1
|
Yang L, Li Q, Ge Z, Fan C, Huang W. DNA Mechanics: From Single Stranded to Self-Assembled. NANO LETTERS 2024. [PMID: 39259830 DOI: 10.1021/acs.nanolett.4c03323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
DNA encodes genetic information and forms various structural conformations with distinct physical, chemical, and biological properties. Over the past 30 years, advancements in force manipulation technology have enabled the precise manipulation of DNA at nanometer and piconewton resolutions. This mini-review discusses these force manipulation techniques for exploring the mechanical properties of DNA at the single-molecule level. We summarize the distinct mechanical features of different DNA forms while considering the impact of the force geometry. We highlight the role of DNA mechanics in origami structures that serve as self-assembled building blocks or mechanically responsive/active nanomachines. Accordingly, we emphasize how DNA mechanics are integral to the functionality of origami structures for achieving mechanical capabilities. Finally, we provide an outlook on the intrinsic mechanical properties of DNA, from single stranded to self-assembled higher-dimensional structures. This understanding is expected to inspire new design strategies in DNA mechanics, paving the way for innovative applications and technologies.
Collapse
Affiliation(s)
- Linfeng Yang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhilei Ge
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wenmao Huang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
2
|
Singh N, Singh A, Dhanka M, Bhatia D. DNA functionalized programmable hybrid biomaterials for targeted multiplexed applications. J Mater Chem B 2024. [PMID: 38973587 DOI: 10.1039/d4tb00287c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
With the advent of DNA nanotechnology, DNA-based biomaterials have emerged as a unique class of materials at the center of various biological advances. Owing to DNA's high modification capacity via programmable Watson-Crick base-pairing, DNA structures of desired design with increased complexity have been developed. However, the limited scalability, along with poor mechanical properties, high synthesis costs, and poor stability, reduced the adaptability of DNA-based materials to complex biological applications. DNA-based hybrid biomaterials were designed to overcome these limitations by conjugating DNA with functional materials. Today, DNA-based hybrid materials have attracted significant attention in biological engineering with broad application prospects in biomedicine, clinical diagnosis, and nanodevices. Here, we summarize the recent advances in DNA-based hybrid materials with an in-depth understanding of general molecular design principles, functionalities, and applications. Finally, the challenges and prospects associated with DNA-based hybrid materials are discussed at the end of this review.
Collapse
Affiliation(s)
- Nihal Singh
- Discipline of Bioengineering, Indian Institute of Technology Gandhinagar, Gujarat, India, 382355.
| | - Ankur Singh
- Discipline of Bioengineering, Indian Institute of Technology Gandhinagar, Gujarat, India, 382355.
| | - Mukesh Dhanka
- Discipline of Bioengineering, Indian Institute of Technology Gandhinagar, Gujarat, India, 382355.
| | - Dhiraj Bhatia
- Discipline of Bioengineering, Indian Institute of Technology Gandhinagar, Gujarat, India, 382355.
| |
Collapse
|
3
|
Hartmann B, Fleischhauer L, Nicolau M, Jensen THL, Taran FA, Clausen-Schaumann H, Reuten R. Profiling native pulmonary basement membrane stiffness using atomic force microscopy. Nat Protoc 2024; 19:1498-1528. [PMID: 38429517 DOI: 10.1038/s41596-024-00955-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 11/27/2023] [Indexed: 03/03/2024]
Abstract
Mammalian cells sense and react to the mechanics of their immediate microenvironment. Therefore, the characterization of the biomechanical properties of tissues with high spatial resolution provides valuable insights into a broad variety of developmental, homeostatic and pathological processes within living organisms. The biomechanical properties of the basement membrane (BM), an extracellular matrix (ECM) substructure measuring only ∼100-400 nm across, are, among other things, pivotal to tumor progression and metastasis formation. Although the precise assignment of the Young's modulus E of such a thin ECM substructure especially in between two cell layers is still challenging, biomechanical data of the BM can provide information of eminent diagnostic potential. Here we present a detailed protocol to quantify the elastic modulus of the BM in murine and human lung tissue, which is one of the major organs prone to metastasis. This protocol describes a streamlined workflow to determine the Young's modulus E of the BM between the endothelial and epithelial cell layers shaping the alveolar wall in lung tissues using atomic force microscopy (AFM). Our step-by-step protocol provides instructions for murine and human lung tissue extraction, inflation of these tissues with cryogenic cutting medium, freezing and cryosectioning of the tissue samples, and AFM force-map recording. In addition, it guides the reader through a semi-automatic data analysis procedure to identify the pulmonary BM and extract its Young's modulus E using an in-house tailored user-friendly AFM data analysis software, the Center for Applied Tissue Engineering and Regenerative Medicine processing toolbox, which enables automatic loading of the recorded force maps, conversion of the force versus piezo-extension curves to force versus indentation curves, calculation of Young's moduli and generation of Young's modulus maps, where the pulmonary BM can be identified using a semi-automatic spatial filtering tool. The entire protocol takes 1-2 d.
Collapse
Affiliation(s)
- Bastian Hartmann
- Munich University of Applied Sciences, Center for Applied Tissue Engineering and Regenerative Medicine - CANTER, Munich, Germany
- Center for Nanoscience, Munich, Germany
| | - Lutz Fleischhauer
- Munich University of Applied Sciences, Center for Applied Tissue Engineering and Regenerative Medicine - CANTER, Munich, Germany
- Center for Nanoscience, Munich, Germany
| | - Monica Nicolau
- Experimental and Clinical Pharmacology and Toxicology, Medical Faculty, University of Freiburg, Freiburg, Germany
- Department of Obstetrics and Gynecology, Medical Center, University of Freiburg, Freiburg, Germany
| | - Thomas Hartvig Lindkær Jensen
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Pathology, Rigshospitalet, Copenhagen, Denmark
| | - Florin-Andrei Taran
- Department of Obstetrics and Gynecology, Medical Center, University of Freiburg, Freiburg, Germany
| | - Hauke Clausen-Schaumann
- Munich University of Applied Sciences, Center for Applied Tissue Engineering and Regenerative Medicine - CANTER, Munich, Germany.
- Center for Nanoscience, Munich, Germany.
| | - Raphael Reuten
- Experimental and Clinical Pharmacology and Toxicology, Medical Faculty, University of Freiburg, Freiburg, Germany.
- Department of Obstetrics and Gynecology, Medical Center, University of Freiburg, Freiburg, Germany.
| |
Collapse
|
4
|
Liu Z, Liu H, Vera AM, Yang B, Tinnefeld P, Nash MA. Engineering an artificial catch bond using mechanical anisotropy. Nat Commun 2024; 15:3019. [PMID: 38589360 PMCID: PMC11001878 DOI: 10.1038/s41467-024-46858-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/13/2024] [Indexed: 04/10/2024] Open
Abstract
Catch bonds are a rare class of protein-protein interactions where the bond lifetime increases under an external pulling force. Here, we report how modification of anchor geometry generates catch bonding behavior for the mechanostable Dockerin G:Cohesin E (DocG:CohE) adhesion complex found on human gut bacteria. Using AFM single-molecule force spectroscopy in combination with bioorthogonal click chemistry, we mechanically dissociate the complex using five precisely controlled anchor geometries. When tension is applied between residue #13 on CohE and the N-terminus of DocG, the complex behaves as a two-state catch bond, while in all other tested pulling geometries, including the native configuration, it behaves as a slip bond. We use a kinetic Monte Carlo model with experimentally derived parameters to simulate rupture force and lifetime distributions, achieving strong agreement with experiments. Single-molecule FRET measurements further demonstrate that the complex does not exhibit dual binding mode behavior at equilibrium but unbinds along multiple pathways under force. Together, these results show how mechanical anisotropy and anchor point selection can be used to engineer artificial catch bonds.
Collapse
Affiliation(s)
- Zhaowei Liu
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
- Department of Bionanoscience, Delft University of Technology, 2629HZ, Delft, the Netherlands
| | - Haipei Liu
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Andrés M Vera
- Faculty of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Byeongseon Yang
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
- Botnar Research Centre for Child Health, 4051, Basel, Switzerland
- National Center for Competence in Research (NCCR) Molecular Systems Engineering, 4058, Basel, Switzerland
| | - Philip Tinnefeld
- Faculty of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael A Nash
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058, Basel, Switzerland.
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland.
- Botnar Research Centre for Child Health, 4051, Basel, Switzerland.
- National Center for Competence in Research (NCCR) Molecular Systems Engineering, 4058, Basel, Switzerland.
- Swiss Nanoscience Institute, 4056, Basel, Switzerland.
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
Sun M, Sun H, Yu C, Lu P, Feng F, Zhang J, Li W, Yao L. Force-Encoding DNA Nanomachines for Simultaneous and Direct Detection of Multiple Pathogenic Bacteria in Blood. Anal Chem 2024; 96:4314-4321. [PMID: 38415347 DOI: 10.1021/acs.analchem.4c00298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Pathogen detection is growing in importance in the early stages of bacterial infection and treatment due to the significant morbidity and mortality associated with bloodstream infections. Although various diagnostic approaches for pathogen detection have been proposed, most of them are time-consuming, with insufficient sensitivity and limited specificity and multiplexing capability for clinical use. Here, we report a force-encoding DNA nanomachine for simultaneous and high-throughput detection of multiple pathogens in blood through force-induced remnant magnetization spectroscopy (FIRMS). The force-encoding DNA nanomachines coupled with DNA walkers enable analytical sensitivity down to a single bacterium via a cascade signal amplification strategy. More importantly, it allows for rapid and specific profiling of various pathogens directly in blood samples, without being affected by factors such as light color and solution properties. We expect that this magnetic sensing platform holds great promise for various applications in biomedical research and clinical diagnostics.
Collapse
Affiliation(s)
- Mengxue Sun
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, Beijing 100190, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Hongxia Sun
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, Beijing 100190, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Chanchan Yu
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, Beijing 100190, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Pan Lu
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, Beijing 100190, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Feng Feng
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, Beijing 100190, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jin Zhang
- Department of Thoracic Surgery, China-Japan Friendship Hospital, Beijing 100029, China
| | - Wenchao Li
- The Seventh Medical Center of Chinese People's Liberation Army General Hospital, Beijing 100010, China
| | - Li Yao
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, Beijing 100190, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
7
|
Liu Y, Wang L, Zhao L, Zhang Y, Li ZT, Huang F. Multiple hydrogen bonding driven supramolecular architectures and their biomedical applications. Chem Soc Rev 2024; 53:1592-1623. [PMID: 38167687 DOI: 10.1039/d3cs00705g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Supramolecular chemistry combines the strength of molecular assembly via various molecular interactions. Hydrogen bonding facilitated self-assembly with the advantages of directionality, specificity, reversibility, and strength is a promising approach for constructing advanced supramolecules. There are still some challenges in hydrogen bonding based supramolecular polymers, such as complexity originating from tautomerism of the molecular building modules, the assembly process, and structure versatility of building blocks. In this review, examples are selected to give insights into multiple hydrogen bonding driven emerging supramolecular architectures. We focus on chiral supramolecular assemblies, multiple hydrogen bonding modules as stimuli responsive sources, interpenetrating polymer networks, multiple hydrogen bonding assisted organic frameworks, supramolecular adhesives, energy dissipators, and quantitative analysis of nano-adhesion. The applications in biomedical materials are focused with detailed examples including drug design evolution for myotonic dystrophy, molecular assembly for advanced drug delivery, an indicator displacement strategy for DNA detection, tissue engineering, and self-assembly complexes as gene delivery vectors for gene transfection. In addition, insights into the current challenges and future perspectives of this field to propel the development of multiple hydrogen bonding facilitated supramolecular materials are proposed.
Collapse
Affiliation(s)
- Yanxia Liu
- School of Materials and Energy, University of Electronic Science and Technology of China, Chengdu 611731, Sichuan, China.
| | - Lulu Wang
- State Key Laboratory of Chemistry and Utilization of Carbon-based Energy Resource, Xinjiang University, Urumqi, Xinjiang 830046, China
| | - Lin Zhao
- School of Materials and Energy, University of Electronic Science and Technology of China, Chengdu 611731, Sichuan, China.
| | - Yagang Zhang
- School of Materials and Energy, University of Electronic Science and Technology of China, Chengdu 611731, Sichuan, China.
| | - Zhan-Ting Li
- Key Laboratory of Synthetic and Self-Assembly Chemistry for Organic Functional Molecules, Shanghai Institute of Organic Chemistry (SIOC), Chinese Academy of Sciences, Shanghai 200032, China
- Department of Chemistry, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, 2205 Songhu Road, Shanghai 200438, China.
| | - Feihe Huang
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310058, China.
- ZJU-Hangzhou Global Scientific and Technological Innovation Center-Hangzhou Zhijiang Silicone Chemicals Co. Ltd. Joint Lab, Zhejiang-Israel Joint Laboratory of Self-Assembling Functional Materials, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| |
Collapse
|
8
|
Lallemang M, Akintayo CO, Wenzel C, Chen W, Sielaff L, Ripp A, Jessen HJ, Balzer BN, Walther A, Hugel T. Hierarchical Mechanical Transduction of Precision-Engineered DNA Hydrogels with Sacrificial Bonds. ACS APPLIED MATERIALS & INTERFACES 2023; 15:59714-59721. [PMID: 38095074 DOI: 10.1021/acsami.3c15135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
Engineering the response to external signals in mechanically switchable hydrogels is important to promote smart materials applications. However, comparably little attention has focused on embedded precision mechanisms for autonomous nonlinear response in mechanical profiles in hydrogels, and we lack understanding of how the behavior from the molecular scale transduces to the macroscale. Here, we design a nonlinear stress-strain response into hydrogels by engineering sacrificial DNA hairpin loops into model network hydrogels formed from star-shaped building blocks. We characterize the force-extension response of single DNA hairpins and are able to describe how the specific topology influences the nonlinear mechanical behavior at different length scales. For this purpose, we utilize force spectroscopy as well as microscopic and macroscopic deformation tests. This study contributes to a better understanding of designing nonlinear strain-adaptive features into hydrogel materials.
Collapse
Affiliation(s)
- Max Lallemang
- Institute of Physical Chemistry, University of Freiburg, Albertstrasse 21, Freiburg 79104, Germany
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, Freiburg 79110, Germany
| | - Cecilia Oluwadunsin Akintayo
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Mainz 55128, Germany
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, Freiburg 79110, Germany
| | - Christiane Wenzel
- Institute of Physical Chemistry, University of Freiburg, Albertstrasse 21, Freiburg 79104, Germany
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, Freiburg 79110, Germany
| | - Weixiang Chen
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Mainz 55128, Germany
| | - Lucca Sielaff
- Institute of Physical Chemistry, University of Freiburg, Albertstrasse 21, Freiburg 79104, Germany
| | - Alexander Ripp
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, Freiburg 79110, Germany
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, Freiburg 79104, Germany
| | - Henning J Jessen
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, Freiburg 79110, Germany
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, Freiburg 79104, Germany
| | - Bizan N Balzer
- Institute of Physical Chemistry, University of Freiburg, Albertstrasse 21, Freiburg 79104, Germany
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, Freiburg 79110, Germany
- Freiburg Materials Research Center (FMF), University of Freiburg, Freiburg 79104, Germany
| | - Andreas Walther
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Mainz 55128, Germany
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, Freiburg 79110, Germany
| | - Thorsten Hugel
- Institute of Physical Chemistry, University of Freiburg, Albertstrasse 21, Freiburg 79104, Germany
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, Freiburg 79110, Germany
| |
Collapse
|
9
|
Zou Z, Liang J, Jia Q, Bai D, Xie W, Wu W, Tan C, Ma J. A versatile and high-throughput flow-cell system combined with fluorescence imaging for simultaneous single-molecule force measurement and visualization. NANOSCALE 2023; 15:17443-17454. [PMID: 37859523 DOI: 10.1039/d3nr03214k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
A flow-cell offers many advantages for single-molecule studies. But, its merit as a quantitative single-molecule tool has long been underestimated. In this work, we developed a gas-pumped fully calibrated flow-cell system combined with fluorescence imaging for simultaneous single-molecule force measurement and visualization. Such a flow-cell system has considered the hydrodynamic drags on biomolecules and hence can apply and measure force up to more than 100 pN in sub-pN precision with an ultra-high force stability (force drift <0.01 pN in 10 minutes) and tuning accuracy (∼0.04 pN). Meanwhile, it also allows acquiring force signals and fluorescence images at the same time, parallelly tracking hundreds of protein motors in real time as well as monitoring the conformational changes of biomolecules under a well-controlled force, as demonstrated by a series of single-molecule experiments in this work, including the studies of DNA overstretching dynamics, transcription under force and DNA folding/unfolding dynamics. Interesting findings, such as the very tight association of single-stranded binding (SSB) proteins with ssDNA and the reversed transcription, have also been made. These results together lay down an essential foundation for a flow-cell to be used as a versatile, quantitative and high-throughput tool for single-molecule manipulation and visualization.
Collapse
Affiliation(s)
- Zhenyu Zou
- School of Physics, Sun Yat-sen University, Guangzhou 510275, P.R. China.
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Jialun Liang
- School of Physics, Sun Yat-sen University, Guangzhou 510275, P.R. China.
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Qian Jia
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, 510006, P.R. China
| | - Di Bai
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng 475001, P.R. China
| | - Wei Xie
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, 510006, P.R. China
| | - Wenqiang Wu
- School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng 475001, P.R. China
| | - Chuang Tan
- School of Physics, Sun Yat-sen University, Guangzhou 510275, P.R. China.
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Jie Ma
- School of Physics, Sun Yat-sen University, Guangzhou 510275, P.R. China.
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510275, P.R. China
| |
Collapse
|
10
|
Sarkar A, Niraula G, LeVine D, Zhao Y, Tu Y, Mollaeian K, Ren J, Que L, Wang X. Development of a Ratiometric Tension Sensor Exclusively Responding to Integrin Tension Magnitude in Live Cells. ACS Sens 2023; 8:3701-3712. [PMID: 37738233 PMCID: PMC10788086 DOI: 10.1021/acssensors.3c00606] [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] [Indexed: 09/24/2023]
Abstract
Integrin tensions are critical for cell mechanotransduction. By converting force to fluorescence, molecular tension sensors image integrin tensions in live cells with a high resolution. However, the fluorescence signal intensity results collectively from integrin tension magnitude, tension dwell time, integrin density, sensor accessibility, and so forth, making it highly challenging to specifically monitor the molecular force level of integrin tensions. Here, a ratiometric tension sensor (RTS) was developed to exclusively monitor the integrin tension magnitude. The RTS consists of two tension-sensing units that are coupled in series and always subject to the same integrin tension. These two units are activated by tension to fluoresce in separate spectra and with different activation rates. The ratio of their activation probabilities, reported by fluorescence ratiometric measurement, is solely determined by the local integrin tension magnitude. RTS responded sensitively to the variation of integrin tension magnitude in platelets and focal adhesions due to different cell plating times, actomyosin inhibition, or vinculin knockout. At last, RTS confirmed that integrin tension magnitude in platelets and focal adhesions decreases monotonically with the substrate rigidity, verifying the rigidity dependence of integrin tensions in live cells and suggesting that integrin tension magnitude could be a key biomechanical factor in cell rigidity sensing.
Collapse
Affiliation(s)
- Anwesha Sarkar
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa 50011, United States
| | - Gopal Niraula
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa 50011, United States
| | - Dana LeVine
- Department of Veterinary Clinical Sciences, Iowa State University, Ames, Iowa 50011, United States
| | - Yuanchang Zhao
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa 50011, United States
| | - Ying Tu
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa 50011, United States
| | - Keyvan Mollaeian
- Department of Mechanical Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Juan Ren
- Department of Mechanical Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Long Que
- Department of Electrical and Computer Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Xuefeng Wang
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa 50011, United States
- Hoxworth Blood Center, College of Medicine, The University of Cincinnati, Cincinnati, Ohio 45219, United States
| |
Collapse
|
11
|
Mondal S, Banerjee S, Dey D, Lahiri H, Mana T, Jana SS, Mukhopadhyay R. Impact of HMGB1 binding on the structural alterations of platinum drug-treated single dsDNA molecule. Biochimie 2023; 213:168-175. [PMID: 37211256 DOI: 10.1016/j.biochi.2023.05.012] [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: 02/15/2023] [Revised: 04/24/2023] [Accepted: 05/18/2023] [Indexed: 05/23/2023]
Abstract
High mobility group B1 (HMGB1) is an architectural protein that recognizes the DNA damage sites formed by the platinum anticancer drugs. However, the impact of HMGB1 binding on the structural alterations of the platinum drug-treated single dsDNA molecules has remained largely unknown. Herein, the structural alterations induced by the platinum drugs, the mononuclear cisplatin and it's analog the trinuclear BBR3464, have been probed in presence of HMGB1, by atomic force microscopy (AFM) and AFM-based force spectroscopy. It is observed that the drug-induced DNA loop formation enhanced upon HMGB1 binding, most likely as a result of HMGB1-induced increase in DNA conformational flexibility that allowed the drug-binding sites to come close and form double adducts, thereby resulting in enhanced loop formation via inter-helix cross-linking. Since HMGB1 enhances DNA flexibility, the near-reversible structural transitions as observed in the force-extension curves (for 1 h drug treatment), generally occurred at lower forces in presence of HMGB1. The DNA structural integrity was largely lost after 24 h drug treatment as no reversible transition could be observed. The Young's modulus of the dsDNA molecules, as estimated from the force-extension analysis, increased upon drug treatment, due to formation of the drug-induced covalent cross-links and consequent reduction in DNA flexibility. The Young's modulus increased further in presence of HMGB1 due to HMGB1-induced enhancement in DNA flexibility that could ease formation of the drug-induced covalent cross-links. To our knowledge, this is the first report that shows an increase in the stiffness of the platinum drug-treated DNA molecules in presence of HMGB1.
Collapse
Affiliation(s)
- Sourav Mondal
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India
| | - Siddhartha Banerjee
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India
| | - Debapriya Dey
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India
| | - Hiya Lahiri
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India
| | - Tanushree Mana
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India
| | - Siddhartha S Jana
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India
| | - Rupa Mukhopadhyay
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India.
| |
Collapse
|
12
|
Suh S, Xing Y, Rottensteiner A, Zhu R, Oh YJ, Howorka S, Hinterdorfer P. Molecular Recognition in Confined Space Elucidated with DNA Nanopores and Single-Molecule Force Microscopy. NANO LETTERS 2023; 23:4439-4447. [PMID: 37166380 PMCID: PMC10214486 DOI: 10.1021/acs.nanolett.3c00743] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/24/2023] [Indexed: 05/12/2023]
Abstract
The binding of ligands to receptors within a nanoscale small space is relevant in biology, biosensing, and affinity filtration. Binding in confinement can be studied with biological systems but under the limitation that essential parameters cannot be easily controlled including receptor type and position within the confinement and its dimensions. Here we study molecular recognition with a synthetic confined nanopore with controllable pore dimension and molecular DNA receptors at different depth positions within the channel. Binding of a complementary DNA strand is studied at the single-molecule level with atomic force microscopy. Following the analysis, kinetic association rates are lower for receptors positioned deeper inside the pore lumen while dissociation is faster and requires less force. The phenomena are explained by the steric constraints on molecular interactions in confinement. Our study is the first to explore recognition in DNA nanostructures with atomic force microscopy and lays out new tools to further quantify the effect of nanoconfinement on molecular interactions.
Collapse
Affiliation(s)
- Saanfor
Hubert Suh
- Department
of Applied Experimental Biophysics, Johannes
Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
| | - Yongzheng Xing
- Department
of Chemistry, University College London,
Institute of Structural and Molecular Biology, 20 Gordon Street, London WC1H OAJ, United Kingdom
| | - Alexia Rottensteiner
- Department
of Chemistry, University College London,
Institute of Structural and Molecular Biology, 20 Gordon Street, London WC1H OAJ, United Kingdom
| | - Rong Zhu
- Department
of Applied Experimental Biophysics, Johannes
Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
| | - Yoo Jin Oh
- Department
of Applied Experimental Biophysics, Johannes
Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
| | - Stefan Howorka
- Department
of Chemistry, University College London,
Institute of Structural and Molecular Biology, 20 Gordon Street, London WC1H OAJ, United Kingdom
| | - Peter Hinterdorfer
- Department
of Applied Experimental Biophysics, Johannes
Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
| |
Collapse
|
13
|
Hu Z, Deng ZY, Feng HJ. Stretching effects on non-adiabatic electron dynamic behavior in poly(dG)-poly(dC) DNA upon the proton irradiation. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2023; 35:285101. [PMID: 37040786 DOI: 10.1088/1361-648x/accbfa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/11/2023] [Indexed: 06/19/2023]
Abstract
The electronic excitations caused by DNA when exposed to ion radiation is essential to DNA damage. In this paper, we investigated the energy deposition and electron excitation process of DNA with reasonable stretching range upon proton irradiation based on time-dependent density functional theory. Stretching changes the strength of hydrogen bonding between the DNA base pairs, which in turn affects the Coulomb interaction between the projectile and DNA. As a semi-flexible molecule, the way of energy deposition is weakly sensitive to the stretching rate of DNA. However, the increase of stretching rate causes the increase of charge density along the trajectory channel, sequentially resulting in an increase in proton resistance along the intruding channel. The Mulliken charge analysis indicates that the guanine base and guanine ribose are ionized, meanwhile the cytosine base and cytosine ribose are reduced at all stretching rates. In a few femtoseconds, there exists an electron flow passing through the guanine ribose, guanine, cytosine base and the cytosine ribose in turn. This electron flow increases electron transfer and DNA ionization, promoting the side chain damage of the DNA upon ion irradiation. Our results provide a theoretical insight for deciphering the physical mechanism of the early stage of the irradiation process, and are also of great significance for the study of particle beam cancer therapy in different biological tissues.
Collapse
Affiliation(s)
- Zhihua Hu
- School of Physics, Northwest University, Xi'an 710127, People's Republic of China
| | - Zun-Yi Deng
- School of Physics, Northwest University, Xi'an 710127, People's Republic of China
| | - Hong-Jian Feng
- School of Physics, Northwest University, Xi'an 710127, People's Republic of China
| |
Collapse
|
14
|
Mills A, Aissaoui N, Finkel J, Elezgaray J, Bellot G. Mechanical DNA Origami to Investigate Biological Systems. Adv Biol (Weinh) 2023; 7:e2200224. [PMID: 36509679 DOI: 10.1002/adbi.202200224] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/25/2022] [Indexed: 12/15/2022]
Abstract
The ability to self-assemble DNA nanodevices with programmed structural dynamics that can sense and respond to the local environment can enable transformative applications in fields including mechanobiology and nanomedicine. The responsive function of biomolecules is often driven by alterations in conformational distributions mediated by highly sensitive interactions with the local environment. In this review, the current state-of-the-art in constructing complex DNA geometries with dynamic and mechanical properties to enable a molecular scale force measurement is first summarized. Next, an overview of engineering modular DNA devices that interact with cell surfaces is highlighted detailing examples of mechanosensitive proteins and the force-induced dynamic molecular interaction on the downstream biochemical signaling. Finally, the challenges and an outlook on this promising class of DNA devices acting as nanomachines to operate at a low piconewton range suitable for a majority of biological effects or as hybrid materials to achieve higher tension exertion required for other biological investigations, are discussed.
Collapse
Affiliation(s)
- Allan Mills
- Centre de Biologie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, 34090, France
| | - Nesrine Aissaoui
- Laboratoire CiTCoM, Faculté de Santé, Université Paris Cité, CNRS, Paris, 75006, France
| | - Julie Finkel
- Centre de Biologie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, 34090, France
| | - Juan Elezgaray
- CRPP, CNRS, UMR 5031, Université de Bordeaux, Pessac, 33600, France
| | - Gaëtan Bellot
- Centre de Biologie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, 34090, France
| |
Collapse
|
15
|
Li T, Dufresne ER, Kröger M, Heyden S. Siloxane Molecules: Nonlinear Elastic Behavior and Fracture Characteristics. Macromolecules 2023; 56:1303-1310. [PMID: 36874533 PMCID: PMC9979691 DOI: 10.1021/acs.macromol.2c02576] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/17/2023] [Indexed: 02/10/2023]
Abstract
Fracture phenomena in soft materials span multiple length and time scales. This poses a major challenge in computational modeling and predictive materials design. To pass quantitatively from molecular to continuum scales, a precise representation of the material response at the molecular level is vital. Here, we derive the nonlinear elastic response and fracture characteristics of individual siloxane molecules using molecular dynamics (MD) studies. For short chains, we find deviations from classical scalings for both the effective stiffness and mean chain rupture times. A simple model of a nonuniform chain of Kuhn segments captures the observed effect and agrees well with MD data. We find that the dominating fracture mechanism depends on the applied force scale in a nonmonotonic fashion. This analysis suggests that common polydimethylsiloxane (PDMS) networks fail at cross-linking points. Our results can be readily lumped into coarse-grained models. Although focusing on PDMS as a model system, our study presents a general procedure to pass beyond the window of accessible rupture times in MD studies employing mean first passage time theory, which can be exploited for arbitrary molecular systems.
Collapse
Affiliation(s)
- Tianchi Li
- Soft and Living Materials, Department of Materials, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Eric R Dufresne
- Soft and Living Materials, Department of Materials, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Martin Kröger
- Polymer Physics, Department of Materials, ETH Zurich, CH-8093 Zurich, Switzerland.,Magnetism and Interface Physics, Department of Materials, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Stefanie Heyden
- Soft and Living Materials, Department of Materials, ETH Zurich, CH-8093 Zurich, Switzerland
| |
Collapse
|
16
|
Fiasconaro A, Falo F. Elastic traits of the extensible discrete wormlike chain model. Phys Rev E 2023; 107:024501. [PMID: 36932488 DOI: 10.1103/physreve.107.024501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Polymer models play the special role of elucidating the elementary features describing the physics of long molecules and become essential to interpret the measurements of their magnitudes. In this work the end-to-end distance of an extensible discrete wormlike chain polymer as a function of the applied force has been calculated both numerically and analytically, the latter as an effective approximation. The numerical evaluation uses the transfer matrix formalism to obtain an exact calculation of the partition function, while the analytic derivations generalize the simple phenomenological formulas largely used up to now. The obtained formulas are simple enough to be implemented in the fit analysis of experimental data of semiflexible extensible polymers, with the result that the elastic parameters obtained are compatible with previous measurements, and more, their accuracy strongly improves in a large range of chain extensibility.
Collapse
Affiliation(s)
- Alessandro Fiasconaro
- Departamento de Física de la Materia Condensada, Universidad de Zaragoza, 50009 Zaragoza, Spain and Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Zaragoza, Spain
| | - Fernando Falo
- Departamento de Física de la Materia Condensada, Universidad de Zaragoza, 50009 Zaragoza, Spain and Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Zaragoza, Spain
| |
Collapse
|
17
|
Mondal A, Bhattacherjee A. Understanding protein diffusion on force-induced stretched DNA conformation. Front Mol Biosci 2022; 9:953689. [PMID: 36545509 PMCID: PMC9760818 DOI: 10.3389/fmolb.2022.953689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 11/22/2022] [Indexed: 12/11/2022] Open
Abstract
DNA morphology is subjected to environmental conditions and is closely coupled with its function. For example, DNA experiences stretching forces during several biological processes, including transcription and genome transactions, that significantly alter its conformation from that of B-DNA. Indeed, a well-defined 1.5 times extended conformation of dsDNA, known as Σ-DNA, has been reported in DNA complexes with proteins such as Rad51 and RecA. A striking feature in Σ-DNA is that the nucleobases are partitioned into triplets of three locally stacked bases separated by an empty rise gap of ∼ 5 Å. The functional role of such a DNA base triplet was hypothesized to be coupled with the ease of recognition of DNA bases by DNA-binding proteins (DBPs) and the physical origin of three letters (codon/anti-codon) in the genetic code. However, the underlying mechanism of base-triplet formation and the ease of DNA base-pair recognition by DBPs remain elusive. To investigate, here, we study the diffusion of a protein on a force-induced stretched DNA using coarse-grained molecular dynamics simulations. Upon pulling at the 3' end of DNA by constant forces, DNA exhibits a conformational transition from B-DNA to a ladder-like S-DNA conformation via Σ-DNA intermediate. The resulting stretched DNA conformations exhibit non-uniform base-pair clusters such as doublets, triplets, and quadruplets, of which triplets are energetically more stable than others. We find that protein favors the triplet formation compared to its unbound form while interacting non-specifically along DNA, and the relative population of it governs the ruggedness of the protein-DNA binding energy landscape and enhances the efficiency of DNA base recognition. Furthermore, we analyze the translocation mechanism of a DBP under different force regimes and underscore the significance of triplet formation in regulating the facilitated diffusion of protein on DNA. Our study, thus, provides a plausible framework for understanding the structure-function relationship between triplet formation and base recognition by a DBP and helps to understand gene regulation in complex regulatory processes.
Collapse
Affiliation(s)
| | - Arnab Bhattacherjee
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| |
Collapse
|
18
|
Basu A, Bobrovnikov DG, Cieza B, Arcon JP, Qureshi Z, Orozco M, Ha T. Deciphering the mechanical code of the genome and epigenome. Nat Struct Mol Biol 2022; 29:1178-1187. [PMID: 36471057 PMCID: PMC10142808 DOI: 10.1038/s41594-022-00877-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 10/18/2022] [Indexed: 12/12/2022]
Abstract
Diverse DNA-deforming processes are impacted by the local mechanical and structural properties of DNA, which in turn depend on local sequence and epigenetic modifications. Deciphering this mechanical code (that is, this dependence) has been challenging due to the lack of high-throughput experimental methods. Here we present a comprehensive characterization of the mechanical code. Utilizing high-throughput measurements of DNA bendability via loop-seq, we quantitatively established how the occurrence and spatial distribution of dinucleotides, tetranucleotides and methylated CpG impact DNA bendability. We used our measurements to develop a physical model for the sequence and methylation dependence of DNA bendability. We validated the model by performing loop-seq on mouse genomic sequences around transcription start sites and CTCF-binding sites. We applied our model to test the predictions of all-atom molecular dynamics simulations and to demonstrate that sequence and epigenetic modifications can mechanically encode regulatory information in diverse contexts.
Collapse
Affiliation(s)
- Aakash Basu
- Department of Biosciences, Durham University, Durham, UK. .,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Dmitriy G Bobrovnikov
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Basilio Cieza
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Juan Pablo Arcon
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Zan Qureshi
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain.,Department of Biochemistry and Biomedicine, Universitat de Barcelona, Barcelona, Spain
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA. .,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA. .,Howard Hughes Medical Institute, Baltimore, MD, USA.
| |
Collapse
|
19
|
Evaluating the predictive character of the method of Constrained Geometries Simulate External Force with Density Functional Theory. FORCES IN MECHANICS 2022. [DOI: 10.1016/j.finmec.2022.100143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
20
|
Chen J, Peng Q, Peng X, Zhang H, Zeng H. Probing and Manipulating Noncovalent Interactions in Functional Polymeric Systems. Chem Rev 2022; 122:14594-14678. [PMID: 36054924 DOI: 10.1021/acs.chemrev.2c00215] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Noncovalent interactions, which usually feature tunable strength, reversibility, and environmental adaptability, have been recognized as driving forces in a variety of biological and chemical processes, contributing to the recognition between molecules, the formation of molecule clusters, and the establishment of complex structures of macromolecules. The marriage of noncovalent interactions and conventional covalent polymers offers the systems novel mechanical, physicochemical, and biological properties, which are highly dependent on the binding mechanisms of the noncovalent interactions that can be illuminated via quantification. This review systematically discusses the nanomechanical characterization of typical noncovalent interactions in polymeric systems, mainly through direct force measurements at microscopic, nanoscopic, and molecular levels, which provide quantitative information (e.g., ranges, strengths, and dynamics) on the binding behaviors. The fundamental understandings of intermolecular and interfacial interactions are then correlated to the macroscopic performances of a series of noncovalently bonded polymers, whose functions (e.g., stimuli-responsiveness, self-healing capacity, universal adhesiveness) can be customized through the manipulation of the noncovalent interactions, providing insights into the rational design of advanced materials with applications in biomedical, energy, environmental, and other engineering fields.
Collapse
Affiliation(s)
- Jingsi Chen
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Qiongyao Peng
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Xuwen Peng
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Hao Zhang
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Hongbo Zeng
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| |
Collapse
|
21
|
Sun M, Lu P, Yu C, Feng F, Li Q, Zhan J, Xu M, Liu Y, Yao L. Force-Coded Strategy for the Simultaneous Detection of Multiple Tumor-Related Proteins. Anal Chem 2022; 94:8992-8998. [PMID: 35713197 DOI: 10.1021/acs.analchem.2c01014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Multiplexed simultaneous detection of various cancer markers is required for accurate diagnosis and treatment of early cancer. In this work, we present a force-coded strategy for the simultaneous detection of tumor-related proteins with tunable dynamic range via magnetic sensing. The multiplexing capability of this method is achieved by designing DNA devices that can recognize different biomarkers and code them with different binding forces measured by the force-induced remnant magnetization spectroscopy, which is not influenced by the color of the light and the solution. Moreover, the force-coded assay with high sensitivity and adjustable detection range is robust, which could be used for practical biological applications such as magnetic sensing, handheld miniaturized systems, and potential in vivo diagnosis.
Collapse
Affiliation(s)
- Mengxue Sun
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pan Lu
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chanchan Yu
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feng Feng
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qilong Li
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinxiu Zhan
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Xu
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yajing Liu
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Yao
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
22
|
Rahman M, Islam KR, Islam MR, Islam MJ, Kaysir MR, Akter M, Rahman MA, Alam SMM. A Critical Review on the Sensing, Control, and Manipulation of Single Molecules on Optofluidic Devices. MICROMACHINES 2022; 13:968. [PMID: 35744582 PMCID: PMC9229244 DOI: 10.3390/mi13060968] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 02/06/2023]
Abstract
Single-molecule techniques have shifted the paradigm of biological measurements from ensemble measurements to probing individual molecules and propelled a rapid revolution in related fields. Compared to ensemble measurements of biomolecules, single-molecule techniques provide a breadth of information with a high spatial and temporal resolution at the molecular level. Usually, optical and electrical methods are two commonly employed methods for probing single molecules, and some platforms even offer the integration of these two methods such as optofluidics. The recent spark in technological advancement and the tremendous leap in fabrication techniques, microfluidics, and integrated optofluidics are paving the way toward low cost, chip-scale, portable, and point-of-care diagnostic and single-molecule analysis tools. This review provides the fundamentals and overview of commonly employed single-molecule methods including optical methods, electrical methods, force-based methods, combinatorial integrated methods, etc. In most single-molecule experiments, the ability to manipulate and exercise precise control over individual molecules plays a vital role, which sometimes defines the capabilities and limits of the operation. This review discusses different manipulation techniques including sorting and trapping individual particles. An insight into the control of single molecules is provided that mainly discusses the recent development of electrical control over single molecules. Overall, this review is designed to provide the fundamentals and recent advancements in different single-molecule techniques and their applications, with a special focus on the detection, manipulation, and control of single molecules on chip-scale devices.
Collapse
Affiliation(s)
- Mahmudur Rahman
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Kazi Rafiqul Islam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Rashedul Islam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Jahirul Islam
- Department of Electrical and Electronic Engineering, Khulna University of Engineering & Technology, Khulna 9203, Bangladesh;
| | - Md. Rejvi Kaysir
- Department of Electrical and Computer Engineering, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada;
- Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada
| | - Masuma Akter
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Arifur Rahman
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - S. M. Mahfuz Alam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| |
Collapse
|
23
|
Lee D, Woo Y, Lim JS, Park I, Park SK, Park JW. Quantification of a Neurological Protein in a Single Cell Without Amplification. ACS OMEGA 2022; 7:20165-20171. [PMID: 35722002 PMCID: PMC9201896 DOI: 10.1021/acsomega.2c02009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
Proteins are key biomolecules that not only play various roles in the living body but also are used as biomarkers. If these proteins can be quantified at the level of a single cell, understanding the role of proteins will be deepened and diagnosing diseases and abnormality will be further upgraded. In this study, we quantified a neurological protein in a single cell using atomic force microscopy (AFM). After capturing specifically disrupted-in-schizophrenia 1 (DISC1) in a single cell onto a microspot immobilizing the corresponding antibody on the surface, force mapping with AFM was followed to visualize individual DISC1. Although a large variation of the number of DISC1 in a cell was observed, the average number is 4.38 × 103, and the number agrees with the ensemble-averaged value. The current AFM approach for the quantitative analysis of proteins in a single cell should be useful to study molecular behavior of proteins in depth and to follow physiological change of individual cells in response to external stimuli.
Collapse
Affiliation(s)
- Donggyu Lee
- Department
of Life Sciences, Pohang University of Science
and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Youngsik Woo
- Department
of Life Sciences, Pohang University of Science
and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Ji-seon Lim
- Department
of Chemistry, Pohang University of Science
and Technology, 77 Cheongam-Ro,
Nam-Gu, Pohang 37673, Republic of Korea
| | - Ikbum Park
- Analysis
and Assessment Research Center, Research
Institute of Industrial Science and Technology, 67 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic
of Korea
| | - Sang Ki Park
- Department
of Life Sciences, Pohang University of Science
and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Joon Won Park
- Department
of Chemistry, Pohang University of Science
and Technology, 77 Cheongam-Ro,
Nam-Gu, Pohang 37673, Republic of Korea
- Institute
of Convergence Science, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic
of Korea
| |
Collapse
|
24
|
Lim JS, Kim HJ, Park I, Woo S, Kim JH, Park JW. Force Mapping Reveals the Spatial Distribution of Individual Proteins in a Neuron. NANO LETTERS 2022; 22:3865-3871. [PMID: 35549313 DOI: 10.1021/acs.nanolett.1c04395] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Conventional methods for studying the spatial distribution and expression level of proteins within neurons have primarily relied on immunolabeling and/or signal amplification. Here, we present an atomic force microscopy (AFM)-based nanoscale force mapping method, where Anti-LIMK1-tethered AFM probes were used to visualize individual LIMK1 proteins in cultured neurons directly through force measurements. We observed that the number density of LIMK1 decreased in neuronal somas after the cells were depolarized. We also elucidated the spatial distribution of LIMK1 in single spine areas and found that the protein predominantly locates at heads of spines rather than dendritic shafts. The study demonstrates that our method enables unveiling of the abundance and spatial distribution of a protein of interest in neurons without signal amplification or labeling. We expected that this approach should facilitate the studies of protein expression phenomena in depth in a wide range of biological systems.
Collapse
Affiliation(s)
- Ji-Seon Lim
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Hyun Jin Kim
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Ikbum Park
- Analysis and Assessment Research Center, Research Institute of Industrial Science and Technology, 67 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Sungwook Woo
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Joung-Hun Kim
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
- Institute of Convergence Science, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Joon Won Park
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
- Institute of Convergence Science, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| |
Collapse
|
25
|
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.
Collapse
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.
| |
Collapse
|
26
|
Engineered Molecular Therapeutics Targeting Fibrin and the Coagulation System: a Biophysical Perspective. Biophys Rev 2022; 14:427-461. [PMID: 35399372 PMCID: PMC8984085 DOI: 10.1007/s12551-022-00950-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/25/2022] [Indexed: 02/07/2023] Open
Abstract
The coagulation cascade represents a sophisticated and highly choreographed series of molecular events taking place in the blood with important clinical implications. One key player in coagulation is fibrinogen, a highly abundant soluble blood protein that is processed by thrombin proteases at wound sites, triggering self-assembly of an insoluble protein hydrogel known as a fibrin clot. By forming the key protein component of blood clots, fibrin acts as a structural biomaterial with biophysical properties well suited to its role inhibiting fluid flow and maintaining hemostasis. Based on its clinical importance, fibrin is being investigated as a potentially valuable molecular target in the development of coagulation therapies. In this topical review, we summarize our current understanding of the coagulation cascade from a molecular, structural and biophysical perspective. We highlight single-molecule studies on proteins involved in blood coagulation and report on the current state of the art in directed evolution and molecular engineering of fibrin-targeted proteins and polymers for modulating coagulation. This biophysical overview will help acclimatize newcomers to the field and catalyze interdisciplinary work in biomolecular engineering toward the development of new therapies targeting fibrin and the coagulation system.
Collapse
|
27
|
Lallemang M, Yu L, Cai W, Rischka K, Hartwig A, Haag R, Hugel T, Balzer BN. Multivalent non-covalent interactions lead to strongest polymer adhesion. NANOSCALE 2022; 14:3768-3776. [PMID: 35171194 DOI: 10.1039/d1nr08338d] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Multivalent interactions play a leading role in biological processes such as the inhibition of inflammation or virus internalization. The multivalent interactions show enhanced strength and better selectivity compared to monovalent interactions, but they are much less understood due to their complexity. Here, we detect molecular interactions in the range of a few piconewtons to several nanonewtons and correlate them with the formation and subsequent breaking of one or several bonds and assign these bonds. This becomes possible by performing atomic force microcopy (AFM)-based single molecule force spectroscopy of a multifunctional polymer covalently attached to an AFM cantilever tip on a substrate bound polymer layer of the multifunctional polymer. Varying the pH value and the crosslinking state of the polymer layer, we find that bonds of intermediate strength (non-covalent), like coordination bonds, give the highest multivalent bond strength, even outperforming strong (covalent) bonds. At the same time, covalent bonds enhance the polymer layer density, increasing in particular the number of non-covalent bonds. In summary, we can show that the key for the design of stable and durable polymer coatings is to provide a variety of multivalent interactions and to keep the number of non-covalent interactions at a high level.
Collapse
Affiliation(s)
- Max Lallemang
- Institute of Physical Chemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany.
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Leixiao Yu
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takusstraße 3, 14195 Berlin, Germany
| | - Wanhao Cai
- Institute of Physical Chemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany.
| | - Klaus Rischka
- Fraunhofer Institute for Manufacturing Technology and Advanced Materials IFAM, Wiener Straße 12, 28359 Bremen, Germany
| | - Andreas Hartwig
- Fraunhofer Institute for Manufacturing Technology and Advanced Materials IFAM, Wiener Straße 12, 28359 Bremen, Germany
- University of Bremen, Department 2 Biology/Chemistry, Leobener Straße 3, 28359 Bremen, Germany
| | - Rainer Haag
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takusstraße 3, 14195 Berlin, Germany
| | - Thorsten Hugel
- Institute of Physical Chemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany.
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Bizan N Balzer
- Institute of Physical Chemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany.
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Freiburg Materials Research Center (FMF), Albert Ludwig University of Freiburg, 79104 Freiburg, Germany
| |
Collapse
|
28
|
Liu Z, Moreira RA, Dujmović A, Liu H, Yang B, Poma AB, Nash MA. Mapping Mechanostable Pulling Geometries of a Therapeutic Anticalin/CTLA-4 Protein Complex. NANO LETTERS 2022; 22:179-187. [PMID: 34918516 PMCID: PMC8759085 DOI: 10.1021/acs.nanolett.1c03584] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/03/2021] [Indexed: 05/27/2023]
Abstract
We used single-molecule AFM force spectroscopy (AFM-SMFS) in combination with click chemistry to mechanically dissociate anticalin, a non-antibody protein binding scaffold, from its target (CTLA-4), by pulling from eight different anchor residues. We found that pulling on the anticalin from residue 60 or 87 resulted in significantly higher rupture forces and a decrease in koff by 2-3 orders of magnitude over a force range of 50-200 pN. Five of the six internal anchor points gave rise to complexes significantly more stable than N- or C-terminal anchor points, rupturing at up to 250 pN at loading rates of 0.1-10 nN s-1. Anisotropic network modeling and molecular dynamics simulations helped to explain the geometric dependency of mechanostability. These results demonstrate that optimization of attachment residue position on therapeutic binding scaffolds can provide large improvements in binding strength, allowing for mechanical affinity maturation under shear stress without mutation of binding interface residues.
Collapse
Affiliation(s)
- Zhaowei Liu
- Institute
of Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Rodrigo A. Moreira
- Biosystems
and Soft Matter Division, Institute of Fundamental
Technological Research, Polish Academy of Sciences, Pawińskiego 5B, 02-106 Warsaw, Poland
| | - Ana Dujmović
- Institute
of Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Haipei Liu
- Institute
of Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Byeongseon Yang
- Institute
of Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Adolfo B. Poma
- Biosystems
and Soft Matter Division, Institute of Fundamental
Technological Research, Polish Academy of Sciences, Pawińskiego 5B, 02-106 Warsaw, Poland
- International
Center for Research on Innovative Biobased Materials (ICRI-BioM)—International
Research Agenda, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland
| | - Michael A. Nash
- Institute
of Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
- National
Center for Competence in Research (NCCR) Molecular Systems Engineering, 4058 Basel, Switzerland
| |
Collapse
|
29
|
Taylor AMK, Okoniewski SR, Uyetake L, Perkins TT. Force-Activated DNA Substrates for In Situ Generation of ssDNA and Designed ssDNA/dsDNA Structures in an Optical-Trapping Assay. Methods Mol Biol 2022; 2478:273-312. [PMID: 36063324 DOI: 10.1007/978-1-0716-2229-2_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Single-molecule force spectroscopy can precisely probe the biomechanical interactions of proteins that unwind duplex DNA and bind to and wrap around single-stranded (ss)DNA. Yet assembly of the required substrates, which often contain a ssDNA segment embedded within a larger double-stranded (ds)DNA construct, can be time-consuming and inefficient, particularly when using a standard three-way hybridization protocol. In this chapter, we detail how to construct a variety of force-activated DNA substrates more efficiently. To do so, we engineered a dsDNA molecule with a designed sequence of specified GC content positioned between two enzymatically induced, site-specific nicks. Partially pulling this substrate into the overstretching transition of DNA (~65 pN) using an optical trap led to controlled dissociation of the ssDNA segment delineated by the two nicks. Here, we describe protocols for generating ssDNA of up to 1000 nucleotides as well as more complex structures, such as a 120-base-pair DNA hairpin positioned next to a 33-nucleotide ssDNA segment. The utility of the hairpin substrate was demonstrated by measuring the motion of E. coli. RecQ, a 3'-to-5' DNA helicase.
Collapse
Affiliation(s)
- Arnulf M K Taylor
- JILA, National Institute of Standards and Technology, and University of Colorado, Boulder, CO, USA
- Department of Physics, University of Colorado, Boulder, CO, USA
| | - Stephen R Okoniewski
- JILA, National Institute of Standards and Technology, and University of Colorado, Boulder, CO, USA
- Department of Physics, University of Colorado, Boulder, CO, USA
| | - Lyle Uyetake
- JILA, National Institute of Standards and Technology, and University of Colorado, Boulder, CO, USA
| | - Thomas T Perkins
- JILA, National Institute of Standards and Technology, and University of Colorado, Boulder, CO, USA.
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA.
| |
Collapse
|
30
|
Kameda T, Awazu A, Togashi Y. Molecular dynamics analysis of biomolecular systems including nucleic acids. Biophys Physicobiol 2022; 19:e190027. [DOI: 10.2142/biophysico.bppb-v19.0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/18/2022] [Indexed: 12/01/2022] Open
Affiliation(s)
| | - Akinori Awazu
- Graduate School of Integrated Sciences for Life, Hiroshima University
| | | |
Collapse
|
31
|
Tripathi S, Brahmachari S, Onuchic JN, Levine H. DNA supercoiling-mediated collective behavior of co-transcribing RNA polymerases. Nucleic Acids Res 2021; 50:1269-1279. [PMID: 34951454 PMCID: PMC8860607 DOI: 10.1093/nar/gkab1252] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 12/02/2021] [Accepted: 12/06/2021] [Indexed: 11/14/2022] Open
Abstract
Multiple RNA polymerases (RNAPs) transcribing a gene have been known to exhibit collective group behavior, causing the transcription elongation rate to increase with the rate of transcription initiation. Such behavior has long been believed to be driven by a physical interaction or ‘push’ between closely spaced RNAPs. However, recent studies have posited that RNAPs separated by longer distances may cooperate by modifying the DNA segment under transcription. Here, we present a theoretical model incorporating the mechanical coupling between RNAP translocation and the DNA torsional response. Using stochastic simulations, we demonstrate DNA supercoiling-mediated long-range cooperation between co-transcribing RNAPs. We find that inhibiting transcription initiation can slow down the already recruited RNAPs, in agreement with recent experimental observations, and predict that the average transcription elongation rate varies non-monotonically with the rate of transcription initiation. We further show that while RNAPs transcribing neighboring genes oriented in tandem can cooperate, those transcribing genes in divergent or convergent orientations can act antagonistically, and that such behavior holds over a large range of intergenic separations. Our model makes testable predictions, revealing how the mechanical interplay between RNAPs and the DNA they transcribe can govern transcriptional dynamics.
Collapse
Affiliation(s)
- Shubham Tripathi
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA.,Center for Theoretical Biological Physics & Department of Physics, Northeastern University, Boston, MA, USA
| | | | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.,Department of Physics and Astronomy, Department of Chemistry, & Department of Biosciences, Rice University, Houston, TX, USA
| | - Herbert Levine
- Center for Theoretical Biological Physics & Department of Physics, Northeastern University, Boston, MA, USA
| |
Collapse
|
32
|
Abstract
Invention of DNA origami has transformed the fabrication and application of biological nanomaterials. In this review, we discuss DNA origami nanoassemblies according to their four fundamental mechanical properties in response to external forces: elasticity, pliability, plasticity and stability. While elasticity and pliability refer to reversible changes in structures and associated properties, plasticity shows irreversible variation in topologies. The irreversible property is also inherent in the disintegration of DNA nanoassemblies, which is manifested by its mechanical stability. Disparate DNA origami devices in the past decade have exploited the mechanical regimes of pliability, elasticity, and plasticity, among which plasticity has shown its dominating potential in biomechanical and physiochemical applications. On the other hand, the mechanical stability of the DNA origami has been used to understand the mechanics of the assembly and disassembly of DNA nano-devices. At the end of this review, we discuss the challenges and future development of DNA origami nanoassemblies, again, from these fundamental mechanical perspectives.
Collapse
Affiliation(s)
- Jiahao Ji
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44240, USA.
| | - Deepak Karna
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44240, USA.
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44240, USA.
| |
Collapse
|
33
|
Loop-seq: A high-throughput technique to measure the mesoscale mechanical properties of DNA. Methods Enzymol 2021; 661:305-326. [PMID: 34776217 DOI: 10.1016/bs.mie.2021.08.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The local mechanical properties of the DNA polymer influence molecular processes in biology that require mechanical deformations of DNA. Lack of suitable high-throughput experimental techniques had precluded measuring how these properties might vary with sequence along the vast lengths of genomes. Here, we present a detailed protocol for a recently developed experimental technique called loop-seq, which measures at least one local mechanical property of DNA-its propensity to cyclize-in genome-scale throughput. Loop-seq has been used to obtain experimentally derived genome-wide maps of a physical property of DNA. Such measurements have revealed that diverse DNA-deforming processes involved in chromatin organization at various genomic loci are regulated by the genetically encoded, sequence-dependent variations in the mechanical properties of DNA.
Collapse
|
34
|
Delamarche E, Pereiro I, Kashyap A, Kaigala GV. Biopatterning: The Art of Patterning Biomolecules on Surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:9637-9651. [PMID: 34347483 DOI: 10.1021/acs.langmuir.1c00867] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Patterning biomolecules on surfaces provides numerous opportunities for miniaturizing biological assays; biosensing; studying proteins, cells, and tissue sections; and engineering surfaces that include biological components. In this Feature Article, we summarize the themes presented in our recent Langmuir Lecture on patterning biomolecules on surfaces, miniaturizing surface assays, and interacting with biointerfaces using three key technologies: microcontact printing, microfluidic networks, and microfluidic probes.
Collapse
Affiliation(s)
- Emmanuel Delamarche
- IBM Research Europe-Zurich, Säumerstrasse 4, Rüschlikon CH-8803, Switzerland
| | - Iago Pereiro
- IBM Research Europe-Zurich, Säumerstrasse 4, Rüschlikon CH-8803, Switzerland
| | - Aditya Kashyap
- IBM Research Europe-Zurich, Säumerstrasse 4, Rüschlikon CH-8803, Switzerland
| | - Govind V Kaigala
- IBM Research Europe-Zurich, Säumerstrasse 4, Rüschlikon CH-8803, Switzerland
| |
Collapse
|
35
|
Majumdar D. Elasticity of a DNA chain dotted with bubbles under force. Phys Rev E 2021; 103:052412. [PMID: 34134228 DOI: 10.1103/physreve.103.052412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 05/04/2021] [Indexed: 11/07/2022]
Abstract
The flexibility and the extension along the direction of the force are shown to be related to the bubble number fluctuation and the average number of bubbles, respectively, when the strands of the DNA are subjected to a force along the same direction, here called a stretching force. The force-temperature phase diagram shows the existence of a tricritical point, where the first-order force-induced zipping transition becomes continuous. On the other hand, when the forces are being applied in opposite directions, here called an unzipping force, the transition remains first order, with the possibility of vanishing of the low-temperature reentrant phase for a semiflexible DNA. Moreover, we found that the bulk elasticity changes only if an external force penetrates the bound phase and affects the bubble states.
Collapse
Affiliation(s)
- Debjyoti Majumdar
- Institute of Physics, Bhubaneswar, Odisha 751005, India and Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| |
Collapse
|
36
|
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.
Collapse
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
| |
Collapse
|
37
|
Penth M, Schellnhuber K, Bennewitz R, Blass J. Nanomechanics of self-assembled DNA building blocks. NANOSCALE 2021; 13:9371-9380. [PMID: 33999986 DOI: 10.1039/d0nr06865a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
DNA has become a powerful platform to design functional nanodevices. DNA nanodevices are often composed of self-assembled DNA building blocks that differ significantly from the structure of native DNA. In this study, we present Flow Force Microscopy as a massively parallel approach to study the nanomechanics of DNA self-assemblies on the single-molecular level. The high-throughput experiments performed in a simple microfluidic channel enable statistically meaningful studies with nanometer scale precision in a time frame of several minutes. A surprisingly high flexibility was observed for a typical construct used in DNA origami, reflected in a persistence length of 10.2 nm, a factor of five smaller than for native DNA. The enhanced flexibility is attributed to the discontinuous backbone of DNA self-assemblies that facilitate base pair opening by thermal fluctuations at the end of hybridized oligomers. We believe that the results will contribute to the fundamental understanding of DNA nanomechanics and help to improve the design of DNA nanodevices with applications in biological analysis and clinical research.
Collapse
Affiliation(s)
- Michael Penth
- INM - Leibniz Institute for New Materials, Campus D22, 66123 Saarbrücken, Germany. and Physics Department, Campus D22, 66123 Saarbrücken, Germany
| | - Kordula Schellnhuber
- INM - Leibniz Institute for New Materials, Campus D22, 66123 Saarbrücken, Germany. and Physics Department, Campus D22, 66123 Saarbrücken, Germany
| | - Roland Bennewitz
- INM - Leibniz Institute for New Materials, Campus D22, 66123 Saarbrücken, Germany. and Physics Department, Campus D22, 66123 Saarbrücken, Germany
| | - Johanna Blass
- INM - Leibniz Institute for New Materials, Campus D22, 66123 Saarbrücken, Germany.
| |
Collapse
|
38
|
Karna D, Pan W, Pandey S, Suzuki Y, Mao H. Mechanochemical properties of DNA origami nanosprings revealed by force jumps in optical tweezers. NANOSCALE 2021; 13:8425-8430. [PMID: 33908965 PMCID: PMC8170849 DOI: 10.1039/d0nr08605c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
By incorporating pH responsive i-motif elements, we have constructed DNA origami nanosprings that respond to pH changes in the environment. Using an innovative force jump approach in optical tweezers, we have directly measured the spring constants and dynamic recoiling responses of the DNA nanosprings under different forces. These DNA nanosprings exhibited 3 times slower recoiling rates compared to duplex DNA backbones. In addition, we observed two distinct force regions which show different spring constants. In the entropic region below 2 pN, a spring constant of ∼0.03 pN nm-1 was obtained, whereas in the enthalpic region above 2 pN, the nanospring was 17 times stronger (0.5 pN nm-1). The force jump gave a more accurate measurement on nanospring constants compared to regular force ramping approaches, which only yielded an average spring constant in a specific force range. Compared to the reported DNA origami nanosprings with a completely different design, our nanospring is up to 50 times stiffer. The drastic increase in the spring constant and the pH responsive feature allow more robust applications of these nanosprings in many mechanobiological processes.
Collapse
Affiliation(s)
- Deepak Karna
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, USA.
| | | | | | | | | |
Collapse
|
39
|
Danielsen SPO, Beech HK, Wang S, El-Zaatari BM, Wang X, Sapir L, Ouchi T, Wang Z, Johnson PN, Hu Y, Lundberg DJ, Stoychev G, Craig SL, Johnson JA, Kalow JA, Olsen BD, Rubinstein M. Molecular Characterization of Polymer Networks. Chem Rev 2021; 121:5042-5092. [PMID: 33792299 DOI: 10.1021/acs.chemrev.0c01304] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Polymer networks are complex systems consisting of molecular components. Whereas the properties of the individual components are typically well understood by most chemists, translating that chemical insight into polymer networks themselves is limited by the statistical and poorly defined nature of network structures. As a result, it is challenging, if not currently impossible, to extrapolate from the molecular behavior of components to the full range of performance and properties of the entire polymer network. Polymer networks therefore present an unrealized, important, and interdisciplinary opportunity to exert molecular-level, chemical control on material macroscopic properties. A barrier to sophisticated molecular approaches to polymer networks is that the techniques for characterizing the molecular structure of networks are often unfamiliar to many scientists. Here, we present a critical overview of the current characterization techniques available to understand the relation between the molecular properties and the resulting performance and behavior of polymer networks, in the absence of added fillers. We highlight the methods available to characterize the chemistry and molecular-level properties of individual polymer strands and junctions, the gelation process by which strands form networks, the structure of the resulting network, and the dynamics and mechanics of the final material. The purpose is not to serve as a detailed manual for conducting these measurements but rather to unify the underlying principles, point out remaining challenges, and provide a concise overview by which chemists can plan characterization strategies that suit their research objectives. Because polymer networks cannot often be sufficiently characterized with a single method, strategic combinations of multiple techniques are typically required for their molecular characterization.
Collapse
Affiliation(s)
- Scott P O Danielsen
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Haley K Beech
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Shu Wang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Bassil M El-Zaatari
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Xiaodi Wang
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | | | | | - Zi Wang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Patricia N Johnson
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Yixin Hu
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - David J Lundberg
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Georgi Stoychev
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Stephen L Craig
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Jeremiah A Johnson
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Julia A Kalow
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Bradley D Olsen
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Michael Rubinstein
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina 27599, United States.,Department of Chemistry, Duke University, Durham, North Carolina 27708, United States.,Departments of Biomedical Engineering and Physics, Duke University, Durham, North Carolina 27708, United States.,World Primer Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, Sapporo, Hokkaido 001-0021, Japan
| |
Collapse
|
40
|
Understanding transcription across scales: From base pairs to chromosomes. Mol Cell 2021; 81:1601-1616. [PMID: 33770487 DOI: 10.1016/j.molcel.2021.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/23/2021] [Accepted: 02/26/2021] [Indexed: 02/07/2023]
Abstract
The influence of genome organization on transcription is central to our understanding of cell type specification. Higher-order genome organization is established through short- and long-range DNA interactions. Coordination of these interactions, from single atoms to entire chromosomes, plays a fundamental role in transcriptional control of gene expression. Loss of this coupling can result in disease. Analysis of transcriptional regulation typically involves disparate experimental approaches, from structural studies that define angstrom-level interactions to cell-biological and genomic approaches that assess mesoscale relationships. Thus, to fully understand the mechanisms that regulate gene expression, it is critical to integrate the findings gained across these distinct size scales. In this review, I illustrate fundamental ways in which cells regulate transcription in the context of genome organization.
Collapse
|
41
|
Basu A, Bobrovnikov DG, Ha T. DNA mechanics and its biological impact. J Mol Biol 2021; 433:166861. [PMID: 33539885 DOI: 10.1016/j.jmb.2021.166861] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 02/06/2023]
Abstract
Almost all nucleoprotein interactions and DNA manipulation events involve mechanical deformations of DNA. Extraordinary progresses in single-molecule, structural, and computational methods have characterized the average mechanical properties of DNA, such as bendability and torsional rigidity, in high resolution. Further, the advent of sequencing technology has permitted measuring, in high-throughput, how such mechanical properties vary with sequence and epigenetic modifications along genomes. We review these recent technological advancements, and discuss how they have contributed to the emerging idea that variations in the mechanical properties of DNA play a fundamental role in regulating, genome-wide, diverse processes involved in chromatin organization.
Collapse
Affiliation(s)
- Aakash Basu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Dmitriy G Bobrovnikov
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA
| |
Collapse
|
42
|
Leitner M, Brummeir J, Plaimer GO, Kefer I, Poturnayova A, Hianik T, Ebner A. DNA building blocks for AFM tip functionalization: An easy, fast and stable strategy. Methods 2021; 197:54-62. [PMID: 33677061 DOI: 10.1016/j.ymeth.2021.02.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 02/13/2021] [Accepted: 02/27/2021] [Indexed: 10/22/2022] Open
Abstract
Biosensing atomic force microscopy (AFM) offers the unique feature to determine the energy landscape of a bimolecular interaction at the real single molecule level. Furthermore, simultaneous and label-free mapping of molecular recognition and the determination of sample topography at the nanoscale gets possible. A prerequisite and one of the major parts in biosensing AFM are the bio-functionalized AFM tips. In the past decades, different approaches for tip functionalization have been developed. Using these functionalization strategies, several biological highly relevant interactions at the single molecule level have been explored. For the most common approach, the use of a heterobifunctional poly(ethylenglycol) crosslinker, a broad range of linkers for different chemical coupling strategies is available. Nonetheless, the time consuming functionalization protocol as well as the broad distribution of rupture length reduces the possibility of automation and may reduce the accuracy of the results. Here we present a stable and fast forward approach based on tetra-functional DNA tetrahedra. A fast functionalization and a sharp defined distribution of rupture length gets possible with low effort and high success rate. We tested the performance on the classical avidin biotin system by using tetrahedra with three disulfide legs for stable and site directed coupling to gold coated tips and a biotinylated end at the fourth vertex. A special advantage appears when working with a DNA aptamer as sensing molecule. In this case, the fourth strand can be extended by a certain DNA sequence complementary to the linkage part of an aptamer. This AFM tip functionalization protocol was applied on thrombin using DNA aptamers directed against the fibrinogen binding side of human thrombin.
Collapse
Affiliation(s)
- Michael Leitner
- Institute of Biophysics, Johannes Kepler University, Gruberstrasse 40, 4020 Linz, Austria
| | - Julian Brummeir
- Institute of Biophysics, Johannes Kepler University, Gruberstrasse 40, 4020 Linz, Austria
| | - Gernot Oswald Plaimer
- Institute of Biophysics, Johannes Kepler University, Gruberstrasse 40, 4020 Linz, Austria
| | - Isabel Kefer
- Institute of Biophysics, Johannes Kepler University, Gruberstrasse 40, 4020 Linz, Austria
| | - Alexandra Poturnayova
- Center of Biosciences, Slovak Academy of Sciences, Dúbravská cesta 9, 840 05 Bratislava, Slovakia
| | - Tibor Hianik
- Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynská dolina F1, 842 48 Bratislava, Slovakia
| | - Andreas Ebner
- Institute of Biophysics, Johannes Kepler University, Gruberstrasse 40, 4020 Linz, Austria.
| |
Collapse
|
43
|
Everaers R, Becker NB, Rosa A. Single-molecule stretching experiments of flexible (wormlike) chain molecules in different ensembles: Theory and a potential application of finite chain length effects to nick-counting in DNA. J Chem Phys 2021; 154:024903. [PMID: 33445920 DOI: 10.1063/5.0028777] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We propose a formalism for deriving force-elongation and elongation-force relations for flexible chain molecules from analytical expressions for their radial distribution function, which provides insight into the factors controlling the asymptotic behavior and finite chain length corrections. In particular, we apply this formalism to our previously developed interpolation formula for the wormlike chain end-to-end distance distribution. The resulting expression for the asymptotic limit of infinite chain length is of similar quality to the numerical evaluation of Marko and Siggia's variational theory and considerably more precise than their interpolation formula. A comparison to numerical data suggests that our analytical finite chain length corrections achieve a comparable accuracy. As an application of our results, we discuss the possibility of inferring the time-dependent number of nicks in single-molecule stretching experiments on double-stranded DNA from the accompanying changes in the effective chain length.
Collapse
Affiliation(s)
- Ralf Everaers
- Université Lyon, ENS de Lyon, CNRS, Laboratoire de Physique and Centre Blaise Pascal, F-69342 Lyon, France
| | - Nils B Becker
- German Cancer Research Center, Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Angelo Rosa
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy
| |
Collapse
|
44
|
Li S, Wang X, Li Z, Huang Z, Lin S, Hu J, Tu Y. Research progress of single molecule force spectroscopy technology based on atomic force microscopy in polymer materials: Structure, design strategy and probe modification. NANO SELECT 2021. [DOI: 10.1002/nano.202000235] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Shi Li
- Guangzhou Institute of Chemistry Chinese Academy of Sciences Guangzhou 510650 PR China
- University of Chinese Academy of Sciences Beijing 100049 PR China
| | - Xiao Wang
- Guangzhou Institute of Chemistry Chinese Academy of Sciences Guangzhou 510650 PR China
- University of Chinese Academy of Sciences Beijing 100049 PR China
| | - Zhihua Li
- Guangzhou Institute of Chemistry Chinese Academy of Sciences Guangzhou 510650 PR China
- University of Chinese Academy of Sciences Beijing 100049 PR China
| | - Zhenzhu Huang
- Guangzhou Institute of Chemistry Chinese Academy of Sciences Guangzhou 510650 PR China
- Guangdong Provincial Key Laboratory of Organic Polymer Materials for Electronics Guangzhou 510650 PR China
- CAS Engineering Laboratory for Special Fine Chemicals Guangzhou 510650 PR China
- Incubator of Nanxiong CAS Co., Ltd. Nanxiong 512400 PR China
- University of Chinese Academy of Sciences Beijing 100049 PR China
| | - Shudong Lin
- Guangzhou Institute of Chemistry Chinese Academy of Sciences Guangzhou 510650 PR China
- Guangdong Provincial Key Laboratory of Organic Polymer Materials for Electronics Guangzhou 510650 PR China
- CAS Engineering Laboratory for Special Fine Chemicals Guangzhou 510650 PR China
- Incubator of Nanxiong CAS Co., Ltd. Nanxiong 512400 PR China
- University of Chinese Academy of Sciences Beijing 100049 PR China
| | - Jiwen Hu
- Guangzhou Institute of Chemistry Chinese Academy of Sciences Guangzhou 510650 PR China
- Guangdong Provincial Key Laboratory of Organic Polymer Materials for Electronics Guangzhou 510650 PR China
- CAS Engineering Laboratory for Special Fine Chemicals Guangzhou 510650 PR China
- Incubator of Nanxiong CAS Co., Ltd. Nanxiong 512400 PR China
- University of Chinese Academy of Sciences Beijing 100049 PR China
| | - Yuanyuan Tu
- Guangzhou Institute of Chemistry Chinese Academy of Sciences Guangzhou 510650 PR China
- Guangdong Provincial Key Laboratory of Organic Polymer Materials for Electronics Guangzhou 510650 PR China
- CAS Engineering Laboratory for Special Fine Chemicals Guangzhou 510650 PR China
- Incubator of Nanxiong CAS Co., Ltd. Nanxiong 512400 PR China
- University of Chinese Academy of Sciences Beijing 100049 PR China
| |
Collapse
|
45
|
Rifaie‐Graham O, Galensowske NFB, Dean C, Pollard J, Balog S, Gouveia MG, Chami M, Vian A, Amstad E, Lattuada M, Bruns N. Shear Stress-Responsive Polymersome Nanoreactors Inspired by the Marine Bioluminescence of Dinoflagellates. Angew Chem Int Ed Engl 2021; 60:904-909. [PMID: 32961006 PMCID: PMC7839717 DOI: 10.1002/anie.202010099] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Indexed: 12/22/2022]
Abstract
Some marine plankton called dinoflagellates emit light in response to the movement of surrounding water, resulting in a phenomenon called milky seas or sea sparkle. The underlying concept, a shear-stress induced permeabilisation of biocatalytic reaction compartments, is transferred to polymer-based nanoreactors. Amphiphilic block copolymers that carry nucleobases in their hydrophobic block are self-assembled into polymersomes. The membrane of the vesicles can be transiently switched between an impermeable and a semipermeable state by shear forces occurring in flow or during turbulent mixing of polymersome dispersions. Nucleobase pairs in the hydrophobic leaflet separate when mechanical force is applied, exposing their hydrogen bonding motifs and therefore making the membrane less hydrophobic and more permeable for water soluble compounds. This polarity switch is used to release payload of the polymersomes on demand, and to activate biocatalytic reactions in the interior of the polymersomes.
Collapse
Affiliation(s)
- Omar Rifaie‐Graham
- Adolphe Merkle InstituteUniversity of FribourgChemin des Verdiers 41700FribourgSwitzerland
- Current address: Department of Materials and Department of BioengineeringInstitute of Biomedical EngineeringImperial College LondonExhibition RoadLondonSW7 2AZUK
| | | | - Charlie Dean
- Adolphe Merkle InstituteUniversity of FribourgChemin des Verdiers 41700FribourgSwitzerland
| | - Jonas Pollard
- Adolphe Merkle InstituteUniversity of FribourgChemin des Verdiers 41700FribourgSwitzerland
| | - Sandor Balog
- Adolphe Merkle InstituteUniversity of FribourgChemin des Verdiers 41700FribourgSwitzerland
| | - Micael G. Gouveia
- Department of Pure and Applied ChemistryUniversity of StrathclydeThomas Graham Building, 295 Cathedral StreetGlasgowG1 1XLUK
| | - Mohamed Chami
- BioEM labCenter of Cellular Imaging and NanoAnalytics (C-CINA)BiozentrumUniversity of BaselMattenstrasse 264058BaselSwitzerland
| | - Antoine Vian
- Soft Materials LaboratoryInstitute of MaterialsÉcole Polytechnique Fédérale de Lausanne, EPFL-STI-IMX-SMALMXC 231 Station 121015LausanneSwitzerland
| | - Esther Amstad
- Soft Materials LaboratoryInstitute of MaterialsÉcole Polytechnique Fédérale de Lausanne, EPFL-STI-IMX-SMALMXC 231 Station 121015LausanneSwitzerland
| | - Marco Lattuada
- Department of ChemistryUniversity of FribourgChemin du Musée 91700FribourgSwitzerland
| | - Nico Bruns
- Adolphe Merkle InstituteUniversity of FribourgChemin des Verdiers 41700FribourgSwitzerland
- Department of Pure and Applied ChemistryUniversity of StrathclydeThomas Graham Building, 295 Cathedral StreetGlasgowG1 1XLUK
| |
Collapse
|
46
|
Razbin M, Mashaghi A. Elasticity of connected semiflexible quadrilaterals. SOFT MATTER 2021; 17:102-112. [PMID: 33150925 DOI: 10.1039/d0sm01719a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Using the positional-orientational propagator of a semiflexible filament in the weakly bending regime, we analytically calculate the probability densities associated with the fluctuating tip and the corners of a grafted system of connected quadrilaterals. We calculate closed analytic expressions for the probability densities within the framework of the worm-like chain model, which are valid in the weakly bending regime. The probability densities give the physical quantities related to the elasticity of the system such as the force-extension relation in the fixed extension ensemble, the Poisson's ratio and the average of the force exerted to a confining stiff planar wall by the fluctuating tip of the system. Our analysis reveals that the force-extension relations depend on the contour length of the system (material content), the bending stiffness (chemical nature), the geometrical angle and the number of the quadrilaterals, while the Poisson's ratio depends only on the geometrical angle and the number of the quadrilaterals, and is thus a purely geometric property of the system.
Collapse
Affiliation(s)
- Mohammadhosein Razbin
- Department of Energy Engineering and Physics, Amirkabir University of Technology, 14588 Tehran, Iran.
| | | |
Collapse
|
47
|
Kameda T, Suzuki MM, Awazu A, Togashi Y. Structural dynamics of DNA depending on methylation pattern. Phys Rev E 2021; 103:012404. [PMID: 33601517 DOI: 10.1103/physreve.103.012404] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 12/14/2020] [Indexed: 06/12/2023]
Abstract
DNA methylation is associated with a number of biological phenomena, and plays crucial roles in epigenetic regulation of eukaryotic gene expression. It is also suggested that DNA methylation alters the mechanical properties of DNA molecules, which is likely to affect epigenetic regulation. However, it has not been systematically investigated how methylation changes the structural and dynamic features of DNA. In this research, to elucidate the effects of methylation on DNA mechanics, a fully atomic molecular dynamics simulation of double-stranded DNA with several methylation patterns was performed. Through the analysis of the relative positioning of the nucleotides (base-step variables), characteristic changes in terms of local flexibility were observed, which further affected the overall DNA geometry and stiffness. These findings may serve as a basis for a discussion on methylation-dependent DNA dynamics in physiological conditions.
Collapse
Affiliation(s)
- Takeru Kameda
- Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
- RIKEN Center for Biosystems Dynamics Research (BDR), Wako, Saitama, Japan
| | - Miho M Suzuki
- Graduate School of Medicine, Nagoya University, Nagoya, Aichi, Japan
| | - Akinori Awazu
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
- Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Yuichi Togashi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
- Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
- RIKEN Center for Biosystems Dynamics Research (BDR), Higashi-Hiroshima, Hiroshima, Japan
| |
Collapse
|
48
|
Rifaie‐Graham O, Galensowske NFB, Dean C, Pollard J, Balog S, Gouveia MG, Chami M, Vian A, Amstad E, Lattuada M, Bruns N. Shear Stress‐Responsive Polymersome Nanoreactors Inspired by the Marine Bioluminescence of Dinoflagellates. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202010099] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Omar Rifaie‐Graham
- Adolphe Merkle Institute University of Fribourg Chemin des Verdiers 4 1700 Fribourg Switzerland
- Current address: Department of Materials and Department of Bioengineering Institute of Biomedical Engineering Imperial College London Exhibition Road London SW7 2AZ UK
| | | | - Charlie Dean
- Adolphe Merkle Institute University of Fribourg Chemin des Verdiers 4 1700 Fribourg Switzerland
| | - Jonas Pollard
- Adolphe Merkle Institute University of Fribourg Chemin des Verdiers 4 1700 Fribourg Switzerland
| | - Sandor Balog
- Adolphe Merkle Institute University of Fribourg Chemin des Verdiers 4 1700 Fribourg Switzerland
| | - Micael G. Gouveia
- Department of Pure and Applied Chemistry University of Strathclyde Thomas Graham Building, 295 Cathedral Street Glasgow G1 1XL UK
| | - Mohamed Chami
- BioEM lab Center of Cellular Imaging and NanoAnalytics (C-CINA) Biozentrum University of Basel Mattenstrasse 26 4058 Basel Switzerland
| | - Antoine Vian
- Soft Materials Laboratory Institute of Materials École Polytechnique Fédérale de Lausanne, EPFL-STI-IMX-SMAL MXC 231 Station 12 1015 Lausanne Switzerland
| | - Esther Amstad
- Soft Materials Laboratory Institute of Materials École Polytechnique Fédérale de Lausanne, EPFL-STI-IMX-SMAL MXC 231 Station 12 1015 Lausanne Switzerland
| | - Marco Lattuada
- Department of Chemistry University of Fribourg Chemin du Musée 9 1700 Fribourg Switzerland
| | - Nico Bruns
- Adolphe Merkle Institute University of Fribourg Chemin des Verdiers 4 1700 Fribourg Switzerland
- Department of Pure and Applied Chemistry University of Strathclyde Thomas Graham Building, 295 Cathedral Street Glasgow G1 1XL UK
| |
Collapse
|
49
|
Zhang X, Zhang Y, Zhang W. Dynamic topology of double-stranded telomeric DNA studied by single-molecule manipulation in vitro. Nucleic Acids Res 2020; 48:6458-6470. [PMID: 32496520 PMCID: PMC7337930 DOI: 10.1093/nar/gkaa479] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/17/2020] [Accepted: 05/27/2020] [Indexed: 12/18/2022] Open
Abstract
The dynamic topological structure of telomeric DNA is closely related to its biological function; however, no such structural information on full-length telomeric DNA has been reported due to difficulties synthesizing long double-stranded telomeric DNA. Herein, we developed an EM-PCR and TA cloning-based approach to synthesize long-chain double-stranded tandem repeats of telomeric DNA. Using mechanical manipulation assays based on single-molecule atomic force microscopy, we found that mechanical force can trigger the melting of double-stranded telomeric DNA and the formation of higher-order structures (G-quadruplexes or i-motifs). Our results show that only when both the G-strand and C-strand of double-stranded telomeric DNA form higher-order structures (G-quadruplexes or i-motifs) at the same time (e.g. in the presence of 100 mM KCl under pH 4.7), that the higher-order structure(s) can remain after the external force is removed. The presence of monovalent K+, single-wall carbon nanotubes (SWCNTs), acidic conditions, or short G-rich fragments (∼30 nt) can shift the transition from dsDNA to higher-order structures. Our results provide a new way to regulate the topology of telomeric DNA.
Collapse
Affiliation(s)
- Xiaonong Zhang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, People's Republic of China
| | - Yingqi Zhang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, People's Republic of China
| | - Wenke Zhang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, People's Republic of China
| |
Collapse
|
50
|
Wang H, Shen B, Song Y, Lee M, Zhang W. Nanomechanical Properties of a Supramolecular Helix Stabilized by Non-Covalent Interactions. Macromol Rapid Commun 2020; 41:e2000453. [PMID: 32902027 DOI: 10.1002/marc.202000453] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 08/30/2020] [Indexed: 11/06/2022]
Abstract
Supramolecular helices have unique properties and many potential applications, such as chiral separation and asymmetric catalysis. Mechanical property (stability) of the supramolecular helix plays important roles in their functions. Due to the limitation of detection method, it is quite challenging to investigate nanomechanical properties of individual supramolecular helices stabilized by pure supramolecular interactions. Here atomic force microscopy (AFM)-based single molecule force spectroscopy (SMFS) is used to study the nanomechanical properties of a thermal-responsive supramolecular helix. The unwinding force plateau is observed in the force-extension curve, and the rupture force of the helix is dependent on the loading rate. In addition, the force-induced unwinding process is reversible and there is almost no energy dissipation in the process. Furthermore, the result of thermal shape-fluctuation analysis shows that the persistence length of the supramolecular helix is about 222 nm, which is much larger than helical structure formed by double-stranded DNA (dsDNA). However, because of its unique backbone structure, the supramolecular helix exhibits higher dynamic flexibility during force-induced deformation, since the persistence length determined from the stretching experiment is much smaller (1.1 nm).
Collapse
Affiliation(s)
- Huijie Wang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, P. R. China
| | - Bowen Shen
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, P. R. China
| | - Yu Song
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, P. R. China
| | - Myongsoo Lee
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, P. R. China
| | - Wenke Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, P. R. China
| |
Collapse
|