI: 10.1038/s41565-023-01536-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 09/26/2023] [Indexed: 11/29/2023]
Abstract
Mutations in SARS-CoV-2 have shown effective evasion of population immunity and increased affinity to the cellular receptor angiotensin-converting enzyme 2 (ACE2). However, in the dynamic environment of the respiratory tract, forces act on the binding partners, which raises the question of whether not only affinity but also force stability of the SARS-CoV-2-ACE2 interaction might be a selection factor for mutations. Using magnetic tweezers, we investigate the impact of amino acid substitutions in variants of concern (Alpha, Beta, Gamma and Delta) and on force-stability and bond kinetic of the receptor-binding domain-ACE2 interface at a single-molecule resolution. We find a higher affinity for all of the variants of concern (>fivefold) compared with the wild type. In contrast, Alpha is the only variant of concern that shows higher force stability (by 17%) compared with the wild type. Using molecular dynamics simulations, we rationalize the mechanistic molecular origins of this increase in force stability. Our study emphasizes the diversity of contributions to the transmissibility of variants and establishes force stability as one of the several factors for fitness. Understanding fitness advantages opens the possibility for the prediction of probable mutations, allowing a rapid adjustment of therapeutics, vaccines and intervention measures.
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Affiliation(s)
- Magnus S Bauer
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Sophia Gruber
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany
| | - Adina Hausch
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany
- Center for Protein Assemblies, TUM School of Natural Sciences, Technical University of Munich, Munich, Germany
| | | | | | - Thomas Nicolaus
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany
| | - Lukas F Milles
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Hermann E Gaub
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany
| | | | - Jan Lipfert
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Munich, Germany.
- Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands.
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7
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Horst M, Meisner J, Yang J, Kouznetsova TB, Craig SL, Martínez TJ, Xia Y. Mechanochemistry of Pterodactylane. J Am Chem Soc 2024; 146:884-891. [PMID: 38131266 DOI: 10.1021/jacs.3c11293] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Pterodactylane is a [4]-ladderane with substituents on the central rung. Comparing the mechanochemistry of the [4]-ladderane structure when pulled from the central rung versus the end rung revealed a striking difference in the threshold force of mechanoactivation: the threshold force is dramatically lowered from 1.9 nN when pulled on the end rung to 0.7 nN when pulled on the central rung. We investigated the bicyclic products formed from the mechanochemical activation of pterodactylane experimentally and computationally, which are distinct from the mechanochemical products of ladderanes being activated from the end rung. We compared the products of pterodactylane's mechanochemical and thermal activation to reveal differences and similarities in the mechanochemical and thermal pathways of pterodactylane transformation. Interestingly, we also discovered the presence of elementary steps that are accelerated or suppressed by force within the same mechanochemical reaction of pterodactylane, suggesting rich mechanochemical manifolds of multicyclic structures. We rationalized the greatly enhanced mechanochemical reactivity of the central rung of pterodactylane and discovered force-free ground state bond length to be a good low-cost predictor of the threshold force for cyclobutane-based mechanophores. These findings advance our understanding of mechanochemical reactivities and pathways, and they will guide future designs of mechanophores with low threshold forces to facilitate their applications in force-responsive materials.
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Affiliation(s)
- Matías Horst
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Jan Meisner
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Institute for Physical Chemistry, Department of Chemistry, Heinrich-Heine-Universität Düsseldorf, Düsseldorf D-40225, Germany
| | - Jinghui Yang
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Tatiana B Kouznetsova
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Stephen L Craig
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Todd J Martínez
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Yan Xia
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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8
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Li R, Madhvacharyula AS, Du Y, Adepu HK, Choi JH. Mechanics of dynamic and deformable DNA nanostructures. Chem Sci 2023; 14:8018-8046. [PMID: 37538812 PMCID: PMC10395309 DOI: 10.1039/d3sc01793a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/05/2023] [Indexed: 08/05/2023] Open
Abstract
In DNA nanotechnology, DNA molecules are designed, engineered, and assembled into arbitrary-shaped architectures with predesigned functions. Static DNA assemblies often have delicate designs with structural rigidity to overcome thermal fluctuations. Dynamic structures reconfigure in response to external cues, which have been explored to create functional nanodevices for environmental sensing and other applications. However, the precise control of reconfiguration dynamics has been a challenge due partly to flexible single-stranded DNA connections between moving parts. Deformable structures are special dynamic constructs with deformation on double-stranded parts and single-stranded hinges during transformation. These structures often have better control in programmed deformation. However, related deformability and mechanics including transformation mechanisms are not well understood or documented. In this review, we summarize the development of dynamic and deformable DNA nanostructures from a mechanical perspective. We present deformation mechanisms such as single-stranded DNA hinges with lock-and-release pairs, jack edges, helicity modulation, and external loading. Theoretical and computational models are discussed for understanding their associated deformations and mechanics. We elucidate the pros and cons of each model and recommend design processes based on the models. The design guidelines should be useful for those who have limited knowledge in mechanics as well as expert DNA designers.
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Affiliation(s)
- Ruixin Li
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Anirudh S Madhvacharyula
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Yancheng Du
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Harshith K Adepu
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Jong Hyun Choi
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
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9
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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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10
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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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11
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Shukla S, Troitskaia A, Swarna N, Maity BK, Tjioe M, Bookwalter CS, Trybus KM, Chemla YR, Selvin PR. High-throughput force measurement of individual kinesin-1 motors during multi-motor transport. NANOSCALE 2022; 14:12463-12475. [PMID: 35980233 PMCID: PMC9983033 DOI: 10.1039/d2nr01701f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Molecular motors often work in teams to move a cellular cargo. Yet measuring the forces exerted by each motor is challenging. Using a sensor made with denatured ssDNA and multi-color fluorescence, we measured picoNewtons of forces and nanometer distances exerted by individual constrained kinesin-1 motors acting together while driving a common microtubule in vitro. We find that kinesins primarily exerted less than 1 pN force, even while the microtubule is bypassing artificial obstacles of 20-100 nanometer size. Occasionally, individual forces increase upon encountering obstacles, although at other times they do not, with the cargo continuing in a directional manner. Our high-throughput technique, which can measure forces by many motors simultaneously, is expected to be useful for many different types of molecular motors.
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Affiliation(s)
- Saurabh Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
| | - Alice Troitskaia
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Nikhila Swarna
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Barun Kumar Maity
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Marco Tjioe
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Carol S Bookwalter
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, VT, USA
| | - Kathleen M Trybus
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, VT, USA
| | - Yann R Chemla
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Paul R Selvin
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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12
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Hübner K, Raab M, Bohlen J, Bauer J, Tinnefeld P. Salt-induced conformational switching of a flat rectangular DNA origami structure. NANOSCALE 2022; 14:7898-7905. [PMID: 35587049 DOI: 10.1039/d1nr07793g] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A rectangular DNA origami structure is one of the most studied and often used motif for applications in DNA nanotechnology. Here, we present two assays to study structural changes in DNA nanostructures and reveal a reversible rolling-up of the rectangular DNA origami structure induced by bivalent cations such as magnesium or calcium. First, we applied one-color and two-color superresolution DNA-PAINT with protruding strands along the long edges of the DNA origami rectangle. At increasing salt concentration, a single line instead of two lines is observed as a first indicator of rolling-up. Two-color measurements also revealed different conformations with parallel and angled edges. Second, we placed a gold nanoparticle and a dye molecule at different positions on the DNA origami structure. Distance dependent fluorescence quenching by the nanoparticle reports on dynamic transitions as well as it provides evidence that the rolling-up occurs preferentially along the diagonal of the DNA origami rectangle. The results will be helpful to test DNA structural models and the assays presented will be useful to study further structural transitions in DNA nanotechnology.
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Affiliation(s)
- Kristina Hübner
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377 München, Germany.
| | - Mario Raab
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377 München, Germany.
| | - Johann Bohlen
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377 München, Germany.
| | - Julian Bauer
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377 München, Germany.
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377 München, Germany.
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13
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Molecular sensors for detection of tumor-stroma crosstalk. Adv Cancer Res 2022; 154:47-91. [PMID: 35459472 DOI: 10.1016/bs.acr.2022.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In most solid tumors, malignant cells coexist with non-cancerous host tissue comprised of a variety of extracellular matrix components and cell types, notably fibroblasts, immune cells, and endothelial cells. It is becoming increasingly evident that the non-cancerous host tissue, often referred to as the tumor stroma or the tumor microenvironment, wields tremendous influence in the proliferation, survival, and metastatic ability of cancer cells. The tumor stroma has an active biological role in the transmission of signals, such as growth factors and chemokines that activate oncogenic signaling pathways by autocrine and paracrine mechanisms. Moreover, the constituents of the stroma define the mechanical properties and the physical features of solid tumors, which influence cancer progression and response to therapy. Inspired by the emerging importance of tumor-stroma crosstalk and oncogenic physical forces, numerous biosensors, or advanced imaging and analysis techniques have been developed and applied to investigate complex and challenging questions in cancer research. These techniques facilitate measurements and biological readouts at scales ranging from subcellular to tissue-level with unprecedented level of spatial and temporal precision. Here we examine the application of biosensor technology for studying the complex and dynamic multiscale interactions of the tumor-host system.
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Abstract
Cellular processes and functions can be regulated by mechanical forces. Nanodevices that can measure and manipulate these forces are critical tools in chemical and cellular biology. Synthetic DNA oligonucleotides have been used to develop a wide range of powerful nanodevices due to their programmable nature and precise and predictable self-assembly. In recent years, various types of DNA-based mechanical nanodevices have been engineered for studying molecular-level forces. With the help of these nanodevices, our understanding of cellular responses to physical forces has been significantly advanced. In this article, we have reviewed some recent developments in DNA-based mechanical sensors and regulators for application in the characterization of cellular biomechanics and the manipulation of cellular morphology, motion and other functions. The design principles discussed in this article can be further used to inspire other types of powerful DNA-based mechanical nanodevices.
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Affiliation(s)
- Qian Tian
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
| | - Puspam Keshri
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
| | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
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15
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Sun W, Gao X, Lei H, Wang W, Cao Y. Biophysical Approaches for Applying and Measuring Biological Forces. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2105254. [PMID: 34923777 PMCID: PMC8844594 DOI: 10.1002/advs.202105254] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Indexed: 05/13/2023]
Abstract
Over the past decades, increasing evidence has indicated that mechanical loads can regulate the morphogenesis, proliferation, migration, and apoptosis of living cells. Investigations of how cells sense mechanical stimuli or the mechanotransduction mechanism is an active field of biomaterials and biophysics. Gaining a further understanding of mechanical regulation and depicting the mechanotransduction network inside cells require advanced experimental techniques and new theories. In this review, the fundamental principles of various experimental approaches that have been developed to characterize various types and magnitudes of forces experienced at the cellular and subcellular levels are summarized. The broad applications of these techniques are introduced with an emphasis on the difficulties in implementing these techniques in special biological systems. The advantages and disadvantages of each technique are discussed, which can guide readers to choose the most suitable technique for their questions. A perspective on future directions in this field is also provided. It is anticipated that technical advancement can be a driving force for the development of mechanobiology.
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Affiliation(s)
- Wenxu Sun
- School of SciencesNantong UniversityNantong226019P. R. China
| | - Xiang Gao
- Key Laboratory of Intelligent Optical Sensing and IntegrationNational Laboratory of Solid State Microstructureand Department of PhysicsCollaborative Innovation Center of Advanced MicrostructuresNanjing UniversityNanjing210023P. R. China
- Institute of Brain ScienceNanjing UniversityNanjing210023P. R. China
| | - Hai Lei
- Key Laboratory of Intelligent Optical Sensing and IntegrationNational Laboratory of Solid State Microstructureand Department of PhysicsCollaborative Innovation Center of Advanced MicrostructuresNanjing UniversityNanjing210023P. R. China
- Institute of Brain ScienceNanjing UniversityNanjing210023P. R. China
- Chemistry and Biomedicine Innovation CenterNanjing UniversityNanjing210023P. R. China
| | - Wei Wang
- Key Laboratory of Intelligent Optical Sensing and IntegrationNational Laboratory of Solid State Microstructureand Department of PhysicsCollaborative Innovation Center of Advanced MicrostructuresNanjing UniversityNanjing210023P. R. China
- Institute of Brain ScienceNanjing UniversityNanjing210023P. R. China
| | - Yi Cao
- Key Laboratory of Intelligent Optical Sensing and IntegrationNational Laboratory of Solid State Microstructureand Department of PhysicsCollaborative Innovation Center of Advanced MicrostructuresNanjing UniversityNanjing210023P. R. China
- Institute of Brain ScienceNanjing UniversityNanjing210023P. R. China
- MOE Key Laboratory of High Performance Polymer Materials and TechnologyDepartment of Polymer Science & EngineeringCollege of Chemistry & Chemical EngineeringNanjing UniversityNanjing210023P. R. China
- Chemistry and Biomedicine Innovation CenterNanjing UniversityNanjing210023P. R. China
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16
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Baek KY, Kim S, Koh HR. Molecular Tension Probes to Quantify Cell-Generated Mechanical Forces. Mol Cells 2022; 45:26-32. [PMID: 35114645 PMCID: PMC8819489 DOI: 10.14348/molcells.2022.2049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/10/2022] [Indexed: 11/27/2022] Open
Abstract
Living cells generate, sense, and respond to mechanical forces through their interaction with neighboring cells or extracellular matrix, thereby regulating diverse cellular processes such as growth, motility, differentiation, and immune responses. Dysregulation of mechanosensitive signaling pathways is found associated with the development and progression of various diseases such as cancer. Yet, little is known about the mechanisms behind mechano-regulation, largely due to the limited availability of tools to study it at the molecular level. The recent development of molecular tension probes allows measurement of cellular forces exerted by single ligandreceptor interaction, which has helped in revealing the hitherto unknown mechanistic details of various mechanosensitive processes in living cells. Here, we provide an introductory overview of two methods based on molecular tension probes, tension gauge tether (TGT), and molecular tension fluorescence microscopy (MTFM). TGT utilizes the irreversible rupture of double-stranded DNA tether upon application of force in the piconewton (pN) range, whereas MTFM utilizes the reversible extension of molecular springs such as polymer or single-stranded DNA hairpin under applied pN forces. Specifically, the underlying principle of how molecular tension probes measure cell-generated mechanical forces and their applications to mechanosensitive biological processes are described.
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Affiliation(s)
- Kyung Yup Baek
- Department of Chemistry, Chung-Ang University, Seoul 06974, Korea
| | - Seohyun Kim
- Department of Chemistry, Chung-Ang University, Seoul 06974, Korea
| | - Hye Ran Koh
- Department of Chemistry, Chung-Ang University, Seoul 06974, Korea
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17
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Sarkar A. Biosensing, Characterization of Biosensors, and Improved Drug Delivery Approaches Using Atomic Force Microscopy: A Review. FRONTIERS IN NANOTECHNOLOGY 2022. [DOI: 10.3389/fnano.2021.798928] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Since its invention, atomic force microscopy (AFM) has come forth as a powerful member of the “scanning probe microscopy” (SPM) family and an unparallel platform for high-resolution imaging and characterization for inorganic and organic samples, especially biomolecules, biosensors, proteins, DNA, and live cells. AFM characterizes any sample by measuring interaction force between the AFM cantilever tip (the probe) and the sample surface, and it is advantageous over other SPM and electron micron microscopy techniques as it can visualize and characterize samples in liquid, ambient air, and vacuum. Therefore, it permits visualization of three-dimensional surface profiles of biological specimens in the near-physiological environment without sacrificing their native structures and functions and without using laborious sample preparation protocols such as freeze-drying, staining, metal coating, staining, or labeling. Biosensors are devices comprising a biological or biologically extracted material (assimilated in a physicochemical transducer) that are utilized to yield electronic signal proportional to the specific analyte concentration. These devices utilize particular biochemical reactions moderated by isolated tissues, enzymes, organelles, and immune system for detecting chemical compounds via thermal, optical, or electrical signals. Other than performing high-resolution imaging and nanomechanical characterization (e.g., determining Young’s modulus, adhesion, and deformation) of biosensors, AFM cantilever (with a ligand functionalized tip) can be transformed into a biosensor (microcantilever-based biosensors) to probe interactions with a particular receptors of choice on live cells at a single-molecule level (using AFM-based single-molecule force spectroscopy techniques) and determine interaction forces and binding kinetics of ligand receptor interactions. Targeted drug delivery systems or vehicles composed of nanoparticles are crucial in novel therapeutics. These systems leverage the idea of targeted delivery of the drug to the desired locations to reduce side effects. AFM is becoming an extremely useful tool in figuring out the topographical and nanomechanical properties of these nanoparticles and other drug delivery carriers. AFM also helps determine binding probabilities and interaction forces of these drug delivery carriers with the targeted receptors and choose the better agent for drug delivery vehicle by introducing competitive binding. In this review, we summarize contributions made by us and other researchers so far that showcase AFM as biosensors, to characterize other sensors, to improve drug delivery approaches, and to discuss future possibilities.
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18
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Wang C, O'Hagan MP, Li Z, Zhang J, Ma X, Tian H, Willner I. Photoresponsive DNA materials and their applications. Chem Soc Rev 2022; 51:720-760. [PMID: 34985085 DOI: 10.1039/d1cs00688f] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Photoresponsive nucleic acids attract growing interest as functional constituents in materials science. Integration of photoisomerizable units into DNA strands provides an ideal handle for the reversible reconfiguration of nucleic acid architectures by light irradiation, triggering changes in the chemical and structural properties of the nanostructures that can be exploited in the development of photoresponsive functional devices such as machines, origami structures and ion channels, as well as environmentally adaptable 'smart' materials including nanoparticle aggregates and hydrogels. Moreover, photoresponsive DNA components allow control over the composition of dynamic supramolecular ensembles that mimic native networks. Beyond this, the modification of nucleic acids with photosensitizer functionality enables these biopolymers to act as scaffolds for spatial organization of electron transfer reactions mimicking natural photosynthesis. This review provides a comprehensive overview of these exciting developments in the design of photoresponsive DNA materials, and showcases a range of applications in catalysis, sensing and drug delivery/release. The key challenges facing the development of the field in the coming years are addressed, and exciting emergent research directions are identified.
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Affiliation(s)
- Chen Wang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Michael P O'Hagan
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Ziyuan Li
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Junji Zhang
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Xiang Ma
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - He Tian
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Itamar Willner
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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19
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Beshay PE, Cortes-Medina MG, Menyhert MM, Song JW. The biophysics of cancer: emerging insights from micro- and nanoscale tools. ADVANCED NANOBIOMED RESEARCH 2022; 2:2100056. [PMID: 35156093 PMCID: PMC8827905 DOI: 10.1002/anbr.202100056] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Cancer is a complex and dynamic disease that is aberrant both biologically and physically. There is growing appreciation that physical abnormalities with both cancer cells and their microenvironment that span multiple length scales are important drivers for cancer growth and metastasis. The scope of this review is to highlight the key advancements in micro- and nano-scale tools for delineating the cause and consequences of the aberrant physical properties of tumors. We focus our review on three important physical aspects of cancer: 1) solid mechanical properties, 2) fluid mechanical properties, and 3) mechanical alterations to cancer cells. Beyond posing physical barriers to the delivery of cancer therapeutics, these properties are also known to influence numerous biological processes, including cancer cell invasion and migration leading to metastasis, and response and resistance to therapy. We comment on how micro- and nanoscale tools have transformed our fundamental understanding of the physical dynamics of cancer progression and their potential for bridging towards future applications at the interface of oncology and physical sciences.
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Affiliation(s)
- Peter E Beshay
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210
| | | | - Miles M Menyhert
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210
| | - Jonathan W Song
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210
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20
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Korobchevskaya K, Colin-York H, Barbieri L, Fritzsche M. Extended mechanical force measurements using structured illumination microscopy. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2021; 379:20200151. [PMID: 33896200 PMCID: PMC7612033 DOI: 10.1098/rsta.2020.0151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/11/2021] [Indexed: 06/12/2023]
Abstract
Quantifying cell generated mechanical forces is key to furthering our understanding of mechanobiology. Traction force microscopy (TFM) is one of the most broadly applied force probing technologies, but its sensitivity is strictly dependent on the spatio-temporal resolution of the underlying imaging system. In previous works, it was demonstrated that increased sampling densities of cell derived forces permitted by super-resolution fluorescence imaging enhanced the sensitivity of the TFM method. However, these recent advances to TFM based on super-resolution techniques were limited to slow acquisition speeds and high illumination powers. Here, we present three novel TFM approaches that, in combination with total internal reflection, structured illumination microscopy and astigmatism, improve the spatial and temporal performance in either two-dimensional or three-dimensional mechanical force quantification, while maintaining low illumination powers. These three techniques can be straightforwardly implemented on a single optical set-up offering a powerful platform to provide new insights into the physiological force generation in a wide range of biological studies. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 1)'.
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Affiliation(s)
- Kseniya Korobchevskaya
- Kennedy Institute for Rheumatology, Roosevelt Drive, University of Oxford, Oxford, OX3 7LF, United Kingdom
| | - Huw Colin-York
- Kennedy Institute for Rheumatology, Roosevelt Drive, University of Oxford, Oxford, OX3 7LF, United Kingdom
| | - Liliana Barbieri
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford. OX3 9DS, United Kingdom
| | - Marco Fritzsche
- Kennedy Institute for Rheumatology, Roosevelt Drive, University of Oxford, Oxford, OX3 7LF, United Kingdom
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford. OX3 9DS, United Kingdom
- Rosalind Franklin Institute, Harwell Campus, Didcot, OX11 0FA, United Kingdom
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21
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Frutiger A, Tanno A, Hwu S, Tiefenauer RF, Vörös J, Nakatsuka N. Nonspecific Binding-Fundamental Concepts and Consequences for Biosensing Applications. Chem Rev 2021; 121:8095-8160. [PMID: 34105942 DOI: 10.1021/acs.chemrev.1c00044] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nature achieves differentiation of specific and nonspecific binding in molecular interactions through precise control of biomolecules in space and time. Artificial systems such as biosensors that rely on distinguishing specific molecular binding events in a sea of nonspecific interactions have struggled to overcome this issue. Despite the numerous technological advancements in biosensor technologies, nonspecific binding has remained a critical bottleneck due to the lack of a fundamental understanding of the phenomenon. To date, the identity, cause, and influence of nonspecific binding remain topics of debate within the scientific community. In this review, we discuss the evolution of the concept of nonspecific binding over the past five decades based upon the thermodynamic, intermolecular, and structural perspectives to provide classification frameworks for biomolecular interactions. Further, we introduce various theoretical models that predict the expected behavior of biosensors in physiologically relevant environments to calculate the theoretical detection limit and to optimize sensor performance. We conclude by discussing existing practical approaches to tackle the nonspecific binding challenge in vitro for biosensing platforms and how we can both address and harness nonspecific interactions for in vivo systems.
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Affiliation(s)
- Andreas Frutiger
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Alexander Tanno
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Stephanie Hwu
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Raphael F Tiefenauer
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - János Vörös
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Nako Nakatsuka
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
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22
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Zhang Y, Wang Z, Kouznetsova TB, Sha Y, Xu E, Shannahan L, Fermen-Coker M, Lin Y, Tang C, Craig SL. Distal conformational locks on ferrocene mechanophores guide reaction pathways for increased mechanochemical reactivity. Nat Chem 2020; 13:56-62. [DOI: 10.1038/s41557-020-00600-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 11/03/2020] [Indexed: 12/14/2022]
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23
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Tu Y, Wang X. Recent Advances in Cell Adhesive Force Microscopy. SENSORS (BASEL, SWITZERLAND) 2020; 20:E7128. [PMID: 33322701 PMCID: PMC7763046 DOI: 10.3390/s20247128] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/03/2020] [Accepted: 12/07/2020] [Indexed: 12/22/2022]
Abstract
Cell adhesive force, exerting on the local matrix or neighboring cells, plays a critical role in regulating many cell functions and physiological processes. In the past four decades, significant efforts have been dedicated to cell adhesive force detection, visualization and quantification. A recent important methodological advancement in cell adhesive force visualization is to adopt force-to-fluorescence conversion instead of force-to-substrate strain conversion, thus greatly improving the sensitivity and resolution of force imaging. This review summarizes the recent development of force imaging techniques (collectively termed as cell adhesive force microscopy or CAFM here), with a particular focus on the improvement of CAFM's spatial resolution and the biomaterial choices for constructing the tension sensors used in force visualization. This review also highlights the importance of DNA-based tension sensors in cell adhesive force imaging and the recent breakthrough in the development of super-resolution CAFM.
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Affiliation(s)
- Ying Tu
- 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 Development Biology Interdepartmental Program, Iowa State University, Ames, IA 50011, USA
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24
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Yin F, Li M, Mao X, Li F, Xiang X, Li Q, Wang L, Zuo X, Fan C, Zhu Y. DNA Framework-Based Topological Cell Sorters. Angew Chem Int Ed Engl 2020; 59:10406-10410. [PMID: 32187784 DOI: 10.1002/anie.202002020] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/02/2020] [Indexed: 12/20/2022]
Abstract
Molecular recognition in cell biological process is characterized with specific locks-and-keys interactions between ligands and receptors, which are ubiquitously distributed on cell membrane with topological clustering. Few topologically-engineered ligand systems enable the exploration of the binding strength between ligand-receptor topological organization. Herein, we generate topologically controlled ligands by developing a family of tetrahedral DNA frameworks (TDFs), so the multiple ligands are stoichiometrically and topologically arranged. This topological control of multiple ligands changes the nature of the molecular recognition by inducing the receptor clustering, so the binding strength is significantly improved (ca. 10-fold). The precise engineering of topological complexes formed by the TDFs are readily translated into effective binding control for cell patterning and binding strength control of cells for cell sorting. This work paves the way for the development of versatile design of topological ligands.
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Affiliation(s)
- Fangfei Yin
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Min Li
- Institute of Molecular Medicine, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Fan Li
- Institute of Molecular Medicine, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xuelin Xiang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Qian Li
- Institute of Molecular Medicine, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Lihua Wang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China.,Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Chunhai Fan
- Institute of Molecular Medicine, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Ying Zhu
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
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25
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Yin F, Li M, Mao X, Li F, Xiang X, Li Q, Wang L, Zuo X, Fan C, Zhu Y. DNA Framework‐Based Topological Cell Sorters. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202002020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Fangfei Yin
- Division of Physical Biology CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Min Li
- Institute of Molecular Medicine Renji Hospital School of Medicine and School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules Shanghai Jiao Tong University Shanghai 200127 China
| | - Xiuhai Mao
- Institute of Molecular Medicine Renji Hospital School of Medicine and School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules Shanghai Jiao Tong University Shanghai 200127 China
| | - Fan Li
- Institute of Molecular Medicine Renji Hospital School of Medicine and School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules Shanghai Jiao Tong University Shanghai 200127 China
| | - Xuelin Xiang
- Institute of Molecular Medicine Renji Hospital School of Medicine and School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules Shanghai Jiao Tong University Shanghai 200127 China
| | - Qian Li
- Institute of Molecular Medicine Renji Hospital School of Medicine and School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules Shanghai Jiao Tong University Shanghai 200127 China
| | - Lihua Wang
- Division of Physical Biology CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
- University of Chinese Academy of Sciences Beijing 100049 China
- Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai 201210 China
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering East China Normal University Shanghai 200241 China
| | - Xiaolei Zuo
- Institute of Molecular Medicine Renji Hospital School of Medicine and School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules Shanghai Jiao Tong University Shanghai 200127 China
| | - Chunhai Fan
- Institute of Molecular Medicine Renji Hospital School of Medicine and School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules Shanghai Jiao Tong University Shanghai 200127 China
| | - Ying Zhu
- Division of Physical Biology CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
- University of Chinese Academy of Sciences Beijing 100049 China
- Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai 201210 China
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Yasunaga A, Murad Y, Li ITS. Quantifying molecular tension-classifications, interpretations and limitations of force sensors. Phys Biol 2019; 17:011001. [PMID: 31387091 DOI: 10.1088/1478-3975/ab38ff] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Molecular force sensors (MFSs) have grown to become an important tool to study the mechanobiology of cells and tissues. They provide a minimally invasive means to optically report mechanical interactions at the molecular level. One of the challenges in molecular force sensor studies is the interpretation of the fluorescence readout. In this review, we divide existing MFSs into three classes based on the force-sensing mechanism (reversibility) and the signal output (analog/digital). From single-molecule force spectroscopy (SMFS) perspectives, we provided a critical discussion on how the sensors respond to force and how the different sensor designs affect the interpretation of their fluorescence readout. Lastly, the review focuses on the limitations and attention one must pay in designing MFSs and biological experiments using them; in terms of their tunability, signal-to-noise ratio (SNR), and perturbation of the biological system under investigation.
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Affiliation(s)
- Adam Yasunaga
- These authors contributed equally to the manuscript (co-first author)
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Blanchard AT, Bazrafshan AS, Yi J, Eisman JT, Yehl KM, Bian T, Mugler A, Salaita K. Highly Polyvalent DNA Motors Generate 100+ pN of Force via Autochemophoresis. NANO LETTERS 2019; 19:6977-6986. [PMID: 31402671 DOI: 10.1021/acs.nanolett.9b02311] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Motor proteins such as myosin, kinesin, and dynein are essential to eukaryotic life and power countless processes including muscle contraction, wound closure, cargo transport, and cell division. The design of synthetic nanomachines that can reproduce the functions of these motors is a longstanding goal in the field of nanotechnology. DNA walkers, which are programmed to "walk" along defined tracks via the burnt bridge Brownian ratchet mechanism, are among the most promising synthetic mimics of these motor proteins. While these DNA-based motors can perform useful tasks such as cargo transport, they have not been shown to be capable of cooperating to generate large collective forces for tasks akin to muscle contraction. In this work, we demonstrate that highly polyvalent DNA motors (HPDMs), which can be viewed as cooperative teams of thousands of DNA walkers attached to a microsphere, can generate and sustain substantial forces in the 100+ pN regime. Specifically, we show that HPDMs can generate forces that can unzip and shear DNA duplexes (∼12 and ∼50 pN, respectively) and rupture biotin-streptavidin bonds (∼100-150 pN). To help explain these results, we present a variant of the burnt-bridge Brownian ratchet mechanism that we term autochemophoresis, wherein many individual force generating units generate a self-propagating chemomechanical gradient that produces large collective forces. In addition, we demonstrate the potential of this work to impact future engineering applications by harnessing HPDM autochemophoresis to deposit "molecular ink" via mechanical bond rupture. This work expands the capabilities of synthetic DNA motors to mimic the force-generating functions of biological motors. Our work also builds upon previous observations of autochemophoresis in bacterial transport processes, indicating that autochemophoresis may be a fundamental mechanism of pN-scale force generation in living systems.
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Affiliation(s)
- Aaron T Blanchard
- Wallace H. Coulter Department of Biomedical Engineering , Georgia Institute of Technology and Emory University , Atlanta , Georgia 30322 , United States
| | - Alisina S Bazrafshan
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Jacob Yi
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Julia T Eisman
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Kevin M Yehl
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Teng Bian
- Department of Physics , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Andrew Mugler
- Department of Physics , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Khalid Salaita
- Wallace H. Coulter Department of Biomedical Engineering , Georgia Institute of Technology and Emory University , Atlanta , Georgia 30322 , United States
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
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28
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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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29
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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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Harrison DL, Fang Y, Huang J. T-Cell Mechanobiology: Force Sensation, Potentiation, and Translation. FRONTIERS IN PHYSICS 2019; 7:45. [PMID: 32601597 PMCID: PMC7323161 DOI: 10.3389/fphy.2019.00045] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A T cell is a sensitive self-referential mechanical sensor. Mechanical forces influence the recognition, activation, differentiation, and function throughout the lifetime of a T cell. T cells constantly perceive and respond to physical stimuli through their surface receptors, cytoskeleton, and subcellular structures. Surface receptors receive physical cues in the form of forces generated through receptor-ligand binding events, which are dynamically regulated by contact tension, shear stress, and substrate rigidity. The resulting mechanotransduction not only influences T-cell recognition and signaling but also possibly modulates cell metabolism and gene expression. Moreover, forces also dynamically regulate the deformation, organization, and translocation of cytoskeleton and subcellular structures, leading to changes in T-cell mobility, migration, and infiltration. However, the roles and mechanisms of how mechanical forces modulate T-cell recognition, signaling, metabolism, and gene expression, are largely unknown and underappreciated. Here, we review recent technological and scientific advances in T-cell mechanobiology, discuss possible roles and mechanisms of T-cell mechanotransduction, and propose new research directions of this emerging field in health and disease.
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Affiliation(s)
- Devin L. Harrison
- The Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL, United States
| | - Yun Fang
- The Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL, United States
- Section of Pulmonary and Critical Care, Department of Medicine, The University of Chicago, Chicago, IL, United States
| | - Jun Huang
- The Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL, United States
- Institute for Molecular Engineering, The University of Chicago, Chicago, IL, United States
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Modular Design of Programmable Mechanofluorescent DNA Hydrogels. Nat Commun 2019; 10:528. [PMID: 30705271 PMCID: PMC6355893 DOI: 10.1038/s41467-019-08428-2] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 01/09/2019] [Indexed: 12/13/2022] Open
Abstract
Mechanosensing systems are ubiquitous in nature and control many functions from cell spreading to wound healing. Biologic systems typically rely on supramolecular transformations and secondary reporter systems to sense weak forces. By contrast, synthetic mechanosensitive materials often use covalent transformations of chromophores, serving both as force sensor and reporter, which hinders orthogonal engineering of their sensitivity, response and modularity. Here, we introduce FRET-based, rationally tunable DNA tension probes into macroscopic 3D all-DNA hydrogels to prepare mechanofluorescent materials with programmable sacrificial bonds and stress relaxation. This design addresses current limitations of mechanochromic system by offering spatiotemporal resolution, as well as quantitative and modular force sensing in soft hydrogels. The programmable force probe design further grants temporal control over the recovery of the mechanofluorescence during stress relaxation, enabling reversible and irreversible strain sensing. We show proof-of-concept applications to study strain fields in composites and to visualize freezing-induced strain patterns in homogeneous hydrogels.
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32
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Lu P, Zhang D, Chai Y, Yu C, Wang X, Tang Y, Ge M, Yao L. Regulatory-sequence mechanical biosensor: A versatile platform for investigation of G-quadruplex/label-free protein interactions and tunable protein detection. Anal Chim Acta 2019; 1045:1-9. [PMID: 30454563 DOI: 10.1016/j.aca.2018.09.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 09/07/2018] [Accepted: 09/10/2018] [Indexed: 11/16/2022]
Abstract
Mechanical biosensors can be used to quantitatively explore DNA-protein binding mechanisms by detecting targets at low concentrations or measuring force in single-molecule force spectroscopy. However, restrictions in single-molecule manipulation and labelling protocols have hindered the application for bulk analysis of label-free protein detection. Here, we present the integration of molecular force measurement and finely tunable detection of label-free proteins into one mechanical sensor. Regulatory-sequence force spectroscopy was obtained to investigate the binding force of DNA G-quadruplexes (GQ) and label-free protein. The dual control of regulatory sequences and mechanical forces induces the structure switching from DNA duplex to GQ/protein complex. It exhibits a synergistic effect, enabling the rational fine-tuning of the dynamic range for biosensing protein concentrations over eight orders of magnitude. Furthermore, this method was exploited to estimate the stability of the human telomeric DNA GQ by Ku protein and ligand methylpyridostatin. The results revealed that human telomeric GQ has two different binding sites for Ku protein and ligand. Force spectroscopy integrating label-free force measurement and tunable target detection holds great promise for use in biosensing, drug screening, targeted therapies, DNA nanotechnology, and fields in which GQ are of rapidly increasing importance.
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Affiliation(s)
- Pan Lu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Di Zhang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yahong Chai
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chanchan Yu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiuyu Wang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yalin Tang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Maofa Ge
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Yao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Abstract
B cells are essential to the adaptive immune system for providing the humoral immunity against cohorts of pathogens. The presentation of antigen to the B cell receptor (BCR) leads to the initiation of B cell activation, which is a process sensitive to the stiffness features of the substrates presenting the antigens. Mechanosensing of the B cells, potentiated through BCR signaling and the adhesion molecules, efficiently regulates B cell activation, proliferation and subsequent antibody responses. Defects in sensing of the antigen-presenting substrates can lead to the activation of autoreactive B cells in autoimmune diseases. The use of high-resolution, high-speed live-cell imaging along with the sophisticated biophysical materials, has uncovered the mechanisms underlying the initiation of B cell activation within seconds of its engagement with the antigen presenting substrates. In this chapter, we reviewed studies that have contributed to uncover the molecular mechanisms of B cell mechanosensing during the initiation of B cell activation.
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Affiliation(s)
- Samina Shaheen
- Center for life sciences, MOE Key Laboratory of Protein Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing Key Lab for Immunological Research on Chronic Diseases, School of Life Sciences, Institute for Immunology, Tsinghua University, Beijing, China
| | - Zhengpeng Wan
- Center for life sciences, MOE Key Laboratory of Protein Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing Key Lab for Immunological Research on Chronic Diseases, School of Life Sciences, Institute for Immunology, Tsinghua University, Beijing, China
| | - Kabeer Haneef
- Center for life sciences, MOE Key Laboratory of Protein Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing Key Lab for Immunological Research on Chronic Diseases, School of Life Sciences, Institute for Immunology, Tsinghua University, Beijing, China
| | - Yingyue Zeng
- Center for life sciences, MOE Key Laboratory of Protein Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing Key Lab for Immunological Research on Chronic Diseases, School of Life Sciences, Institute for Immunology, Tsinghua University, Beijing, China
| | - Wang Jing
- Center for life sciences, MOE Key Laboratory of Protein Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing Key Lab for Immunological Research on Chronic Diseases, School of Life Sciences, Institute for Immunology, Tsinghua University, Beijing, China
| | - Wanli Liu
- Center for life sciences, MOE Key Laboratory of Protein Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing Key Lab for Immunological Research on Chronic Diseases, School of Life Sciences, Institute for Immunology, Tsinghua University, Beijing, China.
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34
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Bergues-Pupo AE, Blank KG, Lipowsky R, Vila Verde A. Trimeric coiled coils expand the range of strength, toughness and dynamics of coiled coil motifs under shear. Phys Chem Chem Phys 2018; 20:29105-29115. [PMID: 30426982 DOI: 10.1039/c8cp04896g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Coiled coils are widespread protein motifs in nature, and promising building blocks for bio-inspired nanomaterials and nanoscale force sensors. Detailed structural insight into their mechanical response is required to understand their role in tissues and to design building blocks for applications. We use all-atom molecular dynamics simulations to elucidate the mechanical response of two types of coiled coils under shear: dimers and trimers. The amino acid sequences of both systems are similar, thus enabling universal (vs. system-specific) features to be identified. The trimer is mechanically more stable - it is both stronger and tougher - than the dimer, withstanding higher forces (127 pN vs. 49 pN at v = 10-3 nm ns-1) and dissipating up to five times more energy before rupture. The deformation mechanism of the trimer at all pull speeds is dominated by progressive helix unfolding. In contrast, at the lowest pull speeds, dimers deform by unfolding/refolding-assisted sliding. The additional helix in the trimer thus both determines the stability of the structure and affects the deformation mechanism, preventing helix sliding. The mechanical response of the coiled coils is not only sensitive to the oligomerization state but also to helix stability: preventing helix unfolding doubles the mechanical strength of the trimer, but decreases its toughness to half. Our results show that coiled coil trimers expand the range of coiled coil responses to an applied shear force. Altering the stability of individual helices against deformation emerges as one possible route towards fine-tuning this response, enabling the use of these motifs as nanomechanical building blocks.
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Affiliation(s)
- Ana E Bergues-Pupo
- Max Planck Institute of Colloids and Interfaces, Department of Theory & Bio-Systems, 14424 Potsdam, Germany.
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35
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Schneider A, Niemeyer CM. DNA Surface Technology: From Gene Sensors to Integrated Systems for Life and Materials Sciences. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201811713] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ann‐Kathrin Schneider
- Institute for Biological Interfaces (IBG 1) Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldshafen Germany
| | - Christof M. Niemeyer
- Institute for Biological Interfaces (IBG 1) Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldshafen Germany
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36
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Schneider A, Niemeyer CM. DNA Surface Technology: From Gene Sensors to Integrated Systems for Life and Materials Sciences. Angew Chem Int Ed Engl 2018; 57:16959-16967. [DOI: 10.1002/anie.201811713] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/15/2018] [Indexed: 01/21/2023]
Affiliation(s)
- Ann‐Kathrin Schneider
- Institute for Biological Interfaces (IBG 1) Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldshafen Germany
| | - Christof M. Niemeyer
- Institute for Biological Interfaces (IBG 1) Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 76344 Eggenstein-Leopoldshafen Germany
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37
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Dutta PK, Zhang Y, Blanchard A, Ge C, Rushdi M, Weiss K, Zhu C, Ke Y, Salaita K. Programmable Multivalent DNA-Origami Tension Probes for Reporting Cellular Traction Forces. NANO LETTERS 2018; 18:4803-4811. [PMID: 29911385 PMCID: PMC6087633 DOI: 10.1021/acs.nanolett.8b01374] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Mechanical forces are central to most, if not all, biological processes, including cell development, immune recognition, and metastasis. Because the cellular machinery mediating mechano-sensing and force generation is dependent on the nanoscale organization and geometry of protein assemblies, a current need in the field is the development of force-sensing probes that can be customized at the nanometer-length scale. In this work, we describe a DNA origami tension sensor that maps the piconewton (pN) forces generated by living cells. As a proof-of-concept, we engineered a novel library of six-helix-bundle DNA-origami tension probes (DOTPs) with a tailorable number of tension-reporting hairpins (each with their own tunable tension response threshold) and a tunable number of cell-receptor ligands. We used single-molecule force spectroscopy to determine the probes' tension response thresholds and used computational modeling to show that hairpin unfolding is semi-cooperative and orientation-dependent. Finally, we use our DOTP library to map the forces applied by human blood platelets during initial adhesion and activation. We find that the total tension signal exhibited by platelets on DOTP-functionalized surfaces increases with the number of ligands per DOTP, likely due to increased total ligand density, and decreases exponentially with the DOTP's force-response threshold. This work opens the door to applications for understanding and regulating biophysical processes involving cooperativity and multivalency.
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Affiliation(s)
- Palash K. Dutta
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, USA
| | - Yun Zhang
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, USA
| | - Aaron Blanchard
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, USA
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, USA
| | - Chenghao Ge
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, USA
| | - Muaz Rushdi
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, USA
| | - Kristin Weiss
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, USA
| | - Cheng Zhu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, USA
- Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, USA
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, USA
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Khalid Salaita
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, USA
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, USA
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38
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Mechanics of antigen extraction in the B cell synapse. Mol Immunol 2018; 101:319-328. [PMID: 30036798 DOI: 10.1016/j.molimm.2018.07.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 07/11/2018] [Indexed: 12/16/2022]
Abstract
B cell encounter with antigen displayed on antigen-presenting cells leads to B cell immune synapse formation, internalisation of the antigen, and stimulation of antibody responses. The sensitivity with which B cells detect antigen, and the quality and quantity of antigen that B cells acquire, depend upon mechanical properties of the immune synapse including interfacial tension, the strength of intermolecular bonds, and the compliance of the molecules and membranes that participate in antigen presentation. In this review, we discuss our current understanding of how these various physical parameters influence B cell antigen extraction in the immune synapse and how a more comprehensive understanding of B cell mechanics may promote the development of new approaches to stimulate the production of desired antibodies.
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39
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Goktas M, Luo C, Sullan RMA, Bergues-Pupo AE, Lipowsky R, Vila Verde A, Blank KG. Molecular mechanics of coiled coils loaded in the shear geometry. Chem Sci 2018; 9:4610-4621. [PMID: 29899954 PMCID: PMC5969510 DOI: 10.1039/c8sc01037d] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 04/19/2018] [Indexed: 01/25/2023] Open
Abstract
Coiled coils are important nanomechanical building blocks in biological and biomimetic materials. A mechanistic molecular understanding of their structural response to mechanical load is essential for elucidating their role in tissues and for utilizing and tuning these building blocks in materials applications. Using a combination of single-molecule force spectroscopy (SMFS) and steered molecular dynamics (SMD) simulations, we have investigated the mechanics of synthetic heterodimeric coiled coils of different length (3-4 heptads) when loaded in shear geometry. Upon shearing, we observe an initial rise in the force, which is followed by a constant force plateau and ultimately strand separation. The force required for strand separation depends on the coiled coil length and the applied loading rate, suggesting that coiled coil shearing occurs out of equilibrium. This out-of-equilibrium behaviour is determined by a complex structural response which involves helix uncoiling, uncoiling-assisted sliding of the helices relative to each other in the direction of the applied force as well as uncoiling-assisted dissociation perpendicular to the force axis. These processes follow a hierarchy of timescales with helix uncoiling being faster than sliding and sliding being faster than dissociation. In SMFS experiments, strand separation is dominated by uncoiling-assisted dissociation and occurs at forces between 25-45 pN for the shortest 3-heptad coiled coil and between 35-50 pN for the longest 4-heptad coiled coil. These values are highly similar to the forces required for shearing apart short double-stranded DNA oligonucleotides, reinforcing the potential role of coiled coils as nanomechanical building blocks in applications where protein-based structures are desired.
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Affiliation(s)
- Melis Goktas
- Max Planck Institute of Colloids and Interfaces , Mechano(bio)chemistry , Science Park Potsdam-Golm , 14424 Potsdam , Germany .
| | - Chuanfu Luo
- Max Planck Institute of Colloids and Interfaces , Department of Theory & Bio-Systems , Science Park Potsdam-Golm , 14424 Potsdam , Germany .
| | - Ruby May A Sullan
- Max Planck Institute of Colloids and Interfaces , Mechano(bio)chemistry , Science Park Potsdam-Golm , 14424 Potsdam , Germany .
| | - Ana E Bergues-Pupo
- Max Planck Institute of Colloids and Interfaces , Department of Theory & Bio-Systems , Science Park Potsdam-Golm , 14424 Potsdam , Germany .
| | - Reinhard Lipowsky
- Max Planck Institute of Colloids and Interfaces , Department of Theory & Bio-Systems , Science Park Potsdam-Golm , 14424 Potsdam , Germany .
| | - Ana Vila Verde
- Max Planck Institute of Colloids and Interfaces , Department of Theory & Bio-Systems , Science Park Potsdam-Golm , 14424 Potsdam , Germany .
| | - Kerstin G Blank
- Max Planck Institute of Colloids and Interfaces , Mechano(bio)chemistry , Science Park Potsdam-Golm , 14424 Potsdam , Germany .
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40
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van de Laar T, Schuurman H, van der Scheer P, Maarten van Doorn J, van der Gucht J, Sprakel J. Light from Within: Sensing Weak Strains and FemtoNewton Forces in Single Molecules. Chem 2018. [DOI: 10.1016/j.chempr.2017.12.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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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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42
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Li H, Bergeron S, Larkin H, Juncker D. Snap Chip for Cross-reactivity-free and Spotter-free Multiplexed Sandwich Immunoassays. J Vis Exp 2017. [PMID: 29155743 DOI: 10.3791/56230] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Multiplexed protein analysis has shown superior diagnostic sensitivity and accuracy compared to single proteins. Antibody microarrays allow for thousands of micro-scale immunoassays performed simultaneously on a single chip. Sandwich assay format improves assay specificity by detecting each target with two antibodies, but suffers from cross-reactivity between reagents thus limiting their multiplexing capabilities. Antibody colocalization microarray (ACM) has been developed for cross-reactivity-free multiplexed protein detection, but requires an expensive spotter on-site for microarray fabrication during assays. In this work, we demonstrate a snap chip technology that transfers reagent from microarray-to-microarray by simply snapping two chips together, thus no spotter is needed during the sample incubation and subsequent application of detection antibodies (dAbs) upon storage of pre-spotted slides, dissociating the slide preparation from assay execution. Both single and double transfer methods are presented to achieve accurate alignment between the two microarrays and the slide fabrication for both methods are described. Results show that <40 μm alignment has been achieved with double transfer, reaching an array density of 625 spots/cm2. A 50-plexed immunoassay has been conducted to demonstrate the usability of the snap chip in multiplexed protein analysis. Limits of detection of 35 proteins are in the range of pg/mL.
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Affiliation(s)
- Huiyan Li
- McGill University and Génome Québec Innovation Centre; Biomedical Engineering Department, McGill University
| | | | - Heidi Larkin
- McGill University and Génome Québec Innovation Centre; Biomedical Engineering Department, McGill University; Parallex BioAssays Inc
| | - David Juncker
- McGill University and Génome Québec Innovation Centre; Biomedical Engineering Department, McGill University;
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43
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Force-activatable biosensor enables single platelet force mapping directly by fluorescence imaging. Biosens Bioelectron 2017; 100:192-200. [PMID: 28915383 DOI: 10.1016/j.bios.2017.09.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 08/25/2017] [Accepted: 09/05/2017] [Indexed: 11/23/2022]
Abstract
Integrin-transmitted cellular forces are critical for platelet adhesion, activation, aggregation and contraction during hemostasis and thrombosis. Measuring and mapping single platelet forces are desired in both research and clinical applications. Conventional force-to-strain based cell traction force microscopies have low resolution which is not ideal for cellular force mapping in small platelets. To enable platelet force mapping with submicron resolution, we developed a force-activatable biosensor named integrative tension sensor (ITS) which directly converts molecular tensions to fluorescent signals, therefore enabling cellular force mapping directly by fluorescence imaging. With ITS, we mapped cellular forces in single platelets at 0.4µm resolution. We found that platelet force distribution has strong polarization which is sensitive to treatment with the anti-platelet drug tirofiban, suggesting that the ITS force map can report anti-platelet drug efficacy. The ITS also calibrated integrin molecular tensions in platelets and revealed two distinct tension levels: 12-54 piconewton (nominal values) tensions generated during platelet adhesion and tensions above 54 piconewton generated during platelet contraction. Overall, the ITS is a powerful biosensor for the study of platelet mechanobiology, and holds great potential in antithrombotic drug development and assessing platelet activity in health and disease.
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44
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Single-molecule force spectroscopy on polyproteins and receptor–ligand complexes: The current toolbox. J Struct Biol 2017; 197:3-12. [DOI: 10.1016/j.jsb.2016.02.011] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 02/08/2016] [Accepted: 02/09/2016] [Indexed: 11/21/2022]
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45
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Zhang J, Yan Y, Samai S, Ginger DS. Dynamic Melting Properties of Photoswitch-Modified DNA: Shearing versus Unzipping. J Phys Chem B 2016; 120:10706-10713. [DOI: 10.1021/acs.jpcb.6b08297] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jie Zhang
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Yunqi Yan
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Soumyadyuti Samai
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - David S. Ginger
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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46
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Nickels PC, Høiberg HC, Simmel SS, Holzmeister P, Tinnefeld P, Liedl T. DNA Origami Seesaws as Comparative Binding Assay. Chembiochem 2016; 17:1093-6. [PMID: 27038073 PMCID: PMC5084756 DOI: 10.1002/cbic.201600059] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Indexed: 11/28/2022]
Abstract
The application of commonly used force spectroscopy in biological systems is often limited by the need for an invasive tether connecting the molecules of interest to a bead or cantilever tip. Here we present a DNA origami-based prototype in a comparative binding assay. It has the advantage of in situ readout without any physical connection to the macroscopic world. The seesaw-like structure has a lever that is able to move freely relative to its base. Binding partners on each side force the structure into discrete and distinguishable conformations. Model experiments with competing DNA hybridisation reactions yielded a drastic shift towards the conformation with the stronger binding interaction. With reference DNA duplexes of tuneable length on one side, this device can be used to measure ligand interactions in comparative assays.
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Affiliation(s)
- Philipp C Nickels
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität (LMU), Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Hans C Høiberg
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität (LMU), Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Stephanie S Simmel
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität (LMU), Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Phil Holzmeister
- Institut für physikalische und theoretische Chemie, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, 38106, Braunschweig, Germany
| | - Philip Tinnefeld
- Institut für physikalische und theoretische Chemie, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, 38106, Braunschweig, Germany
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität (LMU), Geschwister-Scholl-Platz 1, 80539, Munich, Germany.
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47
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Maver U, Velnar T, Gaberšček M, Planinšek O, Finšgar M. Recent progressive use of atomic force microscopy in biomedical applications. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.03.014] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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48
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Karsten SL, Kumemura M, Jalabert L, Lafitte N, Kudo LC, Collard D, Fujita H. Direct electrical and mechanical characterization of in situ generated DNA between the tips of silicon nanotweezers (SNT). LAB ON A CHIP 2016; 16:2099-2107. [PMID: 27161663 DOI: 10.1039/c6lc00309e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Previously, we reported the application of micromachined silicon nanotweezers (SNT) integrated with a comb-drive actuator and capacitive sensors for capturing and mechanical characterization of DNA bundles. Here, we demonstrate direct DNA amplification on such a MEMS structure with subsequent electrical and mechanical characterization of a single stranded DNA (ssDNA) bundle generated between the tips of SNT via isothermal rolling circle amplification (RCA) and dielectrophoresis (DEP). An in situ generated ssDNA bundle was visualized and evaluated via electrical conductivity (I-V) and mechanical frequency response measurements. Colloidal gold nanoparticles significantly enhanced (P < 0.01) the electrical properties of thin ssDNA bundles. The proposed technology allows direct in situ synthesis of DNA with a predefined sequence on the tips of a MEMS sensor device, such as SNT, followed by direct DNA electrical and mechanical characterization. In addition, our data provides a "proof-of-principle" for the feasibility of the on-chip label free DNA detection device that can be used for a variety of biomedical applications focused on sequence specific DNA detection.
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Affiliation(s)
- Stanislav L Karsten
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan. and NeuroInDx. Inc., 20725 S. Western Ave., Suite 100, Torrance, CA 90501, USA.
| | - Momoko Kumemura
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan.
| | - Laurent Jalabert
- LIMMS/CNRS-IIS (UMI 2820), The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan
| | - Nicolas Lafitte
- LIMMS/CNRS-IIS (UMI 2820), The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan
| | - Lili C Kudo
- NeuroInDx. Inc., 20725 S. Western Ave., Suite 100, Torrance, CA 90501, USA.
| | - Dominique Collard
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan. and LIMMS/CNRS-IIS (UMI 2820), The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan and SMMiL-E: Institut pour la Recherche sur le Cancer de Lille, Boulevard du Pr Jules Leclercq, 59 000 Lille, France
| | - Hiroyuki Fujita
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan.
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49
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Karatay DU, Zhang J, Harrison JS, Ginger DS. Classifying Force Spectroscopy of DNA Pulling Measurements Using Supervised and Unsupervised Machine Learning Methods. J Chem Inf Model 2016; 56:621-9. [DOI: 10.1021/acs.jcim.5b00722] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Durmus U. Karatay
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Jie Zhang
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Jeffrey S. Harrison
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - David S. Ginger
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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50
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Sulaiman SAJ, Al-Rasbi GS, Abou-Zied OK. Photophysical properties of hydroxyphenyl benzazoles and their applications as fluorescent probes to study local environment in DNA, protein and lipid. LUMINESCENCE 2016; 31:614-25. [DOI: 10.1002/bio.3106] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 01/01/2016] [Accepted: 01/10/2016] [Indexed: 12/22/2022]
Affiliation(s)
| | - Ghalia S. Al-Rasbi
- Department of Chemistry; Sultan Qaboos University; Muscat Sultanate of Oman
| | - Osama K. Abou-Zied
- Department of Chemistry; Sultan Qaboos University; Muscat Sultanate of Oman
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