1
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Lakadamyali M. From feulgen to modern methods: marking a century of DNA imaging advances. Histochem Cell Biol 2024; 162:13-22. [PMID: 38753186 PMCID: PMC11227465 DOI: 10.1007/s00418-024-02291-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2024] [Indexed: 07/07/2024]
Abstract
The mystery of how human DNA is compactly packaged into a nucleus-a space a hundred thousand times smaller-while still allowing for the regulation of gene function, has long been one of the greatest enigmas in cell biology. This puzzle is gradually being solved, thanks in part to the advent of new technologies. Among these, innovative genome-labeling techniques combined with high-resolution imaging methods have been pivotal. These methods facilitate the visualization of DNA within intact nuclei and have significantly contributed to our current understanding of genome organization. This review will explore various labeling and imaging approaches that are revolutionizing our understanding of the three-dimensional organization of the genome, shedding light on the relationship between its structure and function.
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Affiliation(s)
- Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.
- Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, USA.
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2
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Zhu FY, Mei LJ, Tian R, Li C, Wang YL, Xiang SL, Zhu MQ, Tang BZ. Recent advances in super-resolution optical imaging based on aggregation-induced emission. Chem Soc Rev 2024; 53:3350-3383. [PMID: 38406832 DOI: 10.1039/d3cs00698k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Super-resolution imaging has rapidly emerged as an optical microscopy technique, offering advantages of high optical resolution over the past two decades; achieving improved imaging resolution requires significant efforts in developing super-resolution imaging agents characterized by high brightness, high contrast and high sensitivity to fluorescence switching. Apart from technical requirements in optical systems and algorithms, super-resolution imaging relies on fluorescent dyes with special photophysical or photochemical properties. The concept of aggregation-induced emission (AIE) was proposed in 2001, coinciding with unprecedented advancements and innovations in super-resolution imaging technology. AIE probes offer many advantages, including high brightness in the aggregated state, low background signal, a larger Stokes shift, ultra-high photostability, and excellent biocompatibility, making them highly promising for applications in super-resolution imaging. In this review, we summarize the progress in implementation methods and provide insights into the mechanism of AIE-based super-resolution imaging, including fluorescence switching resulting from photochemically-converted aggregation-induced emission, electrostatically controlled aggregation-induced emission and specific binding-regulated aggregation-induced emission. Particularly, the aggregation-induced emission principle has been proposed to achieve spontaneous fluorescence switching, expanding the selection and application scenarios of super-resolution imaging probes. By combining the aggregation-induced emission principle and specific molecular design, we offer some comprehensive insights to facilitate the applications of AIEgens (AIE-active molecules) in super-resolution imaging.
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Affiliation(s)
- Feng-Yu Zhu
- Wuhan National Laboratory for Optoelectronics, School of Optical and Electronic Information, College of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Li-Jun Mei
- Wuhan National Laboratory for Optoelectronics, School of Optical and Electronic Information, College of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Rui Tian
- Wuhan National Laboratory for Optoelectronics, School of Optical and Electronic Information, College of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Chong Li
- Wuhan National Laboratory for Optoelectronics, School of Optical and Electronic Information, College of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Ya-Long Wang
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, Haikou, 570228, China
| | - Shi-Li Xiang
- Hubei Jiufengshan Laboratory, Wuhan, 430206, China
| | - Ming-Qiang Zhu
- Wuhan National Laboratory for Optoelectronics, School of Optical and Electronic Information, College of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China.
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, Haikou, 570228, China
| | - Ben Zhong Tang
- School of Science and Engineering, Shenzhen Institute of Aggregate Science and Technology, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Guangdong 518172, China.
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3
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Sun N, Jia Y, Bai S, Li Q, Dai L, Li J. The power of super-resolution microscopy in modern biomedical science. Adv Colloid Interface Sci 2023; 314:102880. [PMID: 36965225 DOI: 10.1016/j.cis.2023.102880] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/08/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023]
Abstract
Super-resolution microscopy (SRM) technology that breaks the diffraction limit has revolutionized the field of cell biology since its appearance, which enables researchers to visualize cellular structures with nanometric resolution, multiple colors and single-molecule sensitivity. With the flourishing development of hardware and the availability of novel fluorescent probes, the impact of SRM has already gone beyond cell biology and extended to nanomedicine, material science and nanotechnology, and remarkably boosted important breakthroughs in these fields. In this review, we will mainly highlight the power of SRM in modern biomedical science, discussing how these SRM techniques revolutionize the way we understand cell structures, biomaterials assembly and how assembled biomaterials interact with cellular organelles, and finally their promotion to the clinical pre-diagnosis. Moreover, we also provide an outlook on the current technical challenges and future improvement direction of SRM. We hope this review can provide useful information, inspire new ideas and propel the development both from the perspective of SRM techniques and from the perspective of SRM's applications.
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Affiliation(s)
- Nan Sun
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049
| | - Yi Jia
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
| | - Shiwei Bai
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049
| | - Qi Li
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering Chinese Academy of Sciences, Beijing 100190, China
| | - Luru Dai
- Wenzhou Institute and Wenzhou Key Laboratory of Biophysics, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
| | - Junbai Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049.
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4
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Wang J, Hu C, Chen X, Li Y, Sun J, Czajkowsky DM, Shao Z. Single-Molecule Micromanipulation and Super-Resolution Imaging Resolve Nanodomains Underlying Chromatin Folding in Mitotic Chromosomes. ACS NANO 2022; 16:8030-8039. [PMID: 35485433 DOI: 10.1021/acsnano.2c01025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The folding of interphase chromatin into highly compact mitotic chromosomes is one of the most recognizable changes during the cell cycle. However, the structural organization underlying this drastic compaction remains elusive. Here, we combine several super resolution methods, including structured illumination microscopy (SIM), binding-activated localization microscopy (BALM), and atomic force microscopy (AFM), to examine the structural details of the DNA within the mitotic chromosome, both in the native state and after up to 30-fold extension using single-molecule micromanipulation. Images of native chromosomes reveal widespread ∼125 nm compact granules (CGs) throughout the metaphase chromosome. However, at maximal extensions, we find exclusively ∼90 nm domains (mitotic nanodomains, MNDs) that are unexpectedly resistant to extensive forces of tens of nanonewtons. The DNA content of the MNDs is estimated to be predominantly ∼80 kb, which is comparable to the size of the inner loops predicted by a recent nested loop model of the mitotic chromosome. With this DNA content, the total volume expected of the human genome assuming closely packed MNDs is nearly identical to what is observed. Thus, altogether, these results suggest that these mechanically stable MNDs, and their higher-order assembly into CGs, are the dominant higher-level structures that underlie the compaction of chromatin from interphase to metaphase.
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Affiliation(s)
- Jiabin Wang
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chuansheng Hu
- State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xuecheng Chen
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yaqian Li
- State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jielin Sun
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Daniel M Czajkowsky
- State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhifeng Shao
- State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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5
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Kwon J, Elgawish MS, Shim S. Bleaching-Resistant Super-Resolution Fluorescence Microscopy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2101817. [PMID: 35088584 PMCID: PMC8948665 DOI: 10.1002/advs.202101817] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 01/07/2022] [Indexed: 05/08/2023]
Abstract
Photobleaching is the permanent loss of fluorescence after extended exposure to light and is a major limiting factor in super-resolution microscopy (SRM) that restricts spatiotemporal resolution and observation time. Strategies for preventing or overcoming photobleaching in SRM are reviewed developing new probes and chemical environments. Photostabilization strategies are introduced first, which are borrowed from conventional fluorescence microscopy, that are employed in SRM. SRM-specific strategies are then highlighted that exploit the on-off transitions of fluorescence, which is the key mechanism for achieving super-resolution, which are becoming new routes to address photobleaching in SRM. Off states can serve as a shelter from excitation by light or an exit to release a damaged probe and replace it with a fresh one. Such efforts in overcoming the photobleaching limits are anticipated to enhance resolution to molecular scales and to extend the observation time to physiological lifespans.
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Affiliation(s)
- Jiwoong Kwon
- Department of Biophysics and Biophysical ChemistryJohns Hopkins UniversityBaltimoreMD21205USA
| | - Mohamed Saleh Elgawish
- Department of ChemistryKorea UniversitySeoul02841Republic of Korea
- Medicinal Chemistry DepartmentFaculty of PharmacySuez Canal UniversityIsmailia41522Egypt
| | - Sang‐Hee Shim
- Department of ChemistryKorea UniversitySeoul02841Republic of Korea
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6
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Hulleman CN, Thorsen RØ, Kim E, Dekker C, Stallinga S, Rieger B. Simultaneous orientation and 3D localization microscopy with a Vortex point spread function. Nat Commun 2021; 12:5934. [PMID: 34635658 PMCID: PMC8505439 DOI: 10.1038/s41467-021-26228-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 09/21/2021] [Indexed: 11/08/2022] Open
Abstract
Estimating the orientation and 3D position of rotationally constrained emitters with localization microscopy typically requires polarization splitting or a large engineered Point Spread Function (PSF). Here we utilize a compact modified PSF for single molecule emitter imaging to estimate simultaneously the 3D position, dipole orientation, and degree of rotational constraint from a single 2D image. We use an affordable and commonly available phase plate, normally used for STED microscopy in the excitation light path, to alter the PSF in the emission light path. This resulting Vortex PSF does not require polarization splitting and has a compact PSF size, making it easy to implement and combine with localization microscopy techniques. In addition to a vectorial PSF fitting routine we calibrate for field-dependent aberrations which enables orientation and position estimation within 30% of the Cramér-Rao bound limit over a 66 μm field of view. We demonstrate this technique on reorienting single molecules adhered to the cover slip, λ-DNA with DNA intercalators using binding-activated localization microscopy, and we reveal periodicity on intertwined structures on supercoiled DNA.
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Affiliation(s)
- Christiaan N Hulleman
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Rasmus Ø Thorsen
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Eugene Kim
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
- Max Planck Institute of Biophysics, 60438, Frankfurt, Germany
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Sjoerd Stallinga
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands.
| | - Bernd Rieger
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands.
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7
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Wright JG, Amin MN, Schmidt H, Hawkins AR. Performance Comparison of Flow-Through Optofluidic Biosensor Designs. BIOSENSORS 2021; 11:226. [PMID: 34356697 PMCID: PMC8301811 DOI: 10.3390/bios11070226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/01/2021] [Accepted: 07/03/2021] [Indexed: 12/04/2022]
Abstract
Optofluidic flow-through biosensors are being developed for single particle detection, particularly as a tool for pathogen diagnosis. The sensitivity of the biosensor chip depends on design parameters, illumination format (side vs. top), and flow configuration (parabolic, two- and three-dimensional hydrodynamic focused (2DHF and 3DHF)). We study the signal differences between various combinations of these design aspects. Our model is validated against a sample of physical devices. We find that side-illumination with 3DHF produces the strongest and consistent signal, but parabolic flow devices process a sample volume more quickly. Practical matters of optical alignment are also discussed, which may affect design choice.
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Affiliation(s)
- Joel G. Wright
- Electrical and Computer Engineering, Brigham Young University, 450 Engineering Building, Provo, UT 84602, USA;
| | - Md Nafiz Amin
- Electrical and Computer Engineering, University of California, 1156 High Street, Santa Cruz, CA 95064, USA; (M.N.A.); (H.S.)
| | - Holger Schmidt
- Electrical and Computer Engineering, University of California, 1156 High Street, Santa Cruz, CA 95064, USA; (M.N.A.); (H.S.)
| | - Aaron R. Hawkins
- Electrical and Computer Engineering, Brigham Young University, 450 Engineering Building, Provo, UT 84602, USA;
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8
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Bohrer CH, Yang X, Thakur S, Weng X, Tenner B, McQuillen R, Ross B, Wooten M, Chen X, Zhang J, Roberts E, Lakadamyali M, Xiao J. A pairwise distance distribution correction (DDC) algorithm to eliminate blinking-caused artifacts in SMLM. Nat Methods 2021; 18:669-677. [PMID: 34059826 PMCID: PMC9040192 DOI: 10.1038/s41592-021-01154-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 04/12/2021] [Indexed: 02/04/2023]
Abstract
Single-molecule localization microscopy (SMLM) relies on the blinking behavior of a fluorophore, which is the stochastic switching between fluorescent and dark states. Blinking creates multiple localizations belonging to the same fluorophore, confounding quantitative analyses and interpretations. Here we present a method, termed distance distribution correction (DDC), to eliminate blinking-caused repeat localizations without any additional calibrations. The approach relies on obtaining the true pairwise distance distribution of different fluorophores naturally from the imaging sequence by using distances between localizations separated by a time much longer than the average fluorescence survival time. We show that, using the true pairwise distribution, we can define and maximize the likelihood, obtaining a set of localizations void of blinking artifacts. DDC results in drastic improvements in obtaining the closest estimate of the true spatial organization and number of fluorescent emitters in a wide range of applications, enabling accurate reconstruction and quantification of SMLM images.
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Affiliation(s)
- Christopher H. Bohrer
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Xinxing Yang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Shreyasi Thakur
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Xiaoli Weng
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Brian Tenner
- Department of Pharmacology, University of California San Diego, San Diego, CA, USA
| | - Ryan McQuillen
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Brian Ross
- Department of Pharmacology, University of California San Diego, San Diego, CA, USA
| | - Matthew Wooten
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Xin Chen
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Jin Zhang
- Department of Pharmacology, University of California San Diego, San Diego, CA, USA
| | - Elijah Roberts
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Melike Lakadamyali
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
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9
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Miriklis EL, Rozario AM, Rothenberg E, Bell TDM, Whelan DR. Understanding DNA organization, damage, and repair with super-resolution fluorescence microscopy. Methods Appl Fluoresc 2021; 9. [PMID: 33765677 DOI: 10.1088/2050-6120/abf239] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 03/25/2021] [Indexed: 11/12/2022]
Abstract
Super-resolution microscopy (SRM) comprises a suite of techniques well-suited to probing the nanoscale landscape of genomic function and dysfunction. Offering the specificity and sensitivity that has made conventional fluorescence microscopy a cornerstone technique of biological research, SRM allows for spatial resolutions as good as 10 nanometers. Moreover, single molecule localization microscopies (SMLMs) enable examination of individual molecular targets and nanofoci allowing for the characterization of subpopulations within a single cell. This review describes how key advances in both SRM techniques and sample preparation have enabled unprecedented insights into DNA structure and function, and highlights many of these new discoveries. Ongoing development and application of these novel, highly interdisciplinary SRM assays will continue to expand the toolbox available for research into the nanoscale genomic landscape.
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Affiliation(s)
| | | | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, United States of America
| | - Toby D M Bell
- School of Chemistry, Monash University, Clayton, VIC, Australia
| | - Donna R Whelan
- Department of Pharmacy and Biomedical Sciences, La Trobe Institute for Molecular Science, La Trobe University, Bendigo, VIC, Australia
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10
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Chen B, Huang Q, Qu Z, Li C, Li Q, Shi J, Fan C, Wang L, Zuo X, Shen J, Li J. Probing Transient DNA Conformation Changes with an Intercalative Fluorescent Excimer. Angew Chem Int Ed Engl 2021; 60:6624-6630. [PMID: 33314629 DOI: 10.1002/anie.202014466] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/02/2020] [Indexed: 12/17/2022]
Abstract
Variation of DNA conformation is important in regulating gene expression and mediating drug-DNA interactions. However, directly probing transient DNA conformation changes is challenging owing to the dynamic nature of this process. We show a label-free fluorescence method to monitor transient DNA conformation changes in DNA structures with various lengths and shapes using a DNA intercalator, K21. K21 can form transient excimers on the surface of DNA; the ratiometric emission of monomer and excimer correlate to DNA transient conformation stability in numerous DNA structures, including i-motifs, G-quadruplex structures, and single nucleotide mutation at random position. We analyzed the conformation dynamics of a single plasmid before and after enzyme digestion with confocal fluorescence microscopy. This method provides a label-free fluorescence strategy to probe transient conformation changes of DNA structures and has potential in uncovering transient genomic processes in living cells.
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Affiliation(s)
- Bin Chen
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Qiuling Huang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhibei Qu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Cong Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiye Shi
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lihua Wang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Jianlei Shen
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiang Li
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
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11
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Chen B, Huang Q, Qu Z, Li C, Li Q, Shi J, Fan C, Wang L, Zuo X, Shen J, Li J. Probing Transient DNA Conformation Changes with an Intercalative Fluorescent Excimer. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Bin Chen
- Institute of Molecular Medicine Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Qiuling Huang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Zhibei Qu
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Cong Li
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Qian Li
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Jiye Shi
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Lihua Wang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
- University of Chinese Academy of Sciences Beijing 100049 China
- Bioimaging Center Shanghai Synchrotron Radiation Facility Zhangjiang Laboratory Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai 201210 China
| | - Xiaolei Zuo
- Institute of Molecular Medicine Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Jianlei Shen
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Jiang Li
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
- University of Chinese Academy of Sciences Beijing 100049 China
- Bioimaging Center Shanghai Synchrotron Radiation Facility Zhangjiang Laboratory Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai 201210 China
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12
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Fu F, Liao K, Liu Z, Hong D, Yang H, Tian Y, Wei W, Liu C, Li S, Ma J, Li W. Controlled Fluorescence Enhancement of DNA-Binding Dye Through Chain Length Match between Oligoguanine and TOTO. J Phys Chem B 2021; 125:518-527. [PMID: 33426891 DOI: 10.1021/acs.jpcb.0c09611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Fluorescent DNA-binding dyes are extensively employed as probe and biosensing in biological detection and imaging. Experiments and theoretical calculations of thiazole orange homodimeric (TOTO) dye binding to a single-strand DNA (ssDNA), poly(dG)n (n = 2, 4, 6, 8), reveal that the n = 6 complex shows about 300-fold stronger fluorescence than n = 2, 4 and a slightly stronger one than n = 8 complexes, which is benefited from the length match between TOTO and poly(dG)6. The machine learning, based on molecular dynamics trajectories, indicates that TOTO is featured by the dihedral angle along its backbone and its end-to-end distance, in which the latter one defines the stretch and hairpin structures of TOTO, respectively. The time-dependent density functional theory calculations on the low-lying excited states show that the stretched TOTO with π-π end-stacking binding mode can bring about strong fluorescence with localized π-π* transitions. For the n = 2, 4, and 8 complexes, the linear scaling quantum mechanics calculations indicate that the dominant hairpin TOTO with intercalative binding modes have relatively larger binding energies, leading to fluorescence quenching by intramolecular charge transfer. Our results may provide an insight for modulating the DNA-dye binding modes to tune the degree of charge transfer and designing fluorescent probes for the recognition of specific DNA sequences.
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Affiliation(s)
- Fangjia Fu
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Kang Liao
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Ziteng Liu
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Daocheng Hong
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Haitang Yang
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Yuxi Tian
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Wei Wei
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Chungen Liu
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Jing Ma
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Wei Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
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13
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Lee S, Batjikh I, Kang SH. Toward Sub-Diffraction Imaging of Single-DNA Molecule Sensors Based on Stochastic Switching Localization Microscopy. SENSORS (BASEL, SWITZERLAND) 2020; 20:E6667. [PMID: 33233370 PMCID: PMC7700606 DOI: 10.3390/s20226667] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/14/2020] [Accepted: 11/20/2020] [Indexed: 12/27/2022]
Abstract
The natural characteristics of deoxyribonucleic acid (DNA) enable its advanced applications in nanotechnology as a special tool that can be detected by high-resolution imaging with precise localization. Super-resolution (SR) microscopy enables the examination of nanoscale molecules beyond the diffraction limit. With the development of SR microscopy methods, DNA nanostructures can now be optically assessed. Using the specific binding of fluorophores with their target molecules, advanced single-molecule localization microscopy (SMLM) has been expanded into different fields, allowing wide-range detection at the single-molecule level. This review discusses the recent progress in the SR imaging of DNA nano-objects using SMLM techniques, such as direct stochastic optical reconstruction microscopy, binding-activated localization microscopy, and point accumulation for imaging nanoscale topography. Furthermore, we discuss their advantages and limitations, present applications, and future perspectives.
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Affiliation(s)
| | | | - Seong Ho Kang
- Department of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Korea; (S.L.); (I.B.)
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14
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Ma Y, Ye Z, Zhang C, Wang X, Li HW, Wong MS, Luo HB, Xiao L. Deep Red Blinking Fluorophore for Nanoscopic Imaging and Inhibition of β-Amyloid Peptide Fibrillation. ACS NANO 2020; 14:11341-11351. [PMID: 32857496 DOI: 10.1021/acsnano.0c03400] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Deposition and aggregation of β-amyloid (Aβ) peptides are demonstrated to be closely related to the pathogenesis of Alzheimer's disease (AD). Development of functional molecules capable of visualizing Aβ1-40 aggregates with nanoscale resolution and even modulating Aβ assembly has attracted great attention recently. In this work, we use monocyanine fluorophore as the lead structure to develop a set of deep red carbazole-based cyanine molecules, which can specifically bind with Aβ1-40 fibril via electrostatic and van der Waals interactions. Spectroscopic and microscopic characterizations demonstrate that one of these fluorophores, (E)-1-(2-(2-methoxyethoxy)ethyl)-4-(2-(9-methyl-9H-carbazol-3-yl)vinyl) quinolinium iodide (me-slg) can bind to Aβ1-40 aggregates with strong fluorescence enhancement. The photophysical properties of me-slg at the single-molecule level, including low "on/off" duty cycle, high photon output, and sufficient switching cycles, enable real-time nanoscopic imaging of Aβ1-40 aggregates. Morphology-dependent toxic effect of Aβ1-40 aggregates toward PC12 cells is unveiled from in situ nanoscopic fluorescence imaging. In addition, me-slg displays a strong inhibitory effect on Aβ1-40 fibrillation in a low inhibitor-protein ratio (e.g., I:P = 0.2). A noticeably reduced cytotoxic effect of Aβ1-40 after the addition of me-slg is also confirmed. These results afford promising applications in the design of a nanoscopic imaging probe for amyloid fibril as well as the development of inhibitors to modulate the fibrillation process.
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Affiliation(s)
- Yuanyuan Ma
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Zhongju Ye
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Chen Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Xueli Wang
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
| | - Hung-Wing Li
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
| | - Man Shing Wong
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
| | - Hai-Bin Luo
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Lehui Xiao
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin 300071, China
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15
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Carrington G, Tomlinson D, Peckham M. Exploiting nanobodies and Affimers for superresolution imaging in light microscopy. Mol Biol Cell 2020; 30:2737-2740. [PMID: 31609674 PMCID: PMC6789155 DOI: 10.1091/mbc.e18-11-0694] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Antibodies have long been the main approach used for localizing proteins of interest by light microscopy. In the past 5 yr or so, and with the advent of superresolution microscopy, the diversity of tools for imaging has rapidly expanded. One main area of expansion has been in the area of nanobodies, small single-chain antibodies from camelids or sharks. The other has been the use of artificial scaffold proteins, including Affimers. The small size of nanobodies and Affimers compared with the traditional antibody provides several advantages for superresolution imaging.
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Affiliation(s)
- Glenn Carrington
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Darren Tomlinson
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Michelle Peckham
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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16
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Miller HL, Contera S, Wollman AJM, Hirst A, Dunn KE, Schröter S, O'Connell D, Leake MC. Biophysical characterisation of DNA origami nanostructures reveals inaccessibility to intercalation binding sites. NANOTECHNOLOGY 2020; 31:235605. [PMID: 32125281 DOI: 10.1088/1361-6528/ab7a2b] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Intercalation of drug molecules into synthetic DNA nanostructures formed through self-assembled origami has been postulated as a valuable future method for targeted drug delivery. This is due to the excellent biocompatibility of synthetic DNA nanostructures, and high potential for flexible programmability including facile drug release into or near to target cells. Such favourable properties may enable high initial loading and efficient release for a predictable number of drug molecules per nanostructure carrier, important for efficient delivery of safe and effective drug doses to minimise non-specific release away from target cells. However, basic questions remain as to how intercalation-mediated loading depends on the DNA carrier structure. Here we use the interaction of dyes YOYO-1 and acridine orange with a tightly-packed 2D DNA origami tile as a simple model system to investigate intercalation-mediated loading. We employed multiple biophysical techniques including single-molecule fluorescence microscopy, atomic force microscopy, gel electrophoresis and controllable damage using low temperature plasma on synthetic DNA origami samples. Our results indicate that not all potential DNA binding sites are accessible for dye intercalation, which has implications for future DNA nanostructures designed for targeted drug delivery.
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Affiliation(s)
- Helen L Miller
- Department of Physics, University of York, Heslington, York, YO10 5DD, United Kingdom
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17
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Nguyen HTT, Kang SH. Base Pair Distance in Single‐DNA Molecule via TIRF‐Based Super‐Resolution Radial Fluctuations‐Stream Module. B KOREAN CHEM SOC 2020. [DOI: 10.1002/bkcs.11982] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Huong Thi Thuy Nguyen
- Department of ChemistryGraduate School, Kyung Hee University Yongin‐si 17104 Republic of Korea
| | - Seong Ho Kang
- Department of ChemistryGraduate School, Kyung Hee University Yongin‐si 17104 Republic of Korea
- Department of Applied Chemistry, Institute of Natural SciencesKyung Hee University Yongin‐si 17104 Republic of Korea
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18
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Szczurek A, Birk U, Knecht H, Dobrucki J, Mai S, Cremer C. Super-resolution binding activated localization microscopy through reversible change of DNA conformation. Nucleus 2019; 9:182-189. [PMID: 29297245 PMCID: PMC5973136 DOI: 10.1080/19491034.2017.1419846] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Methods of super-resolving light microscopy (SRM) have found an exponentially growing range of applications in cell biology, including nuclear structure analyses. Recent developments have proven that Single Molecule Localization Microscopy (SMLM), a type of SRM, is particularly useful for enhanced spatial analysis of the cell nucleus due to its highest resolving capability combined with very specific fluorescent labeling. In this commentary we offer a brief review of the latest methodological development in the field of SMLM of chromatin designated DNA Structure Fluctuation Assisted Binding Activated Localization Microscopy (abbreviated as fBALM) as well as its potential future applications in biology and medicine.
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Affiliation(s)
- Aleksander Szczurek
- a Institute of Molecular Biology , Mainz , Germany.,b Department of Cell Biophysics , Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University , Krakow , Poland
| | - Udo Birk
- a Institute of Molecular Biology , Mainz , Germany.,c Physics Department University of Mainz (JGU) , Mainz , Germany
| | - Hans Knecht
- d McGill, Jewish General Hospital , Montreal , Quebec , Canada
| | - Jurek Dobrucki
- b Department of Cell Biophysics , Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University , Krakow , Poland
| | - Sabine Mai
- e University of Manitoba, Cancer Care Manitoba , Winnipeg , Canada
| | - Christoph Cremer
- a Institute of Molecular Biology , Mainz , Germany.,c Physics Department University of Mainz (JGU) , Mainz , Germany.,f Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University , Germany
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19
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Xu J, Liu Y. A guide to visualizing the spatial epigenome with super-resolution microscopy. FEBS J 2019; 286:3095-3109. [PMID: 31127980 DOI: 10.1111/febs.14938] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/24/2019] [Accepted: 05/23/2019] [Indexed: 12/28/2022]
Abstract
Genomic DNA in eukaryotic cells is tightly compacted with histone proteins into nucleosomes, which are further packaged into the higher-order chromatin structure. The physical structuring of chromatin is highly dynamic and regulated by a large number of epigenetic modifications in response to various environmental exposures, both in normal development and pathological processes such as aging and cancer. Higher-order chromatin structure has been indirectly inferred by conventional bulk biochemical assays on cell populations, which do not allow direct visualization of the spatial information of epigenomics (referred to as spatial epigenomics). With recent advances in super-resolution microscopy, the higher-order chromatin structure can now be visualized in vivo at an unprecedent resolution. This opens up new opportunities to study physical compaction of 3D chromatin structure in single cells, maintaining a well-preserved spatial context of tissue microenvironment. This review discusses the recent application of super-resolution fluorescence microscopy to investigate the higher-order chromatin structure of different epigenomic states. We also envision the synergistic integration of super-resolution microscopy and high-throughput genomic technologies for the analysis of spatial epigenomics to fully understand the genome function in normal biological processes and diseases.
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Affiliation(s)
- Jianquan Xu
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yang Liu
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
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20
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Zhang X, Ye Z, Zhang X, Man H, Huang Z, Li N, Xiao Y. A targetable fluorescent probe for dSTORM super-resolution imaging of live cell nucleus DNA. Chem Commun (Camb) 2019; 55:1951-1954. [PMID: 30681076 DOI: 10.1039/c8cc08575g] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
HoeSR, a nucleus specific probe for dSTORM super-resolution imaging of nucleus DNA in live cells, was designed by conjugating a rhodamine fluorophore and a Hoechst tag. HoeSR labels the cell nucleus in a wash-free way and emits intensive fluorescence exclusively in the nucleus. With the aid of HoeSR, nucleus nanostructures at different mitosis stages were observed through super-resolution imaging.
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Affiliation(s)
- Xiaodong Zhang
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China.
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21
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Samanta S, Gong W, Li W, Sharma A, Shim I, Zhang W, Das P, Pan W, Liu L, Yang Z, Qu J, Kim JS. Organic fluorescent probes for stochastic optical reconstruction microscopy (STORM): Recent highlights and future possibilities. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2018.08.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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22
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Abstract
Fluorogenic probes efficiently reduce non-specific background signals, which often results in highly improved signal-to-noise ratios.
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Affiliation(s)
- Eszter Kozma
- Chemical Biology Research Group
- Institute of Organic Chemistry
- Research Centre for Natural Sciences
- Hungarian Academy of Sciences
- 1117 Budapest
| | - Péter Kele
- Chemical Biology Research Group
- Institute of Organic Chemistry
- Research Centre for Natural Sciences
- Hungarian Academy of Sciences
- 1117 Budapest
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23
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Abstract
The past decade has witnessed an explosion in the use of super-resolution fluorescence microscopy methods in biology and other fields. Single-molecule localization microscopy (SMLM) is one of the most widespread of these methods and owes its success in large part to the ability to control the on-off state of fluorophores through various chemical, photochemical, or binding-unbinding mechanisms. We provide here a comprehensive overview of switchable fluorophores in SMLM including a detailed review of all major classes of SMLM fluorophores, and we also address strategies for labeling specimens, considerations for multichannel and live-cell imaging, potential pitfalls, and areas for future development.
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Affiliation(s)
- Honglin Li
- Department of Chemistry, University of Washington, Seattle, Washington, USA, 98195
| | - Joshua C. Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington, USA, 98195
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington, USA, 98195
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24
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Sarmento MJ, Oneto M, Pelicci S, Pesce L, Scipioni L, Faretta M, Furia L, Dellino GI, Pelicci PG, Bianchini P, Diaspro A, Lanzanò L. Exploiting the tunability of stimulated emission depletion microscopy for super-resolution imaging of nuclear structures. Nat Commun 2018; 9:3415. [PMID: 30143630 PMCID: PMC6109149 DOI: 10.1038/s41467-018-05963-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/27/2018] [Indexed: 11/23/2022] Open
Abstract
Imaging of nuclear structures within intact eukaryotic nuclei is imperative to understand the effect of chromatin folding on genome function. Recent developments of super-resolution fluorescence microscopy techniques combine high specificity, sensitivity, and less-invasive sample preparation procedures with the sub-diffraction spatial resolution required to image chromatin at the nanoscale. Here, we present a method to enhance the spatial resolution of a stimulated-emission depletion (STED) microscope based only on the modulation of the STED intensity during the acquisition of a STED image. This modulation induces spatially encoded variations of the fluorescence emission that can be visualized in the phasor plot and used to improve and quantify the effective spatial resolution of the STED image. We show that the method can be used to remove direct excitation by the STED beam and perform dual color imaging. We apply this method to the visualization of transcription and replication foci within intact nuclei of eukaryotic cells.
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Affiliation(s)
- Maria J Sarmento
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
- Department of Biophysical Chemistry, J. Heyrovský Institute of Physical Chemistry of the A.S.C.R. v.v.i., Prague, Czech Republic
| | - Michele Oneto
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Simone Pelicci
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
- Department of Physics, University of Genoa, via Dodecaneso 33, 16146, Genoa, Italy
| | - Luca Pesce
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
- Department of Physics, University of Genoa, via Dodecaneso 33, 16146, Genoa, Italy
| | - Lorenzo Scipioni
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Mario Faretta
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Laura Furia
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Gaetano Ivan Dellino
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20142, Milan, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20142, Milan, Italy
| | - Paolo Bianchini
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Alberto Diaspro
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy.
- Department of Physics, University of Genoa, via Dodecaneso 33, 16146, Genoa, Italy.
| | - Luca Lanzanò
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy.
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25
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Baddeley D, Bewersdorf J. Biological Insight from Super-Resolution Microscopy: What We Can Learn from Localization-Based Images. Annu Rev Biochem 2018; 87:965-989. [PMID: 29272143 DOI: 10.1146/annurev-biochem-060815-014801] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Super-resolution optical imaging based on the switching and localization of individual fluorescent molecules [photoactivated localization microscopy (PALM), stochastic optical reconstruction microscopy (STORM), etc.] has evolved remarkably over the last decade. Originally driven by pushing technological limits, it has become a tool of biological discovery. The initial demand for impressive pictures showing well-studied biological structures has been replaced by a need for quantitative, reliable data providing dependable evidence for specific unresolved biological hypotheses. In this review, we highlight applications that showcase this development, identify the features that led to their success, and discuss remaining challenges and difficulties. In this context, we consider the complex topic of defining resolution for this imaging modality and address some of the more common analytical methods used with this data.
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Affiliation(s)
- David Baddeley
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA; , .,Auckland Bioengineering Institute, University of Auckland, Auckland 1010, New Zealand
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA; , .,Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06520, USA
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26
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Vangindertael J, Camacho R, Sempels W, Mizuno H, Dedecker P, Janssen KPF. An introduction to optical super-resolution microscopy for the adventurous biologist. Methods Appl Fluoresc 2018; 6:022003. [DOI: 10.1088/2050-6120/aaae0c] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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27
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Park G, Chakkarapani SK, Ju S, Ahn S, Kang SH. Super-resolution morphological dissemination of intercalating dye in single DNA molecules via binding activated localization microscopy. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2017.08.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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28
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Pyle JR, Chen J. Photobleaching of YOYO-1 in super-resolution single DNA fluorescence imaging. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2017; 8:2296-2306. [PMID: 29181286 PMCID: PMC5687005 DOI: 10.3762/bjnano.8.229] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/05/2017] [Indexed: 06/07/2023]
Abstract
Super-resolution imaging of single DNA molecules via point accumulation for imaging in nanoscale topography (PAINT) has great potential to visualize fine DNA structures with nanometer resolution. In a typical PAINT video acquisition, dye molecules (YOYO-1) in solution sparsely bind to the target surfaces (DNA) whose locations can be mathematically determined by fitting their fluorescent point spread function. Many YOYO-1 molecules intercalate into DNA and remain there during imaging, and most of them have to be temporarily or permanently fluorescently bleached, often stochastically, to allow for the visualization of a few fluorescent events per DNA per frame of the video. Thus, controlling the fluorescence on-off rate is important in PAINT. In this paper, we study the photobleaching of YOYO-1 and its correlation with the quality of the PAINT images. At a low excitation laser power density, the photobleaching of YOYO-1 is too slow and a minimum required power density was identified, which can be theoretically predicted with the proposed method in this report.
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Affiliation(s)
- Joseph R Pyle
- Department of Chemistry and Biochemistry, Nanoscale and Quantum Phenomena Institute, Ohio University, Athens, Ohio 45701, USA
| | - Jixin Chen
- Department of Chemistry and Biochemistry, Nanoscale and Quantum Phenomena Institute, Ohio University, Athens, Ohio 45701, USA
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29
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Szczurek A, Klewes L, Xing J, Gourram A, Birk U, Knecht H, Dobrucki JW, Mai S, Cremer C. Imaging chromatin nanostructure with binding-activated localization microscopy based on DNA structure fluctuations. Nucleic Acids Res 2017; 45:e56. [PMID: 28082388 PMCID: PMC5416826 DOI: 10.1093/nar/gkw1301] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 01/10/2017] [Indexed: 01/14/2023] Open
Abstract
Advanced light microscopy is an important tool for nanostructure analysis of chromatin. In this report we present a general concept for Single Molecule localization Microscopy (SMLM) super-resolved imaging of DNA-binding dyes based on modifying the properties of DNA and the dye. By careful adjustment of the chemical environment leading to local, reversible DNA melting and hybridization control over the fluorescence signal of the DNA-binding dye molecules can be introduced. We postulate a transient binding as the basis for our variation of binding-activated localization microscopy (BALM). We demonstrate that several intercalating and minor-groove binding DNA dyes can be used to register (optically isolate) only a few DNA-binding dye signals at a time. To highlight this DNA structure fluctuation-assisted BALM (fBALM), we applied it to measure, for the first time, nanoscale differences in nuclear architecture in model ischemia with an anticipated structural resolution of approximately 50 nm. Our data suggest that this approach may open an avenue for the enhanced microscopic analysis of chromatin nano-architecture and hence the microscopic analysis of nuclear structure aberrations occurring in various pathological conditions. It may also become possible to analyse nuclear nanostructure differences in different cell types, stages of development or environmental stress conditions.
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Affiliation(s)
| | - Ludger Klewes
- University of Manitoba, Cancer Care Manitoba, Winnipeg R3E 0V9, Canada
| | - Jun Xing
- Institute of Molecular Biology, 55128 Mainz, Germany
| | - Amine Gourram
- Institute of Molecular Biology, 55128 Mainz, Germany.,Physics Department University Mainz (JGU), 55128 Mainz, Germany
| | - Udo Birk
- Institute of Molecular Biology, 55128 Mainz, Germany.,Physics Department University Mainz (JGU), 55128 Mainz, Germany
| | - Hans Knecht
- Département de Médecine, CHUS, Université de Sherbrooke, 3001-12e Avenue Nord, Sherbrooke, Québec J1H 5N4, Canada.,Department of Medicine, Jewish General Hospital, McGill University, 3755 Côte-Ste-Catherine Road, Montreal, Québec H3T 1E2, Canada
| | - Jurek W Dobrucki
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Sabine Mai
- University of Manitoba, Cancer Care Manitoba, Winnipeg R3E 0V9, Canada
| | - Christoph Cremer
- Institute of Molecular Biology, 55128 Mainz, Germany.,Physics Department University Mainz (JGU), 55128 Mainz, Germany.,Kirchhoff Institute of Physics (KIP), and Institute of Pharmacy & Molecular Biotechnology (IPMB), University Heidelberg, Germany
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30
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Cunningham PD, Bricker WP, Díaz SA, Medintz IL, Bathe M, Melinger JS. Optical determination of the electronic coupling and intercalation geometry of thiazole orange homodimer in DNA. J Chem Phys 2017; 147:055101. [DOI: 10.1063/1.4995431] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Paul D. Cunningham
- Electronics Science and Technology Division, U.S. Naval Research Laboratory, Washington, DC 20375-5320, USA
| | - William P. Bricker
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Sebastián A. Díaz
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Washington, DC 20375-5320, USA
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Washington, DC 20375-5320, USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Joseph S. Melinger
- Electronics Science and Technology Division, U.S. Naval Research Laboratory, Washington, DC 20375-5320, USA
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31
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Abstract
Super-resolution fluorescence imaging by photoactivation or photoswitching of single fluorophores and position determination (single-molecule localization microscopy, SMLM) provides microscopic images with subdiffraction spatial resolution. This technology has enabled new insights into how proteins are organized in a cellular context, with a spatial resolution approaching virtually the molecular level. A unique strength of SMLM is that it delivers molecule-resolved information, along with super-resolved images of cellular structures. This allows quantitative access to cellular structures, for example, how proteins are distributed and organized and how they interact with other biomolecules. Ultimately, it is even possible to determine protein numbers in cells and the number of subunits in a protein complex. SMLM thus has the potential to pave the way toward a better understanding of how cells function at the molecular level. In this review, we describe how SMLM has contributed new knowledge in eukaryotic biology, and we specifically focus on quantitative biological data extracted from SMLM images.
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Affiliation(s)
- Markus Sauer
- Department of Biotechnology & Biophysics, Julius-Maximilian-University of Würzburg , 97074 Würzburg, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt , 60438 Frankfurt, Germany
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32
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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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33
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Bittel AM, Nickerson A, Saldivar IS, Dolman NJ, Nan X, Gibbs SL. Methodology for Quantitative Characterization of Fluorophore Photoswitching to Predict Superresolution Microscopy Image Quality. Sci Rep 2016; 6:29687. [PMID: 27412307 PMCID: PMC4944197 DOI: 10.1038/srep29687] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 06/23/2016] [Indexed: 01/05/2023] Open
Abstract
Single-molecule localization microscopy (SMLM) image quality and resolution strongly depend on the photoswitching properties of fluorophores used for sample labeling. Development of fluorophores with optimized photoswitching will considerably improve SMLM spatial and spectral resolution. Currently, evaluating fluorophore photoswitching requires protein-conjugation before assessment mandating specific fluorophore functionality, which is a major hurdle for systematic characterization. Herein, we validated polyvinyl alcohol (PVA) as a single-molecule environment to efficiently quantify the photoswitching properties of fluorophores and identified photoswitching properties predictive of quality SMLM images. We demonstrated that the same fluorophore photoswitching properties measured in PVA films and using antibody adsorption, a protein-conjugation environment analogous to labeled cells, were significantly correlated to microtubule width and continuity, surrogate measures of SMLM image quality. Defining PVA as a fluorophore photoswitching screening platform will facilitate SMLM fluorophore development and optimal image buffer assessment through facile and accurate photoswitching property characterization, which translates to SMLM fluorophore imaging performance.
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Affiliation(s)
- Amy M Bittel
- Biomedical Engineering Department, Oregon Health &Science University, Portland, OR 97201, USA
| | - Andrew Nickerson
- Biomedical Engineering Department, Oregon Health &Science University, Portland, OR 97201, USA
| | - Isaac S Saldivar
- Biomedical Engineering Department, Oregon Health &Science University, Portland, OR 97201, USA
| | | | - Xiaolin Nan
- Biomedical Engineering Department, Oregon Health &Science University, Portland, OR 97201, USA.,Knight Cancer Institute, Oregon Health &Science University, Portland, OR 97201, USA.,OHSU Center for Spatial Systems Biomedicine, Oregon Health &Science University, Portland, OR 97201, USA
| | - Summer L Gibbs
- Biomedical Engineering Department, Oregon Health &Science University, Portland, OR 97201, USA.,Knight Cancer Institute, Oregon Health &Science University, Portland, OR 97201, USA.,OHSU Center for Spatial Systems Biomedicine, Oregon Health &Science University, Portland, OR 97201, USA
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34
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Szczurek A, Xing J, Birk UJ, Cremer C. Single Molecule Localization Microscopy of Mammalian Cell Nuclei on the Nanoscale. Front Genet 2016; 7:114. [PMID: 27446198 PMCID: PMC4919319 DOI: 10.3389/fgene.2016.00114] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 06/02/2016] [Indexed: 11/13/2022] Open
Abstract
Nuclear texture analysis is a well-established method of cellular pathology. It is hampered, however, by the limits of conventional light microscopy (ca. 200 nm). These limits have been overcome by a variety of super-resolution approaches. An especially promising approach to chromatin texture analysis is single molecule localization microscopy (SMLM) as it provides the highest resolution using fluorescent based methods. At the present state of the art, using fixed whole cell samples and standard DNA dyes, a structural resolution of chromatin in the 50–100 nm range is obtained using SMLM. We highlight how the combination of localization microscopy with standard fluorophores opens the avenue to a plethora of studies including the spatial distribution of DNA and associated proteins in eukaryotic cell nuclei with the potential to elucidate the functional organization of chromatin. These views are based on our experience as well as on recently published research in this field.
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Affiliation(s)
| | - Jun Xing
- Superresolution Microscopy, Institute of Molecular Biology Mainz, Germany
| | - Udo J Birk
- Superresolution Microscopy, Institute of Molecular BiologyMainz, Germany; Department of Physics, University of MainzMainz, Germany; Department of Physics, University of MainzMainz, Germany
| | - Christoph Cremer
- Superresolution Microscopy, Institute of Molecular BiologyMainz, Germany; Department of Physics, University of MainzMainz, Germany; Kirchhoff Institute of Physics, University of HeidelbergHeidelberg, Germany; Institute of Pharmacy and Molecular Biotechnology, University of HeidelbergHeidelberg, Germany
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35
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Backer AS, Lee MY, Moerner WE. Enhanced DNA imaging using super-resolution microscopy and simultaneous single-molecule orientation measurements. OPTICA 2016; 3:3-6. [PMID: 27722186 PMCID: PMC5050005 DOI: 10.1364/optica.3.000659] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Single-molecule orientation measurements provide unparalleled insight into a multitude of biological and polymeric systems. We report a simple, high-throughput technique for measuring the azimuthal orientation and rotational dynamics of single fluorescent molecules, which is compatible with localization microscopy. Our method involves modulating the polarization of an excitation laser, and analyzing the corresponding intensities emitted by single dye molecules and their modulation amplitudes. To demonstrate our approach, we use intercalating and groove-binding dyes to obtain super-resolved images of stretched DNA strands through binding-induced turn-on of fluorescence. By combining our image data with thousands of dye molecule orientation measurements, we develop a means of probing the structure of individual DNA strands, while also characterizing dye-DNA interactions. This approach may hold promise as a method for monitoring DNA conformation changes resulting from DNA-binding proteins.
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Affiliation(s)
- Adam S. Backer
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford CA 94305
- Institute for Computational and Mathematical Engineering, Stanford University, 475 Via Ortega, Stanford CA 94305
| | - Maurice Y. Lee
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford CA 94305
- Biophysics Program, Stanford University, Stanford CA 94305
| | - W. E. Moerner
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford CA 94305
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36
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Chen Y, Gu M, Gunning PW, Russell SM. Dense small molecule labeling enables activator-dependent STORM by proximity mapping. Histochem Cell Biol 2016; 146:255-66. [PMID: 27246003 DOI: 10.1007/s00418-016-1451-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2016] [Indexed: 12/18/2022]
Abstract
Stochastic optical reconstruction microscopy (STORM) enables high-resolution imaging, but multi-channel 3D imaging is problematic because of chromatic aberrations and alignment errors. The use of activator-dependent STORM in which spectrally distinct activators can be coupled with a single reporter can circumvent such issues. However, the standard approach of linking activators and reporters to a single antibody molecule is hampered by low labeling density and the large size of the antibody. We proposed that small molecule labels might enable activator-dependent STORM if the reporter or activator were linked to separate small molecules that bound within 3.5 nm of each other. This would greatly increase the labeling density and therefore improve resolution. We tested various mixtures of phalloidin- or mCling-conjugated fluorophore to demonstrate this feasibility. The specific activation was dependent on the choice of activator, its density, a matching activating laser and its power. In addition to providing an effective means of multi-channel 3D STORM imaging, this method also provides information about the local proximity between labels, potentially enabling super-resolved mapping of the conformation of the labeled structures.
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Affiliation(s)
- Ye Chen
- Immune Signalling Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia.,Centre for Micro-Photonics, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, VIC, Australia
| | - Min Gu
- Centre for Micro-Photonics, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, VIC, Australia.,Artificial-Intelligence Nanophotonics Laboratory, School of Science, RMIT University, Melbourne, VIC, 3001, Australia
| | - Peter W Gunning
- School of Medical Sciences, UNSW Australia, Sydney, NSW, 2052, Australia
| | - Sarah M Russell
- Immune Signalling Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia. .,Centre for Micro-Photonics, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, VIC, Australia. .,Department of Pathology, The University of Melbourne, Parkville, VIC, Australia. .,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia.
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37
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Żurek-Biesiada D, Szczurek AT, Prakash K, Mohana GK, Lee HK, Roignant JY, Birk UJ, Dobrucki JW, Cremer C. Localization microscopy of DNA in situ using Vybrant ® DyeCycle™ Violet fluorescent probe: A new approach to study nuclear nanostructure at single molecule resolution. Exp Cell Res 2016; 343:97-106. [DOI: 10.1016/j.yexcr.2015.08.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 08/27/2015] [Accepted: 08/30/2015] [Indexed: 12/17/2022]
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38
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Abstract
The majority of studies of the living cell rely on capturing images using fluorescence microscopy. Unfortunately, for centuries, diffraction of light was limiting the spatial resolution in the optical microscope: structural and molecular details much finer than about half the wavelength of visible light (~200 nm) could not be visualized, imposing significant limitations on this otherwise so promising method. The surpassing of this resolution limit in far-field microscopy is currently one of the most momentous developments for studying the living cell, as the move from microscopy to super-resolution microscopy or 'nanoscopy' offers opportunities to study problems in biophysical and biomedical research at a new level of detail. This review describes the principles and modalities of present fluorescence nanoscopes, as well as their potential for biophysical and cellular experiments. All the existing nanoscopy variants separate neighboring features by transiently preparing their fluorescent molecules in states of different emission characteristics in order to make the features discernible. Usually these are fluorescent 'on' and 'off' states causing the adjacent molecules to emit sequentially in time. Each of the variants can in principle reach molecular spatial resolution and has its own advantages and disadvantages. Some require specific transitions and states that can be found only in certain fluorophore subfamilies, such as photoswitchable fluorophores, while other variants can be realized with standard fluorescent labels. Similar to conventional far-field microscopy, nanoscopy can be utilized for dynamical, multi-color and three-dimensional imaging of fixed and live cells, tissues or organisms. Lens-based fluorescence nanoscopy is poised for a high impact on future developments in the life sciences, with the potential to help solve long-standing quests in different areas of scientific research.
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39
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Quantitative nanoscale imaging of orientational order in biological filaments by polarized superresolution microscopy. Proc Natl Acad Sci U S A 2016; 113:E820-8. [PMID: 26831082 DOI: 10.1073/pnas.1516811113] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Essential cellular functions as diverse as genome maintenance and tissue morphogenesis rely on the dynamic organization of filamentous assemblies. For example, the precise structural organization of DNA filaments has profound consequences on all DNA-mediated processes including gene expression, whereas control over the precise spatial arrangement of cytoskeletal protein filaments is key for mechanical force generation driving animal tissue morphogenesis. Polarized fluorescence is currently used to extract structural organization of fluorescently labeled biological filaments by determining the orientation of fluorescent labels, however with a strong drawback: polarized fluorescence imaging is indeed spatially limited by optical diffraction, and is thus unable to discriminate between the intrinsic orientational mobility of the fluorophore labels and the real structural disorder of the labeled biomolecules. Here, we demonstrate that quantitative single-molecule polarized detection in biological filament assemblies allows not only to correct for the rotational flexibility of the label but also to image orientational order of filaments at the nanoscale using superresolution capabilities. The method is based on polarized direct stochastic optical reconstruction microscopy, using dedicated optical scheme and image analysis to determine both molecular localization and orientation with high precision. We apply this method to double-stranded DNA in vitro and microtubules and actin stress fibers in whole cells.
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40
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Chakkarapani SK, Park G, Kang SH. Base pair distance analysis in single DNA molecule by direct stochastic optical reconstruction microscopy. CHINESE CHEM LETT 2015. [DOI: 10.1016/j.cclet.2015.10.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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41
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Developing a New Biophysical Tool to Combine Magneto-Optical Tweezers with Super-Resolution Fluorescence Microscopy. PHOTONICS 2015. [DOI: 10.3390/photonics2030758] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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42
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Innovative techniques, sensors, and approaches for imaging biofilms at different scales. Trends Microbiol 2015; 23:233-42. [DOI: 10.1016/j.tim.2014.12.010] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/04/2014] [Accepted: 12/19/2014] [Indexed: 11/19/2022]
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43
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Whelan DR, Bell TDM. Super-Resolution Single-Molecule Localization Microscopy: Tricks of the Trade. J Phys Chem Lett 2015; 6:374-382. [PMID: 26261950 DOI: 10.1021/jz5019702] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Application of single-molecule fluorescence detection has led to the development of light microscopy techniques that make it possible to study fluorescent samples at spatial resolutions significantly improved upon the diffraction limit of light. The biological and materials science applications of these "super-resolution" microscopy methods are vast, causing current demand for them to be high. However, implementation, execution, and interpretation of these techniques, particularly involving biological samples, require a broad interdisciplinary skillset, not often found in a single laboratory. Those already used to interdisciplinary work as well as navigating communication and collaboration between more pure forms of physics, chemistry, and biology are well-positioned to spearhead such efforts. In this Perspective, we describe various aspects of single-molecule super-resolution imaging, discussing, in particular, the role that physical chemistry has so far played in its development and establishment. We also highlight a selection of some of the remarkable recent research achievements in this vibrant field.
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Affiliation(s)
- Donna R Whelan
- School of Chemistry, Monash University, Wellington Road, Clayton, Victoria 3800, Australia
| | - Toby D M Bell
- School of Chemistry, Monash University, Wellington Road, Clayton, Victoria 3800, Australia
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44
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Superresolution imaging of single DNA molecules using stochastic photoblinking of minor groove and intercalating dyes. Methods 2015; 88:81-8. [PMID: 25637032 DOI: 10.1016/j.ymeth.2015.01.010] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 12/08/2014] [Accepted: 01/07/2015] [Indexed: 01/04/2023] Open
Abstract
As proof-of-principle for generating superresolution structural information from DNA we applied a method of localization microscopy utilizing photoblinking comparing intercalating dye YOYO-1 against minor groove binding dye SYTO-13, using a bespoke multicolor single-molecule fluorescence microscope. We used a full-length ∼49 kbp λ DNA construct possessing oligo inserts at either terminus allowing conjugation of digoxigenin and biotin at opposite ends for tethering to a glass coverslip surface and paramagnetic microsphere respectively. We observed stochastic DNA-bound dye photoactivity consistent with dye photoblinking as opposed to binding/unbinding events, evidenced through both discrete simulations and continuum kinetics analysis. We analyzed dye photoblinking images of immobilized DNA molecules using superresolution reconstruction software from two existing packages, rainSTORM and QuickPALM, and compared the results against our own novel home-written software called ADEMS code. ADEMS code generated lateral localization precision values of 30-40 nm and 60-70 nm for YOYO-1 and SYTO-13 respectively at video-rate sampling, similar to rainSTORM, running more slowly than rainSTORM and QuickPALM algorithms but having a complementary capability over both in generating automated centroid distribution and cluster analyses. Our imaging system allows us to observe dynamic topological changes to single molecules of DNA in real-time, such as rapid molecular snapping events. This will facilitate visualization of fluorescently-labeled DNA molecules conjugated to a magnetic bead in future experiments involving newly developed magneto-optical tweezers combined with superresolution microscopy.
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45
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Tuson HH, Biteen JS. Unveiling the inner workings of live bacteria using super-resolution microscopy. Anal Chem 2014; 87:42-63. [PMID: 25380480 DOI: 10.1021/ac5041346] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Hannah H Tuson
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
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46
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Habuchi S. Super-resolution molecular and functional imaging of nanoscale architectures in life and materials science. Front Bioeng Biotechnol 2014; 2:20. [PMID: 25152893 PMCID: PMC4126472 DOI: 10.3389/fbioe.2014.00020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 05/30/2014] [Indexed: 11/13/2022] Open
Abstract
Super-resolution (SR) fluorescence microscopy has been revolutionizing the way in which we investigate the structures, dynamics, and functions of a wide range of nanoscale systems. In this review, I describe the current state of various SR fluorescence microscopy techniques along with the latest developments of fluorophores and labeling for the SR microscopy. I discuss the applications of SR microscopy in the fields of life science and materials science with a special emphasis on quantitative molecular imaging and nanoscale functional imaging. These studies open new opportunities for unraveling the physical, chemical, and optical properties of a wide range of nanoscale architectures together with their nanostructures and will enable the development of new (bio-)nanotechnology.
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Affiliation(s)
- Satoshi Habuchi
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology , Jeddah , Saudi Arabia
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47
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Jungmann R, Avendaño MS, Woehrstein JB, Dai M, Shih WM, Yin P. Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT. Nat Methods 2014; 11:313-8. [PMID: 24487583 PMCID: PMC4153392 DOI: 10.1038/nmeth.2835] [Citation(s) in RCA: 719] [Impact Index Per Article: 71.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 01/03/2014] [Indexed: 12/11/2022]
Abstract
Super-resolution fluorescence microscopy is a powerful tool for biological research, but obtaining multiplexed images for a large number of distinct target species remains challenging. Here we use the transient binding of short fluorescently labeled oligonucleotides (DNA-PAINT, a variation of point accumulation for imaging in nanoscale topography) for simple and easy-to-implement multiplexed super-resolution imaging that achieves sub-10-nm spatial resolution in vitro on synthetic DNA structures. We also report a multiplexing approach (Exchange-PAINT) that allows sequential imaging of multiple targets using only a single dye and a single laser source. We experimentally demonstrate ten-color super-resolution imaging in vitro on synthetic DNA structures as well as four-color two-dimensional (2D) imaging and three-color 3D imaging of proteins in fixed cells.
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Affiliation(s)
- Ralf Jungmann
- 1] Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA. [2] Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA. [3]
| | - Maier S Avendaño
- 1] Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA. [2] Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA. [3]
| | - Johannes B Woehrstein
- 1] Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA. [2]
| | - Mingjie Dai
- 1] Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA. [2] Program in Biophysics, Harvard University, Cambridge, Massachusetts, USA
| | - William M Shih
- 1] Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA. [2] Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA. [3] Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Peng Yin
- 1] Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA. [2] Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
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48
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Whelan DR, Holm T, Sauer M, Bell TDM. Focus on Super-Resolution Imaging with Direct Stochastic Optical Reconstruction Microscopy (dSTORM). Aust J Chem 2014. [DOI: 10.1071/ch13499] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The last decade has seen the development of several microscopic techniques capable of achieving spatial resolutions that are well below the diffraction limit of light. These techniques, collectively referred to as ‘super-resolution’ microscopy, are now finding wide use, particularly in cell biology, routinely generating fluorescence images with resolutions in the order of tens of nanometres. In this highlight, we focus on direct Stochastic Optical Reconstruction Microscopy or dSTORM, one of the localisation super-resolution fluorescence microscopy techniques that are founded on the detection of fluorescence emissions from single molecules. We detail how, with minimal assemblage, a highly functional and versatile dSTORM set-up can be built from ‘off-the-shelf’ components at quite a modest budget, especially when compared with the current cost of commercial systems. We also present some typical super-resolution images of microtubules and actin filaments within cells and discuss sample preparation and labelling methods.
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49
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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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50
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Chen J, Bremauntz A, Kisley L, Shuang B, Landes CF. Super-resolution mbPAINT for optical localization of single-stranded DNA. ACS APPLIED MATERIALS & INTERFACES 2013; 5:9338-43. [PMID: 24073628 PMCID: PMC3934010 DOI: 10.1021/am403984k] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We demonstrate the application of superlocalization microscopy to identify sequence-specific portions of single-stranded DNA (ssDNA) with sequence resolution of 50 nucleotides, corresponding to a spatial resolution of 30 nm. Super-resolution imaging was achieved using a variation of a single-molecule localization method, termed as "motion blur" point accumulation for imaging in nanoscale topography (mbPAINT). The target ssDNA molecules were immobilized on the substrate. Short, dye-labeled, and complementary ssDNA molecules stochastically bound to the target ssDNA, with repeated binding events allowing super-resolution. Sequence specificity was demonstrated via the use of a control, noncomplementary probe. The results support the possibility of employing relatively inexpensive short ssDNAs to identify gene sequence specificity with improved resolution in comparison to the existing methods.
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Affiliation(s)
- Jixin Chen
- Department of Chemistry, Rice University, Houston, TX, 77251-1892, USA
| | - Alberto Bremauntz
- Department of Chemistry, Rice University, Houston, TX, 77251-1892, USA
| | - Lydia Kisley
- Department of Chemistry, Rice University, Houston, TX, 77251-1892, USA
| | - Bo Shuang
- Department of Chemistry, Rice University, Houston, TX, 77251-1892, USA
| | - Christy F. Landes
- Department of Chemistry, Rice University, Houston, TX, 77251-1892, USA
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, 77251-1892, USA
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