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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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Reuter M, Zelensky A, Smal I, Meijering E, van Cappellen WA, de Gruiter HM, van Belle GJ, van Royen ME, Houtsmuller AB, Essers J, Kanaar R, Wyman C. BRCA2 diffuses as oligomeric clusters with RAD51 and changes mobility after DNA damage in live cells. ACTA ACUST UNITED AC 2015; 207:599-613. [PMID: 25488918 PMCID: PMC4259808 DOI: 10.1083/jcb.201405014] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Nuclear BRCA2 is oligomeric and associated with RAD51, possibly sequestering it until it is delivered to DNA damage sites. Genome maintenance by homologous recombination depends on coordinating many proteins in time and space to assemble at DNA break sites. To understand this process, we followed the mobility of BRCA2, a critical recombination mediator, in live cells at the single-molecule level using both single-particle tracking and fluorescence correlation spectroscopy. BRCA2-GFP and -YFP were compared to distinguish diffusion from fluorophore behavior. Diffusive behavior of fluorescent RAD51 and RAD54 was determined for comparison. All fluorescent proteins were expressed from endogenous loci. We found that nuclear BRCA2 existed in oligomeric clusters, and exhibited heterogeneous mobility. DNA damage increased BRCA2 transient binding, presumably including binding to damaged sites. Despite its very different size, RAD51 displayed mobility similar to BRCA2, which indicates physical interaction between these proteins both before and after induction of DNA damage. We propose that BRCA2-mediated sequestration of nuclear RAD51 serves to prevent inappropriate DNA interactions and that all RAD51 is delivered to DNA damage sites in association with BRCA2.
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Affiliation(s)
- Marcel Reuter
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
| | - Alex Zelensky
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
| | - Ihor Smal
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
| | - Erik Meijering
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
| | - Wiggert A van Cappellen
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
| | - H Martijn de Gruiter
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
| | - Gijsbert J van Belle
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
| | - Martin E van Royen
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
| | - Adriaan B Houtsmuller
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
| | - Jeroen Essers
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
| | - Roland Kanaar
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
| | - Claire Wyman
- Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands Department of Genetics, Cancer Genomics Centre Netherlands, Department of Medical Informatics, Department of Radiology, Erasmus Optical Imaging Centre, Department of Pathology, Department of Vascular Surgery, and Department of Radiation Oncology, Erasmus University Medical Centre, 3000 CA Rotterdam, Netherlands
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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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