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Yi HB, Lee S, Seo K, Kim H, Kim M, Lee HS. Cellular and Biophysical Applications of Genetic Code Expansion. Chem Rev 2024. [PMID: 38753805 DOI: 10.1021/acs.chemrev.4c00112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Despite their diverse functions, proteins are inherently constructed from a limited set of building blocks. These compositional constraints pose significant challenges to protein research and its practical applications. Strategically manipulating the cellular protein synthesis system to incorporate novel building blocks has emerged as a critical approach for overcoming these constraints in protein research and application. In the past two decades, the field of genetic code expansion (GCE) has achieved significant advancements, enabling the integration of numerous novel functionalities into proteins across a variety of organisms. This technological evolution has paved the way for the extensive application of genetic code expansion across multiple domains, including protein imaging, the introduction of probes for protein research, analysis of protein-protein interactions, spatiotemporal control of protein function, exploration of proteome changes induced by external stimuli, and the synthesis of proteins endowed with novel functions. In this comprehensive Review, we aim to provide an overview of cellular and biophysical applications that have employed GCE technology over the past two decades.
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Affiliation(s)
- Han Bin Yi
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Seungeun Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Kyungdeok Seo
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyeongjo Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Minah Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
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Kozma E, Kele P. Bioorthogonal Reactions in Bioimaging. Top Curr Chem (Cham) 2024; 382:7. [PMID: 38400853 PMCID: PMC10894152 DOI: 10.1007/s41061-024-00452-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/22/2024] [Indexed: 02/26/2024]
Abstract
Visualization of biomolecules in their native environment or imaging-aided understanding of more complex biomolecular processes are one of the focus areas of chemical biology research, which requires selective, often site-specific labeling of targets. This challenging task is effectively addressed by bioorthogonal chemistry tools in combination with advanced synthetic biology methods. Today, the smart combination of the elements of the bioorthogonal toolbox allows selective installation of multiple markers to selected targets, enabling multicolor or multimodal imaging of biomolecules. Furthermore, recent developments in bioorthogonally applicable probe design that meet the growing demands of superresolution microscopy enable more complex questions to be addressed. These novel, advanced probes enable highly sensitive, low-background, single- or multiphoton imaging of biological species and events in live organisms at resolutions comparable to the size of the biomolecule of interest. Herein, the latest developments in bioorthogonal fluorescent probe design and labeling schemes will be discussed in the context of in cellulo/in vivo (multicolor and/or superresolved) imaging schemes. The second part focuses on the importance of genetically engineered minimal bioorthogonal tags, with a particular interest in site-specific protein tagging applications to answer biological questions.
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Affiliation(s)
- Eszter Kozma
- Chemical Biology Research Group, Institute of Organic Chemistry, HUN-REN Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, Budapest, 1117, Hungary
| | - Péter Kele
- Chemical Biology Research Group, Institute of Organic Chemistry, HUN-REN Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, Budapest, 1117, Hungary.
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Jeong S, Koh D, Gwak E, Srambickal CV, Seo D, Widengren J, Lee JC. Pushing the Resolution Limit of Stimulated Emission Depletion Optical Nanoscopy. Int J Mol Sci 2023; 25:26. [PMID: 38203197 PMCID: PMC10779414 DOI: 10.3390/ijms25010026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/08/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024] Open
Abstract
Optical nanoscopy, also known as super-resolution optical microscopy, has provided scientists with the means to surpass the diffraction limit of light microscopy and attain new insights into nanoscopic structures and processes that were previously inaccessible. In recent decades, numerous studies have endeavored to enhance super-resolution microscopy in terms of its spatial (lateral) resolution, axial resolution, and temporal resolution. In this review, we discuss recent efforts to push the resolution limit of stimulated emission depletion (STED) optical nanoscopy across multiple dimensions, including lateral resolution, axial resolution, temporal resolution, and labeling precision. We introduce promising techniques and methodologies building on the STED concept that have emerged in the field, such as MINSTED, isotropic STED, and event-triggered STED, and evaluate their respective strengths and limitations. Moreover, we discuss trade-off relationships that exist in far-field optical microscopy and how they come about in STED optical nanoscopy. By examining the latest developments addressing these aspects, we aim to provide an updated overview of the current state of STED nanoscopy and its potential for future research.
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Affiliation(s)
- Sejoo Jeong
- Department of New Biology, DGIST, Daegu 42988, Republic of Korea
| | - Dongbin Koh
- School of Undergraduate Studies, DGIST, Daegu 42988, Republic of Korea
| | - Eunha Gwak
- Department of New Biology, DGIST, Daegu 42988, Republic of Korea
| | - Chinmaya V. Srambickal
- Exp. Biomol. Physics, Dept. Applied Physics, KTH—Royal Institute of Technology, 106 91 Stockholm, Sweden
| | - Daeha Seo
- Department of Physics and Chemistry, DGIST, Daegu 42988, Republic of Korea
| | - Jerker Widengren
- Exp. Biomol. Physics, Dept. Applied Physics, KTH—Royal Institute of Technology, 106 91 Stockholm, Sweden
| | - Jong-Chan Lee
- Department of New Biology, DGIST, Daegu 42988, Republic of Korea
- New Biology Research Center, DGIST, Daegu 42988, Republic of Korea
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Helmerich DA, Beliu G, Taban D, Meub M, Streit M, Kuhlemann A, Doose S, Sauer M. Photoswitching fingerprint analysis bypasses the 10-nm resolution barrier. Nat Methods 2022; 19:986-994. [PMID: 35915194 PMCID: PMC9349044 DOI: 10.1038/s41592-022-01548-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 06/13/2022] [Indexed: 12/20/2022]
Abstract
Advances in super-resolution microscopy have demonstrated single-molecule localization precisions of a few nanometers. However, translation of such high localization precisions into sub-10-nm spatial resolution in biological samples remains challenging. Here we show that resonance energy transfer between fluorophores separated by less than 10 nm results in accelerated fluorescence blinking and consequently lower localization probabilities impeding sub-10-nm fluorescence imaging. We demonstrate that time-resolved fluorescence detection in combination with photoswitching fingerprint analysis can be used to determine the number and distance even of spatially unresolvable fluorophores in the sub-10-nm range. In combination with genetic code expansion with unnatural amino acids and bioorthogonal click labeling with small fluorophores, photoswitching fingerprint analysis can be used advantageously to reveal information about the number of fluorophores present and their distances in the sub-10-nm range in cells. Energy transfer between fluorophores is shown to impede SMLM at sub-10-nm spatial resolution. Time-resolved detection and photoswitching fingerprinting analysis are used to determine the number and separation of closely spaced fluorophores.
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Affiliation(s)
- Dominic A Helmerich
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Gerti Beliu
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany.,Rudolf Virchow Center, Research Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
| | - Danush Taban
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Mara Meub
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Marcel Streit
- Rudolf Virchow Center, Research Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
| | - Alexander Kuhlemann
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Sören Doose
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany. .,Rudolf Virchow Center, Research Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany.
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