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Maekawa M, Saito S, Isobe D, Takemoto K, Miura Y, Dobashi Y, Yamasu K. The Oct4-related PouV gene, pou5f3, mediates isthmus development in zebrafish by directly and dynamically regulating pax2a. Cells Dev 2024; 179:203933. [PMID: 38908828 DOI: 10.1016/j.cdev.2024.203933] [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] [Received: 04/14/2024] [Revised: 05/24/2024] [Accepted: 06/13/2024] [Indexed: 06/24/2024]
Abstract
Using a transgenic zebrafish line harboring a heat-inducible dominant-interference pou5f3 gene (en-pou5f3), we reported that this PouV gene is involved in isthmus development at the midbrain-hindbrain boundary (MHB), which patterns the midbrain and cerebellum. Importantly, the functions of pou5f3 reportedly differ before and after the end of gastrulation. In the present study, we examined in detail the effects of en-pou5f3 induction on isthmus development during embryogenesis. When en-pou5f3 was induced around the end of gastrulation (bud stage), the isthmus was abrogated or deformed by the end of somitogenesis (24 hours post-fertilization). At this stage, the expression of MHB markers -- such as pax2a, fgf8a, wnt1, and gbx2 -- was absent in embryos lacking the isthmus structure, whereas it was present, although severely distorted, in embryos with a deformed isthmus. We further found that, after en-pou5f3 induction at late gastrulation, pax2a, fgf8a, and wnt1 were immediately and irreversibly downregulated, whereas the expression of en2a and gbx2 was reduced only weakly and slowly. Induction of en-pou5f3 at early somite stages also immediately downregulated MHB genes, particularly pax2a, but their expression was restored later. Overall, the data suggested that pou5f3 directly upregulates at least pax2a and possibly fgf8a and wnt1, which function in parallel in establishing the MHB, and that the role of pou5f3 dynamically changes around the end of gastrulation. We next examined the transcriptional regulation of pax2a using both in vitro and in vivo reporter analyses; the results showed that two upstream 1.0-kb regions with sequences conserved among vertebrates specifically drove transcription at the MHB. These reporter analyses confirmed that development of the isthmic organizer is regulated by PouV through direct regulation of pax2/pax2a in vertebrate embryos.
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Affiliation(s)
- Masato Maekawa
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Shinji Saito
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan; Institute for Vaccine Research and Development, Hokkaido University, N21, W11, Kita-ku, Sapporo, Hokkaido 001-0021, Japan
| | - Daiki Isobe
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Kazumasa Takemoto
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan; Department of Physiology and Neurobiology, University of Connecticut, 75 North Eagleville Road, U3156, Storrs, CT 06269, USA
| | - Yuhei Miura
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Yurie Dobashi
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Kyo Yamasu
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama City, Saitama 338-8570, Japan.
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2
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Guo J, Chen S, Onishi Y, Shi Q, Song Y, Mei H, Chen L, Kool ET, Zhu RY. RNA Control via Redox-Responsive Acylation. Angew Chem Int Ed Engl 2024; 63:e202402178. [PMID: 38480851 DOI: 10.1002/anie.202402178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Indexed: 04/05/2024]
Abstract
Incorporating stimuli-responsive components into RNA constructs provides precise spatiotemporal control over RNA structures and functions. Despite considerable advancements, the utilization of redox-responsive stimuli for the activation of caged RNAs remains scarce. In this context, we present a novel strategy that leverages post-synthetic acylation coupled with redox-responsive chemistry to exert control over RNA. To achieve this, we design and synthesize a series of acylating reagents specifically tailored for introducing disulfide-containing acyl adducts into the 2'-OH groups of RNA ("cloaking"). Our data reveal that these acyl moieties can be readily appended, effectively blocking RNA catalytic activity and folding. We also demonstrate the traceless release and reactivation of caged RNAs ("uncloaking") through reducing stimuli. By employing this strategy, RNA exhibits rapid cellular uptake, effective distribution and activation in the cytosol without lysosomal entrapment. We anticipate that our methodology will be accessible to laboratories engaged in RNA biology and holds promise as a versatile platform for RNA-based applications.
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Affiliation(s)
- Junsong Guo
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore, 117544, Singapore
| | - Siqin Chen
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore, 117544, Singapore
| | - Yoshiyuki Onishi
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Qi Shi
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore, 117544, Singapore
| | - Yangyang Song
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Dr, Singapore, 117599, Singapore
| | - Hui Mei
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Dr, Singapore, 117599, Singapore
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Ru-Yi Zhu
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore, 117544, Singapore
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3
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Xuan W, Ma JA. Pinpointing Acidic Residues in Proteins. ChemMedChem 2024; 19:e202300623. [PMID: 38303683 DOI: 10.1002/cmdc.202300623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/18/2023] [Indexed: 02/03/2024]
Abstract
It is of great importance to pinpoint specific residues or sites of a protein in biological contexts to enable desired mechanism of action for small molecules or to precisely control protein function. In this regard, acidic residues including aspartic acid (Asp) and glutamic acid (Glu) hold great potential due to their great prevalence and unique function. To unlock the largely untapped potential, great efforts have been made recently by synthetic chemists, chemical biologists and pharmacologists. Herein, we would like to highlight the remarkable progress and particularly introduce the electrophiles that exhibit reactivity to carboxylic acids, the light-induced reactivities to carboxylic acids and the genetically encoded noncanonical amino acids that allow protein manipulations at acidic residues. We also comment on certain unresolved challenges, hoping to draw more attention to this rapidly developing area.
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Affiliation(s)
- Weimin Xuan
- Frontiers Science Center for Synthetic Biology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Jun-An Ma
- Department of Chemistry, Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, 300072, P. R. China
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4
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Liu R, Yao J, Zhou S, Yang J, Zhang Y, Yang X, Li L, Zhang Y, Zhuang Y, Yang Y, Chen X. Spatiotemporal control of RNA metabolism and CRISPR-Cas functions using engineered photoswitchable RNA-binding proteins. Nat Protoc 2024; 19:374-405. [PMID: 38036926 DOI: 10.1038/s41596-023-00920-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 09/19/2023] [Indexed: 12/02/2023]
Abstract
RNA molecules perform various crucial roles in diverse cellular processes, from translating genetic information to decoding the genome, regulating gene expression and catalyzing chemical reactions. RNA-binding proteins (RBPs) play an essential role in regulating the diverse behaviors and functions of RNA in live cells, but techniques for the spatiotemporal control of RBP activities and RNA functions are rarely reported yet highly desirable. We recently reported the development of LicV, a synthetic photoswitchable RBP that can bind to a specific RNA sequence in response to blue light irradiation. LicV has been used successfully for the optogenetic control of RNA localization, splicing, translation and stability, as well as for the photoswitchable regulation of transcription and genomic locus labeling. Compared to classical genetic or pharmacologic perturbations, LicV-based light-switchable effectors have the advantages of large dynamic range between dark and light conditions and submicron and millisecond spatiotemporal resolutions. In this protocol, we provide an easy, efficient and generalizable strategy for engineering photoswitchable RBPs for the spatiotemporal control of RNA metabolism. We also provide a detailed protocol for the conversion of a CRISPR-Cas system to optogenetic control. The protocols typically take 2-3 d, including transfection and results analysis. Most of this protocol is applicable to the development of novel LicV-based photoswitchable effectors for the optogenetic control of other RNA metabolisms and CRISPR-Cas functions.
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Affiliation(s)
- Renmei Liu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
- School of Bioengineering, East China University of Science and Technology, Shanghai, China
| | - Jing Yao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Siyu Zhou
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Jing Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yaqiang Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Xiaoyan Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Leshi Li
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Yunbin Zhang
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yingping Zhuang
- School of Bioengineering, East China University of Science and Technology, Shanghai, China
| | - Yi Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
| | - Xianjun Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
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5
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Takemura S, Shimada N, Maruyama A. Malachite green-derivatized cationic comb-type copolymer acts as a photoresponsive artificial chaperone. JOURNAL OF BIOMATERIALS SCIENCE. POLYMER EDITION 2023; 34:2463-2482. [PMID: 37787160 DOI: 10.1080/09205063.2023.2265127] [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: 12/02/2022] [Accepted: 09/01/2023] [Indexed: 10/04/2023]
Abstract
Molecular chaperones play vital roles in various physiological reactions by regulating the folding and assembly of biomacromolecules. We have demonstrated that cationic comb-type copolymers exhibit chaperone activity for anionic biomolecules including DNA and ionic peptide via the formation of soluble interpolyelectrolyte complexes. The development of smart artificial chaperones that can be spatiotemporally controlled by a remotely guided signal would expand the functions of artificial chaperones. Herein, to enable photocontrol of chaperone activity, a cationic comb-type copolymer bearing malachite green as a photoresponsive unit was designed. We first prepared a series of carboxylic acid derivatives of malachite green identified a derivative that could be quickly and quantitatively converted to the cationic form from the nonionic form by photoirradiation. This derivative was conjugated to the cationic comb-type copolymer, poly(allylamine)-graft-poly(ethylene glycol) through a condensation reaction. Upon photoirradiation, the copolymer bearing 9 mol% malachite green enhanced the membrane disruptive activity of acidic peptide E5 and induced morphological changes in liposomes. This demonstration of photoresponsive activation of chaperoning activity of a copolymer suggests that the installation of carboxyl derivatives of malachite green will impart photoresponsiveness to various materials including biopolymers.
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Affiliation(s)
- Seiya Takemura
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Naohiko Shimada
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Atsushi Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
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6
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Chung K, Booth MJ. Sequence-independent, site-specific incorporation of chemical modifications to generate light-activated plasmids. Chem Sci 2023; 14:12693-12706. [PMID: 38020373 PMCID: PMC10646958 DOI: 10.1039/d3sc02761a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
Plasmids are ubiquitous in biology, where they are used to study gene-function relationships and intricate molecular networks, and hold potential as therapeutic devices. Developing methods to control their function will advance their application in research and may also expedite their translation to clinical settings. Light is an attractive stimulus to conditionally regulate plasmid expression as it is non-invasive, and its properties such as wavelength, intensity, and duration can be adjusted to minimise cellular toxicity and increase penetration. Herein, we have developed a method to site-specifically introduce photocages into plasmids, by resynthesising one strand in a manner similar to Kunkel mutagenesis. Unlike alternative approaches to chemically modify plasmids, this method is sequence-independent at the site of modification and uses commercially available phosphoramidites. To generate our light-activated (LA) plasmids, photocleavable biotinylated nucleobases were introduced at specific sites across the T7 and CMV promoters on plasmids and bound to streptavidin to sterically block access. These LA-plasmids were then successfully used to control expression in both cell-free systems (T7 promoter) and mammalian cells (CMV promoter). These light-activated plasmids might be used to remotely control cellular activity and reduce off-target toxicity for future medical use. Our simple approach to plasmid modification might also be used to introduce novel chemical moieties for advanced function.
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Affiliation(s)
- Khoa Chung
- Department of Chemistry, University of Oxford Mansfield Road OX1 3TA Oxford UK
| | - Michael J Booth
- Department of Chemistry, University of Oxford Mansfield Road OX1 3TA Oxford UK
- Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
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7
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O’Hagan M, Duan Z, Huang F, Laps S, Dong J, Xia F, Willner I. Photocleavable Ortho-Nitrobenzyl-Protected DNA Architectures and Their Applications. Chem Rev 2023; 123:6839-6887. [PMID: 37078690 PMCID: PMC10214457 DOI: 10.1021/acs.chemrev.3c00016] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Indexed: 04/21/2023]
Abstract
This review article introduces mechanistic aspects and applications of photochemically deprotected ortho-nitrobenzyl (ONB)-functionalized nucleic acids and their impact on diverse research fields including DNA nanotechnology and materials chemistry, biological chemistry, and systems chemistry. Specific topics addressed include the synthesis of the ONB-modified nucleic acids, the mechanisms involved in the photochemical deprotection of the ONB units, and the photophysical and chemical means to tune the irradiation wavelength required for the photodeprotection process. Principles to activate ONB-caged nanostructures, ONB-protected DNAzymes and aptamer frameworks are introduced. Specifically, the use of ONB-protected nucleic acids for the phototriggered spatiotemporal amplified sensing and imaging of intracellular mRNAs at the single-cell level are addressed, and control over transcription machineries, protein translation and spatiotemporal silencing of gene expression by ONB-deprotected nucleic acids are demonstrated. In addition, photodeprotection of ONB-modified nucleic acids finds important applications in controlling material properties and functions. These are introduced by the phototriggered fusion of ONB nucleic acid functionalized liposomes as models for cell-cell fusion, the light-stimulated fusion of ONB nucleic acid functionalized drug-loaded liposomes with cells for therapeutic applications, and the photolithographic patterning of ONB nucleic acid-modified interfaces. Particularly, the photolithographic control of the stiffness of membrane-like interfaces for the guided patterned growth of cells is realized. Moreover, ONB-functionalized microcapsules act as light-responsive carriers for the controlled release of drugs, and ONB-modified DNA origami frameworks act as mechanical devices or stimuli-responsive containments for the operation of DNA machineries such as the CRISPR-Cas9 system. The future challenges and potential applications of photoprotected DNA structures are discussed.
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Affiliation(s)
- Michael
P. O’Hagan
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Zhijuan Duan
- State
Key Laboratory of Biogeology and Environmental Geology, Engineering
Research Center of Nano-Geomaterials of Ministry of Education, Faculty
of Materials Science and Chemistry, China
University of Geosciences, Wuhan 430074, China
| | - Fujian Huang
- State
Key Laboratory of Biogeology and Environmental Geology, Engineering
Research Center of Nano-Geomaterials of Ministry of Education, Faculty
of Materials Science and Chemistry, China
University of Geosciences, Wuhan 430074, China
| | - Shay Laps
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Jiantong Dong
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Fan Xia
- State
Key Laboratory of Biogeology and Environmental Geology, Engineering
Research Center of Nano-Geomaterials of Ministry of Education, Faculty
of Materials Science and Chemistry, China
University of Geosciences, Wuhan 430074, China
| | - Itamar Willner
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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8
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Liu Y, Shi Y, Yu L, Wu Z, Jiang JH. Reversible Acylation of RNA Enables Activatable Biosensing. Anal Chem 2023; 95:6490-6495. [PMID: 37053522 DOI: 10.1021/acs.analchem.3c00723] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
There is a high demand to develop chemical tools to control the property and function of RNA. Current methods mainly rely on ultraviolet light-based caging strategies, which may cause phototoxicity in live cell-based experiments. We herein report an endogenous stimulus-responsive RNA acylation approach by introducing boronate ester (BE) groups to 2'-hydroxyls through postsynthetic modification. Treatment with hydrogen peroxide (H2O2) yields a phenol derivative which undergoes a 1,6-eliminaton for the traceless release of 2'-hydroxyl. We demonstrated that the acylation of crRNA enabled conditional regulation of CRISPR/Cas13a activity for activatable detection of target RNA. We also showed that the highly specific acylation of the single RNA in 8-17 DNAzyme allowed reversible control of the catalytic activity of DNAzyme, which was further applied to the cell-selective imaging of metal ions in cancer cells. Thus, our strategy provides a simple, general, and cell-selective method to control RNA activity, affording great potential in the construction of activatable RNA sensors and pre-RNA medicines.
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Affiliation(s)
- Yining Liu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Yang Shi
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Lanxing Yu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Zhenkun Wu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
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9
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Velema WA, Lu Z. Chemical RNA Cross-Linking: Mechanisms, Computational Analysis, and Biological Applications. JACS AU 2023; 3:316-332. [PMID: 36873678 PMCID: PMC9975857 DOI: 10.1021/jacsau.2c00625] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/23/2022] [Accepted: 12/23/2022] [Indexed: 06/18/2023]
Abstract
In recent years, RNA has emerged as a multifaceted biomolecule that is involved in virtually every function of the cell and is critical for human health. This has led to a substantial increase in research efforts to uncover the many chemical and biological aspects of RNA and target RNA for therapeutic purposes. In particular, analysis of RNA structures and interactions in cells has been critical for understanding their diverse functions and druggability. In the last 5 years, several chemical methods have been developed to achieve this goal, using chemical cross-linking combined with high-throughput sequencing and computational analysis. Applications of these methods resulted in important new insights into RNA functions in a variety of biological contexts. Given the rapid development of new chemical technologies, a thorough perspective on the past and future of this field is provided. In particular, the various RNA cross-linkers and their mechanisms, the computational analysis and challenges, and illustrative examples from recent literature are discussed.
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Affiliation(s)
- Willem A. Velema
- Institute
for Molecules and Materials, Radboud University, Nijmegen 6500 HC, The Netherlands
| | - Zhipeng Lu
- Department
of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90033, United States
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10
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Dittmar M, Weissenböck FP, Rentmeister A. Lichtgesteuerte Translation von mRNA in Eukaryoten. BIOSPEKTRUM : ZEITSCHRIFT DER GESELLSCHAFT FUR BIOLOGISHE CHEMIE (GBCH) UND DER VEREINIGUNG FUR ALLGEMEINE UND ANGEWANDTE MIKROBIOLOGIE (VAAM) 2023; 29:31-34. [PMID: 36845577 PMCID: PMC9942070 DOI: 10.1007/s12268-023-1881-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Messenger RNA (mRNA) shows great potential for medical applications, as recently demonstrated by the mRNA-based vaccines against the coronavirus. In addition, it has long been used for ectopic gene expression in cells and model organisms. While numerous methodologies are available for controlling gene expression at the level of transcription, approaches to control translation are scarce. Here we review strategies for direct light-mediated activation of mRNA translation via photocleavable groups and their potential to achieve spatial and temporal control of protein production.
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Affiliation(s)
- Maria Dittmar
- Institut für Biochemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, D-48149 Münster, Deutschland
| | - Florian Peter Weissenböck
- Institut für Biochemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, D-48149 Münster, Deutschland
| | - Andrea Rentmeister
- Institut für Biochemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, D-48149 Münster, Deutschland
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11
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Bollu A, Klöcker N, Špaček P, P Weissenboeck F, Hüwel S, Rentmeister A. Light-Activated Translation of Different mRNAs in Cells via Wavelength-Dependent Photouncaging. Angew Chem Int Ed Engl 2023; 62:e202209975. [PMID: 36417319 PMCID: PMC10107135 DOI: 10.1002/anie.202209975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/20/2022] [Accepted: 11/23/2022] [Indexed: 11/24/2022]
Abstract
The 5' cap is a hallmark of eukaryotic mRNA involved in the initiation of translation. Its modification with a single photo-cleavable group can bring translation of mRNA under the control of light. However, UV irradiation causes cell stress and downregulation of translation. Furthermore, complex processes often involve timed expression of more than one gene. The approach would thus greatly benefit from the ability to photo-cleave by blue light and to control more than one mRNA at a time. We report the synthesis of a 5' cap modified with a 7-(diethylamino)coumarin (CouCap) and adapted conditions for in vitro transcription. Translation of the resulting CouCap-mRNA is muted in vitro and in mammalian cells, and can be initiated by irradiation with 450 nm. The native cap is restored and no non-natural residues nor sequence alterations remain in the mRNA. Multiplexing for two different mRNAs was achieved by combining cap analogs with coumarin- and ortho-nitrobenzyl-based photo-cleavable groups.
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Affiliation(s)
- Amarnath Bollu
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms Universität Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Nils Klöcker
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms Universität Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Petr Špaček
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms Universität Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Florian P Weissenboeck
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms Universität Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Sabine Hüwel
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms Universität Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, Westfälische Wilhelms Universität Münster, Corrensstraße 36, 48149, Münster, Germany
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12
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Klöcker N, Anhäuser L, Rentmeister A. Enzymatic Modification of the 5' Cap with Photocleavable ONB-Derivatives Using GlaTgs V34A. Chembiochem 2023; 24:e202200522. [PMID: 36408753 PMCID: PMC10108117 DOI: 10.1002/cbic.202200522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 11/22/2022]
Abstract
The 5' cap of mRNA plays a critical role in mRNA processing, quality control and turnover. Enzymatic availability of the 5' cap governs translation and could be a tool to investigate cell fate decisions and protein functions or develop protein replacement therapies. We have previously reported on the chemical synthesis of 5' cap analogues with photocleavable groups for this purpose. However, the synthesis is complex and post-synthetic enzymatic installation may make the technique more applicable to biological researchers. Common 5' cap analogues, like the cap 0, are commercially available and routinely used for in vitro transcription. Here, we report a facile enzymatic approach to attach photocleavable groups site-specifically to the N2 position of m7 G of the 5' cap. By expanding the substrate scope of the methyltransferase variant GlaTgs V34A and using synthetic co-substrate analogues, we could enzymatically photocage the 5' cap and recover it after irradiation.
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Affiliation(s)
- Nils Klöcker
- Department of ChemistryInstitute of BiochemistryWestfälische Wilhelms-Universität MünsterCorrensstraße 36MünsterGermany
| | - Lea Anhäuser
- Department of ChemistryInstitute of BiochemistryWestfälische Wilhelms-Universität MünsterCorrensstraße 36MünsterGermany
| | - Andrea Rentmeister
- Department of ChemistryInstitute of BiochemistryWestfälische Wilhelms-Universität MünsterCorrensstraße 36MünsterGermany
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13
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Kennelly SA, Moorthy R, Otero RS, Harki DA. Expanding Catch and Release DNA Decoy (CRDD) Technology with Pyrimidine Mimics. Chemistry 2022; 28:e202201355. [PMID: 35849314 PMCID: PMC9588621 DOI: 10.1002/chem.202201355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Indexed: 01/05/2023]
Abstract
Catch and release DNA decoys (CRDDs) utilize photochemically responsive nucleoside analogues that generate abasic sites upon exposure to light. Herein, we describe the synthesis and evaluation of four candidate CRDD monomers containing nucleobases that mimic endogenous pyrimidines: 2-nitroimidazole (2-NI), 2-nitrobenzene (2-NB), 2-nitropyrrole (2-NP) and 3-nitropyrrole (3-NP). Our studies reveal that 2-NI and 2-NP can function as CRDDs, whereas 3-NP and 2-NB undergo decomposition and transformation to a higher-ordered structure upon photolysis, respectively. When incorporated into DNA, 2-NP undergoes rapid photochemical cleavage of the anomeric bond (1.8 min half-life) to yield an abasic site. Finally, we find that all four pyrimidine mimics show significantly greater stability when base-paired against the previously reported 7-nitroindole CRDD monomer. Our work marks the expansion of CRDD technology to both purine and pyrimidine scaffolds.
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Affiliation(s)
- Samantha A. Kennelly
- Department of Medicinal ChemistryUniversity of Minnesota2231 6th Street SEMinneapolis, MN 55455USA
| | - Ramkumar Moorthy
- Department of Medicinal ChemistryUniversity of Minnesota2231 6th Street SEMinneapolis, MN 55455USA
| | - Ruben Silva Otero
- Department of Medicinal ChemistryUniversity of Minnesota2231 6th Street SEMinneapolis, MN 55455USA
| | - Daniel A. Harki
- Department of Medicinal ChemistryUniversity of Minnesota2231 6th Street SEMinneapolis, MN 55455USA
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14
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Feng Z, Ducos B, Scerbo P, Aujard I, Jullien L, Bensimon D. The Development and Application of Opto-Chemical Tools in the Zebrafish. Molecules 2022; 27:6231. [PMID: 36234767 PMCID: PMC9572478 DOI: 10.3390/molecules27196231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/18/2022] Open
Abstract
The zebrafish is one of the most widely adopted animal models in both basic and translational research. This popularity of the zebrafish results from several advantages such as a high degree of similarity to the human genome, the ease of genetic and chemical perturbations, external fertilization with high fecundity, transparent and fast-developing embryos, and relatively low cost-effective maintenance. In particular, body translucency is a unique feature of zebrafish that is not adequately obtained with other vertebrate organisms. The animal's distinctive optical clarity and small size therefore make it a successful model for optical modulation and observation. Furthermore, the convenience of microinjection and high embryonic permeability readily allow for efficient delivery of large and small molecules into live animals. Finally, the numerous number of siblings obtained from a single pair of animals offers large replicates and improved statistical analysis of the results. In this review, we describe the development of opto-chemical tools based on various strategies that control biological activities with unprecedented spatiotemporal resolution. We also discuss the reported applications of these tools in zebrafish and highlight the current challenges and future possibilities of opto-chemical approaches, particularly at the single cell level.
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Affiliation(s)
- Zhiping Feng
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Bertrand Ducos
- Laboratoire de Physique de l’Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Université de Paris, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
- High Throughput qPCR Core Facility, Ecole Normale Supérieure, Paris Sciences Letters University, 46 Rue d’Ulm, 75005 Paris, France
| | - Pierluigi Scerbo
- Laboratoire de Physique de l’Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Université de Paris, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
- Inovarion, 75005 Paris, France
| | - Isabelle Aujard
- Laboratoire PASTEUR, Département de Chimie, Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
| | - Ludovic Jullien
- Laboratoire PASTEUR, Département de Chimie, Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
| | - David Bensimon
- Laboratoire de Physique de l’Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Université de Paris, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
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15
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Higashi SL, Shintani Y, Ikeda M. Installing Reduction Responsiveness into Biomolecules by Introducing Nitroaryl Groups. Chemistry 2022; 28:e202201103. [DOI: 10.1002/chem.202201103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Sayuri L. Higashi
- United Graduate School of Drug Discovery and Medical Information Sciences Gifu University 1-1 Yanagido Gifu 501-1193 Japan
- Present address: Institut für Physiologische Chemie und Pathobiochemie Universität Münster Waldeyerstraße 15 48149 Münster Germany
| | - Yuki Shintani
- Department of Life Science and Chemistry Graduate School of Natural Science and Technology Gifu University 1-1 Yanagido Gifu 501-1193 Japan
| | - Masato Ikeda
- United Graduate School of Drug Discovery and Medical Information Sciences Gifu University 1-1 Yanagido Gifu 501-1193 Japan
- Department of Life Science and Chemistry Graduate School of Natural Science and Technology Gifu University 1-1 Yanagido Gifu 501-1193 Japan
- Institute for Glyco-core Research (iGCORE) Gifu University 1-1 Yanagido Gifu 501-1193 Japan
- Institute of Nano-Life-Systems Institutes of Innovation for Future Society Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
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16
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Photocaged 5' cap analogues for optical control of mRNA translation in cells. Nat Chem 2022; 14:905-913. [PMID: 35725774 PMCID: PMC7613264 DOI: 10.1038/s41557-022-00972-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 05/11/2022] [Indexed: 11/08/2022]
Abstract
The translation of messenger RNA (mRNA) is a fundamental process in gene expression, and control of translation is important to regulate protein synthesis in cells. The primary hallmark of eukaryotic mRNAs is their 5′ cap, whose molecular contacts to the eukaryotic translation initiation factor eIF4E govern the initiation of translation. Here we report 5′ cap analogues with photo-cleavable groups (FlashCaps) that prohibit binding to eIF4E and resist cleavage by decapping enzymes. These compounds are compatible with the general and efficient production of mRNAs by in vitro transcription. In FlashCap-mRNAs, the single photocaging group abrogates translation in vitro and in mammalian cells without increasing immunogenicity. Irradiation restores the native cap, triggering efficient translation. FlashCaps overcome the problem of remaining sequence or structure changes in mRNA after irradiation that limited previous designs. Together, these results demonstrate that FlashCaps offer a route to regulate the expression of any given mRNA and to dose mRNA therapeutics with spatio-temporal control. ![]()
Analogues of mRNA 5′ caps containing a photo-cleavable group have now been developed. These so-called FlashCaps can be used for routine in vitro transcription to make long mRNAs containing a cap. In cells, the capped mRNAs are translationally muted; however, upon irradiation by light, the photo-cleavable group is removed without leaving any remaining modification and mRNA is then translated into the corresponding protein.
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17
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Site-specific photolabile roadblocks for the study of transcription elongation in biologically complex systems. Commun Biol 2022; 5:457. [PMID: 35552496 PMCID: PMC9098449 DOI: 10.1038/s42003-022-03382-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 04/20/2022] [Indexed: 12/14/2022] Open
Abstract
Transcriptional pausing is crucial for the timely expression of genetic information. Biochemical methods quantify the half-life of paused RNA polymerase (RNAP) by monitoring restarting complexes across time. However, this approach may produce apparent half-lives that are longer than true pause escape rates in biological contexts where multiple consecutive pause sites are present. We show here that the 6-nitropiperonyloxymethyl (NPOM) photolabile group provides an approach to monitor transcriptional pausing in biological systems containing multiple pause sites. We validate our approach using the well-studied his pause and show that an upstream RNA sequence modulates the pause half-life. NPOM was also used to study a transcriptional region within the Escherichia coli thiC riboswitch containing multiple consecutive pause sites. We find that an RNA hairpin structure located upstream to the region affects the half-life of the 5′ most proximal pause site—but not of the 3′ pause site—in contrast to results obtained using conventional approaches not preventing asynchronous transcription. Our results show that NPOM is a powerful tool to study transcription elongation dynamics within biologically complex systems. Transcriptional pausing can be achieved by 6-nitropiperonyloxymethyl modification, which can halt RNAP without causing backtracking and be efficiently removed by short illumination with a moderately intense UV light.
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18
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Liu R, Yang J, Yao J, Zhao Z, He W, Su N, Zhang Z, Zhang C, Zhang Z, Cai H, Zhu L, Zhao Y, Quan S, Chen X, Yang Y. Optogenetic control of RNA function and metabolism using engineered light-switchable RNA-binding proteins. Nat Biotechnol 2022; 40:779-786. [PMID: 34980910 DOI: 10.1038/s41587-021-01112-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 10/01/2021] [Indexed: 12/13/2022]
Abstract
RNA-binding proteins (RBPs) play an essential role in regulating the function of RNAs in a cellular context, but our ability to control RBP activity in time and space is limited. Here, we describe the engineering of LicV, a photoswitchable RBP that binds to a specific RNA sequence in response to blue light irradiation. When fused to various RNA effectors, LicV allows for optogenetic control of RNA localization, splicing, translation and stability in cell culture. Furthermore, LicV-assisted CRISPR-Cas systems allow for efficient and tunable photoswitchable regulation of transcription and genomic locus labeling. These data demonstrate that the photoswitchable RBP LicV can serve as a programmable scaffold for the spatiotemporal control of synthetic RNA effectors.
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Affiliation(s)
- Renmei Liu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Jing Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Jing Yao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Zhou Zhao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Wei He
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Ni Su
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Zeyi Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Chenxia Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Zhuo Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Haibo Cai
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Linyong Zhu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Yuzheng Zhao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Shu Quan
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Xianjun Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- School of Pharmacy, East China University of Science and Technology, Shanghai, China.
- CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
| | - Yi Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
- School of Pharmacy, East China University of Science and Technology, Shanghai, China.
- CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
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Furuta T. Design and Synthesis of Gene-directed Caged Compounds toward Photopharmacology. YAKUGAKU ZASSHI 2022; 142:495-502. [DOI: 10.1248/yakushi.21-00203-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Toshiaki Furuta
- Department of Biomolecular Science, Faculty of Science, Toho University
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20
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Tavakoli A, Min JH. Photochemical modifications for DNA/RNA oligonucleotides. RSC Adv 2022; 12:6484-6507. [PMID: 35424630 PMCID: PMC8982246 DOI: 10.1039/d1ra05951c] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/27/2021] [Indexed: 11/29/2022] Open
Abstract
Light-triggered chemical reactions can provide excellent tools to investigate the fundamental mechanisms important in biology. Light is easily applicable and orthogonal to most cellular events, and its dose and locality can be controlled in tissues and cells. Light-induced conversion of photochemical groups installed on small molecules, proteins, and oligonucleotides can alter their functional states and thus the ensuing biological events. Recently, photochemical control of DNA/RNA structure and function has garnered attention thanks to the rapidly expanding photochemistry used in diverse biological applications. Photoconvertible groups can be incorporated in the backbone, ribose, and nucleobase of an oligonucleotide to undergo various irreversible and reversible light-induced reactions such as cleavage, crosslinking, isomerization, and intramolecular cyclization reactions. In this review, we gather a list of photoconvertible groups used in oligonucleotides and summarize their reaction characteristics, impacts on DNA/RNA thermal stability and structure, as well as their biological applications.
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Affiliation(s)
- Amirrasoul Tavakoli
- Department of Chemistry & Biochemistry, Baylor University Waco TX 76706 USA +1-254-710-2095
| | - Jung-Hyun Min
- Department of Chemistry & Biochemistry, Baylor University Waco TX 76706 USA +1-254-710-2095
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21
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Muralidhar JR, Kodama K, Hirose T, Ito Y, Kawamoto M. Noncovalent Functionalization of Single-Walled Carbon Nanotubes with a Photocleavable Polythiophene Derivative. NANOMATERIALS 2021; 12:nano12010052. [PMID: 35010002 PMCID: PMC8746816 DOI: 10.3390/nano12010052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/22/2021] [Accepted: 12/22/2021] [Indexed: 11/25/2022]
Abstract
Single-walled carbon nanotubes (SWCNTs) have received extensive research attention owing to their extraordinary optical, electrical, and mechanical properties, which make them particularly attractive for application in optoelectronic devices. However, SWCNTs are insoluble in almost all solvents. Therefore, developing methods to solubilize SWCNTs is crucial for their use in solution-based processes. In this study, we developed a photocleavable polythiophene-derivative polymer dispersant for SWCNTs. The noncovalent surface functionalization of SWCNTs with a polymer allows their dispersal in tetrahydrofuran. The resultant solution-processed polymer/SWCNT composite film undergoes a hydrophobic-to-hydrophilic change in surface properties upon light irradiation (313 nm) because hydrophilic carboxyl groups are formed upon photocleavage of the hydrophobic solubilizing units in the polymer. Furthermore, the photocleaved composite film displays a 38-fold increase in electrical conductivity. This is due to the removal of the solubilizing unit, which is electrically insulating.
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Affiliation(s)
- Jyorthana Rajappa Muralidhar
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako 351-0198, Japan;
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan; (K.K.); (T.H.)
| | - Koichi Kodama
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan; (K.K.); (T.H.)
| | - Takuji Hirose
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan; (K.K.); (T.H.)
| | - Yoshihiro Ito
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako 351-0198, Japan;
- Nano Medical Engineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako 351-0198, Japan
- Correspondence: (Y.I.); (M.K.); Tel.: +81-48-467-2752 (Y.I. & M.K.); Fax: +81-48-467-9300 (Y.I. & M.K.)
| | - Masuki Kawamoto
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako 351-0198, Japan;
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan; (K.K.); (T.H.)
- Nano Medical Engineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako 351-0198, Japan
- Correspondence: (Y.I.); (M.K.); Tel.: +81-48-467-2752 (Y.I. & M.K.); Fax: +81-48-467-9300 (Y.I. & M.K.)
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22
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Xiao L, Jun YW, Kool ET. DNA Tiling Enables Precise Acylation‐Based Labeling and Control of mRNA. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202112106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Lu Xiao
- Department of Chemistry Stanford University Stanford CA 94305 USA
| | - Yong Woong Jun
- Department of Chemistry Stanford University Stanford CA 94305 USA
| | - Eric T. Kool
- Department of Chemistry Stanford University Stanford CA 94305 USA
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23
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Xiao L, Jun YW, Kool ET. DNA Tiling Enables Precise Acylation-Based Labeling and Control of mRNA. Angew Chem Int Ed Engl 2021; 60:26798-26805. [PMID: 34624169 PMCID: PMC8649056 DOI: 10.1002/anie.202112106] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/04/2021] [Indexed: 12/15/2022]
Abstract
Methods for the site-selective labeling of long, native RNAs are needed for studying mRNA biology and future therapies. Current approaches involve engineering RNA sequences, which may alter folding, or are limited to specific sequences or bases. Here, we describe a versatile strategy for mRNA conjugation via a novel DNA-tiling approach. The method, TRAIL, exploits a pool of "protector" oligodeoxynucleotides to hybridize and block the mRNA, combined with an "inducer" DNA that extrudes a reactive RNA loop for acylation at a predetermined site. Using TRAIL, an azido-acylimidazole reagent was employed for labeling and controlling RNA for multiple applications in vitro and in cells, including analysis of RNA-binding proteins, imaging mRNA in cells, and analysis and control of translation. The TRAIL approach offers an efficient and accessible way to label and manipulate RNAs of virtually any length or origin without altering native sequence.
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Affiliation(s)
- Lu Xiao
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Yong Woong Jun
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
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24
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Darrah KE, Deiters A. Translational control of gene function through optically regulated nucleic acids. Chem Soc Rev 2021; 50:13253-13267. [PMID: 34739027 DOI: 10.1039/d1cs00257k] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Translation of mRNA into protein is one of the most fundamental processes within biological systems. Gene expression is tightly regulated both in space and time, often involving complex signaling or gene regulatory networks, as most prominently observed in embryo development. Thus, studies of gene function require tools with a matching level of external control. Light is an excellent conditional trigger as it is minimally invasive, can be easily tuned in wavelength and amplitude, and can be applied with excellent spatial and temporal resolution. To this end, modification of established oligonucleotide-based technologies with optical control elements, in the form of photocaging groups and photoswitches, has rendered these tools capable of navigating the dynamic regulatory pathways of mRNA translation in cellular and in vivo models. In this review, we discuss the different optochemical approaches used to generate photoresponsive nucleic acids that activate and deactivate gene expression and function at the translational level.
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Affiliation(s)
- Kristie E Darrah
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA.
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA.
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26
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Hemelíková N, Žukauskaitė A, Pospíšil T, Strnad M, Doležal K, Mik V. Caged Phytohormones: From Chemical Inactivation to Controlled Physiological Response. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:12111-12125. [PMID: 34610745 DOI: 10.1021/acs.jafc.1c02018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Plant hormones, also called phytohormones, are small signaling molecules regulating a wide range of growth and developmental processes. These unique compounds respond to both external (light, temperature, water, nutrition, or pathogen attack) and internal factors (e.g., age) and mediate signal transduction leading to gene expression with the aim of allowing plants to adapt to constantly changing environmental conditions. Within the regulation of biological processes, individual groups of phytohormones act mostly through a web of interconnected responses rather than linear pathways, making elucidation of their mode of action in living organisms quite challenging. To further progress with our knowledge, the development of novel tools for phytohormone research is required. Although plenty of small molecules targeting phytohormone metabolic or signaling pathways (agonists, antagonists, and inhibitors) and labeled or tagged (fluorescently, isotopically, or biotinylated) compounds have been produced, the control over them in vivo is lost at the time of their administration. Caged compounds, on the other hand, represent a new approach to the development of small organic substances for phytohormone research. The term "caged compounds" refers to light-sensitive probes with latent biological activity, where the active molecule can be freed using a light beam in a highly spatio/temporal-, amplitude-, or frequency-defined manner. This review summarizes the up-to-date development in the field of caged plant hormones. Research progress is arranged in chronological order for each phytohormone regardless of the cage compound formulation and bacterial/plant/animal cell applications. Several known drawbacks and possible directions for future research are highlighted.
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Affiliation(s)
- Noemi Hemelíková
- Laboratory of Growth Regulators, The Czech Academy of Sciences, Institute of Experimental Botany & Palacký University, Šlechtitelů 27, Olomouc CZ-78371, Czech Republic
| | - Asta Žukauskaitė
- Department of Chemical Biology, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc CZ-78371, Czech Republic
| | - Tomáš Pospíšil
- Department of Chemical Biology, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc CZ-78371, Czech Republic
| | - Miroslav Strnad
- Laboratory of Growth Regulators, The Czech Academy of Sciences, Institute of Experimental Botany & Palacký University, Šlechtitelů 27, Olomouc CZ-78371, Czech Republic
| | - Karel Doležal
- Department of Chemical Biology, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc CZ-78371, Czech Republic
| | - Václav Mik
- Department of Experimental Biology, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc CZ-78371, Czech Republic
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27
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Park HS, Jash B, Xiao L, Jun YW, Kool ET. Control of RNA with quinone methide reversible acylating reagents. Org Biomol Chem 2021; 19:8367-8376. [PMID: 34528657 PMCID: PMC8609948 DOI: 10.1039/d1ob01713f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Caging RNA by polyacylation (cloaking) has been developed recently as a simple and rapid method to control the function of RNAs. Previous approaches for chemical reversal of acylation (uncloaking) made use of azide reduction followed by amine cyclization, requiring ∼2-4 h for the completion of cyclization. In new studies aimed at improving reversal rates and yields, we have designed novel acylating reagents that utilize quinone methide (QM) elimination for reversal. The QM de-acylation reactions were tested with two bioorthogonally cleavable motifs, azide and vinyl ether, and their acylation and reversal efficiencies were assessed with NMR and mass spectrometry on model small-molecule substrates as well as on RNAs. Successful reversal both with phosphines and strained alkenes was documented. Among the compounds tested, the azido-QM compound A-3 displayed excellent de-acylation efficiency, with t1/2 for de-acylation of less than an hour using a phosphine trigger. To test its function in RNA caging, A-3 was successfully applied to control EGFP mRNA translation in vitro and in HeLa cells. We expect that this molecular caging strategy can serve as a valuable tool for biological investigation and control of RNAs both in vitro and in cells.
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Affiliation(s)
- Hyun Shin Park
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
| | - Biswarup Jash
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
| | - Lu Xiao
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
| | - Yong Woong Jun
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
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28
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Shirakami N, Kawaki Y, Higashi SL, Shibata A, Kitamura Y, Abu Hanifah S, Wah LL, Ikeda M. Introduction of an Oxidation-responsive 4-Boronobenzyl Group into an Oligonucleotide through a Postmodification Approach. CHEM LETT 2021. [DOI: 10.1246/cl.210204] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Nanami Shirakami
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Yugo Kawaki
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Sayuri L. Higashi
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Aya Shibata
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Yoshiaki Kitamura
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Sharina Abu Hanifah
- Department of Chemical Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Selangor, Malaysia
| | - Lim Lee Wah
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Masato Ikeda
- Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- Center for Highly Advanced Integration of Nano and Life Sciences, Gifu University (G-CHAIN), 1-1 Yanagido, Gifu 501-1193, Japan
- Institute for Glyco-core Research (iGCORE), Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
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29
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Shieh P, Hill MR, Zhang W, Kristufek SL, Johnson JA. Clip Chemistry: Diverse (Bio)(macro)molecular and Material Function through Breaking Covalent Bonds. Chem Rev 2021; 121:7059-7121. [PMID: 33823111 DOI: 10.1021/acs.chemrev.0c01282] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In the two decades since the introduction of the "click chemistry" concept, the toolbox of "click reactions" has continually expanded, enabling chemists, materials scientists, and biologists to rapidly and selectively build complexity for their applications of interest. Similarly, selective and efficient covalent bond breaking reactions have provided and will continue to provide transformative advances. Here, we review key examples and applications of efficient, selective covalent bond cleavage reactions, which we refer to herein as "clip reactions." The strategic application of clip reactions offers opportunities to tailor the compositions and structures of complex (bio)(macro)molecular systems with exquisite control. Working in concert, click chemistry and clip chemistry offer scientists and engineers powerful methods to address next-generation challenges across the chemical sciences.
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Affiliation(s)
- Peyton Shieh
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Megan R Hill
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Wenxu Zhang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Samantha L Kristufek
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jeremiah A Johnson
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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30
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Roth S, Trinh PT, Wachtveitl J. Two-photon absorption enhancement for organic acceptor molecules with QD antennas. NANOSCALE 2021; 13:9808-9815. [PMID: 34031687 DOI: 10.1039/d1nr01696b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The photophysics of an inorganic/organic hybrid system was studied by time-resolved optical spectroscopy, focusing on the goal of increasing the two-photon efficiency of photoresponsive systems. The hybrid system consists of CdS/ZnS core/shell quantum dots (QDs) as energy donor and coumarin derivatives as energy acceptor molecules. The spectral overlap of QD emission and coumarin 343 absorption promotes a Förster resonance energy tranfer (FRET) mechanism leading to a FRET efficiency up to nearly 90%. Additionally, time-correlated single photon counting showed a faster fluorescence decay while acceptor molecules were attached to the QD surface. Femtosecond transient absorption measurements demonstrated an ultrafast FRET reaction. Importantly, FRET was observed also after two-photon excitation of the QDs indicating that the chosen QDs can act as two-photon antennas.
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Affiliation(s)
- S Roth
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany.
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31
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Rapp TL, DeForest CA. Targeting drug delivery with light: A highly focused approach. Adv Drug Deliv Rev 2021; 171:94-107. [PMID: 33486009 PMCID: PMC8127392 DOI: 10.1016/j.addr.2021.01.009] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/04/2021] [Accepted: 01/08/2021] [Indexed: 12/23/2022]
Abstract
Light is a uniquely powerful tool for controlling molecular events in biology. No other external input (e.g., heat, ultrasound, magnetic field) can be so tightly focused or so highly regulated as a clinical laser. Drug delivery vehicles that can be photonically activated have been developed across many platforms, from the simplest "caging" of therapeutics in a prodrug form, to more complex micelles and circulating liposomes that improve drug uptake and efficacy, to large-scale hydrogel platforms that can be used to protect and deliver macromolecular agents including full-length proteins. In this Review, we discuss recent innovations in photosensitive drug delivery and highlight future opportunities to engineer and exploit such light-responsive technologies in the clinical setting.
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Affiliation(s)
- Teresa L Rapp
- Department of Chemical Engineering, University of Washington, Seattle, WA 98105, USA
| | - Cole A DeForest
- Department of Chemical Engineering, University of Washington, Seattle, WA 98105, USA; Department of Bioengineering, University of Washington, Seattle, WA 98105, USA; Department of Chemistry, University of Washington, Seattle, WA 98105, USA; Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA 98105, USA.
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32
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The Issue of Tissue: Approaches and Challenges to the Light Control of Drug Activity. CHEMPHOTOCHEM 2021; 5:611-618. [DOI: 10.1002/cptc.202100001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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33
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Yang L, Dmochowski IJ. Conditionally Activated ("Caged") Oligonucleotides. Molecules 2021; 26:1481. [PMID: 33803234 PMCID: PMC7963183 DOI: 10.3390/molecules26051481] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 01/09/2023] Open
Abstract
Conditionally activated ("caged") oligonucleotides provide useful spatiotemporal control for studying dynamic biological processes, e.g., regulating in vivo gene expression or probing specific oligonucleotide targets. This review summarizes recent advances in caging strategies, which involve different stimuli in the activation step. Oligo cyclization is a particularly attractive caging strategy, which simplifies the probe design and affords oligo stabilization. Our laboratory developed an efficient synthesis for circular caged oligos, and a circular caged antisense DNA oligo was successfully applied in gene regulation. A second technology is Transcriptome In Vivo Analysis (TIVA), where caged oligos enable mRNA isolation from single cells in living tissue. We highlight our development of TIVA probes with improved caging stability. Finally, we illustrate the first protease-activated oligo probe, which was designed for caspase-3. This expands the toolkit for investigating the transcriptome under a specific physiologic condition (e.g., apoptosis), particularly in specimens where light activation is impractical.
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Affiliation(s)
| | - Ivan J. Dmochowski
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA;
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34
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Construction of a reduction-responsive oligonucleotide via a post-modification approach utilizing 4-nitrophenyl diazomethane. Polym J 2021. [DOI: 10.1038/s41428-021-00464-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
AbstractHerein, we describe the construction of a reduction-responsive oligonucleotide by post-modification of an oligonucleotide with a diazo compound bearing a 4-nitrobenzyl group as a reduction-responsive cleavable moiety. High-performance liquid chromatography and mass spectrometry were used to reveal the introduction of a 4-nitrobenzyl group to the 5′-phosphate group of an oligonucleotide, and the subsequent reduction-triggered recovery of the original oligonucleotide. The protocol used for the preparation of this reduction-responsive oligonucleotide is simple and it will have various applications in the fields of chemical and synthetic biology.
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35
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Neural and behavioral control in Caenorhabditis elegans by a yellow-light-activatable caged compound. Proc Natl Acad Sci U S A 2021; 118:2009634118. [PMID: 33542099 DOI: 10.1073/pnas.2009634118] [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: 11/18/2022] Open
Abstract
Caenorhabditis elegans is used as a model system to understand the neural basis of behavior, but application of caged compounds to manipulate and monitor the neural activity is hampered by the innate photophobic response of the nematode to short-wavelength light or by the low temporal resolution of photocontrol. Here, we develop boron dipyrromethene (BODIPY)-derived caged compounds that release bioactive phenol derivatives upon illumination in the yellow wavelength range. We show that activation of the transient receptor potential vanilloid 1 (TRPV1) cation channel by spatially targeted optical uncaging of the TRPV1 agonist N-vanillylnonanamide at 580 nm modulates neural activity. Further, neuronal activation by illumination-induced uncaging enables optical control of the behavior of freely moving C. elegans without inducing a photophobic response and without crosstalk between uncaging and simultaneous fluorescence monitoring of neural activity.
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36
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Kato D, Shiraishi T, Kagechika H, Hirano T. 6-Arylcoumarin as a Scaffold of Photofunctional Molecules with OFF-ON-OFF Type Regulation. J Org Chem 2021; 86:2264-2270. [PMID: 33356259 DOI: 10.1021/acs.joc.0c02419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Coumarin has been utilized as a core structure of photofunctional molecules, such as fluorescent sensors and photoremovable protecting groups. Here, we show that the 6-arylcoumarin moiety can provide OFF-ON-OFF type regulatory functionality for such compounds. To illustrate its utility, we synthesized a coumarin derivative bearing two phenolic hydroxy groups at 7-position and on 6-aryl group as a fluorescent sensor showing an OFF-ON-OFF change in fluorescence intensity in response to an increase in pH from a strongly acidic condition. Further, we show that the efficiency of photoreaction of other derivatives with the same hydroxyl groups is switched from "OFF" at pH 3 and 6 to "ON" at pH 9 and then to OFF at pH 12, enabling their application as switchable photoremovable protective groups. These features arise from sequential deprotonation of two hydroxyl groups: the monoanionic form is responsible for the photoinduced fluorescence and photoreaction.
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Affiliation(s)
- Daiki Kato
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Takuya Shiraishi
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Hiroyuki Kagechika
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Tomoya Hirano
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
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37
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Wu Y, Williams J, Calder EDD, Walport LJ. Strategies to expand peptide functionality through hybridisation with a small molecule component. RSC Chem Biol 2021; 2:151-165. [PMID: 34458778 PMCID: PMC8341444 DOI: 10.1039/d0cb00167h] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/09/2020] [Indexed: 02/04/2023] Open
Abstract
Combining different compound classes gives molecular hybrids that can offer access to novel chemical space and unique properties. Peptides provide ideal starting points for such molecular hybrids, which can be easily modified with a variety of molecular entities. The addition of small molecules can improve the potency, stability and cell permeability of therapeutically relevant peptides. Furthermore, they are often applied to create peptide-based tools in chemical biology. In this review, we discuss general methods that allow the discovery of this compound class and highlight key examples of peptide-small molecule hybrids categorised by the application and function of the small molecule entity.
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Affiliation(s)
- Yuteng Wu
- Protein-Protein Interaction Laboratory, The Francis Crick Institute London UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London London UK
| | - Jack Williams
- Protein-Protein Interaction Laboratory, The Francis Crick Institute London UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London London UK
| | - Ewen D D Calder
- Protein-Protein Interaction Laboratory, The Francis Crick Institute London UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London London UK
| | - Louise J Walport
- Protein-Protein Interaction Laboratory, The Francis Crick Institute London UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London London UK
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38
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Wang S, Zhao J, Wang L, Zhang J, Hu H, Yu P, Wang R. Inducible DNA Polymerase Chain Reaction Triggered by Oxidative Species. ASIAN J ORG CHEM 2021. [DOI: 10.1002/ajoc.202000377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Sheng Wang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation School of Pharmacy Tongji Medical College Huazhong University of Science and Technology 13 Hangkong Road Wuhan Hubei 430030 P. R. China
| | - Jizhong Zhao
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation School of Pharmacy Tongji Medical College Huazhong University of Science and Technology 13 Hangkong Road Wuhan Hubei 430030 P. R. China
| | - Li Wang
- Wuhan No.1 Hospital 215 Zhongshan Avenue Wuhan Hubei 430022 P. R. China
| | - Jingwen Zhang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation School of Pharmacy Tongji Medical College Huazhong University of Science and Technology 13 Hangkong Road Wuhan Hubei 430030 P. R. China
| | - Hongmei Hu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation School of Pharmacy Tongji Medical College Huazhong University of Science and Technology 13 Hangkong Road Wuhan Hubei 430030 P. R. China
| | - Ping Yu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation School of Pharmacy Tongji Medical College Huazhong University of Science and Technology 13 Hangkong Road Wuhan Hubei 430030 P. R. China
| | - Rui Wang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation School of Pharmacy Tongji Medical College Huazhong University of Science and Technology 13 Hangkong Road Wuhan Hubei 430030 P. R. China
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39
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Weinstain R, Slanina T, Kand D, Klán P. Visible-to-NIR-Light Activated Release: From Small Molecules to Nanomaterials. Chem Rev 2020; 120:13135-13272. [PMID: 33125209 PMCID: PMC7833475 DOI: 10.1021/acs.chemrev.0c00663] [Citation(s) in RCA: 261] [Impact Index Per Article: 65.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Indexed: 02/08/2023]
Abstract
Photoactivatable (alternatively, photoremovable, photoreleasable, or photocleavable) protecting groups (PPGs), also known as caged or photocaged compounds, are used to enable non-invasive spatiotemporal photochemical control over the release of species of interest. Recent years have seen the development of PPGs activatable by biologically and chemically benign visible and near-infrared (NIR) light. These long-wavelength-absorbing moieties expand the applicability of this powerful method and its accessibility to non-specialist users. This review comprehensively covers organic and transition metal-containing photoactivatable compounds (complexes) that absorb in the visible- and NIR-range to release various leaving groups and gasotransmitters (carbon monoxide, nitric oxide, and hydrogen sulfide). The text also covers visible- and NIR-light-induced photosensitized release using molecular sensitizers, quantum dots, and upconversion and second-harmonic nanoparticles, as well as release via photodynamic (photooxygenation by singlet oxygen) and photothermal effects. Release from photoactivatable polymers, micelles, vesicles, and photoswitches, along with the related emerging field of photopharmacology, is discussed at the end of the review.
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Affiliation(s)
- Roy Weinstain
- School
of Plant Sciences and Food Security, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Tomáš Slanina
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Dnyaneshwar Kand
- School
of Plant Sciences and Food Security, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Petr Klán
- Department
of Chemistry and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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40
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Bollu A, Hassan MK, Dixit M, Sharma NK. The 2'-caged-tethered-siRNA shows light-dependent temporal controlled RNAi activity for GFP gene into HEK293T cells. Bioorg Med Chem 2020; 30:115932. [PMID: 33316720 DOI: 10.1016/j.bmc.2020.115932] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 11/19/2022]
Abstract
Small interfering RNA (siRNA) exhibits gene-specific RNAi activity by the formation of RISC complex with mRNA of gene. The structural modification of siRNA at appropriate positions affects the structure of RISC complex and then RNAi activity. The modified siRNA are mostly prepared from the incorporation of sugar ring modified, and nucleobase modified RNA nucleotides. It is learned that the introduction of the sterically hindered nucleoside at the specific position of siRNA, severely affects siRNA-RISC complex formation. This report describes the syntheses of bulkier siRNA from 2'-caged-tethered-siRNAs, containing bulkier photolabile protecting group (o-nitrobenzyl) at 2'-position of ribose nucleoside. Importantly, these 2'-caged-siRNAs exhibit the light-dependent RNA interference (RNAi) activity into HEK293T cells for the GFP gene expression. The 2'-caged-siRNAs are synthesized by caging the sense and antisense strand of siRNA. The biochemical evaluations of these caged-siRNAs show that antisense-strand caged-siRNAs decrease RNAi activity temporarily in dark while enhancing RNAi activity, almost like control, after exposure withUV- light. However, 2'-caged sense strand siRNA increase RNAi activity temporarily while decreasing RNAi activity after exposure with light. These caged-siRNAs are also stable in the serum (fetal bovine serum) as like native siRNA. Hence these results strongly support that 2'-caged-tethered-siRNAs are promising analogues to control RNAi activity by UV-light.
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Affiliation(s)
- Amarnath Bollu
- National Institute of Science Education and Research (NISER), SCS, Jatni-Campus, Bhubaneswar, Odisha 752050, India; Homi Bhabha National Institute (HBNI), Mumbai 400 094, India
| | - Md Khurshidul Hassan
- National Institute of Science Education and Research (NISER), SBS, Jatni-Campus, Bhubaneswar, Odisha 752050, India; Homi Bhabha National Institute (HBNI), Mumbai 400 094, India
| | - Manjusha Dixit
- National Institute of Science Education and Research (NISER), SBS, Jatni-Campus, Bhubaneswar, Odisha 752050, India; Homi Bhabha National Institute (HBNI), Mumbai 400 094, India
| | - Nagendra K Sharma
- National Institute of Science Education and Research (NISER), SCS, Jatni-Campus, Bhubaneswar, Odisha 752050, India; Homi Bhabha National Institute (HBNI), Mumbai 400 094, India.
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41
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Dai SY, Yang D. A Visible and Near-Infrared Light Activatable Diazocoumarin Probe for Fluorogenic Protein Labeling in Living Cells. J Am Chem Soc 2020; 142:17156-17166. [PMID: 32870680 DOI: 10.1021/jacs.0c08068] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Chemical modification of proteins in living cells permits valuable glimpses into the molecular interactions that underpin dynamic cellular events. While genetic engineering methods are often preferred, selective labeling of endogenous proteins in a complex intracellular milieu with chemical approaches represents a significant challenge. In this study, we report novel diazocoumarin compounds that can be photoactivated by visible (430-490 nm) and near-infrared light (800 nm) irradiation to photo-uncage reactive carbene intermediates, which could subsequently undergo an insertion reaction with concomitant fluorescence "turned on". With these new molecules in hand, we have developed a new approach for rapid, selective, and fluorogenic labeling of endogenous protein in living cells. By using CA-II and eDHFR as model proteins, we demonstrated that subcellular localization of proteins can be precisely visualized by live-cell imaging and protein levels can be reliably quantified in multiple cell types using flow cytometry. Dynamic protein regulations such as hypoxia-induced CA-IX accumulation can also be detected. In addition, by two-photon excitation with an 800 nm laser, cell-selective labeling can also be achieved with spatially controlled irradiation. Our method circumvents the cytotoxicity of UV light and obviates the need for introducing external reporters with "click chemistries". We believe that this approach of fluorescence labeling of endogenous protein by bioorthogonal photoirradiation opens up exciting opportunities for discoveries and mechanistic interrogation in chemical biology.
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Affiliation(s)
- Sheng-Yao Dai
- Morningside Laboratory for Chemical Biology, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Dan Yang
- Morningside Laboratory for Chemical Biology, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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42
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Xiao L, Habibian M, Kool ET. Site-Selective RNA Functionalization via DNA-Induced Structure. J Am Chem Soc 2020; 142:16357-16363. [PMID: 32865995 PMCID: PMC7962339 DOI: 10.1021/jacs.0c06824] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Methods for RNA functionalization at specific sites are in high demand but remain a challenge, particularly for RNAs produced by transcription rather than by total synthesis. Recent studies have described acylimidazole reagents that react in high yields at 2'-OH groups stochastically at nonbase-paired regions, covering much of the RNA in scattered acyl esters. Localized reactions, if possible, could prove useful in many applications, providing functional handles at specific sites and sequences of the biopolymer. Here, we describe a DNA-directed strategy for in vitro functionalization of RNA at site-localized 2'-OH groups. The method, RNA Acylation at Induced Loops (RAIL), utilizes complementary helper DNA oligonucleotides that expose gaps or loops at selected positions while protecting the remainder in DNA-RNA duplexes. Reaction with an acylimidazole reagent is then carried out, providing high yields of 2'-OH conjugation at predetermined sites. Experiments reveal optimal helper oligodeoxynucleotide designs and conditions for the reaction, and tests of the approach are carried out to control localized ribozyme activities and to label RNAs with dual-color fluorescent dyes. The RAIL approach offers a simple and novel strategy for site-selective labeling and control of RNAs, potentially of any length and origin.
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Affiliation(s)
- Lu Xiao
- Department of Chemistry, ChEM-H Institute and Stanford Cancer Institute, Stanford University, Stanford, California 94305, United States
| | - Maryam Habibian
- Department of Chemistry, ChEM-H Institute and Stanford Cancer Institute, Stanford University, Stanford, California 94305, United States
| | - Eric T. Kool
- Department of Chemistry, ChEM-H Institute and Stanford Cancer Institute, Stanford University, Stanford, California 94305, United States
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43
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Hartmann D, Smith JM, Mazzotti G, Chowdhry R, Booth MJ. Controlling gene expression with light: a multidisciplinary endeavour. Biochem Soc Trans 2020; 48:1645-1659. [PMID: 32657338 PMCID: PMC7458398 DOI: 10.1042/bst20200014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 12/21/2022]
Abstract
The expression of a gene to a protein is one of the most vital biological processes. The use of light to control biology offers unparalleled spatiotemporal resolution from an external, orthogonal signal. A variety of methods have been developed that use light to control the steps of transcription and translation of specific genes into proteins, for cell-free to in vivo biotechnology applications. These methods employ techniques ranging from the modification of small molecules, nucleic acids and proteins with photocages, to the engineering of proteins involved in gene expression using naturally light-sensitive proteins. Although the majority of currently available technologies employ ultraviolet light, there has been a recent increase in the use of functionalities that work at longer wavelengths of light, to minimise cellular damage and increase tissue penetration. Here, we discuss the different chemical and biological methods employed to control gene expression, while also highlighting the central themes and the most exciting applications within this diverse field.
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Affiliation(s)
- Denis Hartmann
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
| | - Jefferson M. Smith
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
| | - Giacomo Mazzotti
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
| | - Razia Chowdhry
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
| | - Michael J. Booth
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
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44
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Hu KH, Eichorst JP, McGinnis CS, Patterson DM, Chow ED, Kersten K, Jameson SC, Gartner ZJ, Rao AA, Krummel MF. ZipSeq: barcoding for real-time mapping of single cell transcriptomes. Nat Methods 2020; 17:833-843. [PMID: 32632238 PMCID: PMC7891292 DOI: 10.1038/s41592-020-0880-2] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 05/26/2020] [Indexed: 12/13/2022]
Abstract
Spatial transcriptomics seeks to integrate single cell transcriptomic data within the three-dimensional space of multicellular biology. Current methods to correlate a cell's position with its transcriptome in living tissues have various limitations. We developed an approach, called 'ZipSeq', that uses patterned illumination and photocaged oligonucleotides to serially print barcodes ('zipcodes') onto live cells in intact tissues, in real time and with an on-the-fly selection of patterns. Using ZipSeq, we mapped gene expression in three settings: in vitro wound healing, live lymph node sections and a live tumor microenvironment. In all cases, we discovered new gene expression patterns associated with histological structures. In the tumor microenvironment, this demonstrated a trajectory of myeloid and T cell differentiation from the periphery inward. A combinatorial variation of ZipSeq efficiently scales in the number of regions defined, providing a pathway for complete mapping of live tissues, subsequent to real-time imaging or perturbation.
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Affiliation(s)
- Kenneth H Hu
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - John P Eichorst
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
| | - Chris S McGinnis
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - David M Patterson
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Eric D Chow
- Department of Biochemistry and Biophysics, Center for Advanced Technology, University of California San Francisco, San Francisco, CA, USA
| | - Kelly Kersten
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Stephen C Jameson
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Zev J Gartner
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Arjun A Rao
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
| | - Matthew F Krummel
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA.
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA.
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45
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Zhang D, Jin S, Piao X, Devaraj NK. Multiplexed Photoactivation of mRNA with Single-Cell Resolution. ACS Chem Biol 2020; 15:1773-1779. [PMID: 32484653 DOI: 10.1021/acschembio.0c00205] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We demonstrate sequential optical activation of two types of mRNAs in the same mammalian cell through the sequential photocleavage of small molecule caging groups ("photocages") tethered to the 5'-untranslated region (5'-UTR) of mRNAs. Synthetic photocages were conjugated onto target mRNA using RNA-TAG, an enzymatic site-specific RNA modification technique. Translation of mRNA was severely reduced upon conjugation of the photocages onto the 5'-UTR. However, subsequent photorelease of the cages from the mRNA transcript triggered activation of translation with single-cell spatiotemporal resolution. To achieve sequential photoactivation of two mRNAs in the same cell, we synthesized a pair of photocages that can be selectively cleaved from mRNA upon photoirradiation with different wavelengths of light. Sequential photoactivation of two mRNAs enabled precise optical control of translation of two unique transcripts. We believe that this modular approach to precisely and rapidly control gene expression will serve as a powerful tool in future biological studies that require controlling translation of multiple transcripts with high spatiotemporal resolution.
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Affiliation(s)
- Dongyang Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Shuaijiang Jin
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Xijun Piao
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Neal K. Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
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Wang S, Huang H, Liu J, Wei L, Wu L, Xiong W, Yin P, Tian T, Zhou X. The Manipulation of RNA-Guided Nucleic Acid Cleavage with Ninhydrin Chemistry. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1903770. [PMID: 32670753 PMCID: PMC7341091 DOI: 10.1002/advs.201903770] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 03/22/2020] [Indexed: 06/11/2023]
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats) systems have been established as valuable genome-editing tools. Controlling CRISPR systems has high biological significance and this field has garnered intense interest. There is a considerable need for simple approaches with no need for protein engineering. The CRISPR systems usually require a guide RNA (gRNA) moiety to recruit and direct the nuclease complexes. In this respect, the ninhydrin (1,2,3-indantrione monohydrate) seems to have considerable potential, as yet unexploited, for modifying gRNA. In this study, ninhydrin chemistry is explored for reversible postsynthetic modification of gRNA molecules. It is further shown that ninhydrin chemistry is efficient in modulating two important CRISPR systems. Thus, ninhydrin chemistry exhibits potential applications in future chemical biology studies.
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Affiliation(s)
- Shao‐Ru Wang
- College of Chemistry and Molecular SciencesKey Laboratory of Biomedical Polymers of Ministry of EducationWuhan UniversityWuhanHubei430072China
- Sauvage Center for Molecular SciencesWuhan UniversityWuhan430072China
- Hubei Province Key Laboratory of Allergy and ImmunologyWuhan UniversityWuhan430071China
| | - Hai‐Yan Huang
- College of Chemistry and Molecular SciencesKey Laboratory of Biomedical Polymers of Ministry of EducationWuhan UniversityWuhanHubei430072China
| | - Jian Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene ResearchHuazhong Agricultural UniversityWuhan430070China
| | - Lai Wei
- College of Chemistry and Molecular SciencesKey Laboratory of Biomedical Polymers of Ministry of EducationWuhan UniversityWuhanHubei430072China
| | - Ling‐Yu Wu
- College of Chemistry and Molecular SciencesKey Laboratory of Biomedical Polymers of Ministry of EducationWuhan UniversityWuhanHubei430072China
| | - Wei Xiong
- College of Chemistry and Molecular SciencesKey Laboratory of Biomedical Polymers of Ministry of EducationWuhan UniversityWuhanHubei430072China
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene ResearchHuazhong Agricultural UniversityWuhan430070China
| | - Tian Tian
- College of Chemistry and Molecular SciencesKey Laboratory of Biomedical Polymers of Ministry of EducationWuhan UniversityWuhanHubei430072China
- Hubei Province Key Laboratory of Allergy and ImmunologyWuhan UniversityWuhan430071China
| | - Xiang Zhou
- College of Chemistry and Molecular SciencesKey Laboratory of Biomedical Polymers of Ministry of EducationWuhan UniversityWuhanHubei430072China
- Hubei Province Key Laboratory of Allergy and ImmunologyWuhan UniversityWuhan430071China
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47
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Anhäuser L, Klöcker N, Muttach F, Mäsing F, Špaček P, Studer A, Rentmeister A. A Benzophenone-Based Photocaging Strategy for the N7 Position of Guanosine. Angew Chem Int Ed Engl 2020; 59:3161-3165. [PMID: 31747109 PMCID: PMC7012642 DOI: 10.1002/anie.201914573] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Indexed: 12/11/2022]
Abstract
Selective modification of nucleobases with photolabile caging groups enables the study and control of processes and interactions of nucleic acids. Numerous positions on nucleobases have been targeted, but all involve formal substitution of a hydrogen atom with a photocaging group. Nature, however, also uses ring-nitrogen methylation, such as m7 G and m1 A, to change the electronic structure and properties of RNA and control biomolecular interactions essential for translation and turnover. We report that aryl ketones such as benzophenone and α-hydroxyalkyl ketone are photolabile caging groups if installed at the N7 position of guanosine or the N1 position of adenosine. Common photocaging groups derived from the ortho-nitrobenzyl moiety were not suitable. Both chemical and enzymatic methods for site-specific modification of N7G in nucleosides, dinucleotides, and RNA were developed, thereby opening the door to studying the molecular interactions of m7 G and m1 A with spatiotemporal control.
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Affiliation(s)
- Lea Anhäuser
- Institut für BiochemieWestfälische Wilhelms-Universität MünsterWilhelm-Klemm-Str. 248149MünsterGermany
| | - Nils Klöcker
- Institut für BiochemieWestfälische Wilhelms-Universität MünsterWilhelm-Klemm-Str. 248149MünsterGermany
| | - Fabian Muttach
- Institut für BiochemieWestfälische Wilhelms-Universität MünsterWilhelm-Klemm-Str. 248149MünsterGermany
| | - Florian Mäsing
- Organisch-Chemisches InstitutWestfälische Wilhelms-Universität MünsterCorrensstrasse 4048149MünsterGermany
| | - Petr Špaček
- Institut für BiochemieWestfälische Wilhelms-Universität MünsterWilhelm-Klemm-Str. 248149MünsterGermany
| | - Armido Studer
- Organisch-Chemisches InstitutWestfälische Wilhelms-Universität MünsterCorrensstrasse 4048149MünsterGermany
| | - Andrea Rentmeister
- Institut für BiochemieWestfälische Wilhelms-Universität MünsterWilhelm-Klemm-Str. 248149MünsterGermany
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48
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Regulation of Electromagnetic Perceptive Gene Using Ferromagnetic Particles for the External Control of Calcium Ion Transport. Biomolecules 2020; 10:biom10020308. [PMID: 32075263 PMCID: PMC7072303 DOI: 10.3390/biom10020308] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/08/2020] [Accepted: 02/11/2020] [Indexed: 01/02/2023] Open
Abstract
Developing synthetic biological devices to allow the noninvasive control of cell fate and function, in vivo can potentially revolutionize the field of regenerative medicine. To address this unmet need, we designed an artificial biological “switch” that consists of two parts: (1) the electromagnetic perceptive gene (EPG) and (2) magnetic particles. Our group has recently cloned the EPG from the Kryptopterus bicirrhis (glass catfish). The EPG gene encodes a putative membrane-associated protein that responds to electromagnetic fields (EMFs). This gene’s primary mechanism of action is to raise the intracellular calcium levels or change in flux through EMF stimulation. Here, we developed a system for the remote regulation of [Ca2+]i (i.e., intracellular calcium ion concentration) using streptavidin-coated ferromagnetic particles (FMPs) under a magnetic field. The results demonstrated that the EPG-FMPs can be used as a molecular calcium switch to express target proteins. This technology has the potential for controlled gene expression, drug delivery, and drug developments.
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49
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Anhäuser L, Klöcker N, Muttach F, Mäsing F, Špaček P, Studer A, Rentmeister A. Eine auf dem Benzophenongerüst basierende Strategie für die Photoschützung der N7‐Position des Guanosins. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201914573] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Lea Anhäuser
- Institut für Biochemie Westfälische Wilhelms-Universität Münster Wilhelm-Klemm-Str. 2 48149 Münster Deutschland
| | - Nils Klöcker
- Institut für Biochemie Westfälische Wilhelms-Universität Münster Wilhelm-Klemm-Str. 2 48149 Münster Deutschland
| | - Fabian Muttach
- Institut für Biochemie Westfälische Wilhelms-Universität Münster Wilhelm-Klemm-Str. 2 48149 Münster Deutschland
| | - Florian Mäsing
- Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Corrensstrasse 40 48149 Münster Deutschland
| | - Petr Špaček
- Institut für Biochemie Westfälische Wilhelms-Universität Münster Wilhelm-Klemm-Str. 2 48149 Münster Deutschland
| | - Armido Studer
- Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Corrensstrasse 40 48149 Münster Deutschland
| | - Andrea Rentmeister
- Institut für Biochemie Westfälische Wilhelms-Universität Münster Wilhelm-Klemm-Str. 2 48149 Münster Deutschland
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50
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Wu Z, Zhang L. Photoregulation between small DNAs and reversible photochromic molecules. Biomater Sci 2019; 7:4944-4962. [PMID: 31650136 DOI: 10.1039/c9bm01305a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Oligonucleotides are widely used biological materials in the fields of biomedicine, nanotechnology, and materials science. Due to the demands for the photoregulation of DNA activities, scientists are placing more and more research interest in the interactions between reversible photochromic molecules and DNAs. Photochromic molecules can work as switches for regulating the DNAs' behavior under light irradiation; meanwhile, DNAs also exert influence over the photochromic molecules. The photochromic molecules can be attached to DNAs either by covalent bonds or by noncovalent forces, which results in different regulative functions. Azobenzenes, spiropyrans, diarylethenes, and stilbene-like compounds are important photochromic molecules working as photoswitches. By summarizing their interactions with oligonucleotides, this review intends to facilitate the relevant research on oligonucleotides/photochromic molecules in the biological and medicinal fields and in materials science.
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Affiliation(s)
- Zhongtao Wu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No. 53 Zhengzhou Rd, Qingdao, 266042, PR China.
| | - Lei Zhang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No. 53 Zhengzhou Rd, Qingdao, 266042, PR China.
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