1
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Miranda A, Gómez-Varela AI, Stylianou A, Hirvonen LM, Sánchez H, De Beule PAA. How did correlative atomic force microscopy and super-resolution microscopy evolve in the quest for unravelling enigmas in biology? NANOSCALE 2021; 13:2082-2099. [PMID: 33346312 DOI: 10.1039/d0nr07203f] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
With the invention of the Atomic Force Microscope (AFM) in 1986 and the subsequent developments in liquid imaging and cellular imaging it became possible to study the topography of cellular specimens under nearly physiological conditions with nanometric resolution. The application of AFM to biological research was further expanded with the technological advances in imaging modes where topographical data can be combined with nanomechanical measurements, offering the possibility to retrieve the biophysical properties of tissues, cells, fibrous components and biomolecules. Meanwhile, the quest for breaking the Abbe diffraction limit restricting microscopic resolution led to the development of super-resolution fluorescence microscopy techniques that brought the resolution of the light microscope comparable to the resolution obtained by AFM. The instrumental combination of AFM and optical microscopy techniques has evolved over the last decades from integration of AFM with bright-field and phase-contrast imaging techniques at first to correlative AFM and wide-field fluorescence systems and then further to the combination of AFM and fluorescence based super-resolution microscopy modalities. Motivated by the many developments made over the last decade, we provide here a review on AFM combined with super-resolution fluorescence microscopy techniques and how they can be applied for expanding our understanding of biological processes.
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Affiliation(s)
- Adelaide Miranda
- International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga s/n, Braga, Portugal.
| | - Ana I Gómez-Varela
- International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga s/n, Braga, Portugal. and Department of Applied Physics, University of Santiago de Compostela, E-15782, Santiago de Compostela, Spain.
| | - Andreas Stylianou
- Cancer Biophysics Laboratory, University of Cyprus, Nicosia, Cyprus and School of Sciences, European University Cyprus, Nicosia, Cyprus
| | - Liisa M Hirvonen
- Centre for Microscopy, Characterisation and Analysis (CMCA), The University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Humberto Sánchez
- Faculty of Applied Sciences, Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ, Delft, The Netherlands
| | - Pieter A A De Beule
- International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga s/n, Braga, Portugal.
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2
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Simultaneous co-localized super-resolution fluorescence microscopy and atomic force microscopy: combined SIM and AFM platform for the life sciences. Sci Rep 2020; 10:1122. [PMID: 31980680 PMCID: PMC6981207 DOI: 10.1038/s41598-020-57885-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/07/2020] [Indexed: 01/05/2023] Open
Abstract
Correlating data from different microscopy techniques holds the potential to discover new facets of signaling events in cellular biology. Here we report for the first time a hardware set-up capable of achieving simultaneous co-localized imaging of spatially correlated far-field super-resolution fluorescence microscopy and atomic force microscopy, a feat only obtained until now by fluorescence microscopy set-ups with spatial resolution restricted by the Abbe diffraction limit. We detail system integration and demonstrate system performance using sub-resolution fluorescent beads and applied to a test sample consisting of human bone osteosarcoma epithelial cells, with plasma membrane transporter 1 (MCT1) tagged with an enhanced green fluorescent protein (EGFP) at the N-terminal.
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3
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Frederickx W, Rocha S, Fujita Y, Kennes K, De Keersmaecker H, De Feyter S, Uji-I H, Vanderlinden W. Orthogonal Probing of Single-Molecule Heterogeneity by Correlative Fluorescence and Force Microscopy. ACS NANO 2018; 12:168-177. [PMID: 29257876 DOI: 10.1021/acsnano.7b05405] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Correlative imaging by fluorescence and force microscopy is an emerging technology to acquire orthogonal information at the nanoscale. Whereas atomic force microscopy excels at resolving the envelope structure of nanoscale specimens, fluorescence microscopy can detect specific molecular labels, which enables the unambiguous recognition of molecules in a complex assembly. Whereas correlative imaging at the micrometer scale has been established, it remains challenging to push the technology to the single-molecule level. Here, we used an integrated setup to systematically evaluate the factors that influence the quality of correlative fluorescence and force microscopy. Optimized data processing to ensure accurate drift correction and high localization precision results in image registration accuracies of ∼25 nm on organic fluorophores, which represents a 2-fold improvement over the state of the art in correlative fluorescence and force microscopy. Furthermore, we could extend the Atto532 fluorophore bleaching time ∼2-fold, by chemical modification of the supporting mica surface. In turn, this enables probing the composition of macromolecular complexes by stepwise photobleaching with high confidence. We demonstrate the performance of our method by resolving the stoichiometry of molecular subpopulations in a heterogeneous EcoRV-DNA nucleoprotein ensemble.
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Affiliation(s)
- Wout Frederickx
- Department of Chemistry, Division of Molecular Imaging and Photonics, KU Leuven-University of Leuven , Celestijnenlaan 200F, B-3001, Leuven, Belgium
| | - Susana Rocha
- Department of Chemistry, Division of Molecular Imaging and Photonics, KU Leuven-University of Leuven , Celestijnenlaan 200F, B-3001, Leuven, Belgium
| | - Yasuhiko Fujita
- Department of Chemistry, Division of Molecular Imaging and Photonics, KU Leuven-University of Leuven , Celestijnenlaan 200F, B-3001, Leuven, Belgium
| | - Koen Kennes
- Department of Chemistry, Division of Molecular Imaging and Photonics, KU Leuven-University of Leuven , Celestijnenlaan 200F, B-3001, Leuven, Belgium
| | - Herlinde De Keersmaecker
- Department of Chemistry, Division of Molecular Imaging and Photonics, KU Leuven-University of Leuven , Celestijnenlaan 200F, B-3001, Leuven, Belgium
| | - Steven De Feyter
- Department of Chemistry, Division of Molecular Imaging and Photonics, KU Leuven-University of Leuven , Celestijnenlaan 200F, B-3001, Leuven, Belgium
| | - Hiroshi Uji-I
- Department of Chemistry, Division of Molecular Imaging and Photonics, KU Leuven-University of Leuven , Celestijnenlaan 200F, B-3001, Leuven, Belgium
- Research Institute for Electronic Science, Nanomaterials and Nanoscopy, Hokkaido University , Kita 10 Nishi 20, North Ward, Sapporo 001-0020, Japan
| | - Willem Vanderlinden
- Department of Chemistry, Division of Molecular Imaging and Photonics, KU Leuven-University of Leuven , Celestijnenlaan 200F, B-3001, Leuven, Belgium
- Department of Physics, Nanosystems Initiative Munich, and Center for NanoScience, LMU Munich , Amalienstrasse 54, 80799 Munich, Germany
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4
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Mohan Bangalore D, Tessmer I. Unique insight into protein-DNA interactions from single molecule atomic force microscopy. AIMS BIOPHYSICS 2018. [DOI: 10.3934/biophy.2018.3.194] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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5
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Pirrotta A, Solomon GC, Franco I, Troisi A. Excitonic Coupling Modulated by Mechanical Stimuli. J Phys Chem Lett 2017; 8:4326-4332. [PMID: 28837767 DOI: 10.1021/acs.jpclett.7b01828] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Understanding energy transfer is of vital importance in a diverse range of applications from biological systems to photovoltaics. The ability to tune excitonic coupling in any of these systems, however, is generally limited. In this work, we have simulated a new class of single-molecule spectroscopy in which force microscopy is used to control the excitonic coupling between chromophores. Here we demonstrate that the excitonic coupling can be controlled by mechanical manipulation of the molecule (perylenediimide dimers and terrylenediimide-perylenediimide heterodimers) and can be tuned over a broad range of values (0.02-0.15 eV) that correspond to different regimes of exciton dynamics going from the folded to the elongated structure of the dimer. In all of the systems considered here, the switching from high to low coupling takes place simultaneously with the mechanical deformation detected by a strong increase and subsequent decay of the force. These simulations suggest that single-molecule force spectroscopy can be used to understand and eventually aid the design of excitonic devices.
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Affiliation(s)
- Alessandro Pirrotta
- Nano-Science Center and Department of Chemistry, University of Copenhagen , 2100 Copenhagen Ø, Denmark
| | - Gemma C Solomon
- Nano-Science Center and Department of Chemistry, University of Copenhagen , 2100 Copenhagen Ø, Denmark
| | - Ignacio Franco
- Department of Chemistry, University of Rochester , Rochester, New York 14627-0216, United States
| | - Alessandro Troisi
- Department of Chemistry, University of Liverpool , L69 7DZ Liverpool, United Kingdom
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6
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Beckwitt EC, Kong M, Van Houten B. Studying protein-DNA interactions using atomic force microscopy. Semin Cell Dev Biol 2017; 73:220-230. [PMID: 28673677 DOI: 10.1016/j.semcdb.2017.06.028] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 06/27/2017] [Accepted: 06/29/2017] [Indexed: 12/12/2022]
Abstract
Atomic force microscopy (AFM) has made significant contributions to the study of protein-DNA interactions by making it possible to topographically image biological samples. A single protein-DNA binding reaction imaged by AFM can reveal protein binding specificity and affinity, protein-induced DNA bending, and protein binding stoichiometry. Changes in DNA structure, complex conformation, and cooperativity, can also be analyzed. In this review we highlight some important examples in the literature and discuss the advantages and limitations of these measurements. We also discuss important advances in technology that will facilitate the progress of AFM in the future.
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Affiliation(s)
- Emily C Beckwitt
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA; The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Muwen Kong
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA; The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Bennett Van Houten
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA; The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.
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7
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LeBlanc S, Wilkins H, Li Z, Kaur P, Wang H, Erie DA. Using Atomic Force Microscopy to Characterize the Conformational Properties of Proteins and Protein-DNA Complexes That Carry Out DNA Repair. Methods Enzymol 2017; 592:187-212. [PMID: 28668121 PMCID: PMC5761736 DOI: 10.1016/bs.mie.2017.04.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Atomic force microscopy (AFM) is a scanning probe technique that allows visualization of single biomolecules and complexes deposited on a surface with nanometer resolution. AFM is a powerful tool for characterizing protein-protein and protein-DNA interactions. It can be used to capture snapshots of protein-DNA solution dynamics, which in turn, enables the characterization of the conformational properties of transient protein-protein and protein-DNA interactions. With AFM, it is possible to determine the stoichiometries and binding affinities of protein-protein and protein-DNA associations, the specificity of proteins binding to specific sites on DNA, and the conformations of the complexes. We describe methods to prepare and deposit samples, including surface treatments for optimal depositions, and how to quantitatively analyze images. We also discuss a new electrostatic force imaging technique called DREEM, which allows the visualization of the path of DNA within proteins in protein-DNA complexes. Collectively, these methods facilitate the development of comprehensive models of DNA repair and provide a broader understanding of all protein-protein and protein-nucleic acid interactions. The structural details gleaned from analysis of AFM images coupled with biochemistry provide vital information toward establishing the structure-function relationships that govern DNA repair processes.
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Affiliation(s)
- Sharonda LeBlanc
- University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Hunter Wilkins
- University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Zimeng Li
- University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Parminder Kaur
- North Carolina State University, Raleigh, NC, United States
| | - Hong Wang
- North Carolina State University, Raleigh, NC, United States
| | - Dorothy A Erie
- University of North Carolina at Chapel Hill, Chapel Hill, NC, United States; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.
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8
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Colomb W, Czerski J, Sau JD, Sarkar SK. Estimation of microscope drift using fluorescent nanodiamonds as fiducial markers. J Microsc 2017; 266:298-306. [PMID: 28328030 DOI: 10.1111/jmi.12539] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 01/16/2017] [Accepted: 01/25/2017] [Indexed: 01/10/2023]
Abstract
Fiducial markers are used to correct the microscope drift and should be photostable, be usable at multiple wavelengths and be compatible for multimodal imaging. Fiducial markers such as beads, gold nanoparticles, microfabricated patterns and organic fluorophores lack one or more of these criteria. Moreover, the localization accuracy and drift correction can be degraded by other fluorophores, instrument noise and artefacts due to image processing and tracking algorithms. Estimating mechanical drift by assuming Gaussian distributed noise is not suitable under these circumstances. Here we present a method that uses fluorescent nanodiamonds as fiducial markers and uses an improved maximum likelihood algorithm to estimate the drift with both accuracy and precision within the range 1.55-5.75 nm.
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Affiliation(s)
- W Colomb
- Department of Physics, Colorado School of Mines, Golden, Colorado, U.S.A
| | - J Czerski
- Department of Physics, Colorado School of Mines, Golden, Colorado, U.S.A
| | - J D Sau
- Department of Physics, University of Maryland, College Park, MD, U.S.A
| | - S K Sarkar
- Department of Physics, Colorado School of Mines, Golden, Colorado, U.S.A
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9
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Handschuh-Wang S, Wang T, Zhou X. Recent advances in hybrid measurement methods based on atomic force microscopy and surface sensitive measurement techniques. RSC Adv 2017. [DOI: 10.1039/c7ra08515j] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
This review summaries the recent progress of the combination of optical and non-optical surface sensitive techniques with the atomic force microscopy.
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Affiliation(s)
- Stephan Handschuh-Wang
- College of Chemistry and Environmental Engineering
- Shenzhen University
- Shenzhen 518060
- P. R. China
| | - Tao Wang
- Functional Thin Films Research Center
- Shenzhen Institutes of Advanced Technology
- Chinese Academy of Sciences
- Shenzhen 518055
- P. R. China
| | - Xuechang Zhou
- College of Chemistry and Environmental Engineering
- Shenzhen University
- Shenzhen 518060
- P. R. China
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10
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Bondia P, Casado S, Flors C. Correlative Super-Resolution Fluorescence Imaging and Atomic Force Microscopy for the Characterization of Biological Samples. Methods Mol Biol 2017; 1663:105-113. [PMID: 28924662 DOI: 10.1007/978-1-4939-7265-4_9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Recent advances in imaging tools have greatly improved our ability to analyze the structure and molecular components of a wide range of biological systems at the nanoscale. High resolution imaging can be performed with a handful of techniques, each of them revealing particular features of the sample. A more comprehensive picture of a biological system can be achieved by combining the information provided by complementary imaging methods. Specifically, the correlation between super-resolution fluorescence imaging and atomic force microscopy (AFM) provides high resolution topography as well as specific chemical information, the latter with a spatial resolution that approaches that of AFM. We present a detailed protocol and discuss the requirements and challenges in terms of sample preparation, instrumentation, and image alignment to combine these two powerful techniques. This hybrid nanoscale imaging tool has the potential to provide robust validation for super-resolution methods as well as new insight into biological samples.
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Affiliation(s)
- Patricia Bondia
- Madrid Institute for Advanced Studies in Nanoscience (IMDEA Nanoscience) and Nanobiotechnology Unit Associated to the National Center for Biotechnology (CSIC), C/ Faraday 9, Madrid, 28049, Spain
| | - Santiago Casado
- Madrid Institute for Advanced Studies in Nanoscience (IMDEA Nanoscience) and Nanobiotechnology Unit Associated to the National Center for Biotechnology (CSIC), C/ Faraday 9, Madrid, 28049, Spain
| | - Cristina Flors
- Madrid Institute for Advanced Studies in Nanoscience (IMDEA Nanoscience) and Nanobiotechnology Unit Associated to the National Center for Biotechnology (CSIC), C/ Faraday 9, Madrid, 28049, Spain.
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11
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The molecular choreography of protein synthesis: translational control, regulation, and pathways. Q Rev Biophys 2016; 49:e11. [PMID: 27658712 DOI: 10.1017/s0033583516000056] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Translation of proteins by the ribosome regulates gene expression, with recent results underscoring the importance of translational control. Misregulation of translation underlies many diseases, including cancer and many genetic diseases. Decades of biochemical and structural studies have delineated many of the mechanistic details in prokaryotic translation, and sketched the outlines of eukaryotic translation. However, translation may not proceed linearly through a single mechanistic pathway, but likely involves multiple pathways and branchpoints. The stochastic nature of biological processes would allow different pathways to occur during translation that are biased by the interaction of the ribosome with other translation factors, with many of the steps kinetically controlled. These multiple pathways and branchpoints are potential regulatory nexus, allowing gene expression to be tuned at the translational level. As research focus shifts toward eukaryotic translation, certain themes will be echoed from studies on prokaryotic translation. This review provides a general overview of the dynamic data related to prokaryotic and eukaryotic translation, in particular recent findings with single-molecule methods, complemented by biochemical, kinetic, and structural findings. We will underscore the importance of viewing the process through the viewpoints of regulation, translational control, and heterogeneous pathways.
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12
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Symmetric curvature descriptors for label-free analysis of DNA. Sci Rep 2014; 4:6459. [PMID: 25248631 PMCID: PMC5377314 DOI: 10.1038/srep06459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 08/26/2014] [Indexed: 11/13/2022] Open
Abstract
High-resolution microscopy techniques such as electron microscopy, scanning tunnelling microscopy and atomic force microscopy represent well-established, powerful tools for the structural characterization of adsorbed DNA molecules at the nanoscale. Notably, the analysis of DNA contours allows mapping intrinsic curvature and flexibility along the molecular backbone. This is particularly suited to address the impact of the base-pairs sequence on the local conformation of the strands and plays a pivotal role for investigations relating the inherent DNA shape and flexibility to other functional properties. Here, we introduce novel chain descriptors aimed to characterize the local intrinsic curvature and flexibility of adsorbed DNA molecules with unknown orientation. They consist of stochastic functions that couple the curvatures of two nanosized segments, symmetrically placed on the DNA contour. We show that the fine mapping of the ensemble-averaged functions along the molecular backbone generates characteristic patterns of variation that highlight all pairs of tracts with large intrinsic curvature or enhanced flexibility. We demonstrate the practical applicability of the method for DNA chains imaged by atomic force microscopy. Our approach paves the way for the label-free comparative analysis of duplexes, aimed to detect nanoscale conformational changes of physical or biological relevance in large sample numbers.
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13
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Hughes CD, Simons M, Mackenzie CE, Van Houten B, Kad NM. Single molecule techniques in DNA repair: a primer. DNA Repair (Amst) 2014; 20:2-13. [PMID: 24819596 DOI: 10.1016/j.dnarep.2014.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 02/03/2014] [Indexed: 10/25/2022]
Abstract
A powerful new approach has become much more widespread and offers insights into aspects of DNA repair unattainable with billions of molecules. Single molecule techniques can be used to image, manipulate or characterize the action of a single repair protein on a single strand of DNA. This allows search mechanisms to be probed, and the effects of force to be understood. These physical aspects can dominate a biochemical reaction, where at the ensemble level their nuances are obscured. In this paper we discuss some of the many technical advances that permit study at the single molecule level. We focus on DNA repair to which these techniques are actively being applied. DNA repair is also a process that encompasses so much of what single molecule studies benefit--searching for targets, complex formation, sequential biochemical reactions and substrate hand-off to name just a few. We discuss how single molecule biophysics is poised to transform our understanding of biological systems, in particular DNA repair.
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Affiliation(s)
- Craig D Hughes
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Michelle Simons
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Cassidy E Mackenzie
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Bennett Van Houten
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Neil M Kad
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK.
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14
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Sanchez H, Reuter M, Yokokawa M, Takeyasu K, Wyman C. Taking it one step at a time in homologous recombination repair. DNA Repair (Amst) 2014; 20:110-118. [PMID: 24636751 DOI: 10.1016/j.dnarep.2014.02.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 02/07/2014] [Accepted: 02/11/2014] [Indexed: 01/10/2023]
Abstract
The individual steps in the process of homologous recombination are particularly amenable to analysis by single-molecule imaging and manipulation experiments. Over the past 20 years these have provided a wealth of new information on the DNA transactions that make up this vital process. Exciting progress in developing new tools and techniques to analyze more complex components, dynamic reaction steps and molecular coordination continues at a rapid pace. Here we highlight recent results and indicate some emerging techniques likely to produce the next stage of advanced insight into homologous recombination. In this and related fields the future is bright.
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Affiliation(s)
- Humberto Sanchez
- Department of Genetics, Cancer Genomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marcel Reuter
- Department of Genetics, Cancer Genomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Masatoshi Yokokawa
- Graduate School of Pure and Applied Science, University of Tsukuba, Japan
| | | | - Claire Wyman
- Department of Genetics, Cancer Genomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands; Department of Radiation Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands.
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15
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Multi-modal registration for correlative microscopy using image analogies. Med Image Anal 2013; 18:914-26. [PMID: 24387943 DOI: 10.1016/j.media.2013.12.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 11/22/2013] [Accepted: 12/05/2013] [Indexed: 11/23/2022]
Abstract
Correlative microscopy is a methodology combining the functionality of light microscopy with the high resolution of electron microscopy and other microscopy technologies for the same biological specimen. In this paper, we propose an image registration method for correlative microscopy, which is challenging due to the distinct appearance of biological structures when imaged with different modalities. Our method is based on image analogies and allows to transform images of a given modality into the appearance-space of another modality. Hence, the registration between two different types of microscopy images can be transformed to a mono-modality image registration. We use a sparse representation model to obtain image analogies. The method makes use of corresponding image training patches of two different imaging modalities to learn a dictionary capturing appearance relations. We test our approach on backscattered electron (BSE) scanning electron microscopy (SEM)/confocal and transmission electron microscopy (TEM)/confocal images. We perform rigid, affine, and deformable registration via B-splines and show improvements over direct registration using both mutual information and sum of squared differences similarity measures to account for differences in image appearance.
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16
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Monserrate A, Casado S, Flors C. Correlative Atomic Force Microscopy and Localization-Based Super-Resolution Microscopy: Revealing Labelling and Image Reconstruction Artefacts. Chemphyschem 2013; 15:647-50. [DOI: 10.1002/cphc.201300853] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Indexed: 11/10/2022]
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17
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Buechner CN, Tessmer I. DNA substrate preparation for atomic force microscopy studies of protein-DNA interactions. J Mol Recognit 2013; 26:605-17. [DOI: 10.1002/jmr.2311] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 08/14/2013] [Accepted: 08/15/2013] [Indexed: 12/16/2022]
Affiliation(s)
- Claudia N. Buechner
- Rudolf Virchow Center for Experimental Biomedicine; University of Wuerzburg; Josef Schneider Str. 2 97080 Wuerzburg Germany
| | - Ingrid Tessmer
- Rudolf Virchow Center for Experimental Biomedicine; University of Wuerzburg; Josef Schneider Str. 2 97080 Wuerzburg Germany
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18
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Tessmer I, Kaur P, Lin J, Wang H. Investigating bioconjugation by atomic force microscopy. J Nanobiotechnology 2013; 11:25. [PMID: 23855448 PMCID: PMC3723498 DOI: 10.1186/1477-3155-11-25] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2013] [Accepted: 07/05/2013] [Indexed: 12/15/2022] Open
Abstract
Nanotechnological applications increasingly exploit the selectivity and processivity of biological molecules. Integration of biomolecules such as proteins or DNA into nano-systems typically requires their conjugation to surfaces, for example of carbon-nanotubes or fluorescent quantum dots. The bioconjugated nanostructures exploit the unique strengths of both their biological and nanoparticle components and are used in diverse, future oriented research areas ranging from nanoelectronics to biosensing and nanomedicine. Atomic force microscopy imaging provides valuable, direct insight for the evaluation of different conjugation approaches at the level of the individual molecules. Recent technical advances have enabled high speed imaging by AFM supporting time resolutions sufficient to follow conformational changes of intricately assembled nanostructures in solution. In addition, integration of AFM with different spectroscopic and imaging approaches provides an enhanced level of information on the investigated sample. Furthermore, the AFM itself can serve as an active tool for the assembly of nanostructures based on bioconjugation. AFM is hence a major workhorse in nanotechnology; it is a powerful tool for the structural investigation of bioconjugation and bioconjugation-induced effects as well as the simultaneous active assembly and analysis of bioconjugation-based nanostructures.
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Affiliation(s)
- Ingrid Tessmer
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Str, 2, 97080, Würzburg, Germany.
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19
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Combined optical and topographic imaging reveals different arrangements of human RAD54 with presynaptic and postsynaptic RAD51-DNA filaments. Proc Natl Acad Sci U S A 2013; 110:11385-90. [PMID: 23801766 DOI: 10.1073/pnas.1306467110] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Essential genome transactions, such as homologous recombination, are achieved by concerted and dynamic interactions of multiple protein components with DNA. Which proteins do what and how, will be reflected in their relative arrangements. However, obtaining high-resolution structural information on the variable arrangements of these complex assemblies is a challenge. Here we demonstrate the versatility of a combined total internal reflection fluorescence and scanning force microscope (TIRF-SFM) to pinpoint fluorescently labeled human homologous recombination protein RAD54 interacting with presynaptic (ssDNA) and postsynaptic (dsDNA) human recombinase RAD51 nucleoprotein filaments. Labeled proteins were localized by superresolution imaging on complex structures in the SFM image with high spatial accuracy. We observed some RAD54 at RAD51 filament ends, as expected. More commonly, RAD54 interspersed along RAD51-DNA filaments. RAD54 promotes RAD51-mediated DNA strand exchange and has been described to both stabilize and destabilize RAD51-DNA filaments. The different architectural arrangements we observe for RAD54 with RAD51-DNA filaments may reflect the diverse roles of this protein in homologous recombination.
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Li JJ, Yip CM. Super-resolved FT-IR spectroscopy: Strategies, challenges, and opportunities for membrane biophysics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2272-82. [PMID: 23500349 DOI: 10.1016/j.bbamem.2013.02.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Accepted: 02/25/2013] [Indexed: 01/16/2023]
Abstract
Direct correlation of molecular conformation with local structure is critical to studies of protein- and peptide-membrane interactions, particularly in the context of membrane-facilitated aggregation, and disruption or disordering. Infrared spectroscopy has long been a mainstay for determining molecular conformation, following folding dynamics, and characterizing reactions. While tremendous advances have been made in improving the spectral and temporal resolution of infrared spectroscopy, it has only been with the introduction of scanned-probe techniques that exploit the raster-scanning tip as either a source, scattering tool, or measurement probe that researchers have been able to obtain sub-diffraction limit IR spectra. This review will examine the history of correlated scanned-probe IR spectroscopies, from their inception to their use in studies of molecular aggregates, membrane domains, and cellular structures. The challenges and opportunities that these platforms present for examining dynamic phenomena will be discussed. This article is part of a Special Issue entitled: FTIR in membrane proteins and peptide studies.
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Affiliation(s)
- Jessica J Li
- Department of Chemical Engineering and Applied Chemistry, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada M5S 3E1
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Registration for Correlative Microscopy Using Image Analogies. BIOMEDICAL IMAGE REGISTRATION 2012. [DOI: 10.1007/978-3-642-31340-0_31] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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Caplan J, Niethammer M, Taylor RM, Czymmek KJ. The power of correlative microscopy: multi-modal, multi-scale, multi-dimensional. Curr Opin Struct Biol 2011; 21:686-93. [PMID: 21782417 DOI: 10.1016/j.sbi.2011.06.010] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 06/22/2011] [Indexed: 11/24/2022]
Abstract
Correlative microscopy is a sophisticated approach that combines the capabilities of typically separate, but powerful microscopy platforms: often including, but not limited, to conventional light, confocal and super-resolution microscopy, atomic force microscopy, transmission and scanning electron microscopy, magnetic resonance imaging and micro/nano CT (computed tomography). When targeting rare or specific events within large populations or tissues, correlative microscopy is increasingly being recognized as the method of choice. Furthermore, this multi-modal assimilation of technologies provides complementary and often unique information, such as internal and external spatial, structural, biochemical and biophysical details from the same targeted sample. The development of a continuous stream of cutting-edge applications, probes, preparation methodologies, hardware and software developments will enable realization of the full potential of correlative microscopy.
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Affiliation(s)
- Jeffrey Caplan
- Delaware Biotechnology Institute Bio-Imaging Center, University of Delaware, Newark, DE 19711, United States
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