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Tuma FA, Jari AA, Hasan HA, Badran HA. Synthesis, Surface Morphology, Gas Sensor, DSC Technique and Third-Order Behavior of Conducting Polymer. J Fluoresc 2024; 34:2309-2323. [PMID: 37755630 DOI: 10.1007/s10895-023-03448-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 09/20/2023] [Indexed: 09/28/2023]
Abstract
The compound polyaniline (Poly-ANI) with different concentrations of (H2SO4) sulfuric acid has been synthesized by the chemical polymerization method. The prepared compounds have been characterized using number of techniques including FTIR, FE-SEM, EDS and DSC. Additionally, UV-Vis spectroscopy employed for studying the linear optical properties of polymer with different acid concentrations. Third order optical nonlinearity was characterized using Z-scan at 532 nm. The results showed that the nonlinear refractive index has a negative sign. It was observed that the nonlinear refractive index changes in different ratios of H2SO4. The high value of nonlinear refractive index ( n 2 ) obtained along Z-axis is 74.62 × 10 - 7 cm2/W, and the corresponding χ 3 is 21.5 × 10-5 esu. Also, the Poly-ANI film shows the response to NH3 gas sensing in the range 20 ppm-250 ppm and can be used for NH3 sensing application.
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Affiliation(s)
- Fadhil A Tuma
- Department of Physics, College of Education for Pure Sciences, University of Basrah, Basrah, Iraq
| | - Alyaa A Jari
- Ministry of Education, Directorate of Education, Al-Basma Preparatory School for Girls, Basrah, Iraq
| | - Harith A Hasan
- Department of Material Science, Polymer Research Centre, University of Basrah, Basrah, Iraq
| | - Hussain A Badran
- Department of Physics, College of Education for Pure Sciences, University of Basrah, Basrah, Iraq.
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2
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Maruyama H, Ohniwa RL, Ushijima Y, Morikawa K, Takeyasu K. Atomic Force Microscopy Imaging and Analysis of Prokaryotic Genome Organization. Methods Mol Biol 2024; 2819:263-277. [PMID: 39028511 DOI: 10.1007/978-1-0716-3930-6_13] [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: 07/20/2024]
Abstract
This protocol describes the application of atomic force microscopy for structural analysis of prokaryotic and organellar nucleoids. It is based on a simple cell manipulation procedure that enables stepwise dissection of the nucleoid. The procedure includes (i) on-substrate lysis of cells and (ii) enzyme treatment, followed by atomic force microscopy. This type of dissection analysis permits analysis of nucleoid structure ranging from the fundamental units assembled on DNA to higher-order levels of organization. The combination with molecular-genetic and biochemical techniques further permits analysis of the functions of key nucleoid factors relevant to signal-induced structural reorganization or building up of basic structures, as seen for Dps in Escherichia coli and TrmBL2 in Thermococcus kodakarensis. These systems are described here as examples of the successful application of AFM for this purpose. Moreover, we describe the procedures needed for quantitative analysis of the data.
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Affiliation(s)
- Hugo Maruyama
- Department of Bacteriology, Osaka Dental University, Hirakata, Osaka, Japan
| | - Ryosuke L Ohniwa
- Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yuri Ushijima
- Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Kazuya Morikawa
- Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan.
| | - Kunio Takeyasu
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
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3
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Ghazal M, Susloparova A, Lefebvre C, Daher Mansour M, Ghodhbane N, Melot A, Scholaert C, Guérin D, Janel S, Barois N, Colin M, Buée L, Yger P, Halliez S, Coffinier Y, Pecqueur S, Alibart F. Electropolymerization processing of side-chain engineered EDOT for high performance microelectrode arrays. Biosens Bioelectron 2023; 237:115538. [PMID: 37506488 DOI: 10.1016/j.bios.2023.115538] [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: 03/24/2023] [Revised: 07/04/2023] [Accepted: 07/16/2023] [Indexed: 07/30/2023]
Abstract
Microelectrode Arrays (MEAs) are popular tools for in vitro extracellular recording. They are often optimized by surface engineering to improve affinity with neurons and guarantee higher recording quality and stability. Recently, PEDOT:PSS has been used to coat microelectrodes due to its good biocompatibility and low impedance, which enhances neural coupling. Herein, we investigate on electro-co-polymerization of EDOT with its triglymated derivative to control valence between monomer units and hydrophilic functions on a conducting polymer. Molecular packing, cation complexation, dopant stoichiometry are governed by the glycolation degree of the electro-active coating of the microelectrodes. Optimal monomer ratio allows fine-tuning the material hydrophilicity and biocompatibility without compromising the electrochemical impedance of microelectrodes nor their stability while interfaced with a neural cell culture. After incubation, sensing readout on the modified electrodes shows higher performances with respect to unmodified electropolymerized PEDOT, with higher signal-to-noise ratio (SNR) and higher spike counts on the same neural culture. Reported SNR values are superior to that of state-of-the-art PEDOT microelectrodes and close to that of state-of-the-art 3D microelectrodes, with a reduced fabrication complexity. Thanks to this versatile technique and its impact on the surface chemistry of the microelectrode, we show that electro-co-polymerization trades with many-compound properties to easily gather them into single macromolecular structures. Applied on sensor arrays, it holds great potential for the customization of neurosensors to adapt to environmental boundaries and to optimize extracted sensing features.
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Affiliation(s)
- Mahdi Ghazal
- Institute of Electronics, Microelectronics and Nanotechnology (IEMN, UMR 8520) | Univ. Lille, CNRS, Univ. Polytechnique Hauts-de-France, 59000, Lille, France
| | - Anna Susloparova
- Institute of Electronics, Microelectronics and Nanotechnology (IEMN, UMR 8520) | Univ. Lille, CNRS, Univ. Polytechnique Hauts-de-France, 59000, Lille, France
| | - Camille Lefebvre
- University of Lille, Inserm, CHU Lille, Lille Neuroscience & Cognition, UMR-S1172, Lille, France
| | - Michel Daher Mansour
- Institute of Electronics, Microelectronics and Nanotechnology (IEMN, UMR 8520) | Univ. Lille, CNRS, Univ. Polytechnique Hauts-de-France, 59000, Lille, France
| | - Najami Ghodhbane
- Institute of Electronics, Microelectronics and Nanotechnology (IEMN, UMR 8520) | Univ. Lille, CNRS, Univ. Polytechnique Hauts-de-France, 59000, Lille, France
| | - Alexis Melot
- Laboratoire Nanotechnologies & Nanosystèmes (LN2, UMI 3463) | CNRS, Université de Sherbrooke, J1X0A5, Sherbrooke, Canada
| | - Corentin Scholaert
- Institute of Electronics, Microelectronics and Nanotechnology (IEMN, UMR 8520) | Univ. Lille, CNRS, Univ. Polytechnique Hauts-de-France, 59000, Lille, France
| | - David Guérin
- Institute of Electronics, Microelectronics and Nanotechnology (IEMN, UMR 8520) | Univ. Lille, CNRS, Univ. Polytechnique Hauts-de-France, 59000, Lille, France
| | - Sébastien Janel
- Université de Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017, CIIL-Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Nicolas Barois
- Université de Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR9017, CIIL-Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Morvane Colin
- University of Lille, Inserm, CHU Lille, Lille Neuroscience & Cognition, UMR-S1172, Lille, France
| | - Luc Buée
- University of Lille, Inserm, CHU Lille, Lille Neuroscience & Cognition, UMR-S1172, Lille, France
| | - Pierre Yger
- Plasticity & SubjectivitY Team, Lille Neuroscience & Cognition Research Centre, University of Lille, INSERM U1172, Lille, France; Institut de La Vision, Sorbonne Université, INSERM, Centre National de La Recherche Scientifique, Paris, France
| | - Sophie Halliez
- University of Lille, Inserm, CHU Lille, Lille Neuroscience & Cognition, UMR-S1172, Lille, France
| | - Yannick Coffinier
- Institute of Electronics, Microelectronics and Nanotechnology (IEMN, UMR 8520) | Univ. Lille, CNRS, Univ. Polytechnique Hauts-de-France, 59000, Lille, France.
| | - Sébastien Pecqueur
- Institute of Electronics, Microelectronics and Nanotechnology (IEMN, UMR 8520) | Univ. Lille, CNRS, Univ. Polytechnique Hauts-de-France, 59000, Lille, France.
| | - Fabien Alibart
- Institute of Electronics, Microelectronics and Nanotechnology (IEMN, UMR 8520) | Univ. Lille, CNRS, Univ. Polytechnique Hauts-de-France, 59000, Lille, France; Laboratoire Nanotechnologies & Nanosystèmes (LN2, UMI 3463) | CNRS, Université de Sherbrooke, J1X0A5, Sherbrooke, Canada
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4
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Dubrovin EV. Atomic force microscopy-based approaches for single-molecule investigation of nucleic acid- protein complexes. Biophys Rev 2023; 15:1015-1033. [PMID: 37974971 PMCID: PMC10643717 DOI: 10.1007/s12551-023-01111-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/07/2023] [Indexed: 11/19/2023] Open
Abstract
The interaction of nucleic acids with proteins plays an important role in many fundamental biological processes in living cells, including replication, transcription, and translation. Therefore, understanding nucleic acid-protein interaction is of high relevance in many areas of biology, medicine and technology. During almost four decades of its existence atomic force microscopy (AFM) accumulated a significant experience in investigation of biological molecules at a single-molecule level. AFM has become a powerful tool of molecular biology and biophysics providing unique information about properties, structure, and functioning of biomolecules. Despite a great variety of nucleic acid-protein systems under AFM investigations, there are a number of typical approaches for such studies. This review is devoted to the analysis of the typical AFM-based approaches of investigation of DNA (RNA)-protein complexes with a major focus on transcription studies. The basic strategies of AFM analysis of nucleic acid-protein complexes including investigation of the products of DNA-protein reactions and real-time dynamics of DNA-protein interaction are categorized and described by the example of the most relevant research studies. The described approaches and protocols have many universal features and, therefore, are applicable for future AFM studies of various nucleic acid-protein systems.
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Affiliation(s)
- Evgeniy V. Dubrovin
- Lomonosov Moscow State University, Leninskie Gory 1 Bld. 2, 119991 Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Institutskiy Per. 9, Dolgoprudny, 141700 Russian Federation
- Sirius University of Science and Technology, Olimpiyskiy Ave 1, Township Sirius, Krasnodar Region, 354349 Russia
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5
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Kim J. Characterization of Biocompatibility of Functional Bioinks for 3D Bioprinting. Bioengineering (Basel) 2023; 10:bioengineering10040457. [PMID: 37106644 PMCID: PMC10135811 DOI: 10.3390/bioengineering10040457] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/02/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Three-dimensional (3D) bioprinting with suitable bioinks has become a critical tool for fabricating 3D biomimetic complex structures mimicking physiological functions. While enormous efforts have been devoted to developing functional bioinks for 3D bioprinting, widely accepted bioinks have not yet been developed because they have to fulfill stringent requirements such as biocompatibility and printability simultaneously. To further advance our knowledge of the biocompatibility of bioinks, this review presents the evolving concept of the biocompatibility of bioinks and standardization efforts for biocompatibility characterization. This work also briefly reviews recent methodological advances in image analyses to characterize the biocompatibility of bioinks with regard to cell viability and cell-material interactions within 3D constructs. Finally, this review highlights a number of updated contemporary characterization technologies and future perspectives to further advance our understanding of the biocompatibility of functional bioinks for successful 3D bioprinting.
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Affiliation(s)
- Jinku Kim
- Department of Biological and Chemical Engineering, Hongik University, Sejong 30016, Republic of Korea
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6
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Ovalle-Flores L, Rodríguez-Nieto M, Zárate-Triviño D, Rodríguez-Padilla C, Menchaca JL. Methodologies and models for measuring viscoelastic properties of cancer cells: Towards a universal classification. J Mech Behav Biomed Mater 2023; 140:105734. [PMID: 36848744 DOI: 10.1016/j.jmbbm.2023.105734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023]
Abstract
Different methods and several physical models exist to study cell viscoelasticity with the atomic force microscope (AFM). In search of a robust mechanical classification of cells through AFM, in this work, viscoelastic parameters of the cancer cell lines MDA-MB-231, DU-145, and MG-63 are obtained using two methodologies; through force-distance and force-relaxation curves. Four mechanical models were applied to fit the curves. The results show that both methodologies agree qualitatively on the parameters that quantify elasticity but disagree on the parameters that account for energy dissipation. The Fractional Zener (FZ) model represents well the information given by the Solid Linear Standard and Generalized Maxwell models. The Fractional Kelvin (FK) model concentrates the viscoelastic information mainly in two parameters, which could be an advantage over the other models. Therefore, the FZ and FK models are proposed as the basis for the classification of cancer cells. However, more research using these models is needed to obtain a broader view of the meaning of each parameter and to be able to establish a relationship between the parameters and the cellular components.
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Affiliation(s)
- Lizeth Ovalle-Flores
- Universidad Autónoma de Nuevo León, Centro de Investigación en Ciencias Físico Matemáticas, Facultad de Ciencias Físico Matemáticas, Av. Universidad s/n, San Nicolás de los Garza, 66450, Nuevo León, Mexico
| | - Maricela Rodríguez-Nieto
- Universidad Autónoma de Nuevo León, Centro de Investigación en Ciencias Físico Matemáticas, Facultad de Ciencias Físico Matemáticas, Av. Universidad s/n, San Nicolás de los Garza, 66450, Nuevo León, Mexico
| | - Diana Zárate-Triviño
- Universidad Autónoma de Nuevo León, Laboratorio de Inmunología y Virología, Facultad de Ciencias Biológicas, Av. Manuel L. Barragán s/n, San Nicolás de los Garza, 66450, Nuevo León, Mexico
| | - Cristina Rodríguez-Padilla
- Universidad Autónoma de Nuevo León, Laboratorio de Inmunología y Virología, Facultad de Ciencias Biológicas, Av. Manuel L. Barragán s/n, San Nicolás de los Garza, 66450, Nuevo León, Mexico
| | - Jorge Luis Menchaca
- Universidad Autónoma de Nuevo León, Centro de Investigación en Ciencias Físico Matemáticas, Facultad de Ciencias Físico Matemáticas, Av. Universidad s/n, San Nicolás de los Garza, 66450, Nuevo León, Mexico.
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7
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Haghizadeh A, Iftikhar M, Dandpat SS, Simpson T. Looking at Biomolecular Interactions through the Lens of Correlated Fluorescence Microscopy and Optical Tweezers. Int J Mol Sci 2023; 24:2668. [PMID: 36768987 PMCID: PMC9916863 DOI: 10.3390/ijms24032668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/19/2022] [Accepted: 01/26/2023] [Indexed: 02/01/2023] Open
Abstract
Understanding complex biological events at the molecular level paves the path to determine mechanistic processes across the timescale necessary for breakthrough discoveries. While various conventional biophysical methods provide some information for understanding biological systems, they often lack a complete picture of the molecular-level details of such dynamic processes. Studies at the single-molecule level have emerged to provide crucial missing links to understanding complex and dynamic pathways in biological systems, which are often superseded by bulk biophysical and biochemical studies. Latest developments in techniques combining single-molecule manipulation tools such as optical tweezers and visualization tools such as fluorescence or label-free microscopy have enabled the investigation of complex and dynamic biomolecular interactions at the single-molecule level. In this review, we present recent advances using correlated single-molecule manipulation and visualization-based approaches to obtain a more advanced understanding of the pathways for fundamental biological processes, and how this combination technique is facilitating research in the dynamic single-molecule (DSM), cell biology, and nanomaterials fields.
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8
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Moraille P, Abdali Z, Ramkaran M, Polcari D, Patience GS, Dorval Courchesne N, Badia A. Experimental Methods in Chemical Engineering: Atomic force microscopy—
AFM. CAN J CHEM ENG 2022. [DOI: 10.1002/cjce.24407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Zahra Abdali
- Chemical Engineering, McGill University Québec Canada
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9
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Martinac B, Nikolaev YA, Silvani G, Bavi N, Romanov V, Nakayama Y, Martinac AD, Rohde P, Bavi O, Cox CD. Cell membrane mechanics and mechanosensory transduction. CURRENT TOPICS IN MEMBRANES 2020; 86:83-141. [DOI: 10.1016/bs.ctm.2020.08.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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10
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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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11
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Zuttion F, Sicard D, Dupin L, Vergoten G, Girard-Bock C, Madaoui M, Chevolot Y, Morvan F, Vidal S, Vasseur JJ, Souteyrand E, Phaner-Goutorbe M. Deciphering multivalent glycocluster-lectin interactions through AFM characterization of the self-assembled nanostructures. SOFT MATTER 2019; 15:7211-7218. [PMID: 31475271 DOI: 10.1039/c9sm00371a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Pseudomonas aeruginosa is a human opportunistic pathogen responsible for lung infections in cystic fibrosis patients. The emergence of resistant strains and its ability to form a biofilm seem to give a selective advantage to the bacterium and thus new therapeutic approaches are needed. To infect the lung, the bacterium uses several virulence factors, like LecA lectins. These proteins are involved in bacterial adhesion due to their specific interaction with carbohydrates of the host epithelial cells. The tetrameric LecA lectin specifically binds galactose residues. A new therapeutic approach is based on the development of highly affine synthetic glycoclusters able to selectively link with LecA to interfere with the natural carbohydrate-LecA interaction. In this study, we combined atomic force microscopy imaging and molecular dynamics simulations to visualize and understand the arrangements formed by LecA and five different glycoclusters. Our glycoclusters are small scaffolds characterized by a core and four branches, which terminate in a galactose residue. Depending on the nature of the core and the branches, the glycocluster-lectin interaction can be modulated and the affinity increased. We show that glycocluster-LecA arrangements highly depend on the glycocluster architecture: the core influences the rigidity of the geometry and the directionality of the branches, whereas the nature of the branch determines the compactness of the structure and the ease of binding.
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Affiliation(s)
- Francesca Zuttion
- Université de Lyon, Ecole Centrale de Lyon, Institut des Nanotechnologies de Lyon INL UMR-5270 CNRS, 36 avenue Guy de Collongue, 69134 Ecully, France.
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12
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Abstract
This protocol describes the application of atomic force microscopy for structural analysis of the prokaryotic and organellar nucleoids. It is based on a simple cell manipulation procedure that enables step-wise dissection of the nucleoid. The procedure includes (1) on-substrate-lysis of cells, and (2) enzyme treatment, followed by atomic force microscopy. This type of dissection analysis permits analysis of nucleoid structure ranging from the fundamental units assembled on DNA to higher order levels of organization. The combination with molecular-genetic and biochemical techniques further permits analysis of the functions of key nucleoid factors relevant to signal-induced structural re-organization or building up of basic structures, as seen for Dps in Escherichia coli, and TrmBL2 in Thermococcus kodakarensis. These systems are described here as examples of the successful application of AFM for this purpose. Moreover, we describe the procedures needed for quantitative analysis of the data.
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13
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Lyubchenko YL. Direct AFM Visualization of the Nanoscale Dynamics of Biomolecular Complexes. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2018; 51:403001. [PMID: 30410191 PMCID: PMC6217977 DOI: 10.1088/1361-6463/aad898] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
High-speed AFM (HS-AFM) is an advanced technique with numerous applications in biology, particularly in molecular biophysics. Developed as a time-lapse AFM technique for direct imaging fully hydrated biological molecules, HS-AFM is currently capable of visualizing the dynamics of biological molecules and their complexes at a video-data acquisition rate. Spatial resolution at the nanometer level is another important characteristic of HS-AFM. This review focuses on examples of primarily protein-DNA complexes to illustrate the high temporal and spatial resolution capabilities of HS-AFM that have resulted in novel models and/or the functional mechanisms of these biological systems.
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Affiliation(s)
- Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
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14
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Peng Y, Jin X, Zheng Y, Han D, Liu K, Jiang L. Direct Imaging of Superwetting Behavior on Solid-Liquid-Vapor Triphase Interfaces. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2017; 29. [PMID: 28869679 DOI: 10.1002/adma.201703009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 07/17/2017] [Indexed: 05/11/2023]
Abstract
A solid-liquid-vapor interface dominated by a three-phase contact line usually serves as an active area for interfacial reactions and provides a vital clue to surface behavior. Recently, direct imaging of the triphase interface of superwetting interfaces on the microscale/nanoscale has attracted broad scientific attention for both theoretical research and practical applications, and has gradually become an efficient and intuitive approach to explore the wetting behaviors of various multiphase interfaces. Here, recent progress on characterizing the solid-liquid-vapor triphase interface on the microscale/nanoscale with diverse types of imaging apparatus is summarized. Moreover, the accurate, visible, and quantitative information that can be obtained shows the real interfacial morphology of the wetting behaviors of multiphase interfaces. On the basis of fundamental research, technical innovations in imaging and complicated multiphase interfaces of the superwetting surface are also briefly presented.
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Affiliation(s)
- Yun Peng
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of Ministry of Education, School of Chemistry, Beihang University, Beijing, 100191, P. R. China
| | - Xu Jin
- Research Institute of Petroleum, Exploration and Development, Petro China, Beijing, 100191, P. R. China
| | - Yongmei Zheng
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of Ministry of Education, School of Chemistry, Beihang University, Beijing, 100191, P. R. China
| | - Dong Han
- National Center for Nanoscience and Technology, Beijing, 100190, P. R. China
| | - Kesong Liu
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of Ministry of Education, School of Chemistry, Beihang University, Beijing, 100191, P. R. China
| | - Lei Jiang
- Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of Ministry of Education, School of Chemistry, Beihang University, Beijing, 100191, P. R. China
- Laboratory of Bio-inspired Smart Interface Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
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15
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Kantor Y, Kardar M. Attractive and repulsive polymer-mediated forces between scale-free surfaces. Phys Rev E 2017; 96:022148. [PMID: 28950594 DOI: 10.1103/physreve.96.022148] [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: 11/07/2022]
Abstract
We consider forces acting on objects immersed in, or attached to, long fluctuating polymers. The confinement of the polymer by the obstacles results in polymer-mediated forces that can be repulsive (due to loss of entropy) or attractive (if some or all surfaces are covered by adsorbing layers). The strength and sign of the force in general depends on the detailed shape and adsorption properties of the obstacles but assumes simple universal forms if characteristic length scales associated with the objects are large. This occurs for scale-free shapes (such as a flat plate, straight wire, or cone) when the polymer is repelled by the obstacles or is marginally attracted to it (close to the depinning transition where the absorption length is infinite). In such cases, the separation h between obstacles is the only relevant macroscopic length scale, and the polymer-mediated force equals Ak_{B}T/h, where T is temperature. The amplitude A is akin to a critical exponent, depending only on geometry and universality of the polymer system. The value of A, which we compute for simple geometries and ideal polymers, can be positive or negative. Remarkably, we find A=0 for ideal polymers at the adsorption transition point, irrespective of shapes of the obstacles, i.e., at this special point there is no polymer-mediated force between obstacles (scale free or not).
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Affiliation(s)
- Yacov Kantor
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv 69978, Israel
| | - Mehran Kardar
- Massachusetts Institute of Technology, Department of Physics, Cambridge, Massachusetts 02139, USA
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16
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Yamada Y, Konno H, Shimabukuro K. Demonstration of correlative atomic force and transmission electron microscopy using actin cytoskeleton. Biophys Physicobiol 2017; 14:111-117. [PMID: 28828286 PMCID: PMC5551270 DOI: 10.2142/biophysico.14.0_111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 06/29/2017] [Indexed: 12/01/2022] Open
Abstract
In this study, we present a new technique called correlative atomic force and transmission electron microscopy (correlative AFM/TEM) in which a targeted region of a sample can be observed under AFM and TEM. The ultimate goal of developing this new technique is to provide a technical platform to expand the fields of AFM application to complex biological systems such as cell extracts. Recent advances in the time resolution of AFM have enabled detailed observation of the dynamic nature of biomolecules. However, specifying molecular species, by AFM alone, remains a challenge. Here, we demonstrate correlative AFM/TEM, using actin filaments as a test sample, and further show that immuno-electron microscopy (immuno-EM), to specify molecules, can be integrated into this technique. Therefore, it is now possible to specify molecules, captured under AFM, by subsequent observation using immuno-EM. In conclusion, correlative AFM/TEM can be a versatile method to investigate complex biological systems at the molecular level.
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Affiliation(s)
- Yutaro Yamada
- Department of Chemical and Biological Engineering, National College of Technology, Ube College, Ube, Yamaguchi 755-8555, Japan
| | - Hiroki Konno
- Bio-AFM Frontier Research Center, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Katsuya Shimabukuro
- Department of Chemical and Biological Engineering, National College of Technology, Ube College, Ube, Yamaguchi 755-8555, Japan
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17
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Chen Y, Gao T, Wang Y, Yang G. Investigating the Influence of Magnesium Ions on p53-DNA Binding Using Atomic Force Microscopy. Int J Mol Sci 2017; 18:ijms18071585. [PMID: 28754018 PMCID: PMC5536072 DOI: 10.3390/ijms18071585] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 07/10/2017] [Accepted: 07/18/2017] [Indexed: 12/22/2022] Open
Abstract
p53 is a tumor suppressor protein that plays a significant role in apoptosis and senescence, preserving genomic stability, and preventing oncogene expression. Metal ions, such as magnesium and zinc ions, have important influences on p53–DNA interactions for stabilizing the structure of the protein and enhancing its affinity to DNA. In the present study, we systematically investigated the interaction of full length human protein p53 with DNA in metal ion solution by atomic force microscopy (AFM). The p53–DNA complexes at various p53 concentrations were scanned by AFM and their images are used to measure the dissociation constant of p53–DNA binding by a statistical method. We found that the dissociation constant of p53 binding DNA is 328.02 nmol/L in physiological buffer conditions. The influence of magnesium ions on p53–DNA binding was studied by AFM at various ion strengths through visualization. We found that magnesium ions significantly stimulate the binding of the protein to DNA in a sequence-independent manner, different from that stimulated by zinc. Furthermore, the high concentrations of magnesium ions can promote p53 aggregation and even lead to the formation of self-assembly networks of DNA and p53 proteins. We propose an aggregation and self-assembly model based on the present observation and discuss its biological meaning.
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Affiliation(s)
- Yang Chen
- School of Physics and Electronic Information, Wenzhou University, Wenzhou 325035, China.
| | - Tianyong Gao
- School of Physics and Electronic Information, Wenzhou University, Wenzhou 325035, China.
| | - Yanwei Wang
- School of Physics and Electronic Information, Wenzhou University, Wenzhou 325035, China.
| | - Guangcan Yang
- School of Physics and Electronic Information, Wenzhou University, Wenzhou 325035, China.
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18
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19
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Sajjadi M, Pishkenari HN, Vossoughi G. Dynamic modeling of trolling-mode AFM: Considering effects of cantilever torsion, nanoneedle flexibility and liquid-nanoneedle interactions. Ultramicroscopy 2017; 182:99-111. [PMID: 28667869 DOI: 10.1016/j.ultramic.2017.06.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 05/13/2017] [Accepted: 06/12/2017] [Indexed: 11/17/2022]
Abstract
Trolling mode atomic force microscope (TR-Mode AFM) significantly reduces the hydrodynamic drag generated during operation in liquid environments. This is achieved by utilizing a long nanoneedle and keeping the cantilever out of liquid. In this research, a continuous mathematical model is developed to study TR-Mode AFM dynamics near a sample submerged in the liquid. Effects of cantilever torsion, nanoneedle flexibility, and liquid-nanoneedle interactions are considered in the model. In order to derive the equations of motion, Hamilton's principle and assumed mode method are used. System operation in dynamic mode is numerically simulated and the accuracy of the results is verified by comparison with the results of the finite element method. Displacements of different components of the system are also compared with each other and the dominant displacements are determined.
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Affiliation(s)
- Mohammadreza Sajjadi
- Nanorobotics laboratory, Department of Mechanical engineering, Sharif University of Technology, Tehran, Iran.
| | - Hossein Nejat Pishkenari
- Nanorobotics laboratory, Department of Mechanical engineering, Sharif University of Technology, Tehran, Iran.
| | - Gholamreza Vossoughi
- Department of Mechanical engineering, Sharif University of Technology, Tehran, Iran.
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20
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Direct measurement of IgM-Antigen interaction energy on individual red blood cells. Colloids Surf B Biointerfaces 2017; 155:373-378. [PMID: 28454066 DOI: 10.1016/j.colsurfb.2017.04.038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 04/17/2017] [Accepted: 04/18/2017] [Indexed: 11/24/2022]
Abstract
Most blood grouping tests rely on the principle of red blood cells (RBCs) agglutination. Agglutination is triggered by the binding of specific blood grouping antibodies to the corresponding RBC surface antigen on multiple cells. The interaction energies between blood grouping antibodies and antigens have been poorly defined in immunohaematology. Here for the first time, we functionalized atomic force microscope (AFM) cantilevers with the IgM form of blood grouping antibodies to probe populations of individual RBCs of different groups under physiological conditions. The force-mapping mode of AFM allowed us to measure specific antibody - antigen interactions, and simultaneously localize and quantify antigen sites on the scanned cell surface. This study provides a new insight of the interactions between IgM antibodies and its corresponding antigen. The technique and information can be translated to develop better blood typing diagnostics and optimize target-specific drug delivery for medical applications.
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21
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Marrese M, Guarino V, Ambrosio L. Atomic Force Microscopy: A Powerful Tool to Address Scaffold Design in Tissue Engineering. J Funct Biomater 2017; 8:E7. [PMID: 28208801 PMCID: PMC5371880 DOI: 10.3390/jfb8010007] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 02/07/2017] [Accepted: 02/08/2017] [Indexed: 11/16/2022] Open
Abstract
Functional polymers currently represent a basic component of a large range of biological and biomedical applications including molecular release, tissue engineering, bio-sensing and medical imaging. Advancements in these fields are driven by the use of a wide set of biodegradable polymers with controlled physical and bio-interactive properties. In this context, microscopy techniques such as Atomic Force Microscopy (AFM) are emerging as fundamental tools to deeply investigate morphology and structural properties at micro and sub-micrometric scale, in order to evaluate the in time relationship between physicochemical properties of biomaterials and biological response. In particular, AFM is not only a mere tool for screening surface topography, but may offer a significant contribution to understand surface and interface properties, thus concurring to the optimization of biomaterials performance, processes, physical and chemical properties at the micro and nanoscale. This is possible by capitalizing the recent discoveries in nanotechnologies applied to soft matter such as atomic force spectroscopy to measure surface forces through force curves. By tip-sample local interactions, several information can be collected such as elasticity, viscoelasticity, surface charge densities and wettability. This paper overviews recent developments in AFM technology and imaging techniques by remarking differences in operational modes, the implementation of advanced tools and their current application in biomaterials science, in terms of characterization of polymeric devices in different forms (i.e., fibres, films or particles).
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Affiliation(s)
- Marica Marrese
- Faculty of Sciences, Biophotonics and Medical Imaging group and Laser Lab, VU University Amsterdam, De Boelelaan 1081 HV Amsterdam, The Netherlands.
| | - Vincenzo Guarino
- Institute of Polymers, Composites and Biomaterials, National Research Council of Italy, V.le Kennedy 54, Pad 20, Mostra d'Oltremare, Naples 80125, Italy.
| | - Luigi Ambrosio
- Institute of Polymers, Composites and Biomaterials, National Research Council of Italy, V.le Kennedy 54, Pad 20, Mostra d'Oltremare, Naples 80125, Italy.
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22
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Kreplak L. Introduction to Atomic Force Microscopy (AFM) in Biology. ACTA ACUST UNITED AC 2016; 85:17.7.1-17.7.21. [PMID: 27479503 DOI: 10.1002/cpps.14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The atomic force microscope (AFM) has the unique capability of imaging biological samples with molecular resolution in buffer solution over a wide range of time scales from milliseconds to hours. In addition to providing topographical images of surfaces with nanometer- to angstrom-scale resolution, forces between single molecules and mechanical properties of biological samples can be investigated from the nano-scale to the micro-scale. Importantly, the measurements are made in buffer solutions, allowing biological samples to "stay alive" within a physiological-like environment while temporal changes in structure are measured-e.g., before and after addition of chemical reagents. These qualities distinguish AFM from conventional imaging techniques of comparable resolution, e.g., electron microscopy (EM). This unit provides an introduction to AFM on biological systems and describes specific examples of AFM on proteins, cells, and tissues. The physical principles of the technique and methodological aspects of its practical use and applications are also described. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Laurent Kreplak
- Department of Physics & Atmospheric Science, Dalhousie University, Halifax, Canada
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23
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Evaluation of β1-integrin expression on chondrogenically differentiating human adipose-derived stem cells using atomic force microscopy. Biointerphases 2016; 11:021005. [PMID: 27106564 DOI: 10.1116/1.4947049] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The expression of β1-integrin on human adipose-derived stem cells, differentiating toward a chondrogenic lineage, is hypothesized to decrease when cells are grown under in vivo-like environments due to sufficient extracellular matrix (ECM) buildup in the engineered tissues. The opposite is true when cells are grown in static cultures such as in pellet or micromass. To probe β1-integrin distribution on cellular surfaces, atomic force microscopy cantilevers modified with anti-β1-integrin antibodies were used. Specific antibody-antigen adhesion forces were identified and indicated the locations of β1-integrins on cells. ECM properties were assessed by estimating the Young's modulus of the matrix. Specific single antibody-antigen interactions averaged 78 ± 10 pN with multiple bindings occurring at approximate multiples of 78 pN. The author's results show that upregulated β1-integrin expression coincided with a less robust ECM as assessed by mechanical properties of tissues. In micromass and pellet cultures, transforming growth factor β3(TGF-β3) elicited a decrease in Young's modulus by 3.7- and 4.4-fold while eliciting an increase in β1-integrin count by 1.1- and 1.3-fold, respectively. β1-integrin counts on cells grown in the presence of TGF-β3 with oscillating hydrostatic pressure decreased by a 1.1-fold while the Young's modulus increased by a 1.9-fold. Collectively, our results suggest that cells in insufficiently robust ECM express more integrin perhaps to facilitate cell-ECM adhesion and compensate for a looser less robust ECM.
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24
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Park IS, Kwak TJ, Lee G, Son M, Choi JW, Choi S, Nam K, Lee SY, Chang WJ, Eom K, Yoon DS, Lee S, Bashir R, Lee SW. Biaxial Dielectrophoresis Force Spectroscopy: A Stoichiometric Approach for Examining Intermolecular Weak Binding Interactions. ACS NANO 2016; 10:4011-4019. [PMID: 27007455 DOI: 10.1021/acsnano.5b05286] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The direct quantification of weak intermolecular binding interactions is very important for many applications in biology and medicine. Techniques that can be used to investigate such interactions under a controlled environment, while varying different parameters such as loading rate, pulling direction, rupture event measurements, and the use of different functionalized probes, are still lacking. Herein, we demonstrate a biaxial dielectrophoresis force spectroscopy (BDFS) method that can be used to investigate weak unbinding events in a high-throughput manner under controlled environments and by varying the pulling direction (i.e., transverse and/or vertical axes) as well as the loading rate. With the BDFS system, we can quantitatively analyze binding interactions related to hydrogen bonding or ionic attractions between functionalized microbeads and a surface within a microfluidic device. Our BDFS system allowed for the characterization of the number of bonds involved in an interaction, bond affinity, kinetic rates, and energy barrier heights and widths from different regimes of the energy landscape.
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Affiliation(s)
- In Soo Park
- Department of Biomedical Engineering, Yonsei University , Wonju 220-710, Korea
| | - Tae Joon Kwak
- Mechanical Engineering Department, University of Wisconsin-Milwaukee , Milwaukee, Wisconsin 53211, United States
| | - Gyudo Lee
- T.H. Chan School of Public Health, Harvard University , Boston, Massachusetts 02115, United States
| | - Myeonggu Son
- Department of Biomedical Engineering, Yonsei University , Wonju 220-710, Korea
| | - Jeong Woo Choi
- Department of Biomedical Engineering, Yonsei University , Wonju 220-710, Korea
| | - Seungyeop Choi
- Department of Biomedical Engineering, Yonsei University , Wonju 220-710, Korea
| | - Kihwan Nam
- Biomedical Research Institute, Korea Institute of Science and Technology , Seoul 136-791, Korea
| | - Sei-Young Lee
- Department of Biomedical Engineering, Yonsei University , Wonju 220-710, Korea
| | - Woo-Jin Chang
- Mechanical Engineering Department, University of Wisconsin-Milwaukee , Milwaukee, Wisconsin 53211, United States
| | - Kilho Eom
- Biomechanics Laboratory, College of Sport Science, Sungkyunkwan University , Suwon 440-746, Korea
| | - Dae Sung Yoon
- Department of Bio-convergence Engineering, Korea University , Seoul 136-703, Korea
| | - Sangyoup Lee
- Biomedical Research Institute, Korea Institute of Science and Technology , Seoul 136-791, Korea
- Department of Biomedical Engineering, University of Science and Technology , Daejeon 305-350, Korea
| | - Rashid Bashir
- Department of Bioengineering, Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign Champaign, Illinois 61801, United States
| | - Sang Woo Lee
- Department of Biomedical Engineering, Yonsei University , Wonju 220-710, Korea
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25
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Abstract
This article reviews atomic force microscopy (AFM) studies of DNA structure and dynamics and protein-DNA complexes, including recent advances in the visualization of protein-DNA complexes with the use of cutting-edge, high-speed AFM. Special emphasis is given to direct nanoscale visualization of dynamics of protein-DNA complexes. In the area of DNA structure and dynamics, structural studies of local non-B conformations of DNA and the interplay of local and global DNA conformations are reviewed. The application of time-lapse AFM nanoscale imaging of DNA dynamics is illustrated by studies of Holliday junction branch migration. Structure and dynamics of protein-DNA interactions include problems related to site-specific DNA recombination, DNA replication, and DNA mismatch repair. Studies involving the structure and dynamics of chromatin are also described.
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Affiliation(s)
- Yuri L. Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025
| | - Luda S. Shlyakhtenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025
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26
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Jembrek MJ, Šimić G, Hof PR, Šegota S. Atomic force microscopy as an advanced tool in neuroscience. Transl Neurosci 2015; 6:117-130. [PMID: 28123795 PMCID: PMC4936619 DOI: 10.1515/tnsci-2015-0011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 06/05/2015] [Indexed: 12/16/2022] Open
Abstract
This review highlights relevant issues about applications and improvements of atomic force microscopy (AFM) toward a better understanding of neurodegenerative changes at the molecular level with the hope of contributing to the development of effective therapeutic strategies for neurodegenerative illnesses. The basic principles of AFM are briefly discussed in terms of evaluation of experimental data, including the newest PeakForce Quantitative Nanomechanical Mapping (QNM) and the evaluation of Young’s modulus as the crucial elasticity parameter. AFM topography, revealed in imaging mode, can be used to monitor changes in live neurons over time, representing a valuable tool for high-resolution detection and monitoring of neuronal morphology. The mechanical properties of living cells can be quantified by force spectroscopy as well as by new AFM. A variety of applications are described, and their relevance for specific research areas discussed. In addition, imaging as well as non-imaging modes can provide specific information, not only about the structural and mechanical properties of neuronal membranes, but also on the cytoplasm, cell nucleus, and particularly cytoskeletal components. Moreover, new AFM is able to provide detailed insight into physical structure and biochemical interactions in both physiological and pathophysiological conditions.
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Affiliation(s)
| | - Goran Šimić
- Department for Neuroscience, Croatian Institute for Brain Research, University of Zagreb Medical School, Zagreb, Croatia
| | - Patrick R Hof
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, 10029 New York, USA
| | - Suzana Šegota
- Division for Marine and Environmental Research, Ruđer Bošković Institute, POB 180, Zagreb, Croatia
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27
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Abdi A, Pishkenari HN, Keramati R, Minary-Jolandan M. Dynamics of the nanoneedle probe in trolling mode AFM. NANOTECHNOLOGY 2015; 26:205702. [PMID: 25915451 DOI: 10.1088/0957-4484/26/20/205702] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Atomic force microscopy (AFM), as an indispensable tool for nanoscale characterization, presents major drawbacks for operation in a liquid environment arising from the large hydrodynamic drag on the vibrating cantilever. The newly introduced 'Trolling mode' (TR-mode) AFM resolves this complication by using a specialized nanoneedle cantilever that keeps the cantilever outside of the liquid. Herein, a mechanical model with a lumped mass was developed to capture the dynamics of such a cantilever with a nanoneedle tip. This new developed model was applied to investigate the effects of the needle-liquid interface on the performance of the AFM, including the imaging capability in liquid.
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Affiliation(s)
- Ahmad Abdi
- Center of Excellence in Design, Robotics and Automation (CEDRA), School of Mechanical Engineering, Sharif University of Technology, Tehran, Iran
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28
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Lyubchenko YL, Gall AA, Shlyakhtenko LS. Visualization of DNA and protein-DNA complexes with atomic force microscopy. Methods Mol Biol 2014; 1117:367-84. [PMID: 24357372 DOI: 10.1007/978-1-62703-776-1_17] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
This article describes sample preparation techniques for AFM imaging of DNA and protein-DNA complexes. The approach is based on chemical functionalization of the mica surface with aminopropyl silatrane (APS) to yield an APS-mica surface. This surface binds nucleic acids and nucleoprotein complexes in a wide range of ionic strengths, in the absence of divalent cations, and in a broad range of pH. The chapter describes the methodologies for the preparation of APS-mica surfaces and the preparation of samples for AFM imaging. The protocol for synthesis and purification of APS is also provided. The AFM applications are illustrated with examples of images of DNA and protein-DNA complexes.
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Affiliation(s)
- Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, USA
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29
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Bruxel F, Vilela JMC, Andrade MS, Malachias Â, Perez CA, Magalhães-Paniago R, Oliveira MC, Teixeira HF. Investigation of the structural organization of cationic nanoemulsion/antisense oligonucleotide complexes. Colloids Surf B Biointerfaces 2013; 112:530-6. [PMID: 24079942 DOI: 10.1016/j.colsurfb.2013.08.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 08/21/2013] [Accepted: 08/22/2013] [Indexed: 11/18/2022]
Abstract
Atomic force microscopy image analysis and energy dispersive X-ray diffraction experiments were used to investigate the structural organization of cationic nanoemulsion/oligonucleotide complexes. Oligonucleotides targeting topoisomerase II gene were adsorbed on cationic nanoemulsions obtained by means of spontaneous emulsification procedure. Topographical analysis by atomic force microscopy allowed the observation of the nanoemulsion/oligonucleotide complexes through three-dimensional high-resolution images. Flattening of the oil droplets was observed, which was reduced in the complexes obtained at high amount of adsorbed oligonucleotides. In such conditions, complexes exhibit droplet size in the 600nm range. The oligonucleotides molecules were detected on the surface of the droplets, preventing their fusion during aggregation. A lamellar structure organization was identified by energy dispersive X-ray diffraction experiments. The presence of the nucleic acid molecules led to a disorganization of the lipid arrangement and an expansion in the lattice spacing, which was proportional to the amount of oligonucleotides added.
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Affiliation(s)
- Fernanda Bruxel
- Programa de Pós-graduação em Ciências Farmacêuticas da Universidade Federal do Rio Grande do Sul (UFRGS), Av. Ipiranga 2752, 90610-000 Porto Alegre, Brazil
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30
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Maghrebi MF, Kantor Y, Kardar M. Polymer-mediated entropic forces between scale-free objects. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:061801. [PMID: 23367967 DOI: 10.1103/physreve.86.061801] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Indexed: 06/01/2023]
Abstract
The number of configurations of a polymer is reduced in the presence of a barrier or an obstacle. The resulting loss of entropy adds a repulsive component to other forces generated by interaction potentials. When the obstructions are scale invariant shapes (such as cones, wedges, lines, or planes) the only relevant length scales are the polymer size R(0) and characteristic separations, severely constraining the functional form of entropic forces. Specifically, we consider a polymer (single strand or star) attached to the tip of a cone, at a separation h from a surface (or another cone). At close proximity, such that h << R(0), separation is the only remaining relevant scale and the entropic force must take the form F = Ak(B)T/h. The amplitude A is universal and can be related to exponents η governing the anomalous scaling of polymer correlations in the presence of obstacles. We use analytical, numerical, and ε-expansion techniques to compute the exponent η for a polymer attached to the tip of the cone (with or without an additional plate or cone) for ideal and self-avoiding polymers. The entropic force is of the order of 0.1 pN at 0.1 μm for a single polymer and can be increased for a star polymer.
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Affiliation(s)
- Mohammad F Maghrebi
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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31
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Park IS, Eom K, Son J, Chang WJ, Park K, Kwon T, Yoon DS, Bashir R, Lee SW. Microfluidic multifunctional probe array dielectrophoretic force spectroscopy with wide loading rates. ACS NANO 2012; 6:8665-8673. [PMID: 22967242 DOI: 10.1021/nn302202t] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The simultaneous investigation of a large number of events with different types of intermolecular interactions, from nonequilibrium high-force pulling assays to quasi-equilibrium unbinding events in the same environment, can be very important for fully understanding intermolecular bond-rupture mechanisms. Here, we describe a novel dielectrophoretic force spectroscopy technique that utilizes microsized beads as multifunctional probes for parallel measurement of intermolecular forces with an extremely wide range of force rate (10(-4) to 10(4) pN/s) inside a microfluidic device. In our experiments, various forces, which broadly form the basis of all molecular interactions, were measured across a range of force loading rates by multifunctional probes of various diameters with a throughput of over 600 events per mm(2), simultaneously and in the same environment. Furthermore, the individual bond-rupture forces, the parameters for the characterization of entire energy landscapes, and the effective stiffness of the force spectroscopy were determined on the basis of the measured results. This method of determining intermolecular forces could be very useful for the precise and simultaneous examination of various molecular interactions, as it can be easily and cost-effectively implemented within a microfluidic device for a range of applications including immunoassays, molecular mechanics, chemical and biological screening, and mechanobiology.
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Affiliation(s)
- In Soo Park
- Department of Biomedical Engineering, Yonsei University, Won-Ju, 220-710, Korea
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32
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Mica functionalization for imaging of DNA and protein-DNA complexes with atomic force microscopy. Methods Mol Biol 2012; 931:295-312. [PMID: 23027008 DOI: 10.1007/978-1-62703-056-4_14] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Surface preparation is a key step for reliable and reproducible imaging of DNA and protein-DNA complexes with atomic force microscopy (AFM). This article describes the approaches for chemical functionalization of the mica surface. One approach utilizes 3-aminopropyl-trietoxy silane (APTES), enabling one to obtain a smooth surface termed AP-mica. This surface binds nucleic acids and nucleoprotein complexes in a wide range of ionic strengths, in the absence of divalent cations and in a broad range of pH. Another method utilizes aminopropyl silatrane (APS) to yield an APS-mica surface. The advantage of APS-mica compared with AP-mica is the ability to obtain reliable and reproducible time-lapse images in aqueous solutions. The chapter describes the methodologies for the preparation of AP-mica and APS-mica surfaces and the preparation of samples for AFM imaging. The protocol for synthesis and purification of APS is also provided. The applications are illustrated with a number of examples.
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33
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Chen P, Jiang L, Han D. In situ imaging of multiphase bio-interfaces at the micro-/nanoscale. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2011; 7:2825-2835. [PMID: 21932246 DOI: 10.1002/smll.201100039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Revised: 04/04/2011] [Indexed: 05/31/2023]
Abstract
The multiphase bio-interfacial system constituted by biological surfaces and their surrounding environment is usually considered to be an essential clue for exploring the mysterious relationship between surface architecture and function. As a visualizing method to understand these systems, in situ imaging of multiphase interfaces (e.g., air/liquid/solid and oil/water/solid systems) at the micro-/nanoscale, still remains a huge challenge, as a result of their heterogeneity and complexity. Here, recent progress on real-space micro-/nanoscale imaging of multiphase bio-interfacial systems is reviewed; this includes several techniques and imaging results on bio-interfaces, such as the lotus leaf, fish scale, living cell's surface, and fresh tissue surface. The results evidently show that interfacial structures have a significant impact on the state of the microscopic multiphase interface, further influencing specific functions. Based on this research, technical innovations, some more complicated multiphase interface systems, and structure-function coupling mechanism are proposed.
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Affiliation(s)
- Peipei Chen
- National Center for Nanoscience and Technology, Beijing, People's Republic of China
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34
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Sanchez H, Suzuki Y, Yokokawa M, Takeyasu K, Wyman C. Protein-DNA interactions in high speed AFM: single molecule diffusion analysis of human RAD54. Integr Biol (Camb) 2011; 3:1127-34. [PMID: 21986699 DOI: 10.1039/c1ib00039j] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
High-speed AFM (atomic force microscopy also called scanning force microscopy) provides nanometre spatial resolution and sub-second temporal resolution images of individual molecules. We exploit these features to study diffusion and motor activity of the RAD54 DNA repair factor. Human RAD54 functions at critical steps in recombinational-DNA repair. It is a member of the Swi2/Snf2 family of chromatin remodelers that translocate on DNA using ATP hydrolysis. A detailed single molecular description of DNA-protein interactions shows intermediate states and distribution of variable states, usually hidden by ensemble averaging. We measured the motion of individual proteins using single-particle tracking and observed that random walks were affected by imaging-buffer composition. Non-Brownian diffusion events were characterized in the presence and in the absence of nucleotide cofactors. Double-stranded DNA immobilized on the surface functioned as a trap reducing Brownian motion. Distinct short range slides and hops on DNA were visualized by high-speed AFM. These short-range interactions were usually inaccessible by other methods based on optical resolution. RAD54 monomers displayed a diffusive behavior unrelated to the motor activity.
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Affiliation(s)
- Humberto Sanchez
- Department of Cell Biology and Genetics, Cancer Genomics Center, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands.
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35
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Abstract
Carbon nanotubes are a significant addition to the emerging field of nanotube biotechnology. The biocompatibility, high structural integrity, and unique electronic and mechanical properties of carbon nanotubes complement or surpass those of self-assembled lipid nanotubes, peptide nanotubes, and template-synthesised nanotubes (metals, polymers, semiconductors, and carbons). Carbon nanotubes are candidates for a range of biomolecular applications that is likely to widen considerably in the future.
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Affiliation(s)
- M Baxendale
- Queen Mary, University of London, Physics Department, London, UK
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36
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Wu N, Zhou X, Czajkowsky DM, Ye M, Zeng D, Fu Y, Fan C, Hu J, Li B. In situ monitoring of single molecule binding reactions with time-lapse atomic force microscopy on functionalized DNA origami. NANOSCALE 2011; 3:2481-2484. [PMID: 21526259 DOI: 10.1039/c1nr10181a] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Individual biomolecular binding events were recorded in situ by combining time-lapse atomic force microscopy and DNA origami. Single streptavidin molecules bound to specifically biotinyated DNA origami were simply counted as a function of time to obtain a direct measure of the binding rate.
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Affiliation(s)
- Na Wu
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
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37
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Lyubchenko YL, Shlyakhtenko LS, Ando T. Imaging of nucleic acids with atomic force microscopy. Methods 2011; 54:274-83. [PMID: 21310240 PMCID: PMC3114274 DOI: 10.1016/j.ymeth.2011.02.001] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Revised: 12/07/2010] [Accepted: 02/01/2011] [Indexed: 11/18/2022] Open
Abstract
Atomic force microscopy (AFM) is a key tool of nanotechnology with great importance in applications to DNA nanotechnology and to the recently emerging field of RNA nanotechnology. Advances in the methodology of AFM now enable reliable and reproducible imaging of DNA of various structures, topologies, and DNA and RNA nanostructures. These advances are reviewed here with emphasis on methods utilizing modification of mica to prepare the surfaces enabling reliable and reproducible imaging of DNA and RNA nanostructures. Since the AFM technology for DNA is more mature, AFM imaging of DNA is introduced in this review to provide experience and background for the improvement of AFM imaging of RNA. Examples of imaging different structures of RNA and DNA are discussed and illustrated. Special attention is given to the potential use of AFM to image the dynamics of nucleic acids at the nanometer scale. As such, we review recent advances with the use of time-lapse AFM.
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Affiliation(s)
- Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198-6025, USA.
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38
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Rivetti C. DNA contour length measurements as a tool for the structural analysis of DNA and nucleoprotein complexes. Methods Mol Biol 2011; 749:235-254. [PMID: 21674377 DOI: 10.1007/978-1-61779-142-0_17] [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: 05/30/2023]
Abstract
The atomic force microscope (AFM) is a widely used tool to image DNA and nucleoprotein complexes at the molecular level. This is because the AFM is relatively easy to operate, has the capability to image biomolecules under aqueous solutions, and, most importantly, can image mesoscopic macromolecular structures that are too complex to be studied by X-ray or NMR and too small to be visualized with the optical microscope. Although there are many AFM studies about the structure and the physical properties of DNA, only in few cases a rigorous method has been applied to analyze AFM images. This chapter describes procedures to prepare DNA and nucleoprotein complexes for AFM imaging and methods used to carry out simple image measurements to obtain structural data. In particular, methods to measure DNA contour length and the volume of free or DNA-bound proteins are presented and discussed.
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Affiliation(s)
- Claudio Rivetti
- Department of Biochemistry and Molecular Biology, University of Parma, Parma, Italy.
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39
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Intermediate structure between chromatin fibers and chromosome revealed by mechanical stretching and SPM measurement. Biochem Biophys Res Commun 2010; 400:181-6. [PMID: 20719238 DOI: 10.1016/j.bbrc.2010.08.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Accepted: 08/11/2010] [Indexed: 11/23/2022]
Abstract
The morphology of chromosomes (certain rod-shaped structures) is highly reproducible despite the high condensation of chromatin fibers (∼1 mm) into chromosomes (∼1 μm). However, the mechanism underlying the condensation of chromatin fibers into chromosomes is unclear. We assume that investigation of the internal structure of chromosomes will aid in elucidating the condensation process. In order to observe the detailed structure of a chromosome, we stretched a human chromosome by using a micromanipulator and observed its morphology along the stretched region by scanning probe microscopy (SPM). We found that the chromosome consisted of some fibers that were thicker than chromatin fibers. The found fiber was composed of approximately 90-nm-wide beads that were linked linearly. To explore the components of the fiber, we performed immunofluorescence staining of the stretched chromosome. Fluorescence signals of topoisomerase (Topo) IIα, which is known to interact with and support chromatin fibers, and DNA were detected both on the found fiber and beads. Furthermore, after micrococcal nuclease and trypsin treatments, the fibers were found to be mechanically supported by proteins. These results suggest that chromosome comprises an intermediate structure between chromatin fibers and chromosomes.
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40
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Lyubchenko YL. Preparation of DNA and nucleoprotein samples for AFM imaging. Micron 2010; 42:196-206. [PMID: 20864349 DOI: 10.1016/j.micron.2010.08.011] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Revised: 08/24/2010] [Accepted: 08/24/2010] [Indexed: 02/06/2023]
Abstract
Sample preparation techniques allowing reliable and reproducible imaging of DNA with various structures, topologies and complexes with proteins are reviewed. The major emphasis is given to methods utilizing chemical functionalization of mica, enabling preparation of the surfaces with required characteristics. The methods are illustrated by examples of imaging of different DNA structures. Special attention is given to the possibility of AFM to image the dynamics of DNA at the nanoscale. The capabilities of time-lapse AFM in aqueous solutions are illustrated by imaging of dynamic processes as transitions of local alternative structures (transition of DNA between H and B forms). The application of AFM to studies of protein-DNA complexes is illustrated by a few examples of imaging site-specific complexes, as well as such systems as chromatin. The time-lapse AFM studies of protein-DNA complexes including very recent advances with the use of high-speed AFM are reviewed.
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Affiliation(s)
- Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, United States.
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41
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Roy D, Kwon SH, Kwak JW, Park JW. “Seeing and Counting” Individual Antigens Captured on a Microarrayed Spot with Force-Based Atomic Force Microscopy. Anal Chem 2010; 82:5189-94. [DOI: 10.1021/ac100476b] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dhruvajyoti Roy
- Department of Chemistry, National Core Research Center for Systems Bio-Dynamics, Pohang University of Science and Technology (POSTECH), Pohang 790-784, Korea
| | - Sung Hong Kwon
- Department of Chemistry, National Core Research Center for Systems Bio-Dynamics, Pohang University of Science and Technology (POSTECH), Pohang 790-784, Korea
| | - Ju-Won Kwak
- Department of Chemistry, National Core Research Center for Systems Bio-Dynamics, Pohang University of Science and Technology (POSTECH), Pohang 790-784, Korea
| | - Joon Won Park
- Department of Chemistry, National Core Research Center for Systems Bio-Dynamics, Pohang University of Science and Technology (POSTECH), Pohang 790-784, Korea
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42
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Lostao A, Peleato ML, Gómez-Moreno C, Fillat MF. Oligomerization properties of FurA from the cyanobacterium Anabaena sp. PCC 7120: direct visualization by in situ atomic force microscopy under different redox conditions. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:1723-9. [PMID: 20417733 DOI: 10.1016/j.bbapap.2010.04.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Revised: 04/06/2010] [Accepted: 04/08/2010] [Indexed: 11/16/2022]
Abstract
Fur proteins are global prokaryotic transcriptional regulators. Functional studies of FurA from the cyanobacterium Anabaena sp. PCC 7120 evidenced the influence of the redox environment in the activity of the regulator and its ability to aggregate through disulphide bridges. Atomic force microscopy allows single-molecule imaging and monitorization of the status of FurA under different redox conditions mimicking a physiological environment. The estimated FurA average diameter was of 4 nm. In the absence of reducing agents, the purified FurA is mainly associated as trimers, being 40 degrees the prevalent angle alpha conformed by protein monomers. Reducing conditions induces trimer rearrangement to protein monomers and a major fraction of FurA dimers. Disruption of the dimeric assemblies and appearance of higher order aggregates, namely trimers and tetramers are induced by oxidation with diamide or hydrogen peroxide. The homogeneity of the angles exhibited by the trimeric particles, as well as the occurrence of dimers in the presence of DTT, suggests the participation of relatively specific hydrophobic interactions maintaining the dimer. Direct visualization of the regulator under liquid phase at molecular resolution unravels the importance of non-polar interactions in FurA dynamics and shows that in Anabaena disulphide bridges are not essential for the dimerization of FurA.
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Affiliation(s)
- Anabel Lostao
- Instituto de Nanociencia de Aragón, Universidad de Zaragoza, 50018 Zaragoza, Spain
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43
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Goldsbury CS, Scheuring S, Kreplak L. Introduction to Atomic Force Microscopy (AFM) in Biology. ACTA ACUST UNITED AC 2009; Chapter 17:17.7.1-17.7.19. [DOI: 10.1002/0471140864.ps1707s58] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
| | | | - Laurent Kreplak
- Dalhousie University, Department of Physics & Atmospheric Science Halifax Canada
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44
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Shlyakhtenko LS, Lushnikov AY, Lyubchenko YL. Dynamics of nucleosomes revealed by time-lapse atomic force microscopy. Biochemistry 2009; 48:7842-8. [PMID: 19618963 DOI: 10.1021/bi900977t] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The dynamics of chromatin provides the access to DNA within nucleosomes, and therefore, this process is critically involved in the regulation of chromatin function. However, our knowledge of the large-range dynamics of nucleosomes is limited. Answers to the questions, such as the range of opening of the nucleosome and the mechanism via which the opening occurs and propagates, remain unknown. Here we applied single-molecule time-lapse atomic force microscopy (AFM) imaging to directly visualize the dynamics of nucleosomes and identify the mechanism of the large range DNA exposure. With this technique, we are able to observe the process of unwrapping of nucleosomes. The unwrapping of nucleosomes proceeds from the ends of the particles, allowing for the unwrapping of DNA regions as large as dozens of base pairs. This process may lead to a complete unfolding of nucleosomes and dissociation of the histone core from the complex. The unwrapping occurs in the absence of proteins involved in the chromatin remodeling that require ATP hydrolysis for their function, suggesting that the inherent dynamics of nucleosomes can contribute to the chromatin unwrapping process. These findings shed a new light on molecular mechanisms of nucleosome dynamics and provide novel hypotheses about the understanding of the action of remodeling proteins as well as other intracellular systems in chromatin dynamics.
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Affiliation(s)
- Luda S Shlyakhtenko
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68198-6025, USA
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45
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Vieira G, Henighan T, Chen A, Hauser AJ, Yang FY, Chalmers JJ, Sooryakumar R. Magnetic wire traps and programmable manipulation of biological cells. PHYSICAL REVIEW LETTERS 2009; 103:128101. [PMID: 19792462 PMCID: PMC3928075 DOI: 10.1103/physrevlett.103.128101] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2009] [Indexed: 05/07/2023]
Abstract
We present a multiplex method, based on microscopic programmable magnetic traps in zigzag wires patterned on a platform, to simultaneously apply directed forces on multiple fluid-borne cells or biologically inert magnetic microparticles or nanoparticles. The gentle tunable forces do not produce damage and retain cell viability. The technique is demonstrated with T-lymphocyte cells remotely manipulated (by a joystick) along desired trajectories on a silicon surface with average speeds up to 20 microm/s.
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Affiliation(s)
- G Vieira
- Department of Physics, The Ohio State University, Columbus, Ohio 43210, USA
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46
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Abou-Saleh RH, Connell SD, Harrand R, Ajjan RA, Mosesson MW, Smith DAM, Grant PJ, Ariëns RAS. Nanoscale probing reveals that reduced stiffness of clots from fibrinogen lacking 42 N-terminal Bbeta-chain residues is due to the formation of abnormal oligomers. Biophys J 2009; 96:2415-27. [PMID: 19289066 DOI: 10.1016/j.bpj.2008.12.3913] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2008] [Revised: 12/12/2008] [Accepted: 12/15/2008] [Indexed: 10/21/2022] Open
Abstract
Removal of Bbetal-42 from fibrinogen by Crotalus atrox venom results in a molecule lacking fibrinopeptide B and part of a thrombin binding site. We investigated the mechanism of polymerization of desBbeta1-42 fibrin. Fibrinogen trinodular structure was clearly observed using high resolution noncontact atomic force microscopy. E-regions were smaller in desBbeta1-42 than normal fibrinogen (1.2 nm +/- 0.3 vs. 1.5 nm +/- 0.2), whereas there were no differences between the D-regions (1.7 nm +/- 0.4 vs. 1.7 nm +/- 0.3). Polymerization rate for desBbeta1-42 was slower than normal, resulting in clots with thinner fibers. Differences in oligomers were found, with predominantly lateral associations for desBbeta1-42 and longitudinal associations for normal fibrin. Clot elasticity as measured by magnetic tweezers showed a G' of approximately 1 Pa for desBbeta1-42 compared with approximately 8 Pa for normal fibrin. Spring constants of early stage desBbeta1-42 single fibers determined by atomic force microscopy were approximately 3 times less than normal fibers of comparable dimensions and development. We conclude that Bbeta1-42 plays an important role in fibrin oligomer formation. Absence of Bbeta1-42 influences oligomer structure, affects the structure and properties of the final clot, and markedly reduces stiffness of the whole clot as well as individual fibrin fibers.
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Affiliation(s)
- Radwa H Abou-Saleh
- Molecular and Nanoscale Physics Group, Department of Physics and Astronomy, University of Leeds, Leeds, United Kingdom
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47
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Lyubchenko YL, Shlyakhtenko LS, Gall AA. Atomic force microscopy imaging and probing of DNA, proteins, and protein DNA complexes: silatrane surface chemistry. Methods Mol Biol 2009; 543:337-351. [PMID: 19378175 DOI: 10.1007/978-1-60327-015-1_21] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Despite their rather recent invention, atomic force microscopes are widely available commercially. AFM and its special modifications (tapping mode and noncontact operation in solution) have been successfully used for topographic studies of a large number of biological objects including DNA, RNA, proteins, cell membranes, and even whole cells. AFM was also successfully applied to studies of nucleic acids and various protein DNA complexes. Part of this success is due to the development of reliable sample preparation procedures. This chapter describes one of the approaches based on chemical functionalization of mica surface with 1-(3-aminopropyl) silatrane (APS). One of the most important properties of APS-mica approach is that the sample can be deposited on the surface in a wide range of ionic strengths, in the absence of divalent cations and a broad range of pH. In addition to imaging of dried sample, APS-mica allows reliable and reproducible time lapse imaging in aqueous solutions. Finally, APS mica is terminated with reactive amino groups that can be used for covalent and ionic attachment of molecules for AFM force spectroscopy studies. The protocols for the preparation of APS, functionalization with APS mica and AFM probes, preparation of samples for imaging in air and in aqueous solutions, and force spectroscopy studies are outlined. All these applications are illustrated with a few examples.
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Affiliation(s)
- Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
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48
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Lyubchenko YL, Shlyakhtenko LS. AFM for analysis of structure and dynamics of DNA and protein-DNA complexes. Methods 2008; 47:206-13. [PMID: 18835446 DOI: 10.1016/j.ymeth.2008.09.002] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2008] [Revised: 09/09/2008] [Accepted: 09/10/2008] [Indexed: 10/21/2022] Open
Abstract
This paper describes protocols for studies of structure and dynamics of DNA and protein-DNA complexes with atomic force microscopy (AFM) utilizing the surface chemistry approach. The necessary specifics for the preparation of functionalized surfaces and AFM probes with the use of silanes and silatranes, including the protocols for synthesis of silatranes are provided. The methodology of studies of local and global conformations DNA with the major focus on the time-lapse imaging of DNA in aqueous solutions is illustrated by the study of dynamics of Holliday junctions including branch migration. The analysis of nucleosome dynamics is selected as an example to illustrate the application of the time-lapse AFM to studies of dynamics of protein-DNA complexes. The force spectroscopy is the modality of AFM with a great importance to various fields of biomedical studies. The AFM force spectroscopy approach for studies of specific protein-DNA complexes is illustrated by the data on analysis of dynamics of synaptic SfiI-DNA complexes. When necessary, additional specifics are added to the corresponding example.
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Affiliation(s)
- Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, College of Pharmacy, COP 1012, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA.
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49
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Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy. Nat Methods 2008; 5:491-505. [PMID: 18511917 DOI: 10.1038/nmeth.1218] [Citation(s) in RCA: 1375] [Impact Index Per Article: 85.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Single-molecule force spectroscopy has emerged as a powerful tool to investigate the forces and motions associated with biological molecules and enzymatic activity. The most common force spectroscopy techniques are optical tweezers, magnetic tweezers and atomic force microscopy. Here we describe these techniques and illustrate them with examples highlighting current capabilities and limitations.
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50
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Goldsbury C, Scheuring S. Introduction to atomic force microscopy (AFM) in biology. ACTA ACUST UNITED AC 2008; Chapter 17:17.7.1-17.7.17. [PMID: 18429225 DOI: 10.1002/0471140864.ps1707s29] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The atomic force microscope has the unique capability of imaging biological samples with molecular resolution in buffer solution. In addition to providing topographical images of surfaces with nanometer- to angstrom-scale resolution, forces between single molecules and mechanical properties of biological samples can be investigated. Importantly, the measurements are made in buffer solutions, allowing biological samples to stay alive within a physiological-like environment while temporal changes in structure are measured. This overview provides an introduction to AFM on biological systems and describes specific examples of AFM on proteins. The physical principles of the technique and methodological aspects of its practical use and applications are also described.
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Affiliation(s)
- Claire Goldsbury
- Cytoskeleton Group, Max Planck Unit for Structural Molecular Biology, Hamburg, Germany
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