1
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Mathur N, Singh A, Singh N. Force-induced unzipping of DNA in the presence of solvent molecules. Biophys Chem 2024; 307:107175. [PMID: 38244296 DOI: 10.1016/j.bpc.2024.107175] [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: 10/29/2023] [Revised: 12/22/2023] [Accepted: 01/08/2024] [Indexed: 01/22/2024]
Abstract
The melting of double-stranded DNA (dsDNA) in the presence of solvent molecules is a fundamental process with significant implications for understanding the thermal and mechanical behavior of DNA and its interactions with the surrounding environment. The solvents play an essential role in the structural transformation of DNA subjected to a pulling force. In this study, we simulate the thermal and force induced denaturation of dsDNA and elucidate the solvent dependent melting behavior, identifying key factors that influence the stability of DNA melting in presence of solvent molecules. Using a statistical model, we first find the melting profile of short heterogeneous DNA molecules in the presence of solvent molecules in Force ensemble. We also investigate the effect of solvent's strengths on the melting profile of DNA. In the force ensemble, we consider two homogeneous DNA chains and apply the force on different locations along the chain in the presence of solvent molecules. Different pathways manifest the melting of the molecule in both ensembles, and we found several interesting features of melting DNA in a constant force ensemble, such as lower critical force when the chain is pulled from the base pair close to a solvent molecule. The results provide new insights into the force-induced unzipping of DNA and could be used to develop new methods for controlling the unzipping process. By providing a better understanding of melting and unzipping of dsDNA in the presence of solvent molecules, this study provides valuable guidelines for predicting DNA thermodynamic quantities and for designing DNA nanostructures.
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Affiliation(s)
- Neha Mathur
- Birla Institute of Technology & Science, Pilani 333031, India
| | - Amar Singh
- Birla Institute of Technology & Science, Pilani 333031, India.
| | - Navin Singh
- Birla Institute of Technology & Science, Pilani 333031, India
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2
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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.
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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
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3
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Buche MR, Rimsza JM. Modeling single-molecule stretching experiments using statistical thermodynamics. Phys Rev E 2023; 108:064503. [PMID: 38243517 DOI: 10.1103/physreve.108.064503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/30/2023] [Indexed: 01/21/2024]
Abstract
Single-molecule stretching experiments are widely utilized within the fields of physics and chemistry to characterize the mechanics of individual bonds or molecules, as well as chemical reactions. Analytic relations describing these experiments are valuable, and these relations can be obtained through the statistical thermodynamics of idealized model systems representing the experiments. Since the specific thermodynamic ensembles manifested by the experiments affect the outcome, primarily for small molecules, the stretching device must be included in the idealized model system. Though the model for the stretched molecule might be exactly solvable, including the device in the model often prevents analytic solutions. In the limit of large or small device stiffness, the isometric or isotensional ensembles can provide effective approximations, but the device effects are missing. Here a dual set of asymptotically correct statistical thermodynamic theories are applied to develop accurate approximations for the full model system that includes both the molecule and the device. The asymptotic theories are first demonstrated to be accurate using the freely jointed chain model and then using molecular dynamics calculations of a single polyethylene chain.
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Affiliation(s)
- Michael R Buche
- Computational Solid Mechanics and Structural Dynamics, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - Jessica M Rimsza
- Geochemistry, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
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4
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Chauhan K, Mishra G, Kishore V, Kumar S. Appearance of de Gennes length in force-induced transitions. Phys Rev E 2023; 108:L042501. [PMID: 37978702 DOI: 10.1103/physreve.108.l042501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 06/12/2023] [Indexed: 11/19/2023]
Abstract
Using Langevin dynamic simulations, a simple coarse-grained model of a DNA protein construct is used to study the DNA rupture and the protein unfolding. We identify three distinct states: (i) zipped DNA and collapsed protein, (ii) unzipped DNA and stretched protein, and (iii) unzipped DNA and collapsed protein. Here, we find a phase diagram that shows these states depending on the size of the DNA handle and the protein. For a less stable protein, unfolding is solely governed by the size of the linker DNA, whereas if the protein's stability increases, complete unfolding becomes impossible because the rupture force for DNA has reached a saturation regime influenced by the de Gennes length. We show that unfolding occurs via a few intermediate states by monitoring the force-extension curve of the entire protein. We extend our study to a heterogeneous protein system, where similar intermediate states in two systems can lead to different protein unfolding paths.
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Affiliation(s)
- Keerti Chauhan
- Department of Physics, Banaras Hindu University, Varanasi 221 005, India
| | - Garima Mishra
- Department of Physics, Ashoka University, Sonipat 131 029, India
| | - Vimal Kishore
- Department of Physics, Banaras Hindu University, Varanasi 221 005, India
| | - Sanjay Kumar
- Department of Physics, Banaras Hindu University, Varanasi 221 005, India
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5
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Blanco PM, Narambuena CF, Madurga S, Mas F, Garcés JL. Unusual Aspects of Charge Regulation in Flexible Weak Polyelectrolytes. Polymers (Basel) 2023; 15:2680. [PMID: 37376324 DOI: 10.3390/polym15122680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/07/2023] [Accepted: 06/10/2023] [Indexed: 06/29/2023] Open
Abstract
This article reviews the state of the art of the studies on charge regulation (CR) effects in flexible weak polyelectrolytes (FWPE). The characteristic of FWPE is the strong coupling of ionization and conformational degrees of freedom. After introducing the necessary fundamental concepts, some unconventional aspects of the the physical chemistry of FWPE are discussed. These aspects are: (i) the extension of statistical mechanics techniques to include ionization equilibria and, in particular, the use of the recently proposed Site Binding-Rotational Isomeric State (SBRIS) model, which allows the calculation of ionization and conformational properties on the same foot; (ii) the recent progresses in the inclusion of proton equilibria in computer simulations; (iii) the possibility of mechanically induced CR in the stretching of FWPE; (iv) the non-trivial adsorption of FWPE on ionized surfaces with the same charge sign as the PE (the so-called "wrong side" of the isoelectric point); (v) the influence of macromolecular crowding on CR.
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Affiliation(s)
- Pablo M Blanco
- Physical Chemistry Unit, Materials Science and Physical Chemistry Department & Research Institute of Theoretical and Computational Chemistry (IQTCUB), Barcelona University (UB), 08028 Barcelona, Catalonia, Spain
| | - Claudio F Narambuena
- Grupo de Bionanotecnologia y Sistemas Complejos, Infap-CONICET & Facultad Regional San Rafael, Universidad Tecnológica Nacional, San Rafael 5600, Argentina
| | - Sergio Madurga
- Physical Chemistry Unit, Materials Science and Physical Chemistry Department & Research Institute of Theoretical and Computational Chemistry (IQTCUB), Barcelona University (UB), 08028 Barcelona, Catalonia, Spain
| | - Francesc Mas
- Physical Chemistry Unit, Materials Science and Physical Chemistry Department & Research Institute of Theoretical and Computational Chemistry (IQTCUB), Barcelona University (UB), 08028 Barcelona, Catalonia, Spain
| | - Josep L Garcés
- Chemistry Department, Technical School of Agricultural Engineering & AGROTECNIO, Lleida University (UdL), 25003 Lleida, Catalonia, Spain
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6
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Rudra S, Chauhan K, Singh AR, Kumar S. Force-induced melting of DNA hairpin: Unfolding pathways and phase diagrams. Phys Rev E 2023; 107:054501. [PMID: 37328992 DOI: 10.1103/physreve.107.054501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 04/27/2023] [Indexed: 06/18/2023]
Abstract
Using the exact enumeration technique, we have studied the force-induced melting of a DNA hairpin on the face centered cubic lattice for two different sequences which differ in terms of loop closing base pairs. The melting profiles obtained from the exact enumeration technique is consistent with the Gaussian network model and Langevin dynamics simulations. Probability distribution analysis based on the exact density of states revealed the microscopic details of the opening of the hairpin. We showed the existence of intermediate states near the melting temperature. We further showed that different ensembles used to model single-molecule force spectroscopy setups may give different force-temperature diagrams. We delineate the possible reasons for the observed discrepancies.
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Affiliation(s)
- Sumitra Rudra
- Department of Physics, Banaras Hindu University, Varanasi 221005, India
| | - Keerti Chauhan
- Department of Physics, Banaras Hindu University, Varanasi 221005, India
| | - Amit Raj Singh
- Department of Physics, Graphic Era Hill University, Dehradun 248002, India
| | - Sanjay Kumar
- Department of Physics, Banaras Hindu University, Varanasi 221005, India
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7
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Ordóñez C, Martínez-Zapata D, Santamaria R. Dissociation of the Watson-Crick base pairs in vacuum and in aqueous solution: a first-principles molecular dynamics study. J Biomol Struct Dyn 2022; 40:13207-13217. [PMID: 34629032 DOI: 10.1080/07391102.2021.1987988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The damage of the DNA structure can affect the correct functioning of the cellular processes. This work investigates the required forces to dissociate the Watson-Crick (WC) base pairs AT into A and T, and GC into G and C. The WC base pairs are immersed in water under realistic conditions of temperature, volume, and density that reproduce the main characteristics of a biological system. The simulations are based on first-principles molecular dynamics combined with steering atomic forces. In addition to the force intensities, the charge transfers between the nucleic acid bases, energy variations, and temperature fluctuations in the cleavage moments are reported. With the purpose of evaluating the effects of the aqueous medium, simulations of the WC base pairs in vacuum are included. The results considering the solvated medium are consistent with the experimental measurements, and show the importance of the aqueous solution to regulate the structural modifications of the nucleic acid bases. The investigation contributes with a novel molecular model in molecular simulations, and to better understand the biological processes where the DNA compounds play an active role in life forms.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Cristian Ordóñez
- Department of Theoretical Physics, Institute of Physics, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Daniel Martínez-Zapata
- Department of Theoretical Physics, Institute of Physics, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Ruben Santamaria
- Department of Theoretical Physics, Institute of Physics, Universidad Nacional Autónoma de México, Ciudad de México, México
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8
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Mishra RK, Maganti L. Antitumor drugs effect on the stability of double-stranded DNA: steered molecular dynamics analysis. J Biomol Struct Dyn 2022; 40:11373-11382. [PMID: 34355668 DOI: 10.1080/07391102.2021.1960193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Denaturation of the DNA double helix inside the cell is essential for cellular processes such as replication and transcription for the growth of the cells. However, the growth of unwanted cells, which are responsible for cancerous kind of disease, is one of the biggest challenges of modern therapeutics. DNA cross-linking agents may kill cancer cells by damaging their DNA and stopping them from dividing. In the present study, we have carried out steered molecular dynamics simulations to study the effects of rupture and unzipping forces on the stability of dsDNA in the absence and presence of covalently bonded drugs. We have found that the stability of dsDNA increases strongly in the presence of covalently bonded drugs. The microscopic study of disruption of hydrogen-bonds associated with base-pairs of the dsDNA and the study of the variation of stacking overlap parameters gives evidence of symmetry during the rupture and asymmetry in the unzip event. The significance of the mechanism of force-induced melting study of the dsDNA in the absence and presence of antitumor drugs might have a biological relevance as it provides a pathway to open the double helix in a specific position and may help for the pharmaceutical design of drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rakesh Kumar Mishra
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Lakshmi Maganti
- Computational Science Division, Saha Institute of Nuclear Physics, Kolkata, West Bengal, India
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9
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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: 44] [Impact Index Per Article: 22.0] [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.
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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
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10
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Ramos De Dios SM, Tiwari VK, McCune CD, Dhokale RA, Berkowitz DB. Biomacromolecule-Assisted Screening for Reaction Discovery and Catalyst Optimization. Chem Rev 2022; 122:13800-13880. [PMID: 35904776 DOI: 10.1021/acs.chemrev.2c00213] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Reaction discovery and catalyst screening lie at the heart of synthetic organic chemistry. While there are efforts at de novo catalyst design using computation/artificial intelligence, at its core, synthetic chemistry is an experimental science. This review overviews biomacromolecule-assisted screening methods and the follow-on elaboration of chemistry so discovered. All three types of biomacromolecules discussed─enzymes, antibodies, and nucleic acids─have been used as "sensors" to provide a readout on product chirality exploiting their native chirality. Enzymatic sensing methods yield both UV-spectrophotometric and visible, colorimetric readouts. Antibody sensors provide direct fluorescent readout upon analyte binding in some cases or provide for cat-ELISA (Enzyme-Linked ImmunoSorbent Assay)-type readouts. DNA biomacromolecule-assisted screening allows for templation to facilitate reaction discovery, driving bimolecular reactions into a pseudo-unimolecular format. In addition, the ability to use DNA-encoded libraries permits the barcoding of reactants. All three types of biomacromolecule-based screens afford high sensitivity and selectivity. Among the chemical transformations discovered by enzymatic screening methods are the first Ni(0)-mediated asymmetric allylic amination and a new thiocyanopalladation/carbocyclization transformation in which both C-SCN and C-C bonds are fashioned sequentially. Cat-ELISA screening has identified new classes of sydnone-alkyne cycloadditions, and DNA-encoded screening has been exploited to uncover interesting oxidative Pd-mediated amido-alkyne/alkene coupling reactions.
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Affiliation(s)
| | - Virendra K Tiwari
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Christopher D McCune
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Ranjeet A Dhokale
- Higuchi Biosciences Center, University of Kansas, Lawrence, Kansas 66047, United States
| | - David B Berkowitz
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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11
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Determination of protein-protein interactions at the single-molecule level using optical tweezers. Q Rev Biophys 2022; 55:e8. [PMID: 35946323 DOI: 10.1017/s0033583522000075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Biomolecular interactions are at the base of all physical processes within living organisms; the study of these interactions has led to the development of a plethora of different methods. Among these, single-molecule (in singulo) experiments have become relevant in recent years because these studies can give insight into mechanisms and interactions that are hidden for ensemble-based (in multiplo) methods. The focus of this review is on optical tweezer (OT) experiments, which can be used to apply and measure mechanical forces in molecular systems. OTs are based on optical trapping, where a laser is used to exert a force on a dielectric bead; and optically trap the bead at a controllable position in all three dimensions. Different experimental approaches have been developed to study protein–protein interactions using OTs, such as: (1) refolding and unfolding in trans interaction where one protein is tethered between the beads and the other protein is in the solution; (2) constant force in cis interaction where each protein is bound to a bead, and the tension is suddenly increased. The interaction may break after some time, giving information about the lifetime of the binding at that tension. And (3) force ramp in cis interaction where each protein is attached to a bead and a ramp force is applied until the interaction breaks. With these experiments, parameters such as kinetic constants (koff, kon), affinity values (KD), energy to the transition state ΔG≠, distance to the transition state Δx≠ can be obtained. These parameters characterize the energy landscape of the interaction. Some parameters such as distance to the transition state can only be obtained from force spectroscopy experiments such as those described here.
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12
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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.
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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
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13
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Chauhan K, Singh AR, Kumar S, Granek R. Can one detect intermediate denaturation states of DNA sequences by following the equilibrium open-close dynamic fluctuations of a single base pair? J Chem Phys 2022; 156:164907. [PMID: 35489993 DOI: 10.1063/5.0088109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Melting of DNA sequences may occur through a few major intermediate states, whose influence on the melting curve has been discussed previously, while their effect on the kinetics has not been explored thoroughly. Here, we chose a simple DNA sequence, forming a hairpin in its native (zipped) state, and study it using molecular dynamic (MD) simulations and a model integrating the Gaussian network model with bond-binding energies-the Gaussian binding energy (GBE) model. We find two major partial denaturation states, a bubble state and a partial unzipping state. We demonstrate the influence of these two states on the closing-opening base pair dynamics, as probed by a tagged bond auto-correlation function (ACF). We argue that the latter is measured by fluorescence correlation spectroscopy experiments, in which one base of the pair is linked to a fluorescent dye, while the complementary base is linked to a quencher, similar to the experiment reported by Altan-Bonnet et al. [Phys. Rev. Lett. 90, 138101 (2003)]. We find that tagging certain base pairs at temperatures around the melting temperature results in a multi-step relaxation of the ACF, while tagging other base pairs leads to an effectively single-step relaxation, albeit non-exponential. Only the latter type of relaxation has been observed experimentally, and we suggest which of the other base pairs should be tagged in order to observe multi-step relaxation. We demonstrate that this behavior can be observed with other sequences and argue that the GBE can reliably predict these dynamics for very long sequences, where MD simulations might be limited.
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Affiliation(s)
- Keerti Chauhan
- Department of Physics, Banaras Hindu University, Varanasi 221005, India
| | - Amit Raj Singh
- Department of Physics, Graphic Era Hill University, Dehradun 248002, India
| | - Sanjay Kumar
- Department of Physics, Banaras Hindu University, Varanasi 221005, India
| | - Rony Granek
- The Avram and Stella Goldstein-Goren Department of Biotechnology Engineering and The Ilse Katz Institute for Meso and Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
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14
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Simpson JD, Ray A, Koehler M, Mohammed D, Alsteens D. Atomic force microscopy applied to interrogate nanoscale cellular chemistry and supramolecular bond dynamics for biomedical applications. Chem Commun (Camb) 2022; 58:5072-5087. [PMID: 35315846 DOI: 10.1039/d1cc07200e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding biological interactions at a molecular level grants valuable information relevant to improving medical treatments and outcomes. Among the suite of technologies available, Atomic Force Microscopy (AFM) is unique in its ability to quantitatively probe forces and receptor-ligand interactions in real-time. The ability to assess the formation of supramolecular bonds and intermediates in real-time on surfaces and living cells generates important information relevant to understanding biological phenomena. Combining AFM with fluorescence-based techniques allows for an unprecedented level of insight not only concerning the formation and rupture of bonds, but understanding medically relevant interactions at a molecular level. As the ability of AFM to probe cells and more complex models improves, being able to assess binding kinetics, chemical topographies, and garner spectroscopic information will likely become key to developing further improvements in fields such as cancer, nanomaterials, and virology. The rapid response to the COVID-19 crisis, producing information regarding not just receptor affinities, but also strain-dependent efficacy of neutralizing nanobodies, demonstrates just how viable and integral to the pre-clinical development of information AFM techniques are in this era of medicine.
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Affiliation(s)
- Joshua D Simpson
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium.
| | - Ankita Ray
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium.
| | - Melanie Koehler
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium.
| | - Danahe Mohammed
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium.
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium.
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15
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Wang Y, Le JV, Crocker K, Darcy MA, Halley PD, Zhao D, Andrioff N, Croy C, Poirier MG, Bundschuh R, Castro CE. A nanoscale DNA force spectrometer capable of applying tension and compression on biomolecules. Nucleic Acids Res 2021; 49:8987-8999. [PMID: 34358322 PMCID: PMC8421221 DOI: 10.1093/nar/gkab656] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 06/30/2021] [Accepted: 07/27/2021] [Indexed: 02/04/2023] Open
Abstract
Single molecule force spectroscopy is a powerful approach to probe the structure, conformational changes, and kinetic properties of biological and synthetic macromolecules. However, common approaches to apply forces to biomolecules require expensive and cumbersome equipment and relatively large probes such as beads or cantilevers, which limits their use for many environments and makes integrating with other methods challenging. Furthermore, existing methods have key limitations such as an inability to apply compressive forces on single molecules. We report a nanoscale DNA force spectrometer (nDFS), which is based on a DNA origami hinge with tunable mechanical and dynamic properties. The angular free energy landscape of the nDFS can be engineered across a wide range through substitution of less than 5% of the strand components. We further incorporate a removable strut that enables reversible toggling of the nDFS between open and closed states to allow for actuated application of tensile and compressive forces. We demonstrate the ability to apply compressive forces by inducing a large bend in a 249bp DNA molecule, and tensile forces by inducing DNA unwrapping of a nucleosome sample. These results establish a versatile tool for force spectroscopy and robust methods for designing nanoscale mechanical devices with tunable force application.
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Affiliation(s)
- Yuchen Wang
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Jenny V Le
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Kyle Crocker
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Michael A Darcy
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Patrick D Halley
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Dengke Zhao
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Nick Andrioff
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Cassie Croy
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Michael G Poirier
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Ralf Bundschuh
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Carlos E Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
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16
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Cheng H, Yu J, Wang Z, Ma P, Guo C, Wang B, Zhong W, Xu B. Details of Single-Molecule Force Spectroscopy Data Decoded by a Network-Based Automatic Clustering Algorithm. J Phys Chem B 2021; 125:9660-9667. [PMID: 34425052 DOI: 10.1021/acs.jpcb.1c03552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Atomic force microscopy-single-molecule force spectroscopy (AFM-SMFS) is a powerful methodology to probe intermolecular and intramolecular interactions in biological systems because of its operability in physiological conditions, facile and rapid sample preparation, versatile molecular manipulation, and combined functionality with high-resolution imaging. Since a huge number of AFM-SMFS force-distance curves are collected to avoid human bias and errors and to save time, numerous algorithms have been developed to analyze the AFM-SMFS curves. Nevertheless, there is still a need to develop new algorithms for the analysis of AFM-SMFS data since the current algorithms cannot specify an unbinding force to a corresponding/each binding site due to the lack of networking functionality to model the relationship between the unbinding forces. To address this challenge, herein, we develop an unsupervised method, i.e., a network-based automatic clustering algorithm (NASA), to decode the details of specific molecules, e.g., the unbinding force of each binding site, given the input of AFM-SMFS curves. Using the interaction of heparan sulfate (HS)-antithrombin (AT) on different endothelial cell surfaces as a model system, we demonstrate that NASA is able to automatically detect the peak and calculate the unbinding force. More importantly, NASA successfully identifies three unbinding force clusters, which could belong to three different binding sites, for both Ext1f/f and Ndst1f/f cell lines. NASA has great potential to be applied either readily or slightly modified to other AFM-based SMFS measurements that result in "saw-tooth"-shaped force-distance curves showing jumps related to the force unbinding, such as antibody-antigen interaction and DNA-protein interaction.
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Affiliation(s)
- Huimin Cheng
- Big Data Analytics Lab, Department of Statistics, University of Georgia, Athens, Georgia 30602, United States
| | - Jun Yu
- School of Mathematics and Statistics, Beijing Institute of Technology, Beijing 100081, P. R. China
| | - Zhen Wang
- Big Data Analytics Lab, Department of Statistics, University of Georgia, Athens, Georgia 30602, United States
| | - Ping Ma
- Big Data Analytics Lab, Department of Statistics, University of Georgia, Athens, Georgia 30602, United States
| | - Cunlan Guo
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China.,Single Molecule Study Laboratory, College of Engineering, University of Georgia, Athens, Georgia 30602, United States
| | - Bin Wang
- Single Molecule Study Laboratory, College of Engineering, University of Georgia, Athens, Georgia 30602, United States
| | - Wenxuan Zhong
- Big Data Analytics Lab, Department of Statistics, University of Georgia, Athens, Georgia 30602, United States
| | - Bingqian Xu
- Single Molecule Study Laboratory, College of Engineering, University of Georgia, Athens, Georgia 30602, United States
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17
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Upadhyaya A, Kumar S. Effect of loop sequence on unzipping of short DNA hairpins. Phys Rev E 2021; 103:062411. [PMID: 34271739 DOI: 10.1103/physreve.103.062411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 05/27/2021] [Indexed: 11/07/2022]
Abstract
The dependence of stability on the sequence of a DNA hairpin has been investigated through atomistic simulations. For this, a sequence of 16 bases of a hairpin, which consists of a loop of four bases and a stem of six base pairs, has been considered. We have taken eight different sequences, where the first five base pairs were kept fixed in all sequences, whereas the loop sequence and the identity of the duplex base pair closing the loop have been varied. For these hairpin structures, force-induced melting (unzipping) studies were carried out to investigate the effect of the variables on the stability of hairpin. The temperature at which half of the base pairs are open is termed the melting temperature. We defined the unzipping force F_{h} (half of the base pairs are open) and showed that it may not provide the effect of closing the base pair or loop sequence on the stability of the DNA hairpin. In order to have a better understanding of the stability of a DNA hairpin, the closing base pair or hairpin loop must be open. This requires complete opening of the stem. We defined a force F_{c} at which all base pairs of the stem are open, and we showed that the F_{c} gives better understanding of DNA hairpin stability.
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Affiliation(s)
- Anurag Upadhyaya
- Department of Physics, Banaras Hindu University, Varanasi, 221 005, India
| | - Sanjay Kumar
- Department of Physics, Banaras Hindu University, Varanasi, 221 005, India
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18
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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.
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Affiliation(s)
- Debjyoti Majumdar
- Institute of Physics, Bhubaneswar, Odisha 751005, India and Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
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19
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Nanomechanical mechanisms of Lyme disease spirochete motility enhancement in extracellular matrix. Commun Biol 2021; 4:268. [PMID: 33649506 PMCID: PMC7921401 DOI: 10.1038/s42003-021-01783-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 02/01/2021] [Indexed: 01/31/2023] Open
Abstract
As opposed to pathogens passively circulating in the body fluids of their host, pathogenic species within the Spirochetes phylum are able to actively coordinate their movement in the host to cause systemic infections. Based on the unique morphology and high motility of spirochetes, we hypothesized that their surface adhesive molecules might be suitably adapted to aid in their dissemination strategies. Designing a system that mimics natural environmental signals, which many spirochetes face during their infectious cycle, we observed that a subset of their surface proteins, particularly Decorin binding protein (Dbp) A/B, can strongly enhance the motility of spirochetes in the extracellular matrix of the host. Using single-molecule force spectroscopy, we disentangled the mechanistic details of DbpA/B and decorin/laminin interactions. Our results show that spirochetes are able to leverage a wide variety of adhesion strategies through force-tuning transient molecular binding to extracellular matrix components, which concertedly enhance spirochetal dissemination through the host.
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20
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Mateti S, Mathesh M, Liu Z, Tao T, Ramireddy T, Glushenkov AM, Yang W, Chen YI. Mechanochemistry: A force in disguise and conditional effects towards chemical reactions. Chem Commun (Camb) 2021; 57:1080-1092. [PMID: 33438694 DOI: 10.1039/d0cc06581a] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Mechanochemistry refers to unusual chemical reactions induced by mechanical energy at room temperatures. It has attracted increased attention because of advantages, such as being a solution-free, energy saving, high-productivity and low-temperature process. However, there is limited understanding of the mechanochemical process because mechanochemistry is often conducted using closed milling devices, which are often regarded as a black box. This feature article shows that mechanochemical reactions can be controlled by varying milling parameters, such as the mechanical force, milling intensity, time and atmosphere. New nanomaterials with doped and functionalized structures can be produced under controlled conditions, which provide a critical insight for understanding mechanochemistry. A fundamental mechanism investigation using force microscopy is discussed.
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Affiliation(s)
- Srikanth Mateti
- Institute for Frontier Materials, Deakin University, Waurn Ponds, Vic 3216, Australia.
| | - Motilal Mathesh
- School of Life and Environmental Science, Deakin University, Geelong, Victoria 3216, Australia.
| | - Zhen Liu
- College of Materials Science and Engineering, Institute for Graphene Applied Technology Innovation, Qingdao University, 308 Ningxia Road, Qingdao 266071, P. R. China
| | - Tao Tao
- School of Materials and Energy, Guangdong University of Technology, Guangzhou 510006, P. R. China
| | - Thrinathreddy Ramireddy
- Research School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia
| | - Alexey M Glushenkov
- Research School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia
| | - Wenrong Yang
- School of Life and Environmental Science, Deakin University, Geelong, Victoria 3216, Australia.
| | - Ying Ian Chen
- Institute for Frontier Materials, Deakin University, Waurn Ponds, Vic 3216, Australia.
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21
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Müller DJ, Dumitru AC, Lo Giudice C, Gaub HE, Hinterdorfer P, Hummer G, De Yoreo JJ, Dufrêne YF, Alsteens D. Atomic Force Microscopy-Based Force Spectroscopy and Multiparametric Imaging of Biomolecular and Cellular Systems. Chem Rev 2020; 121:11701-11725. [PMID: 33166471 DOI: 10.1021/acs.chemrev.0c00617] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
During the last three decades, a series of key technological improvements turned atomic force microscopy (AFM) into a nanoscopic laboratory to directly observe and chemically characterize molecular and cell biological systems under physiological conditions. Here, we review key technological improvements that have established AFM as an analytical tool to observe and quantify native biological systems from the micro- to the nanoscale. Native biological systems include living tissues, cells, and cellular components such as single or complexed proteins, nucleic acids, lipids, or sugars. We showcase the procedures to customize nanoscopic chemical laboratories by functionalizing AFM tips and outline the advantages and limitations in applying different AFM modes to chemically image, sense, and manipulate biosystems at (sub)nanometer spatial and millisecond temporal resolution. We further discuss theoretical approaches to extract the kinetic and thermodynamic parameters of specific biomolecular interactions detected by AFM for single bonds and extend the discussion to multiple bonds. Finally, we highlight the potential of combining AFM with optical microscopy and spectroscopy to address the full complexity of biological systems and to tackle fundamental challenges in life sciences.
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Affiliation(s)
- Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Mattenstrasse 28, 4056 Basel, Switzerland
| | - Andra C Dumitru
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
| | - Cristina Lo Giudice
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
| | - Hermann E Gaub
- Applied Physics, Ludwig-Maximilians-Universität Munich, Amalienstrasse 54, 80799 München, Germany
| | - Peter Hinterdorfer
- Institute of Biophysics, Johannes Kepler University of Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics and Department of Physics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - James J De Yoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States.,Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Yves F Dufrêne
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
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22
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Redondo-Morata L, Losada-Pérez P, Giannotti MI. Lipid bilayers: Phase behavior and nanomechanics. CURRENT TOPICS IN MEMBRANES 2020; 86:1-55. [PMID: 33837691 DOI: 10.1016/bs.ctm.2020.08.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lipid membranes are involved in many physiological processes like recognition, signaling, fusion or remodeling of the cell membrane or some of its internal compartments. Within the cell, they are the ultimate barrier, while maintaining the fluidity or flexibility required for a myriad of processes, including membrane protein assembly. The physical properties of in vitro model membranes as model cell membranes have been extensively studied with a variety of techniques, from classical thermodynamics to advanced modern microscopies. Here we review the nanomechanics of solid-supported lipid membranes with a focus in their phase behavior. Relevant information obtained by quartz crystal microbalance with dissipation monitoring (QCM-D) and atomic force microscopy (AFM) as complementary techniques in the nano/mesoscale interface is presented. Membrane morphological and mechanical characterization will be discussed in the framework of its phase behavior, phase transitions and coexistence, in simple and complex models, and upon the presence of cholesterol.
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Affiliation(s)
- Lorena Redondo-Morata
- Center for Infection and Immunity of Lille, INSERM U1019, CNRS UMR 8204, Lille, France
| | - Patricia Losada-Pérez
- Experimental Soft Matter and Thermal Physics (EST) Group, Department of Physics, Université Libre de Bruxelles, Brussels, Belgium
| | - Marina Inés Giannotti
- Biomedical Research Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain; Institut de Bioenginyeria de Catalunya (IBEC), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Departament de Ciència de Materials i Química Física, Universitat de Barcelona, Barcelona, Spain.
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23
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Lansakara TI, Morris HS, Singh P, Kohen A, Tivanski AV. Rigid Double-Stranded DNA Linkers for Single Molecule Enzyme-Drug Interaction Measurements Using Molecular Recognition Force Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:4174-4183. [PMID: 32233509 DOI: 10.1021/acs.langmuir.9b03495] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Single-molecule studies can reveal the distribution of states and interactions between ligand-enzyme complexes not accessible for most studies that measure a large ensemble average response of many molecules. Furthermore, in some biological applications, the information regarding the outliers, not the average of measured properties, can be more important. The high spatial and force resolution provided by atomic force microscopy (AFM) under physiological conditions has been utilized in this study to quantify the force-distance relations of enzyme-drug interactions. Different immobilization techniques of the protein to a surface and the drug to AFM tip were quantitatively compared to improve the accuracy and precision of the measurement. Protein that is directly bound to the surface, forming a monolayer, was compared to enzyme molecules bound to the surface with rigid double-stranded (ds) DNA spacers. These surfaces immobilization techniques were studied with the drug bound directly to the AFM tip and drug bound via flexible poly(ethylene glycol) and rigid dsDNA linkers. The activity of the enzyme was found to be not significantly altered by immobilization methods relative to its activity in solution. The findings indicate that the approach for studying drug-enzyme interaction based on rigid dsDNA linker on the surface and either flexible or rigid linker on the tip affords straightforward, highly specific, reproducible, and accurate force measurements with a potential for single-molecule level studies. The method could facilitate in-depth examination of a broad spectrum of biological targets and potential drugs.
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Affiliation(s)
| | - Holly S Morris
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Priyanka Singh
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Alexei V Tivanski
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
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24
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Alghazeer R, Burwaiss AA, Howell NK, Alansari WS, Shamlan G, Eskandrani AA. Determining the Cytotoxicity of Oxidized Lipids in Cultured Caco-2 Cells Using Bioimaging Techniques. Molecules 2020; 25:molecules25071693. [PMID: 32272768 PMCID: PMC7180719 DOI: 10.3390/molecules25071693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/01/2020] [Accepted: 04/04/2020] [Indexed: 12/02/2022] Open
Abstract
Fish lipids are comprised of considerable quantities of polyunsaturated acids and are prone to oxidation, producing reactive oxygen species and hydroperoxides. This study aimed to evaluate the biochemical and structural alterations in Caco-2 cells following exposure to 100 μg/mL methyl linoleate or fish oil, and then radiated for 24, 48 or 72 h. Electron spin resonance spectroscopy detected free radicals in the lipid membrane, Raman microscopy observed biochemical alterations and atomic force microscopy identified changes in morphology, such as the breakdown of DNA bonds. The study showed that bioimaging and biochemical techniques can be effective at detecting and diagnosing cellular injuries incurred by lipid peroxidation.
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Affiliation(s)
- Rabia Alghazeer
- Chemistry Department, Faculty of Science, University of Tripoli, Tripoli 50676, Libya
- Correspondence:
| | - Abdullah A. Burwaiss
- Medicine Department, Faculty of Human Medicine, University of Tripoli, Tripoli 50676, Libya;
| | - Nazlin K. Howell
- School of Biomedical and Molecular Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK;
| | - Wafa S. Alansari
- Biochemistry Department, Faculty of Science, University of Jeddah, Jeddah 21577, Saudi Arabia;
| | - Ghalia Shamlan
- Department of Food Science and Nutrition, College of Food and agriculture Sciences, King Saud University, Riyadh 11362, Saudi Arabia;
| | - Areej A. Eskandrani
- Chemistry Department, Faculty of Science, Taibah University, Medina 30002, Saudi Arabia;
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25
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Bao Y, Luo Z, Cui S. Environment-dependent single-chain mechanics of synthetic polymers and biomacromolecules by atomic force microscopy-based single-molecule force spectroscopy and the implications for advanced polymer materials. Chem Soc Rev 2020; 49:2799-2827. [PMID: 32236171 DOI: 10.1039/c9cs00855a] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
"The Tao begets the One. One begets all things of the world." This quote from Tao Te Ching is still inspiring for scientists in chemistry and materials science: The "One" can refer to a single molecule. A macroscopic material is composed of numerous molecules. Although the relationship between the properties of the single molecule and macroscopic material is not well understood yet, it is expected that a deeper understanding of the single-chain mechanics of macromolecules will certainly facilitate the development of materials science. Atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) has been exploited extensively as a powerful tool to study the single-chain behaviors of macromolecules. In this review, we summarize the recent advances in the emerging field of environment-dependent single-chain mechanics of synthetic polymers and biomacromolecules by means of AFM-SMFS. First, the single-chain inherent elasticities of several typical linear macromolecules are introduced, which are also confirmed by one of three polymer models with theoretical elasticities of the corresponding macromolecules obtained from quantum mechanical (QM) calculations. Then, the effects of the external environments on the single-chain mechanics of synthetic polymers and biomacromolecules are reviewed. Finally, the impacts of single-chain mechanics of macromolecules on the development of polymer science especially polymer materials are illustrated.
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Affiliation(s)
- Yu Bao
- Key Laboratory of Advanced Technologies of Materials, Ministry of Education, Southwest Jiaotong University, Chengdu 610031, China.
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26
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Liu W, Guo Y, Wang K, Zhou X, Wang Y, Lü J, Shao Z, Hu J, Czajkowsky DM, Li B. Atomic force microscopy-based single-molecule force spectroscopy detects DNA base mismatches. NANOSCALE 2019; 11:17206-17210. [PMID: 31535117 DOI: 10.1039/c9nr05234h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Atomic force microscopy-based single-molecule-force spectroscopy is limited by low throughput. We introduce addressable DNA origami to study multiple target molecules. Six target DNAs that differed by only a single base-pair mismatch were clearly differentiated a rupture force of only 4 pN.
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Affiliation(s)
- Wenjing Liu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yourong Guo
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Kaizhe Wang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xingfei Zhou
- School of Science, Ningbo University, Ningbo 315211, Zhejiang, China
| | - Ying Wang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. and Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Junhong Lü
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. and Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Zhifeng Shao
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Jun Hu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. and Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China and School of Physical Science and Technology, Shanghai Tech University, Shanghai 201204, China
| | - Daniel M Czajkowsky
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Bin Li
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China. and Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
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27
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Xiao M, Lai W, Man T, Chang B, Li L, Chandrasekaran AR, Pei H. Rationally Engineered Nucleic Acid Architectures for Biosensing Applications. Chem Rev 2019; 119:11631-11717. [DOI: 10.1021/acs.chemrev.9b00121] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Tiantian Man
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Binbin Chang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
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28
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Pawlak R, Vilhena JG, Hinaut A, Meier T, Glatzel T, Baratoff A, Gnecco E, Pérez R, Meyer E. Conformations and cryo-force spectroscopy of spray-deposited single-strand DNA on gold. Nat Commun 2019; 10:685. [PMID: 30737410 PMCID: PMC6368621 DOI: 10.1038/s41467-019-08531-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 01/16/2019] [Indexed: 01/02/2023] Open
Abstract
Cryo-electron microscopy can determine the structure of biological matter in vitrified liquids. However, structure alone is insufficient to understand the function of native and engineered biomolecules. So far, their mechanical properties have mainly been probed at room temperature using tens of pico-newton forces with a resolution limited by thermal fluctuations. Here we combine force spectroscopy and computer simulations in cryogenic conditions to quantify adhesion and intra-molecular properties of spray-deposited single-strand DNA oligomers on Au(111). Sub-nanometer resolution images reveal folding conformations confirmed by simulations. Lifting shows a decay of the measured stiffness with sharp dips every 0.2-0.3 nm associated with the sequential peeling and detachment of single nucleotides. A stiffness of 30-35 N m-1 per stretched repeat unit is deduced in the nano-newton range. This combined study suggests how to better control cryo-force spectroscopy of adsorbed heterogeneous (bio)polymer and to potentially enable single-base recognition in DNA strands only few nanometers long.
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Affiliation(s)
- Rémy Pawlak
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056, Basel, Switzerland.
| | - J G Vilhena
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056, Basel, Switzerland.,Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049, Madrid, Spain
| | - Antoine Hinaut
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056, Basel, Switzerland
| | - Tobias Meier
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056, Basel, Switzerland
| | - Thilo Glatzel
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056, Basel, Switzerland
| | - Alexis Baratoff
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056, Basel, Switzerland
| | - Enrico Gnecco
- Otto Schott Institute of Materials Research, Friedrich Schiller University Jena, D-07742, Jena, Germany
| | - Rubén Pérez
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049, Madrid, Spain. .,Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049, Madrid, Spain.
| | - Ernst Meyer
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056, Basel, Switzerland.
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29
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Oh YJ, Koehler M, Lee Y, Mishra S, Park JW, Hinterdorfer P. Ultra-Sensitive and Label-Free Probing of Binding Affinity Using Recognition Imaging. NANO LETTERS 2019; 19:612-617. [PMID: 30560669 DOI: 10.1021/acs.nanolett.8b04883] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Reliable quantification of binding affinity is important in biotechnology and pharmacology and increasingly coupled with a demand for ultrasensitivity, nanoscale resolution, and minute sample amounts. Standard techniques are not able to meet these criteria. This study provides a new platform based on atomic force microscopy (AFM)-derived recognition imaging to determine affinity by visualizing single molecular bindings on nanosize dendrons. Using DNA hybridization as a demonstrator, an AFM sensor adorned with a cognate binding strand senses and localizes target DNAs at nanometer resolution. To overcome the limitations of speed and resolution, the AFM cantilever is sinusoidally oscillated close to resonance conditions at small amplitudes. The equilibrium dissociation constant of capturing DNA duplexes was obtained, yielding 2.4 × 10-10 M. Our label-free single-molecular biochemical analysis approach evidences the utility of recognition imaging and analysis in quantifying biomolecular interactions of just a few hundred molecules.
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Affiliation(s)
- Yoo Jin Oh
- Institute of Biophysics , Johannes Kepler University Linz , Gruberstrasse 40 , A-4020 Linz , Austria
| | - Melanie Koehler
- Institute of Biophysics , Johannes Kepler University Linz , Gruberstrasse 40 , A-4020 Linz , Austria
| | - Yoonhee Lee
- Department of Chemistry , Pohang University of Science and Technology , 77 Cheongam-Ro , Nam-Gu, Pohang 37673 , Republic of Korea
| | - Sourav Mishra
- Department of Chemistry , 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
| | - Peter Hinterdorfer
- Institute of Biophysics , Johannes Kepler University Linz , Gruberstrasse 40 , A-4020 Linz , Austria
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30
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Oh YJ, Hinterdorfer P. Investigation of Bacterial Curli Production and Adhesion Using AFM. Methods Mol Biol 2019; 1886:221-231. [PMID: 30374870 DOI: 10.1007/978-1-4939-8894-5_12] [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: 06/08/2023]
Abstract
Escherichia coli cells containing the amyloid curli protein CsgA bind to abiotic surfaces and the extracellular matrix protein fibronectin. Here we describe procedures for following bacterial attachment to glass surfaces and provide protocols for coupling bacterial cells to AFM tips. Using single microbial cell force spectroscopy in physiological environment, we show methods to probe mechanical parameters and the dissociation of curliated E. coli cells from fibronectin surfaces by quantifying Young's modulus, unbinding forces, and de-adhesion works.
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Affiliation(s)
- Yoo Jin Oh
- Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria.
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31
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Sumbul F, Rico F. Single-Molecule Force Spectroscopy: Experiments, Analysis, and Simulations. Methods Mol Biol 2019; 1886:163-189. [PMID: 30374867 DOI: 10.1007/978-1-4939-8894-5_9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The mechanical properties of cells and of subcellular components are important to obtain a mechanistic molecular understanding of biological processes. The quantification of mechanical resistance of cells and biomolecules using biophysical methods matured thanks to the development of nanotechnologies such as optical and magnetic tweezers, the biomembrane force probe, and atomic force microscopy (AFM). The quantitative nature of force spectroscopy measurements has converted AFM into a valuable tool in biophysics. Force spectroscopy allows the determination of the forces required to unfold protein domains and to disrupt individual receptor/ligand bonds. Molecular simulations as a computational microscope allow investigation of similar biological processes with an atomistic detail. In this chapter, we first provide a step-by-step protocol of force spectroscopy experiments using AFM, including sample preparation, measurements, and analysis and interpretation of the resulting dynamic force spectrum in terms of available theories. Next, we present the background for molecular dynamics (MD) simulations focusing on steered molecular dynamics (SMD) and the importance of bridging computational tools with experimental techniques.
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Affiliation(s)
- Fidan Sumbul
- LAI, Aix-Marseille Université, INSERM UMR_S 1067, CNRS UMR 7333, 163 Avenue de Luminy, Marseille, 13009, France
| | - Felix Rico
- LAI, Aix-Marseille Université, INSERM UMR_S 1067, CNRS UMR 7333, 163 Avenue de Luminy, Marseille, 13009, France.
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32
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Zdravković S, Satarić MV, Parkhomenko AY, Bugay AN. Demodulated standing solitary wave and DNA-RNA transcription. CHAOS (WOODBURY, N.Y.) 2018; 28:113103. [PMID: 30501228 DOI: 10.1063/1.5046772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 10/12/2018] [Indexed: 06/09/2023]
Abstract
Nonlinear dynamics of DNA molecule at segments where DNA-RNA transcription occurs is studied. Our basic idea is that the solitary wave, moving along the chain, transforms into a demodulated one at these segments. The second idea is that the wave becomes a standing one due to interaction with DNA surrounding, e.g., RNA polymerase molecules. We explain why this is biologically convenient and show that our results match the experimental ones. In addition, we suggest how to experimentally determine crucial constant describing covalent bonds within DNA.
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Affiliation(s)
- S Zdravković
- Institut za nuklearne nauke Vinča, Univerzitet u Beogradu, 11001 Beograd, Serbia
| | - M V Satarić
- Department of Mathematics, Physics and Geosciences, Serbian Academy of Sciences and Arts, 11000 Beograd, Serbia
| | - A Yu Parkhomenko
- Joint Institute for Nuclear Research, Joliot-Curie 6, 141980 Dubna, Moscow Region, Russia
| | - A N Bugay
- Joint Institute for Nuclear Research, Joliot-Curie 6, 141980 Dubna, Moscow Region, Russia
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33
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Mishra S, Lee Y, Park JW. Direct Quantification of Trace Amounts of a Chronic Myeloid Leukemia Biomarker Using Locked Nucleic Acid Capture Probes. Anal Chem 2018; 90:12824-12831. [PMID: 30272952 DOI: 10.1021/acs.analchem.8b03350] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular monitoring is indispensable for the clinical management of chronic myeloid leukemia (CML) patients. Real-time quantitative polymerase chain reaction (RT-qPCR) is the gold standard for the quantitative assessment of BCR-ABL transcript levels, which are critical in clinical decision-making. However, the frequent recurrence of the disease after drug discontinuation for 60% of patients has necessitated more sensitive and specific techniques to detect residual BCR-ABL transcripts. Here, we describe a quantification method for the detection of BCR-ABL targets at very low concentrations (<10 copies/sample) in the presence of a million copies of normal BCR and ABL genes. In this method, a fully modified locked nucleic acid (LNA) and a LNA/DNA chimera were used as capture probes, and the quantitative imaging mode of atomic force microscopy (AFM) was employed. Targets with one of the major breakpoints (found in more than 95% of CML patients), b3a2 and b2a2, were quantified. The BCR-ABL target captured on a miniaturized LNA-probe spot was scanned at nanometric resolution, and the samples containing one to ten copies of the BCR-ABL genes were examined. It was observed that the highest sensitivity, i.e., the detection of a single copy of the target gene, could be achieved through multiple runs, and the observed cluster number was well correlative (adjusted R2 = 0.999) to the target copy number in the sample solution. This observation clearly demonstrates that the LNA-based platform is effective in quantifying BCR-ABL targets with extremely low copy numbers, highlighting the potential applicability of AFM for use in the direct quantification of such targets without amplification or labeling.
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Affiliation(s)
- Sourav Mishra
- Department of Chemistry , Pohang University of Science and Technology , 77 Cheongam-Ro , Nam-Gu, Pohang 37673 , Republic of Korea
| | - Yoonhee Lee
- Department of Chemistry , 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
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34
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Sensing the Ultrastructure of Bacterial Surfaces and Their Molecular Binding Forces Using AFM. Methods Mol Biol 2018. [PMID: 29956243 DOI: 10.1007/978-1-4939-8591-3_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
In this protocol, we provide a detailed step-by-step bacterial surface imaging and molecular analysis procedure. With SPM (scanning probe microscopy)-based dynamic force microscopy (DFM) imaging, we achieved a so far unprecedented resolution of ~1 nm on the outer surface layer of Tannerella forsythia and monitored the production of curli fibers on Escherichia coli in physiological conditions. Moreover, using these immobilization methods, single-molecule force spectroscopy experiments were conducted on living bacterial cells.
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35
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Upadhyaya A, Nath S, Kumar S. Force-induced rupture of double-stranded DNA in the absence and presence of covalently bonded anti-tumor drugs: Insights from molecular dynamics simulations. J Chem Phys 2018; 148:215105. [DOI: 10.1063/1.5024975] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- Anurag Upadhyaya
- Department of Physics, Banaras Hindu University, Varanasi 221 005, India
| | - Shesh Nath
- Department of Physics, Banaras Hindu University, Varanasi 221 005, India
| | - Sanjay Kumar
- Department of Physics, Banaras Hindu University, Varanasi 221 005, India
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36
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Kurus NN, Dultsev FN. Determination of the Thermodynamic Parameters of DNA Double Helix Unwinding with the Help of Mechanical Methods. ACS OMEGA 2018; 3:2793-2797. [PMID: 30023851 PMCID: PMC6044692 DOI: 10.1021/acsomega.7b01815] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 02/26/2018] [Indexed: 06/08/2023]
Abstract
For the first time, rupture event scanning (REVS) procedure based on quartz crystal microbalance (QCM) and involving only mechanical action was used to determine the height of the energy barrier for dsDNA unwinding. Melting point was determined with the help of this procedure. To determine the thermodynamic parameters including enthalpy, DNA denaturation was represented as a unimolecular process. This allowed us to recover the energy profiles from the experimental data obtained by force measurements at different scanning times (reaction times) for different temperatures. The thus obtained results were compared with the data obtained with the help of another mechanical method, namely, atomic force microscopy. The mechanism of DNA unwinding in QCM-based experiments through the unzipping mode, as proposed by us in previous works, was confirmed. Thus, we demonstrated that REVS procedure may be used to assess the thermodynamic parameters of dsDNA unwinding.
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Affiliation(s)
- Nina N. Kurus
- Institute
of Semiconductor Physics, SB RAS, 13 Lavrentyev Avenue, 630090 Novosibirsk, Russia
| | - Fedor N. Dultsev
- Institute
of Semiconductor Physics, SB RAS, 13 Lavrentyev Avenue, 630090 Novosibirsk, Russia
- Novosibirsk
State University, 2 Pirogov
Street, 630090 Novosibirsk, Russia
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37
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Posch S, Obser T, König G, Schneppenheim R, Tampé R, Hinterdorfer P. Interaction of von Willebrand factor domains with collagen investigated by single molecule force spectroscopy. J Chem Phys 2018; 148:123310. [DOI: 10.1063/1.5007313] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Sandra Posch
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Tobias Obser
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Gesa König
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Reinhard Schneppenheim
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe-University Frankfurt, Frankfurt/Main, Germany
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38
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Walder R, Van Patten WJ, Adhikari A, Perkins TT. Going Vertical To Improve the Accuracy of Atomic Force Microscopy Based Single-Molecule Force Spectroscopy. ACS NANO 2018; 12:198-207. [PMID: 29244486 DOI: 10.1021/acsnano.7b05721] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Single-molecule force spectroscopy (SMFS) is a powerful technique to characterize the energy landscape of individual proteins, the mechanical properties of nucleic acids, and the strength of receptor-ligand interactions. Atomic force microscopy (AFM)-based SMFS benefits from ongoing progress in improving the precision and stability of cantilevers and the AFM itself. Underappreciated is that the accuracy of such AFM studies remains hindered by inadvertently stretching molecules at an angle while measuring only the vertical component of the force and extension, degrading both measurements. This inaccuracy is particularly problematic in AFM studies using double-stranded DNA and RNA due to their large persistence length (p ≈ 50 nm), often limiting such studies to other SMFS platforms (e.g., custom-built optical and magnetic tweezers). Here, we developed an automated algorithm that aligns the AFM tip above the DNA's attachment point to a coverslip. Importantly, this algorithm was performed at low force (10-20 pN) and relatively fast (15-25 s), preserving the connection between the tip and the target molecule. Our data revealed large uncorrected lateral offsets for 100 and 650 nm DNA molecules [24 ± 18 nm (mean ± standard deviation) and 180 ± 110 nm, respectively]. Correcting this offset yielded a 3-fold improvement in accuracy and precision when characterizing DNA's overstretching transition. We also demonstrated high throughput by acquiring 88 geometrically corrected force-extension curves of a single individual 100 nm DNA molecule in ∼40 min and versatility by aligning polyprotein- and PEG-based protein-ligand assays. Importantly, our software-based algorithm was implemented on a commercial AFM, so it can be broadly adopted. More generally, this work illustrates how to enhance AFM-based SMFS by developing more sophisticated data-acquisition protocols.
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Affiliation(s)
- Robert Walder
- JILA, National Institute of Standards and Technology , and University of Colorado, Boulder, Colorado 80309, United States
| | - William J Van Patten
- JILA, National Institute of Standards and Technology , and University of Colorado, Boulder, Colorado 80309, United States
| | - Ayush Adhikari
- JILA, National Institute of Standards and Technology , and University of Colorado, Boulder, Colorado 80309, United States
| | - Thomas T Perkins
- JILA, National Institute of Standards and Technology , and University of Colorado, Boulder, Colorado 80309, United States
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado , Boulder, Colorado 80309, United States
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39
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Fujishiro S, Minamino D, Obataya I, Saitoh N, Hosokawa Y, Ajiro H. Observation of Polylactide Stereocomplex by Atomic Force Microscopy. CHEM LETT 2018. [DOI: 10.1246/cl.170863] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Shinya Fujishiro
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Daiki Minamino
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Ikuo Obataya
- JPK Instruments Japanese Branch, 3-9-15 Iwamoto, Chiyoda-ku, Tokyo 101-0032, Japan
| | - Nobuhiro Saitoh
- JPK Instruments Japanese Branch, 3-9-15 Iwamoto, Chiyoda-ku, Tokyo 101-0032, Japan
| | - Yoichiroh Hosokawa
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Hiroharu Ajiro
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
- Institute for Research Initiatives, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
- JST-PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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40
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Leader A, Mandler D, Reches M. The role of hydrophobic, aromatic and electrostatic interactions between amino acid residues and a titanium dioxide surface. Phys Chem Chem Phys 2018; 20:29811-29816. [DOI: 10.1039/c8cp05775c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Understanding the nature of interactions between inorganic surfaces and biomolecules, such as amino acids and peptides, can enhance the development of new materials.
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Affiliation(s)
- Avia Leader
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology
- The Hebrew University of Jerusalem
- Edmond Safra Campus
- Jerusalem 919041
- Israel
| | - Daniel Mandler
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology
- The Hebrew University of Jerusalem
- Edmond Safra Campus
- Jerusalem 919041
- Israel
| | - Meital Reches
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology
- The Hebrew University of Jerusalem
- Edmond Safra Campus
- Jerusalem 919041
- Israel
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41
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Zhu R, Gruber HJ, Hinterdorfer P. Two Ligand Binding Sites in Serotonin Transporter Revealed by Nanopharmacological Force Sensing. Methods Mol Biol 2018; 1814:19-33. [PMID: 29956224 DOI: 10.1007/978-1-4939-8591-3_2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The number of ligand binding sites in neurotransmitter-sodium symporters has been determined by crystal structure analysis and molecular pharmacology with controversial results. Here, we designed molecular tools to measure the interaction forces between the serotonin transporter (SERT) and S-citalopram on the single-molecule level by means of atomic force microscopy. Force spectroscopy allows for the extraction of dynamic information under physiological conditions which is inaccessible via X-ray crystallography. Two populations of distinctly different binding strength between S-citalopram and SERT were demonstrated in Na+-containing buffer. In Li+-containing buffer, SERT showed merely low-force interactions, whereas the vestibular mutant SERT-G402H only displayed the high force population. These observations provide physical evidence for the existence of two different binding sites in SERT when tested under near-physiological conditions.
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Affiliation(s)
- Rong Zhu
- Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Hermann J Gruber
- Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Peter Hinterdorfer
- Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria.
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42
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Traxler L, Rathner P, Fahrner M, Stadlbauer M, Faschinger F, Charnavets T, Müller N, Romanin C, Hinterdorfer P, Gruber HJ. Multiple Evidenz für einen ungewöhnlichen Wechselwirkungsmodus zwischen Calmodulin und Orai-Proteinen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201708667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Lukas Traxler
- Institut für Biophysik; Johannes Kepler Universität; Gruberstrasse 40 4020 Linz Österreich
| | - Petr Rathner
- Institut für Organische Chemie; Johannes Kepler Universität; Altenberger Strasse 69 4020 Linz Österreich
| | - Marc Fahrner
- Institut für Biophysik; Johannes Kepler Universität; Gruberstrasse 40 4020 Linz Österreich
| | - Michael Stadlbauer
- Institut für Biophysik; Johannes Kepler Universität; Gruberstrasse 40 4020 Linz Österreich
| | - Felix Faschinger
- Institut für Biophysik; Johannes Kepler Universität; Gruberstrasse 40 4020 Linz Österreich
| | - Tatsiana Charnavets
- CF Centre of Molecular Structure, BIOCEV; Průmyslová 595 252 50 Vestec Tschechische Republik
| | - Norbert Müller
- Institut für Organische Chemie; Johannes Kepler Universität; Altenberger Strasse 69 4020 Linz Österreich
- Faculty of Science; University of South Bohemia; Branišovská 31 370 05 České Budějovice Tschechische Republik
| | - Christoph Romanin
- Institut für Biophysik; Johannes Kepler Universität; Gruberstrasse 40 4020 Linz Österreich
| | - Peter Hinterdorfer
- Institut für Biophysik; Johannes Kepler Universität; Gruberstrasse 40 4020 Linz Österreich
| | - Hermann J. Gruber
- Institut für Biophysik; Johannes Kepler Universität; Gruberstrasse 40 4020 Linz Österreich
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43
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Traxler L, Rathner P, Fahrner M, Stadlbauer M, Faschinger F, Charnavets T, Müller N, Romanin C, Hinterdorfer P, Gruber HJ. Detailed Evidence for an Unparalleled Interaction Mode between Calmodulin and Orai Proteins. Angew Chem Int Ed Engl 2017; 56:15755-15759. [PMID: 29024298 DOI: 10.1002/anie.201708667] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Indexed: 12/12/2022]
Abstract
Calmodulin (CaM) binds most of its targets by wrapping around an amphipathic α-helix. The N-terminus of Orai proteins contains a conserved CaM-binding segment but the binding mechanism has been only partially characterized. Here, microscale thermophoresis (MST), surface plasmon resonance (SPR), and atomic force microscopy (AFM) were employed to study the binding equilibria, the kinetics, and the single-molecule interaction forces involved in the binding of CaM to the conserved helical segments of Orai1 and Orai3. The results consistently indicated stepwise binding of two separate target peptides to the two lobes of CaM. An unparalleled high affinity was found when two Orai peptides were dimerized or immobilized at high lateral density, thereby mimicking the close proximity of the N-termini in native Orai oligomers. The analogous experiments with smooth muscle myosin light chain kinase (smMLCK) showed only the expected 1:1 binding, confirming the validity of our methods.
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Affiliation(s)
- Lukas Traxler
- Institute of Biophysics, Johannes Kepler University, Gruberstrasse 40, 4020, Linz, Austria
| | - Petr Rathner
- Institute of Organic Chemistry, Johannes Kepler University, Altenberger Strasse 69, 4020, Linz, Austria
| | - Marc Fahrner
- Institute of Biophysics, Johannes Kepler University, Gruberstrasse 40, 4020, Linz, Austria
| | - Michael Stadlbauer
- Institute of Biophysics, Johannes Kepler University, Gruberstrasse 40, 4020, Linz, Austria
| | - Felix Faschinger
- Institute of Biophysics, Johannes Kepler University, Gruberstrasse 40, 4020, Linz, Austria
| | - Tatsiana Charnavets
- CF Centre of Molecular Structure, BIOCEV, Průmyslová 595, 252 50, Vestec, Czech Republic
| | - Norbert Müller
- Institute of Organic Chemistry, Johannes Kepler University, Altenberger Strasse 69, 4020, Linz, Austria.,Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Christoph Romanin
- Institute of Biophysics, Johannes Kepler University, Gruberstrasse 40, 4020, Linz, Austria
| | - Peter Hinterdorfer
- Institute of Biophysics, Johannes Kepler University, Gruberstrasse 40, 4020, Linz, Austria
| | - Hermann J Gruber
- Institute of Biophysics, Johannes Kepler University, Gruberstrasse 40, 4020, Linz, Austria
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44
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Dultsev FN, Kurus NN. Temperature dependence of unwinding forces between complementary oligonucleotides. J Microbiol Methods 2017; 143:94-97. [PMID: 29079297 DOI: 10.1016/j.mimet.2017.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 10/23/2017] [Accepted: 10/23/2017] [Indexed: 11/18/2022]
Abstract
Rupture Event Scanning (REVS) was used to study oligonucleotide unwinding under mechanical load. Oligonucleotide melting temperature was successfully estimated using this method. To estimate the enthalpy of reaction, we represented denaturation process as a unimolecular reaction. This gave us the possibility to recover the force profile from the experimental data obtained in force measurements at different scanning time (reaction time) for different temperatures.
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Affiliation(s)
- Fedor N Dultsev
- Institute of Semiconductor Physics, SB RAS, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia.
| | - Nina N Kurus
- Institute of Semiconductor Physics, SB RAS, Novosibirsk 630090, Russia
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Biomolecular stiffness detection based on positive frequency shift of CMOS compatible gigahertz solidly mounted resonators. Biosens Bioelectron 2017; 96:206-212. [DOI: 10.1016/j.bios.2017.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 04/25/2017] [Accepted: 05/02/2017] [Indexed: 01/15/2023]
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Singh AR, Granek R. Manipulation of double-stranded DNA melting by force. Phys Rev E 2017; 96:032417. [PMID: 29347050 DOI: 10.1103/physreve.96.032417] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Indexed: 01/03/2023]
Abstract
By integrating elasticity-as described by the Gaussian network model-with bond binding energies that distinguish between different base-pair identities and stacking configurations, we study the force induced melting of a double-stranded DNA (dsDNA). Our approach is a generalization of our previous study of thermal dsDNA denaturation [J. Chem. Phys. 145, 144101 (2016)JCPSA60021-960610.1063/1.4964285] to that induced by force at finite temperatures. It allows us to obtain semimicroscopic information about the opening of the chain, such as whether the dsDNA opens from one of the ends or from the interior, forming an internal bubble. We study different types of force manipulation: (i) "end unzipping," with force acting at a single end base pair perpendicular to the helix, (ii) "midunzipping," with force acting at a middle base pair perpendicular to the helix, and (iii) "end shearing," where the force acts at opposite ends along the helix. By monitoring the free-energy landscape and probability distribution of intermediate denaturation states, we show that different dominant intermediate states are stabilized depending on the type of force manipulation used. In particular, the bubble state of the sequence L60B36, which we have previously found to be a stable state during thermal denaturation, is absent for end unzipping and end shearing, whereas very similar bubbles are stabilized by midunzipping, or when the force location is near the middle of the chain. Ours results offer a simple tool for stabilizing bubbles and loops using force manipulations at different temperatures, and may implicate on the mechanism in which DNA enzymes or motors open regions of the chain.
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Affiliation(s)
- Amit Raj Singh
- The Stella and Avram Goren-Goldstein Department of Biotechnology Engineering, Ben-Gurion University of The Negev, Beer Sheva 84105, Israel
| | - Rony Granek
- The Stella and Avram Goren-Goldstein Department of Biotechnology Engineering, Ben-Gurion University of The Negev, Beer Sheva 84105, Israel.,The Ilse Katz Institute for Meso and Nanoscale Science and Technology, Ben-Gurion University of The Negev, Beer Sheva 84105, Israel
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Muramatsu H, Shimada S, Okada T. Direct measurement of interaction forces between a platinum dichloride complex and DNA molecules. J Biol Phys 2017; 43:355-365. [PMID: 28664286 DOI: 10.1007/s10867-017-9456-5] [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: 12/21/2016] [Accepted: 05/18/2017] [Indexed: 11/26/2022] Open
Abstract
The interaction forces between a platinum dichloride complex and DNA molecules have been studied using atomic force microscopy (AFM). The platinum dichloride complex, di-dimethylsulfoxide-dichloroplatinum (II) (Pt(DMSO)2Cl2), was immobilized on an AFM probe by coordinating the platinum to two amino groups to form a complex similar to Pt(en)Cl2, which is structurally similar to cisplatin. The retraction forces were measured between the platinum complex and DNA molecules immobilized on mica plates using force curve measurements. The histogram of the retraction force for λ-DNA showed several peaks; the unit retraction force was estimated to be 130 pN for a pulling rate of 60 nm/s. The retraction forces were also measured separately for four single-base DNA oligomers (adenine, guanine, thymine, and cytosine). Retraction forces were frequently observed in the force curves for the DNA oligomers of guanine and adenine. For the guanine DNA oligomer, the most frequent retraction force was slightly lower than but very similar to the retraction force for λ-DNA. A higher retraction force was obtained for the adenine DNA oligomer than for the guanine oligomer. This result is consistent with a higher retraction activation energy of adenine with the Pt complex being than that of guanine because the kinetic rate constant for retraction correlates to exp(FΔx - ΔE) where ΔE is an activation energy, F is an applied force, and Δx is a displacement of distance.
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Affiliation(s)
- Hiroshi Muramatsu
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura, Hachioji, Tokyo, 192-0982, Japan.
| | - Shogo Shimada
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura, Hachioji, Tokyo, 192-0982, Japan
- New Histo. Science Laboratory Co., Ltd, 2-979-2 Kurosawa, Ohme, Tokyo, 198-0005, Japan
| | - Tomoko Okada
- Graduate School of Health Sciences, Komazawa University, 1-23-1 Komazawa, Setagayaku, Tokyo, 154-8525, Japan
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Dufrêne YF, Ando T, Garcia R, Alsteens D, Martinez-Martin D, Engel A, Gerber C, Müller DJ. Imaging modes of atomic force microscopy for application in molecular and cell biology. NATURE NANOTECHNOLOGY 2017; 12:295-307. [PMID: 28383040 DOI: 10.1038/nnano.2017.45] [Citation(s) in RCA: 478] [Impact Index Per Article: 68.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 02/23/2017] [Indexed: 05/22/2023]
Abstract
Atomic force microscopy (AFM) is a powerful, multifunctional imaging platform that allows biological samples, from single molecules to living cells, to be visualized and manipulated. Soon after the instrument was invented, it was recognized that in order to maximize the opportunities of AFM imaging in biology, various technological developments would be required to address certain limitations of the method. This has led to the creation of a range of new imaging modes, which continue to push the capabilities of the technique today. Here, we review the basic principles, advantages and limitations of the most common AFM bioimaging modes, including the popular contact and dynamic modes, as well as recently developed modes such as multiparametric, molecular recognition, multifrequency and high-speed imaging. For each of these modes, we discuss recent experiments that highlight their unique capabilities.
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Affiliation(s)
- Yves F Dufrêne
- Institute of Life Sciences and Walloon Excellence in Life Sciences and Biotechnology (WELBIO), Université catholique de Louvain, Croix du Sud 4-5, bte L7.07.06., B-1348 Louvain-la-Neuve, Belgium
| | - Toshio Ando
- Department of Physics, Kanazawa University, Kanazawa 920-1192, Japan
| | - Ricardo Garcia
- Instituto de Ciencia de Materiales de Madrid, CSIC, Sor Juana Inés de la Cruz 3, 28049 Madrid, Spain
| | - David Alsteens
- Institute of Life Sciences and Walloon Excellence in Life Sciences and Biotechnology (WELBIO), Université catholique de Louvain, Croix du Sud 4-5, bte L7.07.06., B-1348 Louvain-la-Neuve, Belgium
| | - David Martinez-Martin
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Mattenstrasse 28, 4056 Basel, Switzerland
| | - Andreas Engel
- Department of BioNanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Christoph Gerber
- Swiss Nanoscience Institute, University of Basel, Klingelbergstrasse 80, 4057 Basel, Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Mattenstrasse 28, 4056 Basel, Switzerland
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Affiliation(s)
- Adam K. Sieradzan
- Chemistry
Department, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland
| | - Paweł Krupa
- Chemistry
Department, University of Gdańsk, Wita Stwosza 63, Gdańsk 80-308, Poland
- Institute
of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668 Warsaw, Poland
| | - David J. Wales
- Department
of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, U.K
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