1
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Kraemer S, Schneider DJ, Paterson C, Perry D, Westacott MJ, Hagar Y, Katilius E, Lynch S, Russell TM, Johnson T, Astling DP, DeLisle RK, Cleveland J, Gold L, Drolet DW, Janjic N. Crossing the Halfway Point: Aptamer-Based, Highly Multiplexed Assay for the Assessment of the Proteome. J Proteome Res 2024. [PMID: 39038188 DOI: 10.1021/acs.jproteome.4c00411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Measuring responses in the proteome to various perturbations improves our understanding of biological systems. The value of information gained from such studies is directly proportional to the number of proteins measured. To overcome technical challenges associated with highly multiplexed measurements, we developed an affinity reagent-based method that uses aptamers with protein-like side chains along with an assay that takes advantage of their unique properties. As hybrid affinity reagents, modified aptamers are fully comparable to antibodies in terms of binding characteristics toward proteins, including epitope size, shape complementarity, affinity and specificity. Our assay combines these intrinsic binding properties with serial kinetic proofreading steps to allow highly effective partitioning of stable specific complexes from unstable nonspecific complexes. The use of these orthogonal methods to enhance specificity effectively overcomes the severe limitation to multiplexing inherent to the use of sandwich-based methods. Our assay currently measures half of the unique proteins encoded in the human genome with femtomolar sensitivity, broad dynamic range and exceptionally high reproducibility. Using machine learning to identify patterns of change, we have developed tests based on measurement of multiple proteins predictive of current health states and future disease risk to guide a holistic approach to precision medicine.
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Affiliation(s)
- Stephan Kraemer
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Daniel J Schneider
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Clare Paterson
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Darryl Perry
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Matthew J Westacott
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Yolanda Hagar
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Evaldas Katilius
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Sean Lynch
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Theresa M Russell
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Ted Johnson
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - David P Astling
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Robert Kirk DeLisle
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Jason Cleveland
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Larry Gold
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Daniel W Drolet
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Nebojsa Janjic
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
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2
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Prakash K, Baddeley D, Eggeling C, Fiolka R, Heintzmann R, Manley S, Radenovic A, Smith C, Shroff H, Schermelleh L. Resolution in super-resolution microscopy - definition, trade-offs and perspectives. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00755-7. [PMID: 38951703 DOI: 10.1038/s41580-024-00755-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2024] [Indexed: 07/03/2024]
Affiliation(s)
- Kirti Prakash
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
- The Royal Marsden NHS Foundation Trust, London, UK.
| | - David Baddeley
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand.
| | - Christian Eggeling
- Institute of Applied Optics and Biophysics and Abbe Center of Photonics, Friedrich-Schiller-University Jena, Jena, Germany.
- Leibniz Institute of Photonic Technology, Jena, Germany.
| | - Reto Fiolka
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Rainer Heintzmann
- Leibniz Institute of Photonic Technology, Jena, Germany.
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University Jena, Jena, Germany.
| | - Suliana Manley
- Laboratory of Experimental Biophysics, School of Basic Sciences, Institute of Physics, Interfaculty Institute of Bioengineering, EPFL SB-LEB, Lausanne, Switzerland.
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, School of Engineering, Institute of Bioengineering, EPFL STI IBI-STI LBEN, Lausanne, Switzerland.
| | - Carlas Smith
- Delft Center for Systems and Control, Faculty of Mechanical, Maritime, and Materials Engineering, Technische Universiteit Delft, Delft, The Netherlands.
| | - Hari Shroff
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA.
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3
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Stein J, Ericsson M, Nofal M, Magni L, Aufmkolk S, McMillan RB, Breimann L, Herlihy CP, Lee SD, Willemin A, Wohlmann J, Arguedas-Jimenez L, Yin P, Pombo A, Church GM, Wu CK. Cryosectioning-enabled super-resolution microscopy for studying nuclear architecture at the single protein level. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.576943. [PMID: 38370628 PMCID: PMC10871237 DOI: 10.1101/2024.02.05.576943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
DNA-PAINT combined with total Internal Reflection Fluorescence (TIRF) microscopy enables the highest localization precisions, down to single nanometers in thin biological samples, due to TIRF's unique method for optical sectioning and attaining high contrast. However, most cellular targets elude the accessible TIRF range close to the cover glass and thus require alternative imaging conditions, affecting resolution and image quality. Here, we address this limitation by applying ultrathin physical cryosectioning in combination with DNA-PAINT. With "tomographic & kinetically-enhanced" DNA-PAINT (tokPAINT), we demonstrate the imaging of nuclear proteins with sub-3 nanometer localization precision, advancing the quantitative study of nuclear organization within fixed cells and mouse tissues at the level of single antibodies. We believe that ultrathin sectioning combined with the versatility and multiplexing capabilities of DNA-PAINT will be a powerful addition to the toolbox of quantitative DNA-based super-resolution microscopy in intracellular structural analyses of proteins, RNA and DNA in situ.
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Affiliation(s)
- Johannes Stein
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Maria Ericsson
- Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Michel Nofal
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
| | - Lorenzo Magni
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
| | - Sarah Aufmkolk
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ryan B. McMillan
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
| | - Laura Breimann
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - S. Dean Lee
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Andréa Willemin
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
- Humboldt-Universität zu Berlin, Institute for Biology, Berlin, Germany
| | - Jens Wohlmann
- Department of Biosciences, University of Oslo, Norway
| | - Laura Arguedas-Jimenez
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
| | - Peng Yin
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
| | - Ana Pombo
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany
- Humboldt-Universität zu Berlin, Institute for Biology, Berlin, Germany
| | - George M. Church
- Wyss Institute of Biologically Inspired Engineering, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Chao-Kng Wu
- Department of Genetics, Harvard Medical School, Boston, MA, USA
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4
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Lin B, Xiao F, Jiang J, Zhao Z, Zhou X. Engineered aptamers for molecular imaging. Chem Sci 2023; 14:14039-14061. [PMID: 38098720 PMCID: PMC10718180 DOI: 10.1039/d3sc03989g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/07/2023] [Indexed: 12/17/2023] Open
Abstract
Molecular imaging, including quantification and molecular interaction studies, plays a crucial role in visualizing and analysing molecular events occurring within cells or organisms, thus facilitating the understanding of biological processes. Moreover, molecular imaging offers promising applications for early disease diagnosis and therapeutic evaluation. Aptamers are oligonucleotides that can recognize targets with a high affinity and specificity by folding themselves into various three-dimensional structures, thus serving as ideal molecular recognition elements in molecular imaging. This review summarizes the commonly employed aptamers in molecular imaging and outlines the prevalent design approaches for their applications. Furthermore, it highlights the successful application of aptamers to a wide range of targets and imaging modalities. Finally, the review concludes with a forward-looking perspective on future advancements in aptamer-based molecular imaging.
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Affiliation(s)
- Bingqian Lin
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University Wuhan 430072 China
| | - Feng Xiao
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University Wuhan 430072 China
| | - Jinting Jiang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University Wuhan 430072 China
| | - Zhengjia Zhao
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University Wuhan 430072 China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University Wuhan 430072 China
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5
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Ji D, Feng H, Liew SW, Kwok CK. Modified nucleic acid aptamers: development, characterization, and biological applications. Trends Biotechnol 2023; 41:1360-1384. [PMID: 37302912 DOI: 10.1016/j.tibtech.2023.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/30/2023] [Accepted: 05/18/2023] [Indexed: 06/13/2023]
Abstract
Aptamers are single-stranded oligonucleotides that bind to their targets via specific structural interactions. To improve the properties and performance of aptamers, modified nucleotides are incorporated during or after a selection process such as systematic evolution of ligands by exponential enrichment (SELEX). We summarize the latest modified nucleotides and strategies used in modified (mod)-SELEX and post-SELEX to develop modified aptamers, highlight the methods used to characterize aptamer-target interactions, and present recent progress in modified aptamers that recognize different targets. We discuss the challenges and perspectives in further advancing the methodologies and toolsets to accelerate the discovery of modified aptamers, improve the throughput of aptamer-target characterization, and expand the functional diversity and complexity of modified aptamers.
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Affiliation(s)
- Danyang Ji
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China
| | - Hengxin Feng
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China
| | - Shiau Wei Liew
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China; Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China.
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6
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Lu X, Wu Y, Li PH, Fang T, Schalek RL, Su Y, Carter JD, Gupta S, Jain V, Janjic N, Lichtman JW. Probing Molecular Diversity and Ultrastructure of Brain Cells with Fluorescent Aptamers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558240. [PMID: 37781608 PMCID: PMC10541122 DOI: 10.1101/2023.09.18.558240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Detergent-free immunolabeling has been proven feasible for correlated light and electron microscopy, but its application is restricted by the availability of suitable affinity reagents. Here we introduce CAptVE, a method using slow off-rate modified aptamers for cell fluorescence labeling on ultrastructurally reconstructable electron micrographs. CAptVE provides labeling for a wide range of biomarkers, offering a pathway to integrate molecular analysis into recent approaches to delineate neural circuits via connectomics.
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Affiliation(s)
- Xiaotang Lu
- Department of Molecular and Cellular Biology and The Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Yuelong Wu
- Department of Molecular and Cellular Biology and The Center for Brain Science, Harvard University, Cambridge, MA, USA
| | | | - Tao Fang
- Program of Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA
| | - Richard L Schalek
- Department of Molecular and Cellular Biology and The Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Yaxin Su
- Department of Molecular and Cellular Biology and The Center for Brain Science, Harvard University, Cambridge, MA, USA
| | | | | | | | | | - Jeff W Lichtman
- Department of Molecular and Cellular Biology and The Center for Brain Science, Harvard University, Cambridge, MA, USA
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7
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DeRosa M, Lin A, Mallikaratchy P, McConnell E, McKeague M, Patel R, Shigdar S. In vitro selection of aptamers and their applications. NATURE REVIEWS. METHODS PRIMERS 2023; 3:55. [PMID: 37969927 PMCID: PMC10647184 DOI: 10.1038/s43586-023-00247-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
The introduction of the in-vitro evolution method known as SELEX (Systematic Evolution of Ligands by Exponential enrichment) more than 30 years ago led to the conception of versatile synthetic receptors known as aptamers. Offering many benefits such as low cost, high stability and flexibility, aptamers have sparked innovation in molecular diagnostics, enabled advances in synthetic biology and have facilitated new therapeutic approaches. The SELEX method itself is inherently adaptable and offers near limitless possibilities in yielding functional nucleic acid ligands. This Primer serves to provide guidance on experimental design and highlight new growth areas for this impactful technology.
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Affiliation(s)
- M.C. DeRosa
- Department of Chemistry and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada K1T2S2
| | - A. Lin
- Department of Chemistry, Faculty of Sciences, McGill University, Montreal, QC, Canada, H3A 0B8
| | - P. Mallikaratchy
- Department of Molecular, Cellular, and Biomedical Sciences, City University of New York School of Medicine, New York, NY 10031, USA
- Ph.D. Programs in Chemistry and Biochemistry, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA
- Ph.D. Program in Molecular, Cellular and Developmental Biology, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA
| | - E.M. McConnell
- Department of Chemistry and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada K1T2S2
| | - M. McKeague
- Department of Chemistry, Faculty of Sciences, McGill University, Montreal, QC, Canada, H3A 0B8
- Department of Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada, H3G 1Y6
| | - R. Patel
- Ph.D. Programs in Chemistry and Biochemistry, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA
| | - S. Shigdar
- School of Medicine, Deakin University, Geelong, VIC 3220, Australia
- Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin University, Geelong, VIC 3220, Australia
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8
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Tholen MME, Tas RP, Wang Y, Albertazzi L. Beyond DNA: new probes for PAINT super-resolution microscopy. Chem Commun (Camb) 2023; 59:8332-8342. [PMID: 37306078 PMCID: PMC10318573 DOI: 10.1039/d3cc00757j] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/26/2023] [Indexed: 06/13/2023]
Abstract
In the last decade, point accumulation for imaging in nanoscale topography (PAINT) has emerged as a versatile tool for single-molecule localization microscopy (SMLM). Currently, DNA-PAINT is the most widely used, in which a transient stochastically binding DNA docking-imaging pair is used to reconstruct specific characteristics of biological or synthetic materials on a single-molecule level. Slowly, the need for PAINT probes that are not dependent on DNA has emerged. These probes can be based on (i) endogenous interactions, (ii) engineered binders, (iii) fusion proteins, or (iv) synthetic molecules and provide complementary applications for SMLM. Therefore, researchers have been expanding the PAINT toolbox with new probes. In this review, we provide an overview of the currently existing probes that go beyond DNA and their applications and challenges.
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Affiliation(s)
- Marrit M E Tholen
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.
| | - Roderick P Tas
- Department of Chemical Engineering and Chemistry, Laboratory of Self-Organizing Soft Matter, Eindhoven University of Technology, Eindhoven, 5612 AP, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Yuyang Wang
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
- Department of Applied Physics, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Lorenzo Albertazzi
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.
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9
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Ge D, Chen J, Zhao Z, Sui B, Liang F, Wang H. Characterizing the function-related specific assembly pattern of matrix metalloproteinase-14 by dSTORM imaging. Talanta 2023; 260:124523. [PMID: 37105082 DOI: 10.1016/j.talanta.2023.124523] [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: 02/18/2023] [Revised: 03/29/2023] [Accepted: 04/01/2023] [Indexed: 04/29/2023]
Abstract
As transmembrane proteolytic enzyme, matrix metalloproteinase-14 (MMP14) regulates cell migration and cancer metastasis, but how it works at the single molecule level is unclear. Molecular localization is closely related to its function, and revealing its spatial assemble details is thus helpful to understand bio-function. Here, we apply aptamer probe and dSTORM to characterize MMP14 distribution. With demonstrating labeling properties of the probe, we investigate the specific distributed pattern of MMP14 on various cell membranes with different migratory capacities, and find that MMP14 mostly aggregate in clustering state, which becomes more significant with enhancing its hydrolysis efficiency on high-migratory cells. Lots of MMP14 are revealed to be co-localized with its substrate PTK7, and this colocalization decreases with weakening cell migration, suggesting that MMP14 may coordinate cell migration by altering its spatial relationship with substrate proteins. This work will promote a deep understanding of the roles of MMP14 in cell migration and cancer metastasis.
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Affiliation(s)
- Dian Ge
- Improve-WUST Joint Laboratory of Advanced Technology for Point-of-Care Testing and Precision Medicine, School of Chemistry & Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Street, Wuhan, Hubei, 430081, China
| | - Junling Chen
- Improve-WUST Joint Laboratory of Advanced Technology for Point-of-Care Testing and Precision Medicine, School of Chemistry & Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Street, Wuhan, Hubei, 430081, China.
| | - Zhiyong Zhao
- Improve-WUST Joint Laboratory of Advanced Technology for Point-of-Care Testing and Precision Medicine, School of Chemistry & Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Street, Wuhan, Hubei, 430081, China
| | - Binglin Sui
- Improve-WUST Joint Laboratory of Advanced Technology for Point-of-Care Testing and Precision Medicine, School of Chemistry & Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Street, Wuhan, Hubei, 430081, China
| | - Feng Liang
- Improve-WUST Joint Laboratory of Advanced Technology for Point-of-Care Testing and Precision Medicine, School of Chemistry & Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Street, Wuhan, Hubei, 430081, China.
| | - Hongda Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Research Center of Biomembranomics, 5625 Renmin Street, Changchun, Jilin, 130022, China.
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10
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Banerjee A, Anand M, Ganji M. Labeling approaches for DNA-PAINT super-resolution imaging. NANOSCALE 2023; 15:6563-6580. [PMID: 36942769 DOI: 10.1039/d2nr06541j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Super-resolution imaging is becoming a commonly employed tool to visualize biological targets in unprecedented detail. DNA-PAINT is one of the single-molecule localization microscopy-based super-resolution imaging modalities allowing the ultra-high-resolution imaging with superior multiplexing capabilities. We discuss the importance of patterned DNA nanostructures in demonstrating the capabilities of DNA-PAINT and the design of various combinations of imager-docking strand pairs for imaging. Central to the implementation of DNA-PAINT imaging in a biological context is the generation of docking strand-conjugated binders against the target molecules. Several researchers have developed a variety of labelling probes for improving resolution while also providing multiplexing capabilities for the broader application of DNA-PAINT. This review provides a comprehensive summary of the repertoire of labelling probes used for DNA-PAINT in cells and the strategies implemented to chemically modify them with a docking strand.
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Affiliation(s)
- Abhinav Banerjee
- Department of Biochemistry, Indian Institute of Science, Malleshwaram, Bengaluru 560012, India.
| | - Micky Anand
- Department of Biochemistry, Indian Institute of Science, Malleshwaram, Bengaluru 560012, India.
| | - Mahipal Ganji
- Department of Biochemistry, Indian Institute of Science, Malleshwaram, Bengaluru 560012, India.
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11
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Maity BK, Nall D, Lee Y, Selvin PR. Peptide-PAINT Using a Transfected-Docker Enables Live- and Fixed-Cell Super-Resolution Imaging. SMALL METHODS 2023; 7:e2201181. [PMID: 36734194 PMCID: PMC10121774 DOI: 10.1002/smtd.202201181] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/19/2022] [Indexed: 05/22/2023]
Abstract
Point accumulation for imaging in nanoscale topography (PAINT) is a single-molecule technique for super-resolution microscopy, which uses exchangeable single stranded DNA oligos or peptide-pairs to create blinking phenomenon and achieves ≈5-25 nanometer resolution. Here, it is shown that by transfecting the protein-of-interest with a docker-coil, rather than by adding the docker externally-as is the norm when using DNA tethers or antibodies as dockers-similar localization can be achieved, ≈10 nm. However, using a transfected docker has several experimental advances and simplifications. Most importantly, it allows Peptide-PAINT to be applied to transfected live cells for imaging surface proteins in mammalian cells and neurons under physiological conditions. The enhanced resolution of Peptide-PAINT is also shown for organelles in fixed cells to unravel structural details including ≈40-nm and ≈60-nm axial repeats in vimentin filaments in the cytoplasm, and fiber shapes of sub-100-nm histone-rich regions in the nucleus.
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Affiliation(s)
- Barun Kumar Maity
- Department of Physics, University of Illinois at Urbana Champaign, Urbana, United States
| | - Duncan Nall
- Department of Physics, University of Illinois at Urbana Champaign, Urbana, United States
| | - Yongjae Lee
- Center for Physics of Living Cell, University of Illinois at Urbana Champaign, Urbana, United States
| | - Paul R Selvin
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana- Champaign, Urbana, United States
- Center for Physics of Living Cell, University of Illinois at Urbana Champaign, Urbana, United States
- Department of Physics, University of Illinois at Urbana Champaign, Urbana, United States
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12
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Eklund AS, Jungmann R. Optimized Coiled-Coil Interactions for Multiplexed Peptide-PAINT. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206347. [PMID: 36642829 DOI: 10.1002/smll.202206347] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Super-resolution microscopy has revolutionized how researchers characterize samples in the life sciences in the last decades. Amongst methods employing single-molecule localization microscopy, DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) is a relatively easy-to-implement method that uses the programmable and repetitive binding of dye-labeled DNA imager strands to their respective docking strands. Recently developed Peptide-PAINT replaces the interaction of oligonucleotides by short coiled-coil peptide sequences leading to an improved labeling scheme by reducing linkage errors to target proteins. However, only one coiled-coil pair is currently available for Peptide-PAINT, preventing multiplexed imaging. In this study, the initial Peptide-PAINT E/K coil is improved by modifying its length for optimized binding kinetics leading to improved localization precisions. Additionally, an orthogonal P3/P4 coil pair is introduced, enabling 2-plex Peptide-PAINT imaging and benchmarking its performance and orthogonality using single-molecule and DNA origami assays. Finally, the P3/P4 peptide pair is used to image the human epidermal growth factor receptors 2 (ErbB2/Her2) in 2D and 3D at the single receptor level using genetically encoded peptide tags.
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Affiliation(s)
- Alexandra S Eklund
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Planegg, Germany
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Ralf Jungmann
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Planegg, Germany
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
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13
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Youn Y, Lau GW, Lee Y, Maity BK, Gouaux E, Chung HJ, Selvin PR. Quantitative DNA-PAINT imaging of AMPA receptors in live neurons. CELL REPORTS METHODS 2023; 3:100408. [PMID: 36936077 PMCID: PMC10014303 DOI: 10.1016/j.crmeth.2023.100408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 09/25/2022] [Accepted: 01/25/2023] [Indexed: 02/18/2023]
Abstract
DNA-point accumulation for imaging at nanoscale topography (DNA-PAINT) can image fixed biological specimens with nanometer resolution and absolute stoichiometry. In living systems, however, the usage of DNA-PAINT has been limited due to high salt concentration in the buffer required for specific binding of the imager to the docker attached to the target. Here, we used multiple binding motifs of the docker, from 2 to 16, to accelerate the binding speed of the imager under physiological buffer conditions without compromising spatial resolution and maintaining the basal level homeostasis during the measurement. We imaged endogenous α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) in cultured neurons-critical proteins involved in nerve communication-by DNA-PAINT in 3-dimensions using a monovalent single-chain variable fragment (scFv) to the GluA1 subunit of AMPAR. We found a heterogeneous distribution of synaptic AMPARs: ≈60% are immobile, primarily in nanodomains, defined as AMPARs that are within 0.3 μm of the Homer1 protein in the postsynaptic density; the other ∼40% of AMPARs have restricted mobility and trajectory.
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Affiliation(s)
- Yeoan Youn
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gloria W. Lau
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yongjae Lee
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Barun Kumar Maity
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Eric Gouaux
- Vollum Institute, Oregon Health & Science University, Portland, OR, USA
- Howard Hughes Medical Institute, Portland, OR, USA
| | - Hee Jung Chung
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Paul R. Selvin
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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14
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Galiani S, Eggeling C, Reglinski K. Super-resolution microscopy and studies of peroxisomes. Biol Chem 2023; 404:87-106. [PMID: 36698322 DOI: 10.1515/hsz-2022-0314] [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: 10/18/2022] [Accepted: 01/06/2023] [Indexed: 01/27/2023]
Abstract
Fluorescence microscopy is an important tool for studying cellular structures such as organelles. Unfortunately, many details in the corresponding images are hidden due to the resolution limit of conventional lens-based far-field microscopy. An example is the study of peroxisomes, where important processes such as molecular organization during protein important can simply not be studied with conventional far-field microscopy methods. A remedy is super-resolution fluorescence microscopy, which is nowadays a well-established technique for the investigation of inner-cellular structures but has so far to a lesser extent been applied to the study of peroxisomes. To help advancing the latter, we here give an overview over the different super-resolution microscopy approaches and their potentials and challenges in cell-biological research, including labelling issues and a focus on studies on peroxisomes. Here, we also highlight experiments beyond simple imaging such as observations of diffusion dynamics of peroxisomal proteins.
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Affiliation(s)
- Silvia Galiani
- Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, UK
| | - Christian Eggeling
- Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, UK.,Leibniz Institute of Photonic Technology e.V., Albert-Einstein Strasse 9, D-07745 Jena, Germany, Member of the Leibniz Centre for Photonics in Infection Research (LPI), Jena, Germany.,Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Max-Wien-Platz 1, D-07743 Jena, Germany.,Jena Center for Soft Matter, Philosophenweg 7, D-07743 Jena, Germany
| | - Katharina Reglinski
- Leibniz Institute of Photonic Technology e.V., Albert-Einstein Strasse 9, D-07745 Jena, Germany, Member of the Leibniz Centre for Photonics in Infection Research (LPI), Jena, Germany.,Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Max-Wien-Platz 1, D-07743 Jena, Germany.,University Clinics Jena, Bachstraße 18, D-07743 Jena, Germany
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15
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Regulation of ribosomal RNA gene copy number, transcription and nucleolus organization in eukaryotes. Nat Rev Mol Cell Biol 2023; 24:414-429. [PMID: 36732602 DOI: 10.1038/s41580-022-00573-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2022] [Indexed: 02/04/2023]
Abstract
One of the first biological machineries to be created seems to have been the ribosome. Since then, organisms have dedicated great efforts to optimize this apparatus. The ribosomal RNA (rRNA) contained within ribosomes is crucial for protein synthesis and maintenance of cellular function in all known organisms. In eukaryotic cells, rRNA is produced from ribosomal DNA clusters of tandem rRNA genes, whose organization in the nucleolus, maintenance and transcription are strictly regulated to satisfy the substantial demand for rRNA required for ribosome biogenesis. Recent studies have elucidated mechanisms underlying the integrity of ribosomal DNA and regulation of its transcription, including epigenetic mechanisms and a unique recombination and copy-number control system to stably maintain high rRNA gene copy number. In this Review, we disucss how the crucial maintenance of rRNA gene copy number through control of gene amplification and of rRNA production by RNA polymerase I are orchestrated. We also discuss how liquid-liquid phase separation controls the architecture and function of the nucleolus and the relationship between rRNA production, cell senescence and disease.
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16
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Bhaskar H, Kleinjan D, Oi C, Gidden Z, Rosser SJ, Horrocks MH, Regan L. Live-cell super-resolution imaging of actin using LifeAct-14 with a PAINT-based approach. Protein Sci 2023; 32:e4558. [PMID: 36585831 PMCID: PMC9878614 DOI: 10.1002/pro.4558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 01/01/2023]
Abstract
We present direct-LIVE-PAINT, an easy-to-implement approach for the nanoscopic imaging of protein structures in live cells using labeled binding peptides. We demonstrate the feasibility of direct-LIVE-PAINT with an actin-binding peptide fused to EGFP, the location of which can be accurately determined as it transiently binds to actin filaments. We show that direct-LIVE-PAINT can be used to image actin structures below the diffraction-limit of light and have used it to observe the dynamic nature of actin in live cells. We envisage a similar approach could be applied to imaging other proteins within live mammalian cells.
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Affiliation(s)
- Haresh Bhaskar
- The School of Biological SciencesUniversity of EdinburghEdinburghUK,EaStCHEM School of ChemistryUniversity of EdinburghEdinburghUK
| | - Dirk‐Jan Kleinjan
- Centre for Synthetic and Systems Biology and UK Centre for Mammalian Synthetic Biology, School of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Curran Oi
- Department of Genome SciencesUniversity of WashingtonSeattleWashingtonUSA
| | - Zoe Gidden
- The School of Biological SciencesUniversity of EdinburghEdinburghUK,EaStCHEM School of ChemistryUniversity of EdinburghEdinburghUK
| | - Susan J. Rosser
- Centre for Synthetic and Systems Biology and UK Centre for Mammalian Synthetic Biology, School of Biological SciencesUniversity of EdinburghEdinburghUK
| | | | - Lynne Regan
- The School of Biological SciencesUniversity of EdinburghEdinburghUK
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17
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Riera R, Archontakis E, Cremers G, de Greef T, Zijlstra P, Albertazzi L. Precision and Accuracy of Receptor Quantification on Synthetic and Biological Surfaces Using DNA-PAINT. ACS Sens 2023; 8:80-93. [PMID: 36655822 PMCID: PMC9887648 DOI: 10.1021/acssensors.2c01736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Characterization of the number and distribution of biological molecules on 2D surfaces is of foremost importance in biology and biomedicine. Synthetic surfaces bearing recognition motifs are a cornerstone of biosensors, while receptors on the cell surface are critical/vital targets for the treatment of diseases. However, the techniques used to quantify their abundance are qualitative or semi-quantitative and usually lack sensitivity, accuracy, or precision. Detailed herein a simple and versatile workflow based on super-resolution microscopy (DNA-PAINT) was standardized to improve the quantification of the density and distribution of molecules on synthetic substrates and cell membranes. A detailed analysis of accuracy and precision of receptor quantification is presented, based on simulated and experimental data. We demonstrate enhanced accuracy and sensitivity by filtering out non-specific interactions and artifacts. While optimizing the workflow to provide faithful counting over a broad range of receptor densities. We validated the workflow by specifically quantifying the density of docking strands on a synthetic sensor surface and the densities of PD1 and EGF receptors (EGFR) on two cellular models.
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Affiliation(s)
- Roger Riera
- Department
of Biomedical Engineering, Institute for Complex Molecular Systems
(ICMS), Eindhoven University of Technology, P.O. Box 513, Eindhoven5600 MB, Netherlands
| | - Emmanouil Archontakis
- Department
of Biomedical Engineering, Institute for Complex Molecular Systems
(ICMS), Eindhoven University of Technology, P.O. Box 513, Eindhoven5600 MB, Netherlands
| | - Glenn Cremers
- Laboratory
of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, Eindhoven5600 MB, The Netherlands,Computational
Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology,
P.O. Box 513, Eindhoven5600 MB, The Netherlands
| | - Tom de Greef
- Laboratory
of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, Eindhoven5600 MB, The Netherlands,Computational
Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology,
P.O. Box 513, Eindhoven5600 MB, The Netherlands,Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, AJ Nijmegen6525, The Netherlands
| | - Peter Zijlstra
- Department
of Applied Physics and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, Eindhoven5600 MB, The Netherlands,
| | - Lorenzo Albertazzi
- Department
of Biomedical Engineering, Institute for Complex Molecular Systems
(ICMS), Eindhoven University of Technology, P.O. Box 513, Eindhoven5600 MB, Netherlands,Nanoscopy
for Nanomedicine, Institute for Bioengineering
of Catalonia, Barcelona08028, Spain,
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18
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Strauss S, Jungmann R. Slow-Off-Rate-Modified Aptamer Labeling for Fluorescence Microscopy and DNA-PAINT. Methods Mol Biol 2023; 2570:177-185. [PMID: 36156782 DOI: 10.1007/978-1-0716-2695-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Super-resolution microscopy methods enable the visualization of biological processes on the level of a few nanometers. However, the application of these techniques in biological systems is limited by the availability of small affinity reagents. Slow off-rate-modified aptamers as nucleic acid analogues to antibodies have been successfully applied to improve the resolution and quantification of DNA-PAINT. In this chapter, we describe a protocol for using SOMAmers as labeling reagents for super-resolution microscopy.
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Affiliation(s)
- Sebastian Strauss
- Max Planck Institute of Biochemistry, Martinsried, Germany
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany
| | - Ralf Jungmann
- Max Planck Institute of Biochemistry, Martinsried, Germany.
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany.
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19
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Huang Y, Ryssy J, Nguyen MK, Loo J, Hällsten S, Kuzyk A. Measuring the Affinities of RNA and DNA Aptamers with DNA Origami-Based Chiral Plasmonic Probes. Anal Chem 2022; 94:17577-17586. [PMID: 36480745 PMCID: PMC9773176 DOI: 10.1021/acs.analchem.2c04034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Reliable characterization of binding affinities is crucial for selected aptamers. However, the limited repertoire of universal approaches to obtain the dissociation constant (KD) values often hinders the further development of aptamer-based applications. Herein, we present a competitive hybridization-based strategy to characterize aptamers using DNA origami-based chiral plasmonic assemblies as optical reporters. We incorporated aptamers and partial complementary strands blocking different regions of the aptamers into the reporters and measured the kinetic behaviors of the target binding to gain insights on aptamers' functional domains. We introduced a reference analyte and developed a thermodynamic model to obtain a relative dissociation constant of an aptamer-target pair. With this approach, we characterized RNA and DNA aptamers binding to small molecules with low and high affinities.
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Affiliation(s)
- Yike Huang
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076Aalto, Finland,E-mail:
| | - Joonas Ryssy
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076Aalto, Finland
| | - Minh-Kha Nguyen
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076Aalto, Finland,Faculty
of Chemical Engineering, Ho Chi Minh City
University of Technology (HCMUT), 268 Ly Thuong Kiet St., Dist. 10, Ho Chi Minh
City700000, Vietnam,Vietnam
National University Ho Chi Minh City, Linh Trung Ward, Thu Duc Dist., Ho Chi Minh
City700000, Vietnam
| | - Jacky Loo
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076Aalto, Finland
| | - Susanna Hällsten
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076Aalto, Finland
| | - Anton Kuzyk
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076Aalto, Finland,E-mail:
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20
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Zhang L, Chu M, Ji C, Wei J, Yang Y, Huang Z, Tan W, Tan J, Yuan Q. In Situ Visualization of Epidermal Growth Factor Receptor Nuclear Translocation with Circular Bivalent Aptamer. Anal Chem 2022; 94:17413-17421. [PMID: 36469021 DOI: 10.1021/acs.analchem.2c02762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Epidermal growth factor receptor (EGFR) nuclear translocation correlates with the abnormal proliferation, migration, and anti-apoptosis of tumor cells. Monitoring EGFR nuclear translocation provides insights into the molecular mechanisms underlying cancers. EGFR nuclear translocation includes two processes, EGFR phosphorylation and phosphorylated EGFR translocation to the nucleus. With the help of aptamers, probes that can achieve the first step of anchoring phosphorylated EGFR have been developed. However, the EGFR nuclear translocation can last for hours, posing a challenge to monitor the entire nuclear translocation in living cells. Herein, we designed a circular bivalent aptamer-functionalized optical probe with greatly enhanced stability for long-term visualization of EGFR nuclear translocation in situ. The results of cell experiments show that the probe could monitor the entire nuclear translocation of EGFR. The findings of tissue and in vivo experiments demonstrate that the probe can evaluate the development and progression of tumors by imaging EGFR nuclear translocation in situ. The proposed approach allows us to monitor EGFR nuclear translocation in the long term, indicating its great potential in investigating the mechanisms of cancers and guiding for tumor treatment.
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Affiliation(s)
- Lei Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Mengge Chu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Cailing Ji
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Junyuan Wei
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Yanbing Yang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Zhongnan Huang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China.,The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.,Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China.,College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
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21
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Zhang J, Wang D, Chen H, Yuan X, Jiang X, Ai L, He J, Chen F, Xie S, Cui C, Tan W. A pH-Responsive Covalent Nanoscale Device Enhancing Temporal and Force Stability for Specific Tumor Imaging. NANO LETTERS 2022; 22:9441-9449. [PMID: 36442508 DOI: 10.1021/acs.nanolett.2c03487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Approaches to DNA probe-mediated precision medicine have been extensively explored for the diagnosis and treatment of diverse types of cancer. Despite this, simple nanoscale devices with the required recognition specificity and sensitivity for clinical application have remained elusive until now. Here, we report a pH-driven covalent nanoscale device that integrates pH-responsive, switchable structure and proximity-driven covalent cross-linking. A tumor acidic, pH-driven mechanism eliminates "on-target, off-tumor" nonspecific recognition. By manipulating covalent binding to target molecule on the cell surface, this nanodevice avoids binding-then-shedding to improve the sensitivity of tumor recognition. We envision that this pH-driven covalent nanoscale device will inspire more clinical applications toward specific, long-term tumor imaging in the cancer microenvironment.
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Affiliation(s)
- Jing Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan410082, China
| | - Dan Wang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan410082, China
| | - Hong Chen
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan410082, China
| | - Xi Yuan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan410082, China
| | - Xinyi Jiang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan410082, China
| | - Lili Ai
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan410082, China
| | - Jiaxuan He
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang310022, China
| | - Fengming Chen
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan410082, China
| | - Sitao Xie
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang310022, China
| | - Cheng Cui
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan410082, China
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang310022, China
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai200240, China
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22
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Recent Advances in Proteomics-Based Approaches to Studying Age-Related Macular Degeneration: A Systematic Review. Int J Mol Sci 2022; 23:ijms232314759. [PMID: 36499086 PMCID: PMC9735888 DOI: 10.3390/ijms232314759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Age-related macular degeneration (AMD) is a common ocular disease characterized by degeneration of the central area of the retina in the elderly population. Progression and response to treatment are influenced by genetic and non-genetic factors. Proteomics is a powerful tool to study, at the molecular level, the mechanisms underlying the progression of the disease, to identify new therapeutic targets and to establish biomarkers to monitor progression and treatment effectiveness. In this work, we systematically review the use of proteomics-based approaches for the study of the molecular mechanisms underlying the development of AMD, as well as the progression of the disease and on-treatment patient monitoring. The Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) reporting guidelines were followed. Proteomic approaches have identified key players in the onset of the disease, such as complement components and proteins involved in lipid metabolism and oxidative stress, but also in the progression to advanced stages, including factors related to extracellular matrix integrity and angiogenesis. Although anti-vascular endothelial growth factor (anti-VEGF)-based therapy has been crucial in the treatment of neovascular AMD, it is necessary to deepen our understanding of the underlying disease mechanisms to move forward to next-generation therapies for later-stage forms of this multifactorial disease.
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23
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Glogger M, Wang D, Kompa J, Balakrishnan A, Hiblot J, Barth HD, Johnsson K, Heilemann M. Synergizing Exchangeable Fluorophore Labels for Multitarget STED Microscopy. ACS NANO 2022; 16:17991-17997. [PMID: 36223885 PMCID: PMC9706782 DOI: 10.1021/acsnano.2c07212] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
Investigating the interplay of cellular proteins with optical microscopy requires multitarget labeling. Spectral multiplexing using high-affinity or covalent labels is limited in the number of fluorophores that can be discriminated in a single imaging experiment. Advanced microscopy methods such as STED microscopy additionally demand balanced excitation, depletion, and emission wavelengths for all fluorophores, further reducing multiplexing capabilities. Noncovalent, weak-affinity labels bypass this "spectral barrier" through label exchange and sequential imaging of different targets. Here, we combine exchangeable HaloTag ligands, weak-affinity DNA hybridization, and hydrophophic and protein-peptide interactions to increase labeling flexibility and demonstrate six-target STED microscopy in single cells. We further show that exchangeable labels reduce photobleaching as well as facilitate long acquisition times and multicolor live-cell and high-fidelity 3D STED microscopy. The synergy of different types of exchangeable labels increases the multiplexing capabilities in fluorescence microscopy, and by that, the information content of microscopy images.
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Affiliation(s)
- Marius Glogger
- Institute
of Physical and Theoretical Chemistry, Goethe
University Frankfurt, Max-von-Laue Str. 7, 60438 Frankfurt, Germany
| | - Dongni Wang
- Institute
of Physical and Theoretical Chemistry, Goethe
University Frankfurt, Max-von-Laue Str. 7, 60438 Frankfurt, Germany
| | - Julian Kompa
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Ashwin Balakrishnan
- Institute
of Physical and Theoretical Chemistry, Goethe
University Frankfurt, Max-von-Laue Str. 7, 60438 Frankfurt, Germany
| | - Julien Hiblot
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Hans-Dieter Barth
- Institute
of Physical and Theoretical Chemistry, Goethe
University Frankfurt, Max-von-Laue Str. 7, 60438 Frankfurt, Germany
| | - Kai Johnsson
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
- Institute
of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Mike Heilemann
- Institute
of Physical and Theoretical Chemistry, Goethe
University Frankfurt, Max-von-Laue Str. 7, 60438 Frankfurt, Germany
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24
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Lv X, Gong L, Lin S, Jin P, Huang Z. Super-resolution stimulated Raman scattering microscopy with the phase-shifted spatial frequency modulation. OPTICS LETTERS 2022; 47:4552-4555. [PMID: 36048702 DOI: 10.1364/ol.463087] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
We present a unique super-resolution stimulated Raman scattering (SRS) microscopy technique based on phase-shifted spatial frequency modulation (PSFM) under wide-field illumination, permitting super-resolution chemical imaging with single-pixel detection. Through projecting a series of the pump and Stokes laser patterns with varying spatial frequencies onto the sample and combining with the proposed π-phase shift, the higher spatial information can be rapidly retrieved by implementing the fast inverse Fourier-transform on the spatial frequency-encoded SRS data. We have derived the theory of the PSFM-SRS technique for super-resolution imaging. Our further modeling results confirm that PSFM-SRS microscopy provides a ∼2.2-fold improvement in spatial resolution but with a much-reduced laser excitation power density required as compared with conventional point-scan SRS microscopy, suggesting its potential for label-free super-resolution chemical imaging in cells and tissue.
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25
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Illuminating membrane structural dynamics of fusion and endocytosis with advanced light imaging techniques. Biochem Soc Trans 2022; 50:1157-1167. [PMID: 35960003 PMCID: PMC9444071 DOI: 10.1042/bst20210263] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/24/2022] [Accepted: 07/27/2022] [Indexed: 11/17/2022]
Abstract
Visualization of cellular dynamics using fluorescent light microscopy has become a reliable and indispensable source of experimental evidence for biological studies. Over the past two decades, the development of super-resolution microscopy platforms coupled with innovations in protein and molecule labeling led to significant biological findings that were previously unobservable due to the barrier of the diffraction limit. As a result, the ability to image the dynamics of cellular processes is vastly enhanced. These imaging tools are extremely useful in cellular physiology for the study of vesicle fusion and endocytosis. In this review, we will explore the power of stimulated emission depletion (STED) and confocal microscopy in combination with various labeling techniques in real-time observation of the membrane transformation of fusion and endocytosis, as well as their underlying mechanisms. We will review how STED and confocal imaging are used to reveal fusion and endocytic membrane transformation processes in live cells, including hemi-fusion; hemi-fission; hemi-to-full fusion; fusion pore opening, expansion, constriction and closure; shrinking or enlargement of the Ω-shape membrane structure after vesicle fusion; sequential compound fusion; and the sequential endocytic membrane transformation from flat- to O-shape via the intermediate Λ- and Ω-shape transition. We will also discuss how the recent development of imaging techniques would impact future studies in the field.
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26
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Minagawa H, Sawa H, Fujita T, Kato S, Inaguma A, Hirose M, Orba Y, Sasaki M, Tabata K, Nomura N, Shingai M, Suzuki Y, Horii K. A high-affinity aptamer with base-appended base-modified DNA bound to isolated authentic SARS-CoV-2 strains wild-type and B.1.617.2 (delta variant). Biochem Biophys Res Commun 2022; 614:207-212. [PMID: 35617879 PMCID: PMC9060713 DOI: 10.1016/j.bbrc.2022.04.071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 04/15/2022] [Indexed: 11/02/2022]
Abstract
Simple, highly sensitive detection technologies for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are crucial for the effective implementation of public health policies. We used the systematic evolution of ligands by exponential enrichment with a modified DNA library, including a base-appended base (uracil with a guanine base at its fifth position), to create an aptamer with a high affinity for the receptor-binding domain (RBD) of the SARS-CoV-2 spike glycoprotein. The aptamer had a dissociation constant of 1.2 and < 1 nM for the RBD and spike trimer, respectively. Furthermore, enzyme-linked aptamer assays confirmed that the aptamer binds to isolated authentic SARS-CoV-2 wild-type and B.1.617.2 (delta variant). The binding signal was larger that of commercially available anti-SARS-CoV-2 RBD antibody. Thus, this aptamer as a sensing element will enable the highly sensitive detection of SARS-CoV-2.
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Affiliation(s)
- Hirotaka Minagawa
- NEC Solution Innovators, Ltd., 1-18-7, Shinkiba, Koto-ku, Tokyo, 136-8627, Japan.
| | - Hirofumi Sawa
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo, 001-0020, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo, 001-0020, Japan; One Health Research Center, Hokkaido University, N20, W10, Kita-ku, Sapporo, 001-0020, Japan.
| | - Tomoko Fujita
- NEC Solution Innovators, Ltd., 1-18-7, Shinkiba, Koto-ku, Tokyo, 136-8627, Japan.
| | - Shintaro Kato
- NEC Solution Innovators, Ltd., 1-18-7, Shinkiba, Koto-ku, Tokyo, 136-8627, Japan.
| | - Asumi Inaguma
- NEC Solution Innovators, Ltd., 1-18-7, Shinkiba, Koto-ku, Tokyo, 136-8627, Japan.
| | - Miwako Hirose
- NEC Solution Innovators, Ltd., 1-18-7, Shinkiba, Koto-ku, Tokyo, 136-8627, Japan.
| | - Yasuko Orba
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo, 001-0020, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo, 001-0020, Japan.
| | - Michihito Sasaki
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo, 001-0020, Japan.
| | - Koshiro Tabata
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo, 001-0020, Japan.
| | - Naoki Nomura
- Laboratory for Biologics Development, International Institute for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo, 001-0020, Japan.
| | - Masashi Shingai
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo, 001-0020, Japan; Laboratory for Biologics Development, International Institute for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo, 001-0020, Japan.
| | - Yasuhiko Suzuki
- Division of Bioresource, International Institute for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo, 001-0020, Japan.
| | - Katsunori Horii
- NEC Solution Innovators, Ltd., 1-18-7, Shinkiba, Koto-ku, Tokyo, 136-8627, Japan.
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27
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Dai Z, Xie X, Gao Z, Li Q. DNA‐PAINT Super‐Resolution Imaging for Characterization of Nucleic Acid Nanostructures. Chempluschem 2022; 87:e202200127. [DOI: 10.1002/cplu.202200127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/12/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Zheze Dai
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering CHINA
| | - Xiaodong Xie
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering 200240 Shanghai CHINA
| | - Zhaoshuai Gao
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering 200240 Shanghai CHINA
| | - Qian Li
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering Dongchuan Road 800中国 200240 Shanghai CHINA
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28
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Zheng J, Wang Q, Shi L, Shi L, Li T. Calcium-Differentiated Cellular Internalization of Allosteric Framework Nucleic Acids for Targeted Payload Delivery. Anal Chem 2022; 94:9097-9105. [PMID: 35709364 DOI: 10.1021/acs.analchem.2c01434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Target delivery systems have extensively shown promising applications in cancer therapy, and many of them function smartly by responding to the cancer cell microenvironment. Here, we for the first time report Ca2+-differentiated cellular internalization of 2D/3D framework nucleic acids (FNAs), enabling the engineering of a conceptually new target delivery system using an allosteric FNA nanovehicle. The FNA vehicle is subject to a 2D-to-3D transformation on the cancer cell surface via G-quadruplexes responding to environmental K+ and thereby allows its cell entry to be more efficiently promoted by Ca2+. This design enables the FNA vehicle to target cancer cells and selectively deliver an antisense strand-containing cargo for live-cell mRNA imaging. It would open new avenues toward targeted drug delivery and find extensive applications in precise disease treatment.
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Affiliation(s)
- Jiao Zheng
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Qiwei Wang
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Lin Shi
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Lili Shi
- Department of Chemistry, Anhui University, 111 Jiulong Road, Hefei, Anhui 230601, China
| | - Tao Li
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
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29
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Wu KB, Skrodzki CJA, Su Q, Lin J, Niu J. "Click handle"-modified 2'-deoxy-2'-fluoroarabino nucleic acid as a synthetic genetic polymer capable of post-polymerization functionalization. Chem Sci 2022; 13:6873-6881. [PMID: 35774169 PMCID: PMC9200136 DOI: 10.1039/d2sc00679k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 05/16/2022] [Indexed: 01/01/2023] Open
Abstract
The functions of natural nucleic acids such as DNA and RNA have transcended genetic information carriers and now encompass affinity reagents, molecular catalysts, nanostructures, data storage, and many others. However, the vulnerability of natural nucleic acids to nuclease degradation and the lack of chemical functionality have imposed a significant constraint on their ever-expanding applications. Herein, we report the synthesis and polymerase recognition of a 5-(octa-1,7-diynyl)uracil 2′-deoxy-2′-fluoroarabinonucleic acid (FANA) triphosphate. The DNA-templated, polymerase-mediated primer extension using this “click handle”-modified FANA (cmFANA) triphosphate and other FANA nucleotide triphosphates consisting of canonical nucleobases efficiently generated full-length products. The resulting cmFANA polymers exhibited excellent nuclease resistance and the ability to undergo efficient click conjugation with azide-functionalized molecules, thereby becoming a promising platform for serving as a programmable and evolvable synthetic genetic polymer capable of post-polymerization functionalization. Polymerase-mediated incorporation of a “click handle”-modified fluoroarabinonucleic acid (cmFANA) triphosphate produces a new class of nuclease-resistant, evolvable genetic polymers that can be functionalized with azide-containing molecules.![]()
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Affiliation(s)
- Kevin B Wu
- Department of Chemistry, Boston College 2609 Beacon Street, Chestnut Hill MA 20467 USA
| | | | - Qiwen Su
- Department of Chemistry, Boston College 2609 Beacon Street, Chestnut Hill MA 20467 USA
| | - Jennifer Lin
- Department of Chemistry, Boston College 2609 Beacon Street, Chestnut Hill MA 20467 USA
| | - Jia Niu
- Department of Chemistry, Boston College 2609 Beacon Street, Chestnut Hill MA 20467 USA
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30
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Yang Q, Chang X, Lee JY, Olivera TR, Saji M, Wisniewski H, Kim S, Zhang F. Recent Advances in Self-Assembled DNA Nanostructures for Bioimaging. ACS APPLIED BIO MATERIALS 2022; 5:4652-4667. [PMID: 35559619 DOI: 10.1021/acsabm.2c00128] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
DNA nanotechnology has been proven to be a powerful platform to assist the development of imaging probes for biomedical research. The attractive features of DNA nanostructures, such as nanometer precision, controllable size, programmable functions, and biocompatibility, have enabled researchers to design and customize DNA nanoprobes for bioimaging applications. However, DNA probes with low molecular weights (e.g., 10-100 nt) generally suffer from low stability in physiological buffer environments. To improve the stability of DNA nanoprobes in such environments, DNA nanostructures can be designed with relatively larger sizes and defined shapes. In addition, the established modification methods for DNA nanostructures are also essential in enhancing their properties and performances in a physiological environment. In this review, we begin with a brief recap of the development of DNA nanostructures including DNA tiles, DNA origami, and multifunctional DNA nanostructures with modifications. Then we highlight the recent advances of DNA nanostructures for bioimaging, emphasizing the latest developments in probe modifications and DNA-PAINT imaging. Multiple imaging modules for intracellular biomolecular imaging and cell membrane biomarkers recognition are also summarized. In the end, we discuss the advantages and challenges of applying DNA nanostructures in bioimaging research and speculate on its future developments.
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Affiliation(s)
- Qi Yang
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Xu Chang
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Jung Yeon Lee
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Tiffany R Olivera
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Minu Saji
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Henry Wisniewski
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Suchan Kim
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Fei Zhang
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
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31
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Tagliatti E, Cortese K. Imaging Endocytosis Dynamics in Health and Disease. MEMBRANES 2022; 12:membranes12040393. [PMID: 35448364 PMCID: PMC9028293 DOI: 10.3390/membranes12040393] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/16/2022] [Accepted: 03/29/2022] [Indexed: 02/06/2023]
Abstract
Endocytosis is a critical process for cell growth and viability. It mediates nutrient uptake, guarantees plasma membrane homeostasis, and generates intracellular signaling cascades. Moreover, it plays an important role in dead cell clearance and defense against external microbes. Finally, endocytosis is an important cellular route for the delivery of nanomedicines for therapeutic treatments. Thus, it is not surprising that both environmental and genetic perturbation of endocytosis have been associated with several human conditions such as cancer, neurological disorders, and virus infections, among others. Over the last decades, a lot of research has been focused on developing advanced imaging methods to monitor endocytosis events with high resolution in living cells and tissues. These include fluorescence imaging, electron microscopy, and correlative and super-resolution microscopy. In this review, we outline the major endocytic pathways and briefly discuss how defects in the molecular machinery of these pathways lead to disease. We then discuss the current imaging methodologies used to study endocytosis in different contexts, highlighting strengths and weaknesses.
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Affiliation(s)
- Erica Tagliatti
- Laboratory of Pharmacology and Brain Pathology, Humanitas Clinical and Research Center, Via Manzoni 56, 20089 Milano, Italy
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, University College London, London WC1E 6BT, UK
- Correspondence: (E.T.); (K.C.)
| | - Katia Cortese
- Cellular Electron Microscopy Laboratory, Department of Experimental Medicine (DIMES), Human Anatomy, Università di Genova, Via Antonio de Toni 14, 16132 Genova, Italy
- Correspondence: (E.T.); (K.C.)
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32
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Louch WE, Perdreau-Dahl H, Edwards AG. Image-Driven Modeling of Nanoscopic Cardiac Function: Where Have We Come From, and Where Are We Going? Front Physiol 2022; 13:834211. [PMID: 35356084 PMCID: PMC8959215 DOI: 10.3389/fphys.2022.834211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/31/2022] [Indexed: 11/24/2022] Open
Abstract
Complementary developments in microscopy and mathematical modeling have been critical to our understanding of cardiac excitation–contraction coupling. Historically, limitations imposed by the spatial or temporal resolution of imaging methods have been addressed through careful mathematical interrogation. Similarly, limitations imposed by computational power have been addressed by imaging macroscopic function in large subcellular domains or in whole myocytes. As both imaging resolution and computational tractability have improved, the two approaches have nearly merged in terms of the scales that they can each be used to interrogate. With this review we will provide an overview of these advances and their contribution to understanding ventricular myocyte function, including exciting developments over the last decade. We specifically focus on experimental methods that have pushed back limits of either spatial or temporal resolution of nanoscale imaging (e.g., DNA-PAINT), or have permitted high resolution imaging on large cellular volumes (e.g., serial scanning electron microscopy). We also review the progression of computational approaches used to integrate and interrogate these new experimental data sources, and comment on near-term advances that may unify understanding of the underlying biology. Finally, we comment on several outstanding questions in cardiac physiology that stand to benefit from a concerted and complementary application of these new experimental and computational methods.
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Affiliation(s)
- William E. Louch
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, Oslo, Norway
- K.G. Jebsen Centre for Cardiac Research, University of Oslo, Oslo, Norway
| | - Harmonie Perdreau-Dahl
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, Oslo, Norway
- K.G. Jebsen Centre for Cardiac Research, University of Oslo, Oslo, Norway
| | - Andrew G. Edwards
- Simula Research Laboratory, Lysaker, Norway
- *Correspondence: Andrew G. Edwards,
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33
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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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34
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Unterauer EM, Jungmann R. Quantitative Imaging With DNA-PAINT for Applications in Synaptic Neuroscience. Front Synaptic Neurosci 2022; 13:798267. [PMID: 35197837 PMCID: PMC8860300 DOI: 10.3389/fnsyn.2021.798267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/21/2021] [Indexed: 12/02/2022] Open
Abstract
Super-resolution (SR) microscopy techniques have been advancing the understanding of neuronal protein networks and interactions. Unraveling the arrangement of proteins with molecular resolution provided novel insights into neuron cytoskeleton structure and actin polymerization dynamics in synaptic spines. Recent improvements in quantitative SR imaging have been applied to synaptic protein clusters and with improved multiplexing technology, the interplay of multiple protein partners in synaptic active zones has been elucidated. While all SR techniques come with benefits and drawbacks, true molecular quantification is a major challenge with the most complex requirements for labeling reagents and careful experimental design. In this perspective, we provide an overview of quantitative SR multiplexing and discuss in greater detail the quantification and multiplexing capabilities of the SR technique DNA-PAINT. Using predictable binding kinetics of short oligonucleotides, DNA-PAINT provides two unique approaches to address multiplexed molecular quantification: qPAINT and Exchange-PAINT. With precise and accurate quantification and spectrally unlimited multiplexing, DNA-PAINT offers an attractive route to unravel complex protein interaction networks in neurons. Finally, while the SR community has been pushing technological advances from an imaging technique perspective, the development of universally available, small, efficient, and quantitative labels remains a major challenge in the field.
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Affiliation(s)
- Eduard M. Unterauer
- Max Planck Institute of Biochemistry, Martinsried, Germany
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany
| | - Ralf Jungmann
- Max Planck Institute of Biochemistry, Martinsried, Germany
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany
- *Correspondence: Ralf Jungmann,
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35
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Farrell MV, Nunez AC, Yang Z, Pérez-Ferreros P, Gaus K, Goyette J. Protein-PAINT: Superresolution microscopy with signaling proteins. Sci Signal 2022; 15:eabg9782. [PMID: 35104163 DOI: 10.1126/scisignal.abg9782] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Superresolution techniques have advanced our understanding of complex cellular structures and processes but require the attachment of fluorophores to targets through tags or antibodies, which can be bulky and result in underlabeling. To overcome these limitations, we developed a technique to visualize the nanoscale binding locations of signaling proteins by taking advantage of their native interaction domains. Here, we demonstrated that pPAINT (protein point accumulation in nanoscale topography) is a new, single-molecule localization microscopy (SMLM) technique and used it to investigate T cell signaling by visualizing the Src homology 2 (SH2) domain, which is common in signaling molecules. When SH2 domain-containing proteins relocate to the plasma membrane, the domains selectively, transiently, and reversibly bind to preferred phosphorylated tyrosine residues on receptors. This transient binding yields the stochastic blinking events necessary for SMLM when observed with total internal reflection microscopy and enables quantification of binding coefficients in intact cells. We used pPAINT to reveal the binding sites of several T cell receptor-proximal signaling molecules, including Zap70, PI3K, Grb2, Syk, Eat2, and SHP2, and showed that the probes could be multiplexed. We showed that the binding half-life of the tandem SH2 domain of PI3K correlated with binding site cluster size at the immunological synapses of T cells, but that longer binding lifetimes were associated with smaller clusters for the monovalent SH2 domain of Eat2. These results demonstrate the potential of pPAINT for investigating phosphotyrosine-mediated signaling processes at the plasma membrane.
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Affiliation(s)
- Megan V Farrell
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Andrea C Nunez
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Zhengmin Yang
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Pablo Pérez-Ferreros
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Katharina Gaus
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Jesse Goyette
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, Australia
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36
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Gunasekara H, Munaweera R, Novotná L, Lillemeier BF, Hu YS. Chaotropic Perturbation of Noncovalent Interactions of the Hemagglutinin Tag Monoclonal Antibody Fragment Enables Superresolution Molecular Census. ACS NANO 2022; 16:129-139. [PMID: 34797055 PMCID: PMC11196025 DOI: 10.1021/acsnano.1c04237] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Antibody-antigen interactions represent one of the most exploited biomolecular interactions in experimental biology. While numerous techniques harnessed immobilized antibodies for nanoscale fluorescence imaging, few utilized their reversible binding kinetics. Here, we investigated noncovalent interactions of the monoclonal hemagglutinin (HA) epitope tag antibody, 12CA5, in the fixed cellular environment. We observed that the use of a chaotropic agent, potassium thiocyanate (KSCN), promoted the dissociation of the 12CA5 antibody fragment (Fab), which already displayed faster dissociation compared to its immunoglobulin G (IgG) counterpart. Molecular dynamic simulations revealed notable root-mean-square deviations and destabilizations in the presence of KSCN, while the hydrogen-bonding network remained primarily unaffected at the antigen-binding site. The reversible interactions enabled us to achieve a superresolution molecular census of local populations of 3xHA tagged microtubule fibers with improved molecular quantification consistency compared to single-molecule localization microscopy (SMLM) techniques utilizing standard immunofluorescence staining for sample labeling. Our technique, termed superresolution census of molecular epitope tags (SR-COMET), highlights the utilization of reversible antibody-antigen interactions for SMLM-based quantitative superresolution imaging.
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Affiliation(s)
- Hirushi Gunasekara
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois at Chicago, Chicago, IL, 60607-7061, United States
| | - Rangika Munaweera
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois at Chicago, Chicago, IL, 60607-7061, United States
| | - Lucie Novotná
- Nomis Center for Immunobiology and Microbial Pathogenesis & Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Björn F. Lillemeier
- Nomis Center for Immunobiology and Microbial Pathogenesis & Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, California 92037, United States
- Faculty of Biology and Centre for Integrative Biological Signalling Studies (CIBSS), Albert-Ludwigs-University of Freiburg, Freiburg 79104, Germany
| | - Ying S. Hu
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois at Chicago, Chicago, IL, 60607-7061, United States
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Qi S, Duan N, Khan IM, Dong X, Zhang Y, Wu S, Wang Z. Strategies to manipulate the performance of aptamers in SELEX, post-SELEX and microenvironment. Biotechnol Adv 2022; 55:107902. [DOI: 10.1016/j.biotechadv.2021.107902] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/21/2021] [Accepted: 12/30/2021] [Indexed: 02/07/2023]
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38
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Masullo LA, Szalai AM, Lopez LF, Stefani FD. Fluorescence nanoscopy at the sub-10 nm scale. Biophys Rev 2021; 13:1101-1112. [PMID: 35059030 PMCID: PMC8724505 DOI: 10.1007/s12551-021-00864-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 10/20/2021] [Indexed: 12/14/2022] Open
Abstract
Fluorescence nanoscopy represented a breakthrough for the life sciences as it delivers 20-30 nm resolution using far-field fluorescence microscopes. This resolution limit is not fundamental but imposed by the limited photostability of fluorophores under ambient conditions. This has motivated the development of a second generation of fluorescence nanoscopy methods that aim to deliver sub-10 nm resolution, reaching the typical size of structural proteins and thus providing true molecular resolution. In this review, we present common fundamental aspects of these nanoscopies, discuss the key experimental factors that are necessary to fully exploit their capabilities, and discuss their current and future challenges.
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Affiliation(s)
- Luciano A. Masullo
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Argentina
- Departamento de Física, Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires, Güiraldes 2620, C1428EHA Ciudad Autónoma de Buenos Aires, Argentina
| | - Alan M. Szalai
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Argentina
| | - Lucía F. Lopez
- Departamento de Física, Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires, Güiraldes 2620, C1428EHA Ciudad Autónoma de Buenos Aires, Argentina
| | - Fernando D. Stefani
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Argentina
- Departamento de Física, Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires, Güiraldes 2620, C1428EHA Ciudad Autónoma de Buenos Aires, Argentina
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39
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Abstract
Super-resolution fluorescence microscopy and Förster Resonance Energy Transfer (FRET) form a well-established family of techniques that has provided unique tools to study the dynamic architecture and functionality of biological systems, as well as to investigate nanomaterials. In the last years, the integration of super-resolution methods with FRET measurements has generated advances in two fronts. On the one hand, FRET-based probes have enhanced super-resolution imaging. On the other, the development of super-resolved FRET imaging methods has allowed the visualization of molecular interaction patterns with higher spatial resolution, less averaging and higher dynamic range. Here, we review these advances and discuss future perspectives, including the possible integration of FRET with next generation super-resolution techniques capable of reaching true molecular-scale spatial resolution.
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Affiliation(s)
- Alan M Szalai
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Argentina.
| | - Cecilia Zaza
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Argentina.
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Güiraldes 2620, C1428EHA Ciudad Autónoma de Buenos Aires, Argentina
| | - Fernando D Stefani
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD Ciudad Autónoma de Buenos Aires, Argentina.
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Güiraldes 2620, C1428EHA Ciudad Autónoma de Buenos Aires, Argentina
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40
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Perfilov MM, Gavrikov AS, Lukyanov KA, Mishin AS. Transient Fluorescence Labeling: Low Affinity-High Benefits. Int J Mol Sci 2021; 22:11799. [PMID: 34769228 PMCID: PMC8583718 DOI: 10.3390/ijms222111799] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/15/2021] [Accepted: 10/28/2021] [Indexed: 12/20/2022] Open
Abstract
Fluorescent labeling is an established method for visualizing cellular structures and dynamics. The fundamental diffraction limit in image resolution was recently bypassed with the development of super-resolution microscopy. Notably, both localization microscopy and stimulated emission depletion (STED) microscopy impose tight restrictions on the physico-chemical properties of labels. One of them-the requirement for high photostability-can be satisfied by transiently interacting labels: a constant supply of transient labels from a medium replenishes the loss in the signal caused by photobleaching. Moreover, exchangeable tags are less likely to hinder the intrinsic dynamics and cellular functions of labeled molecules. Low-affinity labels may be used both for fixed and living cells in a range of nanoscopy modalities. Nevertheless, the design of optimal labeling and imaging protocols with these novel tags remains tricky. In this review, we highlight the pros and cons of a wide variety of transiently interacting labels. We further discuss the state of the art and future perspectives of low-affinity labeling methods.
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Affiliation(s)
| | | | | | - Alexander S. Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (M.M.P.); (A.S.G.); (K.A.L.)
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41
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Zong S, Ye X, Zong J, Li J, Wang Z, Cui Y. Telomerase detection using a DNA-PAINT strategy. NANOTECHNOLOGY 2021; 32:505507. [PMID: 34488200 DOI: 10.1088/1361-6528/ac23f6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Abstract
Telomerase plays an important role in maintaining the length of telomere during cell division and is recognized as a new kind of biomarkers for cancer diagnosis. In this work, we present a brand new telomerase detection strategy based on a DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) like strategy. With an extraordinary spatial resolution (∼10 nm), the DNA-PAINT based strategy offers several advantages. First, it avoids complicated polymerase chain reaction and electrophoresis procedures. Second, it enables super resolution imaging of the reaction products with a high signal-to-noise ratio and facilitates the location of telomeric elongation sites on the single particle level, which results in a high sensitivity. Third, the detection scheme of the DNA-PAINT strategy allows directin situvisualization of the telomeric elongation process, which has never been achieved before. All these advantages make the DNA-PAINT telomerase detection strategy significant for dynamic investigation of telomerase related physiological processes as well as cancer diagnosis.
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Affiliation(s)
- Shenfei Zong
- Advanced Photonics Center, Southeast University, Nanjing 210096, Jiangsu, People's Republic of China
| | - Xiangyu Ye
- Advanced Photonics Center, Southeast University, Nanjing 210096, Jiangsu, People's Republic of China
| | - Junzhu Zong
- Advanced Photonics Center, Southeast University, Nanjing 210096, Jiangsu, People's Republic of China
| | - Jia Li
- Department of Ultrasonography, Zhongda Hospital, Medical School Southeast University, Nanjing 210009, People's Republic of China
| | - Zhuyuan Wang
- Advanced Photonics Center, Southeast University, Nanjing 210096, Jiangsu, People's Republic of China
| | - Yiping Cui
- Advanced Photonics Center, Southeast University, Nanjing 210096, Jiangsu, People's Republic of China
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42
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Kopylov AM, Fab LV, Antipova O, Savchenko EA, Revishchin AV, Parshina VV, Pavlova SV, Kireev II, Golovin AV, Usachev DY, Pavlova GV. RNA Aptamers for Theranostics of Glioblastoma of Human Brain. BIOCHEMISTRY (MOSCOW) 2021; 86:1012-1024. [PMID: 34488577 DOI: 10.1134/s0006297921080113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Conventional approaches for studying and molecular typing of tumors include PCR, blotting, omics, immunocytochemistry, and immunohistochemistry. The last two methods are the most used, as they enable detecting both tumor protein markers and their localizations within the cells. In this study, we have investigated a possibility of using RNA aptamers, in particular, 2'-F-pyrimidyl-RNA aptamer ME07 (48 nucleotides long), specific to the receptor of epidermal growth factor (EGFR, ErbB1, Her1), as an alternative to monoclonal antibodies for aptacytochemistry and aptahistochemistry for human glioblastoma multiforme (GBM). A specificity of binding of FAM-ME07 to the receptor on the tumor cells has been demonstrated by flow cytometry; an apparent dissociation constant for the complex of aptamer - EGFR on the cell has been determined; a number of EGFR molecules has been semi-quantitatively estimated for the tumor cell lines having different amount of EGFR: A431 (106 copies per cell), U87 (104 copies per cell), MCF7 (103 copies per cell), and ROZH, primary GBM cell culture derived from patient (104 copies per cell). According to fluorescence microscopy, FAM-ME07 interacts directly with the receptors on A431 cells, followed by its internalization into the cytoplasm and translocation to the nucleolus; this finding opens a possibility of ME07 application as an escort aptamer for a delivery of therapeutic agents into tumor cells. FAM-ME07 efficiently stains sections of GBM clinical specimens, which enables an identification of EGFR-positive clones within a heterogeneous tumor; and providing a potential for further studying animal models of GBM.
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Affiliation(s)
- Alexey M Kopylov
- Chemistry Department, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Lika V Fab
- Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, Moscow, 117485, Russia
| | - Olga Antipova
- Chemistry Department, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Ekaterina A Savchenko
- Burdenko National Medical Research Center of Neurosurgery, Ministry of Health of the Russian Federation, Moscow, 125047, Russia
| | - Alexander V Revishchin
- Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, Moscow, 117485, Russia
| | - Viktoriya V Parshina
- Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, Moscow, 117485, Russia
| | - Svetlana V Pavlova
- Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, Moscow, 117485, Russia
| | - Igor I Kireev
- Chemistry Department, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Andrey V Golovin
- Chemistry Department, Lomonosov Moscow State University, Moscow, 119991, Russia.,Sechenov First Moscow State Medical University, Moscow, 119991, Russia
| | - Dmitry Y Usachev
- Burdenko National Medical Research Center of Neurosurgery, Ministry of Health of the Russian Federation, Moscow, 125047, Russia
| | - Galina V Pavlova
- Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, Moscow, 117485, Russia.,Burdenko National Medical Research Center of Neurosurgery, Ministry of Health of the Russian Federation, Moscow, 125047, Russia.,Sechenov First Moscow State Medical University, Moscow, 119991, Russia
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43
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Valli J, Sanderson J. Super-Resolution Fluorescence Microscopy Methods for Assessing Mouse Biology. Curr Protoc 2021; 1:e224. [PMID: 34436832 DOI: 10.1002/cpz1.224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Super-resolution (diffraction unlimited) microscopy was developed 15 years ago; the developers were awarded the Nobel Prize in Chemistry in recognition of their work in 2014. Super-resolution microscopy is increasingly being applied to diverse scientific fields, from single molecules to cell organelles, viruses, bacteria, plants, and animals, especially the mammalian model organism Mus musculus. In this review, we explain how super-resolution microscopy, along with fluorescence microscopy from which it grew, has aided the renaissance of the light microscope. We cover experiment planning and specimen preparation and explain structured illumination microscopy, super-resolution radial fluctuations, stimulated emission depletion microscopy, single-molecule localization microscopy, and super-resolution imaging by pixel reassignment. The final section of this review discusses the strengths and weaknesses of each super-resolution technique and how to choose the best approach for your research. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC.
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Affiliation(s)
- Jessica Valli
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom
| | - Jeremy Sanderson
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom
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44
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Rovira-Clavé X, Jiang S, Bai Y, Zhu B, Barlow G, Bhate S, Coskun AF, Han G, Ho CMK, Hitzman C, Chen SY, Bava FA, Nolan GP. Subcellular localization of biomolecules and drug distribution by high-definition ion beam imaging. Nat Commun 2021; 12:4628. [PMID: 34330905 PMCID: PMC8324837 DOI: 10.1038/s41467-021-24822-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 06/02/2021] [Indexed: 12/03/2022] Open
Abstract
Simultaneous visualization of the relationship between multiple biomolecules and their ligands or small molecules at the nanometer scale in cells will enable greater understanding of how biological processes operate. We present here high-definition multiplex ion beam imaging (HD-MIBI), a secondary ion mass spectrometry approach capable of high-parameter imaging in 3D of targeted biological entities and exogenously added structurally-unmodified small molecules. With this technology, the atomic constituents of the biomolecules themselves can be used in our system as the “tag” and we demonstrate measurements down to ~30 nm lateral resolution. We correlated the subcellular localization of the chemotherapy drug cisplatin simultaneously with five subnuclear structures. Cisplatin was preferentially enriched in nuclear speckles and excluded from closed-chromatin regions, indicative of a role for cisplatin in active regions of chromatin. Unexpectedly, cells surviving multi-drug treatment with cisplatin and the BET inhibitor JQ1 demonstrated near total cisplatin exclusion from the nucleus, suggesting that selective subcellular drug relocalization may modulate resistance to this important chemotherapeutic treatment. Multiplexed high-resolution imaging techniques, such as HD-MIBI, will enable studies of biomolecules and drug distributions in biologically relevant subcellular microenvironments by visualizing the processes themselves in concert, rather than inferring mechanism through surrogate analyses. Multiplexed ion beam imaging can provide subcellular localisation information but with limited resolution. Here the authors report an ion beam imaging method with nanoscale resolution which they use to assess the subcellular distribution of cisplatin.
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Affiliation(s)
- Xavier Rovira-Clavé
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA
| | - Sizun Jiang
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA
| | - Yunhao Bai
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA
| | - Bokai Zhu
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA
| | - Graham Barlow
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA
| | - Salil Bhate
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA.,Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Ahmet F Coskun
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA
| | - Guojun Han
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA
| | - Chin-Min Kimmy Ho
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA.,Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Chuck Hitzman
- Stanford Nano Shared Facility, Stanford University, Stanford, CA, USA
| | - Shih-Yu Chen
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA.,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Felice-Alessio Bava
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA
| | - Garry P Nolan
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA. .,Department of Pathology, Stanford University, Stanford, CA, USA.
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45
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Tracking single particles for hours via continuous DNA-mediated fluorophore exchange. Nat Commun 2021; 12:4432. [PMID: 34290254 PMCID: PMC8295357 DOI: 10.1038/s41467-021-24223-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 06/07/2021] [Indexed: 01/13/2023] Open
Abstract
Monitoring biomolecules in single-particle tracking experiments is typically achieved by employing fixed organic dyes or fluorescent fusion proteins linked to a target of interest. However, photobleaching typically limits observation times to merely a few seconds, restricting downstream statistical analysis and observation of rare biological events. Here, we overcome this inherent limitation via continuous fluorophore exchange using DNA-PAINT, where fluorescently-labeled oligonucleotides reversibly bind to a single-stranded DNA handle attached to the target molecule. Such versatile and facile labeling allows uninterrupted monitoring of single molecules for extended durations. We demonstrate the power of our approach by observing DNA origami on membranes for tens of minutes, providing perspectives for investigating cellular processes on physiologically relevant timescales. The length of single-particle tracking experiments are limited due to photobleaching. Here the authors achieve long-term single-particle tracking with continuous fluorophore exchange in DNA-PAINT and use this to observe DNA origami on lipid bilayers for tens of minutes.
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46
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van Wee R, Filius M, Joo C. Completing the canvas: advances and challenges for DNA-PAINT super-resolution imaging. Trends Biochem Sci 2021; 46:918-930. [PMID: 34247944 DOI: 10.1016/j.tibs.2021.05.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/16/2021] [Accepted: 05/31/2021] [Indexed: 01/02/2023]
Abstract
Single-molecule localization microscopy (SMLM) is a potent tool to examine biological systems with unprecedented resolution, enabling the investigation of increasingly smaller structures. At the forefront of these developments is DNA-based point accumulation for imaging in nanoscale topography (DNA-PAINT), which exploits the stochastic and transient binding of fluorescently labeled DNA probes. In its early stages the implementation of DNA-PAINT was burdened by low-throughput, excessive acquisition time, and difficult integration with live-cell imaging. However, recent advances are addressing these challenges and expanding the range of applications of DNA-PAINT. We review the current state of the art of DNA-PAINT in light of these advances and contemplate what further developments remain indispensable to realize live-cell imaging.
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Affiliation(s)
- Raman van Wee
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Mike Filius
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Chirlmin Joo
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
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47
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Fu S, Zhang T, Jiang H, Xu Y, Chen J, Zhang L, Su X. DNA nanotechnology enhanced single-molecule biosensing and imaging. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116267] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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48
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Ganji M, Schlichthaerle T, Eklund AS, Strauss S, Jungmann R. Quantitative Assessment of Labeling Probes for Super-Resolution Microscopy Using Designer DNA Nanostructures. Chemphyschem 2021; 22:911-914. [PMID: 33720501 PMCID: PMC8251534 DOI: 10.1002/cphc.202100185] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Indexed: 12/22/2022]
Abstract
Improving labeling probes for state-of-the-art super-resolution microscopy is becoming of major importance. However, there is currently a lack of tools to quantitatively evaluate probe performance regarding efficiency, precision, and achievable resolution in an unbiased yet modular fashion. Herein, we introduce designer DNA origami structures combined with DNA-PAINT to overcome this issue and evaluate labeling efficiency, precision, and quantification using antibodies and nanobodies as exemplary labeling probes. Whereas current assessment of binders is mostly qualitative, e. g. based on an expected staining pattern, we herein present a quantitative analysis platform of the antigen labeling efficiency and achievable resolution, allowing researchers to choose the best performing binder. The platform can furthermore be readily adapted for discovery and precise quantification of a large variety of additional labeling probes.
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Affiliation(s)
- Mahipal Ganji
- Faculty of Physics and Center for Nanoscience, LMU Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
- Current Address: Department of Biochemistry, Indian Institute of Science, CV Raman Road, 560012, Bengaluru, India
| | - Thomas Schlichthaerle
- Faculty of Physics and Center for Nanoscience, LMU Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
- Current Address: Department of Biochemistry, Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alexandra S Eklund
- Faculty of Physics and Center for Nanoscience, LMU Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Sebastian Strauss
- Faculty of Physics and Center for Nanoscience, LMU Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Ralf Jungmann
- Faculty of Physics and Center for Nanoscience, LMU Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
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49
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Schlichthaerle T, Lindner C, Jungmann R. Super-resolved visualization of single DNA-based tension sensors in cell adhesion. Nat Commun 2021; 12:2510. [PMID: 33947854 PMCID: PMC8097079 DOI: 10.1038/s41467-021-22606-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 03/18/2021] [Indexed: 01/07/2023] Open
Abstract
Cell-extracellular matrix sensing plays a crucial role in cellular behavior and leads to the formation of a macromolecular protein complex called the focal adhesion. Despite their importance in cellular decision making, relatively little is known about cell-matrix interactions and the intracellular transduction of an initial ligand-receptor binding event on the single-molecule level. Here, we combine cRGD-ligand-decorated DNA tension sensors with DNA-PAINT super-resolution microscopy to study the mechanical engagement of single integrin receptors and the downstream influence on actin bundling. We uncover that integrin receptor clustering is governed by a non-random organization with complexes spaced at 20–30 nm distances. The DNA-based tension sensor and analysis framework provide powerful tools to study a multitude of receptor-ligand interactions where forces are involved in ligand-receptor binding. Relatively little is known about cell-matrix interactions and the intracellular transduction of an initial ligand-receptor binding event on the single-molecule level. Here authors combine ligand-decorated DNA tension sensors with DNA-PAINT super-resolution microscopy to study the mechanical engagement of single integrin receptors and the downstream influence on actin bundling.
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Affiliation(s)
- Thomas Schlichthaerle
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany.,Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Caroline Lindner
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany.,Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ralf Jungmann
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany. .,Max Planck Institute of Biochemistry, Martinsried, Germany.
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50
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Zong S, Liu Y, Yang K, Yang Z, Wang Z, Cui Y. Eliminating nonspecific binding sites for highly reliable immunoassay via super-resolution multicolor fluorescence colocalization. NANOSCALE 2021; 13:6624-6634. [PMID: 33885541 DOI: 10.1039/d0nr08103e] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Non-specific adsorption in immunoassays has always been a major problem that affects the reliability of assay results. Despite the emergence of various methods that can reduce nonspecific adsorption, a universal and effective method to reduce the influence of nonspecific adsorption is still lacking. Hence, we propose here an optical super-resolution imaging based immunoassay strategy, named super-resolution multicolor fluorescence colocalization (SR-MFC), which can generate a low false-positive rate. Taking advantages of the high spatial resolution of single-molecule localization microscopy (SMLM), SR-MFC can directly visualize the assay results and thus effectively exclude the nonspecific binding sites. In other words, even if nonspecific interactions do happen, SR-MFC ensures that the nonspecific reaction sites are visualized and abandoned, which has never been achieved before. To verify its practicability, exosomes, which are important cancer biomarkers, were used as model targets and detected using SR-MFC. Compared with common immunofluorescence assay, the accuracy and reliability of the detection results are greatly improved. The detection limit of exosomes was 38 particles per μL. More importantly, the SR-MFC method can also be generalized for the detection of other biomarkers (e.g. proteins, DNAs, etc.), which is a significant and promising new strategy for immunoassay based diagnosis.
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Affiliation(s)
- Shenfei Zong
- Advanced Photonics Center, Southeast University, Nanjing 210096, China.
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