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Ghosh B, Chatterjee J, Paul RR, Acuña S, Lahiri P, Pal M, Mitra P, Agarwal K. Molecular histopathology of matrix proteins through autofluorescence super-resolution microscopy. Sci Rep 2024; 14:10524. [PMID: 38719976 PMCID: PMC11078950 DOI: 10.1038/s41598-024-61178-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 05/02/2024] [Indexed: 05/12/2024] Open
Abstract
Extracellular matrix diseases like fibrosis are elusive to diagnose early on, to avoid complete loss of organ function or even cancer progression, making early diagnosis crucial. Imaging the matrix densities of proteins like collagen in fixed tissue sections with suitable stains and labels is a standard for diagnosis and staging. However, fine changes in matrix density are difficult to realize by conventional histological staining and microscopy as the matrix fibrils are finer than the resolving capacity of these microscopes. The dyes further blur the outline of the matrix and add a background that bottlenecks high-precision early diagnosis of matrix diseases. Here we demonstrate the multiple signal classification method-MUSICAL-otherwise a computational super-resolution microscopy technique to precisely estimate matrix density in fixed tissue sections using fibril autofluorescence with image stacks acquired on a conventional epifluorescence microscope. We validated the diagnostic and staging performance of the method in extracted collagen fibrils, mouse skin during repair, and pre-cancers in human oral mucosa. The method enables early high-precision label-free diagnosis of matrix-associated fibrotic diseases without needing additional infrastructure or rigorous clinical training.
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Affiliation(s)
- Biswajoy Ghosh
- Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India.
- UiT - The Arctic University of Norway, 9019, Tromsø, Norway.
| | | | - Ranjan Rashmi Paul
- Guru Nanak Institute of Dental Sciences and Research, Kolkata, West Bengal, 700114, India
| | | | - Pooja Lahiri
- Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Mousumi Pal
- Guru Nanak Institute of Dental Sciences and Research, Kolkata, West Bengal, 700114, India
| | - Pabitra Mitra
- Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Krishna Agarwal
- UiT - The Arctic University of Norway, 9019, Tromsø, Norway.
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Weidner J, Neitzel C, Gote M, Deck J, Küntzelmann K, Pilarczyk G, Falk M, Hausmann M. Advanced image-free analysis of the nano-organization of chromatin and other biomolecules by Single Molecule Localization Microscopy (SMLM). Comput Struct Biotechnol J 2023; 21:2018-2034. [PMID: 36968017 PMCID: PMC10030913 DOI: 10.1016/j.csbj.2023.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/08/2023] [Accepted: 03/08/2023] [Indexed: 03/11/2023] Open
Abstract
The cell as a system of many components, governed by the laws of physics and chemistry drives molecular functions having an impact on the spatial organization of these systems and vice versa. Since the relationship between structure and function is an almost universal rule not only in biology, appropriate methods are required to parameterize the relationship between the structure and function of biomolecules and their networks, the mechanisms of the processes in which they are involved, and the mechanisms of regulation of these processes. Single molecule localization microscopy (SMLM), which we focus on here, offers a significant advantage for the quantitative parametrization of molecular organization: it provides matrices of coordinates of fluorescently labeled biomolecules that can be directly subjected to advanced mathematical analytical procedures without the need for laborious and sometimes misleading image processing. Here, we propose mathematical tools for comprehensive quantitative computer data analysis of SMLM point patterns that include Ripley distance frequency analysis, persistent homology analysis, persistent 'imaging', principal component analysis and co-localization analysis. The application of these methods is explained using artificial datasets simulating different, potentially possible and interpretatively important situations. Illustrative analyses of real complex biological SMLM data are presented to emphasize the applicability of the proposed algorithms. This manuscript demonstrated the extraction of features and parameters quantifying the influence of chromatin (re)organization on genome function, offering a novel approach to study chromatin architecture at the nanoscale. However, the ability to adapt the proposed algorithms to analyze essentially any molecular organizations, e.g., membrane receptors or protein trafficking in the cytosol, offers broad flexibility of use.
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Huszka G, Gijs MA. Super-resolution optical imaging: A comparison. MICRO AND NANO ENGINEERING 2019. [DOI: 10.1016/j.mne.2018.11.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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4
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Dose enhancement effects of gold nanoparticles specifically targeting RNA in breast cancer cells. PLoS One 2018; 13:e0190183. [PMID: 29346397 PMCID: PMC5773234 DOI: 10.1371/journal.pone.0190183] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 12/08/2017] [Indexed: 01/02/2023] Open
Abstract
Localization microscopy has shown to be capable of systematic investigations on the arrangement and counting of cellular uptake of gold nanoparticles (GNP) with nanometer resolution. In this article, we show that the application of specially modified RNA targeting gold nanoparticles ("SmartFlares") can result in ring like shaped GNP arrangements around the cell nucleus. Transmission electron microscopy revealed GNP accumulation in vicinity to the intracellular membrane structures including them of the endoplasmatic reticulum. A quantification of the radio therapeutic dose enhancement as a proof of principle was conducted with γH2AX foci analysis: The application of both-SmartFlares and unmodified GNPs-lead to a significant dose enhancement with a factor of up to 1.2 times the dose deposition compared to non-treated breast cancer cells. This enhancement effect was even more pronounced for SmartFlares. Furthermore, it was shown that a magnetic field of 1 Tesla simultaneously applied during irradiation has no detectable influence on neither the structure nor the dose enhancement dealt by gold nanoparticles.
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Oleksiuk O, Abba M, Tezcan KC, Schaufler W, Bestvater F, Patil N, Birk U, Hafner M, Altevogt P, Cremer C, Allgayer H. Single-Molecule Localization Microscopy allows for the analysis of cancer metastasis-specific miRNA distribution on the nanoscale. Oncotarget 2016; 6:44745-57. [PMID: 26561203 PMCID: PMC4792589 DOI: 10.18632/oncotarget.6297] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 10/23/2015] [Indexed: 01/03/2023] Open
Abstract
We describe a novel approach for the detection of small non-coding RNAs in single cells by Single-Molecule Localization Microscopy (SMLM). We used a modified SMLM–setup and applied this instrument in a first proof-of-principle concept to human cancer cell lines. Our method is able to visualize single microRNA (miR)-molecules in fixed cells with a localization accuracy of 10–15 nm, and is able to quantify and analyse clustering and localization in particular subcellular sites, including exosomes. We compared the metastasis-site derived (SW620) and primary site derived (SW480) human colorectal cancer (CRC) cell lines, and (as a proof of principle) evaluated the metastasis relevant miR-31 as a first example. We observed that the subcellular distribution of miR-31 molecules in both cell lines was very heterogeneous with the largest subpopulation of optically acquired weakly metastatic cells characterized by a low number of miR-31 molecules, as opposed to a significantly higher number in the majority of the highly metastatic cells. Furthermore, the highly metastatic cells had significantly more miR-31-molecules in the extracellular space, which were visualized to co-localize with exosomes in significantly higher numbers. From this study, we conclude that miRs are not only aberrantly expressed and regulated, but also differentially compartmentalized in cells with different metastatic potential. Taken together, this novel approach, by providing single molecule images of miRNAs in cellulo can be used as a powerful supplementary tool in the analysis of miRNA function and behaviour and has far reaching potential in defining metastasis-critical subpopulations within a given heterogeneous cancer cell population.
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Affiliation(s)
- Olga Oleksiuk
- Department of Experimental Surgery, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany.,Centre for Biomedicine and Medical Technology Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Mohammed Abba
- Department of Experimental Surgery, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany.,Centre for Biomedicine and Medical Technology Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Kerem Can Tezcan
- Department of Experimental Surgery, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany.,Centre for Biomedicine and Medical Technology Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Wladimir Schaufler
- Light Microscopy Facility, German Cancer Research Centre (DKFZ), Heidelberg, Germany.,Karlsruhe Institute of Technology, Karlsruhe University, Karlsruhe, Germany
| | - Felix Bestvater
- Light Microscopy Facility, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Nitin Patil
- Department of Experimental Surgery, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany.,Centre for Biomedicine and Medical Technology Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Udo Birk
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Mathias Hafner
- Institute for Molecular and Cellular Biology, Mannheim University of Applied Sciences, Mannheim, Germany
| | - Peter Altevogt
- Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg and Dept. of Dermatology, Venereology and Allergology, UMM, University of Heidelberg, Heidelberg, Germany
| | - Christoph Cremer
- Institute of Molecular Biology (IMB), Mainz, Germany.,Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg, Germany
| | - Heike Allgayer
- Department of Experimental Surgery, Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany.,Centre for Biomedicine and Medical Technology Mannheim, University of Heidelberg, Heidelberg, Germany
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Superresolution intrinsic fluorescence imaging of chromatin utilizing native, unmodified nucleic acids for contrast. Proc Natl Acad Sci U S A 2016; 113:9716-21. [PMID: 27535934 DOI: 10.1073/pnas.1602202113] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Visualizing the nanoscale intracellular structures formed by nucleic acids, such as chromatin, in nonperturbed, structurally and dynamically complex cellular systems, will help expand our understanding of biological processes and open the next frontier for biological discovery. Traditional superresolution techniques to visualize subdiffractional macromolecular structures formed by nucleic acids require exogenous labels that may perturb cell function and change the very molecular processes they intend to study, especially at the extremely high label densities required for superresolution. However, despite tremendous interest and demonstrated need, label-free optical superresolution imaging of nucleotide topology under native nonperturbing conditions has never been possible. Here we investigate a photoswitching process of native nucleotides and present the demonstration of subdiffraction-resolution imaging of cellular structures using intrinsic contrast from unmodified DNA based on the principle of single-molecule photon localization microscopy (PLM). Using DNA-PLM, we achieved nanoscopic imaging of interphase nuclei and mitotic chromosomes, allowing a quantitative analysis of the DNA occupancy level and a subdiffractional analysis of the chromosomal organization. This study may pave a new way for label-free superresolution nanoscopic imaging of macromolecular structures with nucleotide topologies and could contribute to the development of new DNA-based contrast agents for superresolution imaging.
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Dong B, Almassalha L, Urban BE, Nguyen TQ, Khuon S, Chew TL, Backman V, Sun C, Zhang HF. Super-resolution spectroscopic microscopy via photon localization. Nat Commun 2016; 7:12290. [PMID: 27452975 PMCID: PMC4962472 DOI: 10.1038/ncomms12290] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 06/20/2016] [Indexed: 11/16/2022] Open
Abstract
Traditional photon localization microscopy analyses only the spatial distributions of photons emitted by individual molecules to reconstruct super-resolution optical images. Unfortunately, however, the highly valuable spectroscopic information from these photons have been overlooked. Here we report a spectroscopic photon localization microscopy that is capable of capturing the inherent spectroscopic signatures of photons from individual stochastic radiation events. Spectroscopic photon localization microscopy achieved higher spatial resolution than traditional photon localization microscopy through spectral discrimination to identify the photons emitted from individual molecules. As a result, we resolved two fluorescent molecules, which were 15 nm apart, with the corresponding spatial resolution of 10 nm-a four-fold improvement over photon localization microscopy. Using spectroscopic photon localization microscopy, we further demonstrated simultaneous multi-colour super-resolution imaging of microtubules and mitochondria in COS-7 cells and showed that background autofluorescence can be identified through its distinct emission spectra.
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Affiliation(s)
- Biqin Dong
- Biomedical Engineering Department, Northwestern University, Evanston, Illinois 60208, USA
- Mechanical Engineering Department, Northwestern University, Evanston, Illinois 60208, USA
| | - Luay Almassalha
- Biomedical Engineering Department, Northwestern University, Evanston, Illinois 60208, USA
| | - Ben E. Urban
- Biomedical Engineering Department, Northwestern University, Evanston, Illinois 60208, USA
| | - The-Quyen Nguyen
- Biomedical Engineering Department, Northwestern University, Evanston, Illinois 60208, USA
| | - Satya Khuon
- Advanced Imaging Center, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Teng-Leong Chew
- Advanced Imaging Center, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Vadim Backman
- Biomedical Engineering Department, Northwestern University, Evanston, Illinois 60208, USA
| | - Cheng Sun
- Mechanical Engineering Department, Northwestern University, Evanston, Illinois 60208, USA
| | - Hao F. Zhang
- Biomedical Engineering Department, Northwestern University, Evanston, Illinois 60208, USA
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Moser F, Hildenbrand G, Müller P, Al Saroori A, Biswas A, Bach M, Wenz F, Cremer C, Burger N, Veldwijk MR, Hausmann M. Cellular Uptake of Gold Nanoparticles and Their Behavior as Labels for Localization Microscopy. Biophys J 2016; 110:947-53. [PMID: 26910431 PMCID: PMC4776034 DOI: 10.1016/j.bpj.2016.01.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 12/21/2015] [Accepted: 01/04/2016] [Indexed: 10/22/2022] Open
Abstract
Gold nanoparticles (GNPs) enhance the damaging absorbance effects of high-energy photons in radiation therapy by increasing the emission of Auger-photoelectrons in the nm-μm range. It has been shown that the incorporation of GNPs has a significant effect on radiosensitivity of cells and their dose-dependent clonogenic survival. One major characteristic of GNPs is also their diameter-dependent cellular uptake and retention. In this article, we show by means of an established embodiment of localization microscopy, spectral position determination microscopy (SPDM), that imaging with nanometer resolution and systematic counting of GNPs becomes feasible, because optical absorption and plasmon resonance effects result in optical blinking of GNPs at a size-dependent wavelength. To quantify cellular uptake and retention or release, SPDM with GNPs that have diameters of 10 and 25 nm was performed after 2 h and after 18 h. The uptake of the GNPs in HeLa cells was either achieved via incubation or transfection via DNA labeling. On average, the uptake by incubation after 2 h was approximately double for 10 nm GNPs as compared to 25 nm GNPs. In contrast, the uptake of 25 nm GNPs by transfection was approximately four times higher after 2 h. The spectral characteristics of the fluorescence of the GNPs seem to be environment-dependent. In contrast to fluorescent dyes that show blinking characteristics due to reversible photobleaching, the blinking of GNPs seems to be stable for long periods of time, and this facilitates their use as an appropriate dye analog for SPDM imaging.
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Affiliation(s)
- Felipe Moser
- Kirchhoff-Institute for Physics, Faculty of Physics and Astronomy, Medical Faculty Mannheim, Universitätsmedizin Mannheim
| | - Georg Hildenbrand
- Kirchhoff-Institute for Physics, Faculty of Physics and Astronomy, Medical Faculty Mannheim, Universitätsmedizin Mannheim; Department of Radiation Oncology, Medical Faculty Mannheim, Universitätsmedizin Mannheim
| | - Patrick Müller
- Kirchhoff-Institute for Physics, Faculty of Physics and Astronomy, Medical Faculty Mannheim, Universitätsmedizin Mannheim
| | - Alexander Al Saroori
- Kirchhoff-Institute for Physics, Faculty of Physics and Astronomy, Medical Faculty Mannheim, Universitätsmedizin Mannheim
| | - Abin Biswas
- Kirchhoff-Institute for Physics, Faculty of Physics and Astronomy, Medical Faculty Mannheim, Universitätsmedizin Mannheim; Department of Radiation Oncology, Medical Faculty Mannheim, Universitätsmedizin Mannheim
| | - Margund Bach
- Kirchhoff-Institute for Physics, Faculty of Physics and Astronomy, Medical Faculty Mannheim, Universitätsmedizin Mannheim
| | - Frederik Wenz
- Department of Radiation Oncology, Medical Faculty Mannheim, Universitätsmedizin Mannheim
| | - Christoph Cremer
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany; Institute of Molecular Biology, Mainz, Germany
| | - Nina Burger
- Department of Radiation Oncology, Medical Faculty Mannheim, Universitätsmedizin Mannheim
| | - Marlon R Veldwijk
- Department of Radiation Oncology, Medical Faculty Mannheim, Universitätsmedizin Mannheim
| | - Michael Hausmann
- Kirchhoff-Institute for Physics, Faculty of Physics and Astronomy, Medical Faculty Mannheim, Universitätsmedizin Mannheim.
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Samuel N. Images as tools. On visual epistemic practices in the biological sciences. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2013; 44:225-236. [PMID: 23591051 DOI: 10.1016/j.shpsc.2013.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Contemporary visual epistemic practices in the biological sciences raise new questions of how to transform an iconic data measurements into images, and how the process of an imaging technique may change the material it is 'depicting'. This case-oriented study investigates microscopic imagery, which is used by system and synthetic biologists alike. The core argument is developed around the analysis of two recent methods, developed between 2003 and 2006: localization microscopy and photo-induced cell death. Far from functioning merely as illustrations of work done by other means, images can be determined as tools for discovery in their own right and as objects of investigation. Both methods deploy different constellations of intended and unintended interactions between visual appearance and underlying biological materiality. To characterize these new ways of interaction, the article introduces the notions of 'operational images' and 'operational agency'. Despite all their novelty, operational images are still subject to conventions of seeing and depicting: Phenomena emerging with the new method of localization microscopy have to be designed according to image traditions of older, conventional fluorescence microscopy to function properly as devices for communication between physicists and biologists. The article emerged from a laboratory study based on interviews conducted with researchers from the Kirchhoff-Institute for Physics and German Cancer Research Center (DKFZ) at Bioquant, Heidelberg, in 2011.
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Affiliation(s)
- Nina Samuel
- Bard Graduate Center: Decorative Arts, Design History, Material Culture, 38 West 86th Street, New York, NY 10024, USA.
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Cremer C, Kaufmann R, Gunkel M, Pres S, Weiland Y, Müller P, Ruckelshausen T, Lemmer P, Geiger F, Degenhard S, Wege C, Lemmermann NAW, Holtappels R, Strickfaden H, Hausmann M. Superresolution imaging of biological nanostructures by spectral precision distance microscopy. Biotechnol J 2011; 6:1037-51. [DOI: 10.1002/biot.201100031] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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COMBO-FISH enables high precision localization microscopy as a prerequisite for nanostructure analysis of genome loci. Int J Mol Sci 2010; 11:4094-105. [PMID: 21152322 PMCID: PMC2996811 DOI: 10.3390/ijms11104094] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Revised: 10/16/2010] [Accepted: 10/18/2010] [Indexed: 12/28/2022] Open
Abstract
With the completeness of genome databases, it has become possible to develop a novel FISH (Fluorescence in Situ Hybridization) technique called COMBO-FISH (COMBinatorial Oligo FISH). In contrast to other FISH techniques, COMBO-FISH makes use of a bioinformatics approach for probe set design. By means of computer genome database searching, several oligonucleotide stretches of typical lengths of 15–30 nucleotides are selected in such a way that all uniquely colocalize at the given genome target. The probes applied here were Peptide Nucleic Acids (PNAs)—synthetic DNA analogues with a neutral backbone—which were synthesized under high purity conditions. For a probe repetitively highlighted in centromere 9, PNAs labeled with different dyes were tested, among which Alexa 488® showed reversible photobleaching (blinking between dark and bright state) a prerequisite for the application of SPDM (Spectral Precision Distance/Position Determination Microscopy) a novel technique of high resolution fluorescence localization microscopy. Although COMBO-FISH labeled cell nuclei under SPDM conditions sometimes revealed fluorescent background, the specific locus was clearly discriminated by the signal intensity and the resulting localization accuracy in the range of 10–20 nm for a detected oligonucleotide stretch. The results indicate that COMBO-FISH probes with blinking dyes are well suited for SPDM, which will open new perspectives on molecular nanostructural analysis of the genome.
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