1
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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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2
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Singh AK, Mengji R, Nair AV, Shah SS, Avijit J, Singh NDP. Photoactivable AIEgen-based Lipid-Droplet-Specific Drug Delivery Model for Live Cell Imaging and Two-Photon Light-Triggered Anticancer Drug Delivery. ACS APPLIED BIO MATERIALS 2023; 6:4372-4382. [PMID: 37791981 DOI: 10.1021/acsabm.3c00580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Lipid droplets (LDs) are dynamic complex organelles involved in various physiological processes, and their number and activity are linked to multiple diseases, including cancer. In this study, we have developed LD-specific near-infrared (NIR) light-responsive nano-drug delivery systems (DDSs) based on chalcone derivatives for cancer treatment. The reported nano-DDSs localized inside the cancer microenvironment of LDs, and upon exposure to light, they delivered the anticancer drug valproic acid in a spatiotemporally controlled manner. The developed systems, namely, 2'-hydroxyacetophenone-dimethylaminobenzaldehyde-valproic (HA-DAB-VPA) and 2'-hydroxyacetophenone-diphenylaminobenzaldehyde-valproic (HA-DPB-VPA) ester conjugates, required only two simple synthetic steps. Our reported DDSs exhibited interesting properties such as excited-state intramolecular proton transfer (ESIPT) and aggregation-induced emission (AIE) phenomena, which provided advantages such as AIE-initiated photorelease and ESIPT-enhanced rate of photorelease upon exposure to one- or two-photon light. Further, colocalization studies of the nano-DDSs by employing two cancerous cell lines (MCF-7 cell line and CT-26 cell line) and one normal cell line (HEK cell line) revealed LD concentration-dependent enhanced fluorescence intensity. Furthermore, systematic investigations of both the nano-DDSs in the presence and absence of oleic acid inside the cells revealed that nano-DDS HA-DPB-VPA accumulated more selectively in the LDs. This unique selectivity by the nano-DDS HA-DPB-VPA toward the LDs is due to the hydrophobic nature of the diphenylaminobenzaldehyde (mimicking the LD core), which significantly leads to the aggregation and ESIPT (at 90% volume of fw, ΦF = 20.4% and in oleic acid ΦF = 24.6%), respectively. Significantly, we used this as a light-triggered anticancer drug delivery model to take advantage of the high selectivity and accumulation of the nano-DDS HA-DPB-VPA inside the LDs. Hence, these findings give a prototype for designing drug delivery models for monitoring LD-related intracellular activities and significantly triggering the release of LD-specific drugs in the biological field.
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Affiliation(s)
- Amit Kumar Singh
- Department of Chemistry, Photochemistry Laboratory, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Rakesh Mengji
- Department of Natural Products and Medicinal Chemistry, CSIR-Indian Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Asha V Nair
- Department of Chemistry, Photochemistry Laboratory, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Sk Sheriff Shah
- Department of Chemistry, Photochemistry Laboratory, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Jana Avijit
- Department of Natural Products and Medicinal Chemistry, CSIR-Indian Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - N D Pradeep Singh
- Department of Chemistry, Photochemistry Laboratory, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
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3
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Hamerla C, Mondal P, Hegger R, Burghardt I. Controlled destabilization of caged circularized DNA oligonucleotides predicted by replica exchange molecular dynamics simulations. Phys Chem Chem Phys 2023; 25:26132-26144. [PMID: 37740309 DOI: 10.1039/d3cp02961a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Spatiotemporal control is a critical issue in the design of strategies for the photoregulation of oligonucleotide activity. Efficient uncaging, i.e., activation by removal of photolabile protecting groups (PPGs), often necessitates multiple PPGs. An alternative approach is based on circularization strategies, exemplified by intrasequential circularization, also denoted photo-tethering, as introduced in [Seyfried et al., Angew. Chem., Int. Ed., 2017, 56, 359]. Here, we develop a computational protocol, relying on replica exchange molecular dynamics (REMD), in order to characterize the destabilization of a series of circularized, caged DNA oligonucleotides addressed in the aforementioned study. For these medium-sized (32 nt) oligonucleotides, melting temperatures are computed, whose trend is in good agreement with experiment, exhibiting a large destabilization and, hence, reduction of the melting temperature of the order of ΔTm ∼ 30 K as compared with the native species. The analysis of free energy landscapes confirms the destabilization pattern experienced by the circularized oligonucleotides. The present study underscores that computational protocols that capture controlled destabilization and uncaging of oligonucleotides are promising as predictive tools in the tailored photocontrol of nucleic acids.
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Affiliation(s)
- Carsten Hamerla
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany.
| | - Padmabati Mondal
- Department of Chemistry and Center for Atomic, Molecular, and Optical Sciences and Technologies (CAMOST), Indian Institute of Science Education and Research (IISER) Tirupati, Panguru (G.P), Yerpedu Mandal, 517619 - Tirupati Dist., Andhra Pradesh, India
| | - Rainer Hegger
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany.
| | - Irene Burghardt
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany.
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4
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Francis RM, DeForest CA. 4D Biochemical Photocustomization of Hydrogel Scaffolds for Biomimetic Tissue Engineering. ACCOUNTS OF MATERIALS RESEARCH 2023; 4:704-715. [PMID: 39071987 PMCID: PMC11271249 DOI: 10.1021/accountsmr.3c00062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Programmable engineered tissues and the materials that support them are instrumental to the development of next-generation therapeutics and gaining new understanding of human biology. Toward these ends, recent years have brought a growing emphasis on the creation of "4D" hydrogel culture platforms-those that can be customized in 3D space and on demand over time. Many of the most powerful 4D-tunable biomaterials are photochemically regulated, affording users unmatched spatiotemporal modulation through high-yielding, synthetically tractable, and cytocompatible reactions. Precise physicochemical manipulation of gel networks has given us the ability to drive critical changes in cell fate across a diverse range of distance and time scales, including proliferation, migration, and differentiation through user-directed intracellular and intercellular signaling. This Account provides a survey of the numerous creative approaches taken by our lab and others to recapitulate the dynamically heterogeneous biochemistry underpinning in vivo extracellular matrix (ECM)-cell interactions via light-based network (de)decoration with biomolecules (e.g., peptides, proteins) and in situ protein activation/generation. We believe the insights gained from these studies can motivate disruptive improvements to emerging technologies, including low-variability organoid generation and culture, high-throughput drug screening, and personalized medicine. As photolithography and chemical modification strategies continue to mature, access to and control over new and increasingly complex biological pathways are being unlocked. The earliest hydrogel photopatterning efforts selectively encapsulated bioactive peptides and drugs into rudimentary gel volumes. Through continued exploration and refinement, next-generation materials now boast reversible, multiplexed, and/or Boolean logic-based biomolecule presentation, as well as functional activation at subcellular resolutions throughout 3D space. Lithographic hardware and software technologies, particularly those enabling image-guided patterning, allow researchers to precisely replicate complex biological structures within engineered tissue environments. The advent of bioorthogonal click chemistries has expanded 4D tissue engineering toolkits, permitting diverse constructs to be independently customized in the vicinity of any cell that is amenable to hydrogel-based culture. Additionally, the adoption of modern protein engineering techniques including genetic code expansion and chemoenzymatic alteration provides a roadmap toward site-specific modification of nearly any recombinant or isolated protein, affording installation of photoreactive and click handles without sacrificing their bioactivity. While the established bind, release, (de)activate paradigm in hydrogel photolithography continues to thrive alongside these modern engineering techniques, new studies are also demonstrating photocontrol of more complex or nonclassical operations, including engineered material-microorganism interfaces and functional protein photoassembly. Such creative approaches offer exciting new avenues for the field, including spatial control of on-demand biomolecule production from cellular depots and patterned bioactivity using a growing array of split protein pairs. Taken together, these technologies provide the foundation for truly biomimetic photopatterning of engineered tissues.
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Affiliation(s)
- Ryan M Francis
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98105, United States
| | - Cole A DeForest
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98105, United States; Department of Bioengineering, Department of Chemistry, Institute of Stem Cell & Regenerative Medicine, Molecular Engineering & Sciences Institute, and Institute for Protein Design, University of Washington, Seattle, Washington 98105, United States
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5
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Kaufmann J, Sinsel F, Heckel A. Chromatic Selectivity of Coumarin-Caged Oligonucleotides. Chemistry 2023; 29:e202204014. [PMID: 36562762 DOI: 10.1002/chem.202204014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/24/2022]
Abstract
A system of two coumarin-based caging groups is presented - one absorbing in the blue (400-450 nm) and the other absorbing in the green (480-550 nm) part of the visible spectrum. Together they form a pair, which allows to selectively photoactivate the one or the other in oligonucleotides. A numerical characterization defining the term "chromatic selectivity" was proposed, and it was shown how chromatically selective uncaging can literally be titrated in a kinetic reaction scheme.
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Affiliation(s)
- Janik Kaufmann
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt, Germany
| | - Fabian Sinsel
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt, Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt, Germany
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6
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Rizzo R, Petelinšek N, Bonato A, Zenobi‐Wong M. From Free-Radical to Radical-Free: A Paradigm Shift in Light-Mediated Biofabrication. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2205302. [PMID: 36698304 PMCID: PMC10015869 DOI: 10.1002/advs.202205302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/25/2022] [Indexed: 06/17/2023]
Abstract
In recent years, the development of novel photocrosslinking strategies and photoactivatable materials has stimulated widespread use of light-mediated biofabrication techniques. However, despite great progress toward more efficient and biocompatible photochemical strategies, current photoresins still rely on photoinitiators (PIs) producing radical-initiating species to trigger the so-called free-radical crosslinking/polymerization. In the context of bioprinting, where cells are encapsulated in the bioink, the presence of radicals raises concerns of potential cytotoxicity. In this work, a universal, radical-free (RF) photocrosslinking strategy to be used for light-based technologies is presented. Leveraging RF uncaging mechanisms and Michael addition, cell-laden constructs are photocrosslinked by means of one- and two-photon excitation with high biocompatibility. A hydrophilic coumarin-based group is used to cage a universal RF photocrosslinker based on 4-arm-PEG-thiol (PEG4SH). Upon light exposure, thiols are uncaged and react with an alkene counterpart to form a hydrogel. RF photocrosslinker is shown to be highly stable, enabling potential for off-the-shelf products. While PI-based systems cause a strong upregulation of reactive oxygen species (ROS)-associated genes, ROS are not detected in RF photoresins. Finally, optimized RF photoresin is successfully exploited for high resolution two-photon stereolithography (2P-SL) using remarkably low polymer concentration (<1.5%), paving the way for a shift toward radical-free light-based bioprinting.
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Affiliation(s)
- Riccardo Rizzo
- Tissue Engineering + Biofabrication LaboratoryDepartment of Health Sciences & TechnologyETH ZürichOtto‐Stern‐Weg 7Zürich8093Switzerland
| | - Nika Petelinšek
- Tissue Engineering + Biofabrication LaboratoryDepartment of Health Sciences & TechnologyETH ZürichOtto‐Stern‐Weg 7Zürich8093Switzerland
| | - Angela Bonato
- Tissue Engineering + Biofabrication LaboratoryDepartment of Health Sciences & TechnologyETH ZürichOtto‐Stern‐Weg 7Zürich8093Switzerland
| | - Marcy Zenobi‐Wong
- Tissue Engineering + Biofabrication LaboratoryDepartment of Health Sciences & TechnologyETH ZürichOtto‐Stern‐Weg 7Zürich8093Switzerland
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7
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Weber R, Chok K, Junek S, Glaubitz C, Heckel A. Rhodamine-Sensitized Two-Photon Activation of a Red Light-Absorbing BODIPY Photocage. Chemistry 2023; 29:e202300149. [PMID: 36785982 DOI: 10.1002/chem.202300149] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/08/2023] [Accepted: 02/13/2023] [Indexed: 02/15/2023]
Abstract
Two-photon (2P) activatable probes are of high value in biological and medical chemistry since near infrared (NIR) light can penetrate deeply even in blood-perfused tissue and due to the intrinsic three-dimensional activation properties. Designing two-photon chromophores is challenging. However, the two-photon absorption qualities of a photocage can be improved with an intramolecular sensitizer, which transfers the absorbed light onto the cage. We herein present the synthesis and photophysical characterization of a 2P-sensitive uncaging dyad based on rhodamine 101 as donor fluorophore and a redshifted BODIPY as acceptor photocage. Liberation of p-nitroaniline (PNA) upon one-photon photolysis was confirmed by HPLC analysis. The photoreaction was found to be accompanied by a considerable change of the fluorescence properties of the chromophores. The possibility of a fluorescent read-out enabled the detection of two-photon induced uncaging by confocal fluorescence microscopy.
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Affiliation(s)
- Rebekka Weber
- Goethe University Frankfurt, Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany
| | - Kerby Chok
- Goethe University Frankfurt, Institute for Biophysical Chemistry, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Stephan Junek
- Max Planck Institute for Brain Research, Max-von-Laue-Str. 4, 60438, Frankfurt am Main, Germany
| | - Clemens Glaubitz
- Goethe University Frankfurt, Institute for Biophysical Chemistry, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Alexander Heckel
- Goethe University Frankfurt, Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany
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8
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Xiong H, Xu Y, Kim B, Rha H, Zhang B, Li M, Yang GF, Kim JS. Photo-controllable biochemistry: Exploiting the photocages in phototherapeutic window. Chem 2022. [DOI: 10.1016/j.chempr.2022.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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9
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Chen L, Liu Y, Guo W, Liu Z. Light responsive nucleic acid for biomedical application. EXPLORATION 2022; 2:20210099. [PMCID: PMC10190984 DOI: 10.1002/exp.20210099] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 03/03/2022] [Indexed: 06/16/2023]
Affiliation(s)
- Liwei Chen
- Department of Pharmaceutical Engineering College of Chemistry and Chemical Engineering Central South University Changsha Hunan Province P. R. China
| | - Yanfei Liu
- Department of Pharmaceutical Engineering College of Chemistry and Chemical Engineering Central South University Changsha Hunan Province P. R. China
| | - Weisheng Guo
- Department of Minimally Invasive Interventional Radiology Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease School of Pharmaceutical Sciences & The Second Affiliated Hospital Guangzhou Medical University Guangzhou Guangdong Province P. R. China
| | - Zhenbao Liu
- Department of Pharmaceutics Xiangya School of Pharmaceutical Sciences Central South University Changsha Hunan Province P. R. China
- Molecular Imaging Research Center of Central South University Changsha Hunan Province P. R. China
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10
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Dorsey PJ, Scalise D, Schulman R. A model of spatio-temporal regulation within biomaterials using DNA reaction-diffusion waveguides. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220200. [PMID: 36016917 PMCID: PMC9399693 DOI: 10.1098/rsos.220200] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
In multi-cellular organisms, cells and tissues coordinate biochemical signal propagation across length scales spanning micrometres to metres. Designing synthetic materials with similar capacities for coordinated signal propagation could allow these systems to adaptively regulate themselves across space and over time. Here, we combine ideas from cell signalling and electronic circuitry to propose a biochemical waveguide that transmits information in the form of a concentration of a DNA species on a directed path. The waveguide could be seamlessly integrated into a soft material because there is virtually no difference between the chemical or physical properties of the waveguide and the material it is embedded within. We propose the design of DNA strand displacement reactions to construct the system and, using reaction-diffusion models, identify kinetic and diffusive parameters that enable super-diffusive transport of DNA species via autocatalysis. Finally, to support experimental waveguide implementation, we propose a sink reaction and spatially inhomogeneous DNA concentrations that could mitigate the spurious amplification of an autocatalyst within the waveguide, allowing for controlled waveguide triggering. Chemical waveguides could facilitate the design of synthetic biomaterials with distributed sensing machinery integrated throughout their structure and enable coordinated self-regulating programmes triggered by changing environmental conditions.
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Affiliation(s)
- Phillip J. Dorsey
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Dominic Scalise
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Rebecca Schulman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
- Department of Computer Science, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
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11
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Hermanns V, Scheurer M, Kersten NF, Abdellaoui C, Wachtveitl J, Dreuw A, Heckel A. Rethinking Uncaging: A New Antiaromatic Photocage Driven by a Gain of Resonance Energy. Chemistry 2021; 27:14121-14127. [PMID: 34363415 PMCID: PMC8519059 DOI: 10.1002/chem.202102351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Indexed: 12/31/2022]
Abstract
Photoactivatable compounds for example photoswitches or photolabile protecting groups (PPGs, photocages) for spatiotemporal light control, play a crucial role in different areas of research. For each application, parameters such as the absorption spectrum, solubility in the respective media and/or photochemical quantum yields for several competing processes need to be optimized. The design of new photochemical tools therefore remains an important task. In this study, we exploited the concept of excited-state-aromaticity, first described by N. Colin Baird in 1971, to investigate a new class of photocages, based on cyclic, ground-state-antiaromatic systems. Several thio- and nitrogen-functionalized compounds were synthesized, photochemically characterized and further optimized, supported by quantum chemical calculations. After choosing the optimal scaffold, which shows an excellent uncaging quantum yield of 28 %, we achieved a bathochromic shift of over 100 nm, resulting in a robust, well accessible, visible light absorbing, compact new photocage with a clean photoreaction and a high quantum product (ϵ⋅Φ) of 893 M-1 cm-1 at 405 nm.
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Affiliation(s)
- Volker Hermanns
- Institute of Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Lau-Str. 760438FrankfurtGermany
| | - Maximilian Scheurer
- Interdisciplinary Center for Scientific ComputingHeidelberg UniversityIm Neuenheimer Feld 20569120HeidelbergGermany
| | - Nils Frederik Kersten
- Institute of Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Lau-Str. 760438FrankfurtGermany
| | - Chahinez Abdellaoui
- Institute of Physical and Theoretical ChemistryGoethe University FrankfurtMax-von-Laue-Str. 760438FrankfurtGermany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical ChemistryGoethe University FrankfurtMax-von-Laue-Str. 760438FrankfurtGermany
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific ComputingHeidelberg UniversityIm Neuenheimer Feld 20569120HeidelbergGermany
| | - Alexander Heckel
- Institute of Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Lau-Str. 760438FrankfurtGermany
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12
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Cannon J, Tang S, Choi SK. Caged Oxime Reactivators Designed for the Light Control of Acetylcholinesterase Reactivation †. Photochem Photobiol 2021; 98:334-346. [PMID: 34558680 DOI: 10.1111/php.13530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/17/2021] [Accepted: 09/22/2021] [Indexed: 01/13/2023]
Abstract
Despite its promising role in the active control of biological functions by light, photocaging remains untested in acetylcholinesterase (AChE), a key enzyme in the cholinergic family. Here, we describe synthesis, photochemical properties and biochemical activities of two caged oxime compounds applied in the photocontrolled reactivation of the AChE inactivated by reactive organophosphate. Each of these consists of a photocleavable coumarin cage tethered to a known oxime reactivator for AChE that belongs in an either 2-(hydroxyimino)acetamide or pyridiniumaldoxime class. Of these, the first caged compound was able to successfully go through oxime uncaging upon irradiation at long-wavelength ultraviolet light (365 nm) or visible light (420 nm). It was further evaluated in AChE assays in vitro under variable light conditions to define its activity in the photocontrolled reactivation of paraoxon-inactivated AChE. This assay result showed its lack of activity in the dark but its induction of activity under light conditions only. In summary, this article reports a first class of light-activatable modulators for AChE and it offers assay methods and novel insights that help to achieve an effective design of caged compounds in the enzyme control.
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Affiliation(s)
- Jayme Cannon
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan Medical School, Ann Arbor, Michigan, USA.,Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Shengzhuang Tang
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan Medical School, Ann Arbor, Michigan, USA.,Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Seok Ki Choi
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan Medical School, Ann Arbor, Michigan, USA.,Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
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13
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Lechner VM, Nappi M, Deneny PJ, Folliet S, Chu JCK, Gaunt MJ. Visible-Light-Mediated Modification and Manipulation of Biomacromolecules. Chem Rev 2021; 122:1752-1829. [PMID: 34546740 DOI: 10.1021/acs.chemrev.1c00357] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chemically modified biomacromolecules-i.e., proteins, nucleic acids, glycans, and lipids-have become crucial tools in chemical biology. They are extensively used not only to elucidate cellular processes but also in industrial applications, particularly in the context of biopharmaceuticals. In order to enable maximum scope for optimization, it is pivotal to have a diverse array of biomacromolecule modification methods at one's disposal. Chemistry has driven many significant advances in this area, and especially recently, numerous novel visible-light-induced photochemical approaches have emerged. In these reactions, light serves as an external source of energy, enabling access to highly reactive intermediates under exceedingly mild conditions and with exquisite spatiotemporal control. While UV-induced transformations on biomacromolecules date back decades, visible light has the unmistakable advantage of being considerably more biocompatible, and a spectrum of visible-light-driven methods is now available, chiefly for proteins and nucleic acids. This review will discuss modifications of native functional groups (FGs), including functionalization, labeling, and cross-linking techniques as well as the utility of oxidative degradation mediated by photochemically generated reactive oxygen species. Furthermore, transformations at non-native, bioorthogonal FGs on biomacromolecules will be addressed, including photoclick chemistry and DNA-encoded library synthesis as well as methods that allow manipulation of the activity of a biomacromolecule.
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Affiliation(s)
- Vivian M Lechner
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Manuel Nappi
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Patrick J Deneny
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Sarah Folliet
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - John C K Chu
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Matthew J Gaunt
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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14
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Le Bescont J, Mouawad L, Boddaert T, Bombard S, Piguel S. Photoactivatable Small‐Molecule Inhibitors for Light‐Controlled TAM Kinase Activity. CHEMPHOTOCHEM 2021. [DOI: 10.1002/cptc.202100131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Julie Le Bescont
- Institut Curie Université PSL CNRS UMR 9187 INSERM U1196 Chimie et Modélisation pour la Biologie du Cancer 91405 Orsay France
- Université Paris-Saclay CNRS UMR 9187 INSERM U1196 Chimie et Modélisation pour la Biologie du Cancer 91405 Orsay France
| | - Liliane Mouawad
- Institut Curie Université PSL CNRS UMR 9187 INSERM U1196 Chimie et Modélisation pour la Biologie du Cancer 91405 Orsay France
- Université Paris-Saclay CNRS UMR 9187 INSERM U1196 Chimie et Modélisation pour la Biologie du Cancer 91405 Orsay France
| | - Thomas Boddaert
- Université Paris-Saclay CNRS UMR 8182 ICMMO CP3A Organic Synthesis Group 91405 Orsay France
| | - Sophie Bombard
- Institut Curie Université PSL CNRS UMR 9187 INSERM U1196 Chimie et Modélisation pour la Biologie du Cancer 91405 Orsay France
- Université Paris-Saclay CNRS UMR 9187 INSERM U1196 Chimie et Modélisation pour la Biologie du Cancer 91405 Orsay France
| | - Sandrine Piguel
- Institut Curie Université PSL CNRS UMR 9187 INSERM U1196 Chimie et Modélisation pour la Biologie du Cancer 91405 Orsay France
- Université Paris-Saclay CNRS UMR 9187 INSERM U1196 Chimie et Modélisation pour la Biologie du Cancer 91405 Orsay France
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15
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Abstract
DNA-based Boolean logic gates (for example, AND, OR, and NOT) can be assembled into complex computational circuits that generate an output signal in response to specific patterns of oligonucleotide inputs. However, the fundamental nature of NOT gates, which convert the absence of an input into an output, makes their implementation within DNA-based circuits difficult. Premature execution of a NOT gate before completion of its upstream computation introduces an irreversible error into the circuit. By utilizing photocaging groups, we developed a novel DNA gate design that prevents gate function until irradiation at a certain time point. Optical activation provides temporal control over circuit performance by preventing premature computation and is orthogonal to all other components of DNA computation devices. Using this approach, we designed NAND and NOR logic gates that respond to synthetic microRNA sequences. We further demonstrate the utility of the NOT gate within multilayer circuits in response to a specific pattern of four microRNAs.
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Affiliation(s)
- Cole Emanuelson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Anirban Bardhan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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16
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Huang F, Chen M, Zhou Z, Duan R, Xia F, Willner I. Spatiotemporal patterning of photoresponsive DNA-based hydrogels to tune local cell responses. Nat Commun 2021; 12:2364. [PMID: 33888708 PMCID: PMC8062675 DOI: 10.1038/s41467-021-22645-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 03/25/2021] [Indexed: 12/12/2022] Open
Abstract
Understanding the spatiotemporal effects of surface topographies and modulated stiffness and anisotropic stresses of hydrogels on cell growth remains a biophysical challenge. Here we introduce the photolithographic patterning or two-photon laser scanning confocal microscopy patterning of a series of o-nitrobenzylphosphate ester nucleic acid-based polyacrylamide hydrogel films generating periodically-spaced circular patterned domains surrounded by continuous hydrogel matrices. The patterning processes lead to guided modulated stiffness differences between the patterned domains and the surrounding hydrogel matrices, and to the selective functionalization of sub-regions of the films with nucleic acid anchoring tethers. HeLa cells are deposited on the circularly-shaped domains functionalized with the MUC-1 aptamers. Initiation of the hybridization chain reaction by nucleic acid tethers associated with the continuous hydrogel matrix results in stress-induced ordered orthogonal shape-changes on the patterned domains, leading to ordered shapes of cell aggregates bound to the patterns.
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Affiliation(s)
- 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, China.
| | - Mengxi Chen
- 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, China
| | - Zhixin Zhou
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ruilin 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, China
| | - 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, China.
| | - Itamar Willner
- Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, Israel.
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17
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Uhl E, Wolff F, Mangal S, Dube H, Zanin E. Light-Controlled Cell-Cycle Arrest and Apoptosis. Angew Chem Int Ed Engl 2020; 60:1187-1196. [PMID: 33035402 PMCID: PMC7839536 DOI: 10.1002/anie.202008267] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Indexed: 12/19/2022]
Abstract
Cell‐cycle interference by small molecules has widely been used to study fundamental biological mechanisms and to treat a great variety of diseases, most notably cancer. However, at present only limited possibilities exist for spatio‐temporal control of the cell cycle. Here we report on a photocaging strategy to reversibly arrest the cell cycle at metaphase or induce apoptosis using blue‐light irradiation. The versatile proteasome inhibitor MG132 is photocaged directly at the reactive aldehyde function effectively masking its biological activity. Upon irradiation reversible cell‐cycle arrest in the metaphase is demonstrated to take place in vivo. Similarly, apoptosis can efficiently be induced by irradiation of human cancer cells. With the developed photopharmacological approach spatio‐temporal control of the cell cycle is thus enabled with very high modulation, as caged MG132 shows no effect on proliferation in the dark. In addition, full compatibility of photo‐controlled uncaging with dynamic microscopy techniques in vivo is demonstrated. This visible‐light responsive tool should be of great value for biological as well as medicinal approaches in need of high‐precision targeting of the proteasome and thereby the cell cycle and apoptosis.
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Affiliation(s)
- Edgar Uhl
- Ludwig-Maximilians-Universität München, Department of Chemistry and Center for Integrated Protein Science CIPSM, Butenandtstr. 5-13, 81377, München, Germany
| | - Friederike Wolff
- Ludwig-Maximilians-Universität München, Center for Integrated Protein Science CIPSM, Department Biology II, Planegg-Martinsried, 82152, München, Germany
| | - Sriyash Mangal
- Ludwig-Maximilians-Universität München, Center for Integrated Protein Science CIPSM, Department Biology II, Planegg-Martinsried, 82152, München, Germany
| | - Henry Dube
- Ludwig-Maximilians-Universität München, Department of Chemistry and Center for Integrated Protein Science CIPSM, Butenandtstr. 5-13, 81377, München, Germany.,Current address: Friedrich-Alexander-Universität Erlangen-Nürnberg, Department of Chemistry and Pharmacy, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Esther Zanin
- Ludwig-Maximilians-Universität München, Center for Integrated Protein Science CIPSM, Department Biology II, Planegg-Martinsried, 82152, München, Germany
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18
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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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19
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Uhl E, Wolff F, Mangal S, Dube H, Zanin E. Light‐Controlled Cell‐Cycle Arrest and Apoptosis. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Edgar Uhl
- Ludwig-Maximilians-Universität München Department of Chemistry and Center for Integrated Protein Science CIPSM Butenandtstr. 5–13 81377 München Germany
| | - Friederike Wolff
- Ludwig-Maximilians-Universität München Center for Integrated Protein Science CIPSM Department Biology II Planegg-Martinsried 82152 München Germany
| | - Sriyash Mangal
- Ludwig-Maximilians-Universität München Center for Integrated Protein Science CIPSM Department Biology II Planegg-Martinsried 82152 München Germany
| | - Henry Dube
- Ludwig-Maximilians-Universität München Department of Chemistry and Center for Integrated Protein Science CIPSM Butenandtstr. 5–13 81377 München Germany
- Current address: Friedrich-Alexander-Universität Erlangen-Nürnberg Department of Chemistry and Pharmacy Nikolaus-Fiebiger-Str. 10 91058 Erlangen Germany
| | - Esther Zanin
- Ludwig-Maximilians-Universität München Center for Integrated Protein Science CIPSM Department Biology II Planegg-Martinsried 82152 München Germany
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20
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Sasaki M, Tran Bao Nguyen L, Yabumoto S, Nakagawa T, Abe M. Structural Transformation of the 2‐(
p
‐Aminophenyl)‐1‐hydroxyinden‐3‐ylmethyl Chromophore as a Photoremovable Protecting Group. CHEMPHOTOCHEM 2020. [DOI: 10.1002/cptc.202000149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Miyu Sasaki
- Department of Chemistry, Graduate School of Science Hiroshima University 1-3-1 Kagamiyama, Higashi-Hiroshima Hiroshima 739-8526 Japan
| | - Linh Tran Bao Nguyen
- Department of Chemistry, Graduate School of Science Hiroshima University 1-3-1 Kagamiyama, Higashi-Hiroshima Hiroshima 739-8526 Japan
| | | | | | - Manabu Abe
- Department of Chemistry, Graduate School of Science Hiroshima University 1-3-1 Kagamiyama, Higashi-Hiroshima Hiroshima 739-8526 Japan
- Hiroshima University Research Centre for Photo-Drug-Delivery Systems (HiU−P-DDS) Hiroshima University 1-3-1 Kagamiyama, Higashi-Hiroshima Hiroshima 739-8526 Japan
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21
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Chakrapani A, Vaňková Hausnerová V, Ruiz-Larrabeiti O, Pohl R, Krásný L, Hocek M. Photocaged 5-(Hydroxymethyl)pyrimidine Nucleoside Phosphoramidites for Specific Photoactivatable Epigenetic Labeling of DNA. Org Lett 2020; 22:9081-9085. [PMID: 33156631 DOI: 10.1021/acs.orglett.0c03462] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
5-Hydroxymethylcytosine and uracil are epigenetic nucleobases, but their biological roles are still unclear. We present the synthesis of 2-nitrobenzyl photocaged 5-hydroxymethyl-2'-deoxycytidine and uridine 3'-O-phosphoramidites and their use in automated solid-phase synthesis of oligonucleotides (ONs) modified at specific positions. The ONs were used as primers for PCR to construct DNA templates modified in the promoter region that allowed switching of transcription through photochemical uncaging.
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Affiliation(s)
- Aswathi Chakrapani
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000 Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843 Prague 2, Czech Republic
| | - Viola Vaňková Hausnerová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic
| | - Olatz Ruiz-Larrabeiti
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000 Prague 6, Czech Republic
| | - Libor Krásný
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000 Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843 Prague 2, Czech Republic
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22
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Nakad EA, Chaud J, Morville C, Bolze F, Specht A. Monitoring of uncaging processes by designing photolytical reactions. Photochem Photobiol Sci 2020; 19:1122-1133. [PMID: 32756690 DOI: 10.1039/d0pp00169d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The use of photolabile protecting groups (PPGs) has been growing in emphasis for decades, and nowadays they enable cutting-edge results in numerous fields ranging from organic synthesis to neurosciences. PPGs are chemical entities that can be conjugated to a biomolecule to hide its biological activity, forming a stable so called "caged compound". This conjugate can be simply cleaved by light and therefore, the functionality of the biomolecule is restored with the formation of a PPG by-product. However, there is a sizeable need for PPGs that are able to quantify the "uncaging" process. In this review, we will discuss several strategies leading to an acute quantification of the uncaging events by fluorescence. In particular, we will focus on how molecular engineering of PPG could open new opportunities by providing easy access to photoactivation protocols.
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Affiliation(s)
- E Abou Nakad
- Laboratoire de Conception et Application de Molécules Bioactives, Equipe de Chimie et Neurobiologie Moléculaire, Université de Strasbourg, CNRS, CAMB UMR 7199, F-67000, Strasbourg, France
| | - J Chaud
- Laboratoire de Conception et Application de Molécules Bioactives, Equipe de Chimie et Neurobiologie Moléculaire, Université de Strasbourg, CNRS, CAMB UMR 7199, F-67000, Strasbourg, France
| | - C Morville
- Laboratoire de Conception et Application de Molécules Bioactives, Equipe de Chimie et Neurobiologie Moléculaire, Université de Strasbourg, CNRS, CAMB UMR 7199, F-67000, Strasbourg, France
| | - F Bolze
- Laboratoire de Conception et Application de Molécules Bioactives, Equipe de Chimie et Neurobiologie Moléculaire, Université de Strasbourg, CNRS, CAMB UMR 7199, F-67000, Strasbourg, France.
| | - A Specht
- Laboratoire de Conception et Application de Molécules Bioactives, Equipe de Chimie et Neurobiologie Moléculaire, Université de Strasbourg, CNRS, CAMB UMR 7199, F-67000, Strasbourg, France
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23
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Lee M, Rizzo R, Surman F, Zenobi-Wong M. Guiding Lights: Tissue Bioprinting Using Photoactivated Materials. Chem Rev 2020; 120:10950-11027. [DOI: 10.1021/acs.chemrev.0c00077] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Mihyun Lee
- Tissue Engineering + Biofabrication HPL J22, ETH Zürich, Otto-Stern-Weg 7, 8093 Zürich, Switzerland
| | - Riccardo Rizzo
- Tissue Engineering + Biofabrication HPL J22, ETH Zürich, Otto-Stern-Weg 7, 8093 Zürich, Switzerland
| | - František Surman
- Tissue Engineering + Biofabrication HPL J22, ETH Zürich, Otto-Stern-Weg 7, 8093 Zürich, Switzerland
| | - Marcy Zenobi-Wong
- Tissue Engineering + Biofabrication HPL J22, ETH Zürich, Otto-Stern-Weg 7, 8093 Zürich, Switzerland
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24
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Moroz-Omori E, Satyapertiwi D, Ramel MC, Høgset H, Sunyovszki IK, Liu Z, Wojciechowski JP, Zhang Y, Grigsby CL, Brito L, Bugeon L, Dallman MJ, Stevens MM. Photoswitchable gRNAs for Spatiotemporally Controlled CRISPR-Cas-Based Genomic Regulation. ACS CENTRAL SCIENCE 2020; 6:695-703. [PMID: 32490186 PMCID: PMC7256956 DOI: 10.1021/acscentsci.9b01093] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Indexed: 05/06/2023]
Abstract
The recently discovered CRISPR-Cas gene editing system and its derivatives have found numerous applications in fundamental biology research and pharmaceutical sciences. The need for precise external control over the gene editing and regulatory events has driven the development of inducible CRISPR-Cas systems. While most of the light-controllable CRISPR-Cas systems are based on protein engineering, we developed an alternative synthetic approach based on modification of crRNA/tracrRNA duplex (guide RNA or gRNA) with photocaging groups, preventing the gRNA from recognizing its genome target sequence until its deprotection is induced within seconds of illumination. This approach relies on a straightforward solid-phase synthesis of the photocaged gRNAs, with simpler purification and characterization processes in comparison to engineering a light-responsive protein. We have demonstrated the feasibility of photocaging of gRNAs and light-mediated DNA cleavage upon brief exposure to light in vitro. We have achieved light-mediated spatiotemporally resolved gene editing as well as gene activation in cells, whereas photocaged gRNAs showed virtually no detectable gene editing or activation in the absence of light irradiation. Finally, we have applied this system to spatiotemporally control gene editing in zebrafish embryos in vivo, enabling the use of this strategy for developmental biology and tissue engineering applications.
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Affiliation(s)
- Elena
V. Moroz-Omori
- Department
of Materials, Department of Bioengineering and Institute of Biomedical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Dwiantari Satyapertiwi
- Department
of Materials, Department of Bioengineering and Institute of Biomedical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Marie-Christine Ramel
- Department
of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Håkon Høgset
- Department
of Materials, Department of Bioengineering and Institute of Biomedical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Ilona K. Sunyovszki
- Department
of Materials, Department of Bioengineering and Institute of Biomedical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
- Division
of Cardiovascular Sciences, Myocardial Function, National Heart and
Lung Institute, Imperial College London, London W12 0NN, United Kingdom
| | - Ziqian Liu
- Department
of Materials, Department of Bioengineering and Institute of Biomedical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Jonathan P. Wojciechowski
- Department
of Materials, Department of Bioengineering and Institute of Biomedical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Yueyun Zhang
- Department
of Materials, Department of Bioengineering and Institute of Biomedical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Christopher L. Grigsby
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Liliana Brito
- Department
of Materials, Department of Bioengineering and Institute of Biomedical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
- Division
of Cardiovascular Sciences, Myocardial Function, National Heart and
Lung Institute, Imperial College London, London W12 0NN, United Kingdom
| | - Laurence Bugeon
- Department
of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Margaret J. Dallman
- Department
of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Molly M. Stevens
- Department
of Materials, Department of Bioengineering and Institute of Biomedical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 65, Sweden
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25
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Tang S, Cannon J, Yang K, Krummel MF, Baker JR, Choi SK. Spacer-Mediated Control of Coumarin Uncaging for Photocaged Thymidine. J Org Chem 2020; 85:2945-2955. [PMID: 32020803 PMCID: PMC7293860 DOI: 10.1021/acs.joc.9b02617] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Despite its importance in the design of photocaged molecules, less attention is focused on linker chemistry than the cage itself. Here, we describe unique uncaging properties displayed by two coumarin-caged thymidine compounds, each conjugated with (2) or without (1) an extended, self-immolative spacer. Photolysis of 1 using long-wavelength UVA (365 nm) or visible (420, 455 nm) light led to the release of free thymidine along with the competitive generation of a thymidine-bearing recombination product. The occurrence of this undesired side reaction, which is previously unreported, was not present with the photolysis of 2, which released thymidine exclusively with higher quantum efficiency. We propose that the spatial separation between the cage and the substrate molecule conferred by the extended linker can play a critical role in circumventing this unproductive reaction. This report reinforces the importance of linker selection in the design of coumarin-caged oligonucleosides and other conjugates.
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Affiliation(s)
- Shengzhuang Tang
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, Ann Arbor, Michigan 48109, United States of America
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States of America
| | - Jayme Cannon
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, Ann Arbor, Michigan 48109, United States of America
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States of America
| | - Kelly Yang
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States of America
| | - Matthew F. Krummel
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, HSW512, San Francisco, California 94143, United States of America
| | - James R. Baker
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, Ann Arbor, Michigan 48109, United States of America
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States of America
| | - Seok Ki Choi
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, Ann Arbor, Michigan 48109, United States of America
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States of America
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26
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Feeney MJ, Thomas SW. Combining Top-Down and Bottom-Up with Photodegradable Layer-by-Layer Films. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:13791-13804. [PMID: 31487186 DOI: 10.1021/acs.langmuir.9b02005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Layer-by-layer (LbL) self-assembly of polymer coatings is a bottom-up fabrication technique with broad applicability across a wide range of materials and applications that require control over interfacial properties. While most LbL coatings are chemically uniform in directions both tangent and perpendicular to their substrate, control over the properties of surface coatings as a function of space can enhance their function. To contribute to this rapidly advancing field, our group has focused on the top-down spatiotemporal control possible with photochemically reactive LbL coatings, harnessed through charge-shifting polyelectrolytes enabled by photocleavable ester pendants. The photolysis of the photocleavable esters degrades LbL films containing these polyelectrolytes. The chemical structures of the photocleavable groups dictate the wavelengths responsible for disrupting these coatings, ranging from ultraviolet to near-infrared in our work. In addition, spatially segregating reactive groups into "compartments" within LbL films has enabled us to fabricate reactive free-standing polymer films and multiheight photopatterned coatings. Overall, by combining bottom-up and top-down approaches, photoreactive LbL films enable precise control over the interfacial properties of polymer and composite coatings.
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Affiliation(s)
- Matthew J Feeney
- Department of Chemistry , Tufts University , 62 Talbot Avenue , Medford , Massachusetts 02155 , United States
| | - Samuel W Thomas
- Department of Chemistry , Tufts University , 62 Talbot Avenue , Medford , Massachusetts 02155 , United States
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27
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Dorsey PJ, Rubanov M, Wang W, Schulman R. Digital Maskless Photolithographic Patterning of DNA-Functionalized Poly(ethylene glycol) Diacrylate Hydrogels with Visible Light Enabling Photodirected Release of Oligonucleotides. ACS Macro Lett 2019; 8:1133-1140. [PMID: 35619455 DOI: 10.1021/acsmacrolett.9b00450] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Soft biomaterials possessing structural hierarchy have growing applications in lab-on-chip devices, artificial tissues, and micromechanical and chemomechanical systems. The ability to integrate sets of biomolecules, specifically DNA, within hydrogel substrates at precise locations could offer the potential to form and modulate complex biochemical processes with DNA-based molecular switches in such materials and provide a means of creating dynamic spatial patterns, thus enabling spatiotemporal control of a wide array of reaction-diffusion phenomena prevalent in biological systems. Here we develop a means of photopatterning two-dimensional DNA-functionalized poly(ethylene glycol) diacrylate (PEGDA) hydrogel architectures with an aim toward these applications. While PEGDA photopatterning methods are well-established for the fabrication of hydrogels, including those containing oligonucleotides, the photoinitiators typically used have significant crosstalk with many UV-photoswitchable chemistries including nitrobenzyl derivatives. We demonstrate the digital photopatterning of PEGDA-co-DNA hydrogels using a blue light-absorbing (470 nm peak) photoinitiator system and macromer comprised of camphorquinone, triethanolamine, and poly(ethylene glycol) diacrylate (Mn = 575) that minimizes absorption in the UV-A wavelength range commonly used to trigger photoswitchable chemistries. We demonstrate this method using digital maskless photolithography within microfluidic devices that allows for the reliable construction of multidomain structures. The method achieves feature resolutions as small as 25 μm, and the resulting materials allow for lateral isotropic bulk diffusion of short single-stranded (ss) DNA oligonucleotides. Finally, we show how the use of these photoinitiators allows for orthogonal control of photopolymerization and UV-photoscission of acrylate-modified DNA containing a 1-(2-nitrophenyl) ethyl spacer to selectively cleave DNA from regions of a PEGDA substrate.
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28
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Müller P, Seyfried P, Frühauf A, Heckel A. Phosphodiester photo-tethers for the (multi-)cyclic conformational caging of oligonucleotides. Methods Enzymol 2019; 624:89-111. [PMID: 31370937 DOI: 10.1016/bs.mie.2019.04.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The ability to address the function of oligonucleotides with light is highly desirable since they are often used experimentally in the regulation of biological processes that need to be controlled in time, space and activation level. Here we present an extension of our initial approach of using photo-tethers that force single strands of nucleic acids into a circle, thus making them unable to form a duplex with a complementary DNA- or RNA-strand. Due to the persistence length a single strand can form a circle of, for example, 30 nucleotides, but a duplex cannot. We show that these new photo-tethers can also be easily installed on the phosphodiester backbone. This simplifies the approach considerably and leads to temporarily inhibited oligonucleotides that can only form a duplex after linearization by photoactivation.
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Affiliation(s)
- Patricia Müller
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Patrick Seyfried
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Anton Frühauf
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany.
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29
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Menzel JP, Feist F, Tuten B, Weil T, Blinco JP, Barner-Kowollik C. Light-Controlled Orthogonal Covalent Bond Formation at Two Different Wavelengths. Angew Chem Int Ed Engl 2019; 58:7470-7474. [PMID: 30916368 DOI: 10.1002/anie.201901275] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Indexed: 11/12/2022]
Abstract
We report light-induced reactions in a two-chromophore system capable of sequence-independent λ-orthogonal reactivity relying solely on the choice of wavelength and solvent. In a solution of water and acetonitrile, LED irradiation at λmax =285 nm leads to full conversion of 2,5-diphenyltetrazoles with N-ethylmaleimide to the pyrazoline ligation products. Simultaneously present o-methylbenzaldehyde thioethers are retained. Conversely, LED irradiation at λmax =382 nm is used to induce ligation of the o-methylbenzaldehydes in acetonitrile with N-ethylmaleimide via o-quinodimethanes, while 2,5-diphenyltetrazoles also present are retained. This unprecedented photochemical selectivity is achieved through control of the number and wavelength of incident photons as well as favorable optical properties and quantum yields of the reactants in their environment.
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Affiliation(s)
- Jan P Menzel
- School of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology (QUT), Brisbane, QLD, 4000, Australia
| | - Florian Feist
- School of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology (QUT), Brisbane, QLD, 4000, Australia.,Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Bryan Tuten
- School of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology (QUT), Brisbane, QLD, 4000, Australia
| | - Tanja Weil
- Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - James P Blinco
- School of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology (QUT), Brisbane, QLD, 4000, Australia.,Macromolecular Architectures, Institut für Technische Chemie und Polymerchemie, Karlsruhe Institute of Technology (KIT), Engesserstrasse 18, 76131, Karlsruhe, Germany
| | - Christopher Barner-Kowollik
- School of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology (QUT), Brisbane, QLD, 4000, Australia.,Macromolecular Architectures, Institut für Technische Chemie und Polymerchemie, Karlsruhe Institute of Technology (KIT), Engesserstrasse 18, 76131, Karlsruhe, Germany
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30
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Menzel JP, Feist F, Tuten B, Weil T, Blinco JP, Barner‐Kowollik C. Lichtinduzierte orthogonale Bildung kovalenter Bindungen durch zwei Wellenlängen. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901275] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jan P. Menzel
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) Brisbane QLD 4000 Australien
| | - Florian Feist
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) Brisbane QLD 4000 Australien
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| | - Bryan Tuten
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) Brisbane QLD 4000 Australien
| | - Tanja Weil
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| | - James P. Blinco
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) Brisbane QLD 4000 Australien
- Macromolecular Architectures Institut für Technische Chemie und Polymerchemie Karlsruher Institut für Technologie (KIT) Engesserstraße 18 76131 Karlsruhe Deutschland
| | - Christopher Barner‐Kowollik
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) Brisbane QLD 4000 Australien
- Macromolecular Architectures Institut für Technische Chemie und Polymerchemie Karlsruher Institut für Technologie (KIT) Engesserstraße 18 76131 Karlsruhe Deutschland
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31
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Abou Nakad E, Bolze F, Specht A. o-Nitrobenzyl photoremovable groups with fluorescence uncaging reporting properties. Org Biomol Chem 2019; 16:6115-6122. [PMID: 30094422 DOI: 10.1039/c8ob01330f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
o-Nitrobenzyl (o-NB) derivatives are the most widely applied photoremovable groups for the study of dynamic biological processes. By introducing different substituents to the benzylic position we were able to generate a fluorescence signal upon irradiation. This signal originates from the formation of a nitrosoketone by-product able to achieve a keto-enol tautomerism leading to pi-conjugated α-hydroxystilbene derivatives. These o-NB caging groups can be used to directly monitor the uncaging event by the release of a detectable fluorescent side-product.
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Affiliation(s)
- E Abou Nakad
- Laboratoire de Conception et Application de Molécules Bioactives, Equipe de Chimie et Neurobiologie Moléculaire, Université de Strasbourg, CNRS, CAMB UMR 7199, F-67000 Strasbourg, France.
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32
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Vaníková Z, Janoušková M, Kambová M, Krásný L, Hocek M. Switching transcription with bacterial RNA polymerase through photocaging, photorelease and phosphorylation reactions in the major groove of DNA. Chem Sci 2019; 10:3937-3942. [PMID: 31015933 PMCID: PMC6457204 DOI: 10.1039/c9sc00205g] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/01/2019] [Indexed: 12/14/2022] Open
Abstract
We report proof of principle biomimetic switching of transcription in vitro through non-natural chemical reactions in the major groove of DNA templates. Photocaged DNA templates containing nitrobenzyl-protected 5-hydroxymethyluracil or - cytosine permitted no transcription with E. coli RNA polymerase (OFF state). Their irradiation with 400 nm light resulted in DNA templates containing hydroxymethylpyrimidines, which switched transcription ON with a higher yield (250-350%) compared to non-modified DNA. Phosphorylation of templates containing 5-hydroxymethyluracil (but not 5-hydroxymethylcytosine) then turned transcription OFF again. It is the first step towards artificial bioorthogonal chemical epigenetics.
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Affiliation(s)
- Zuzana Vaníková
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nam. 2 , 16610 Prague 6 , Czech Republic . .,Department of Organic Chemistry , Faculty of Science , Charles University in Prague , Hlavova 8 , CZ-12843 Prague 2 , Czech Republic
| | - Martina Janoušková
- Dept. of Molecular Genetics of Bacteria , Institute of Microbiology , Czech Academy of Sciences , CZ-14220 Prague 4 , Czech Republic .
| | - Milada Kambová
- Dept. of Molecular Genetics of Bacteria , Institute of Microbiology , Czech Academy of Sciences , CZ-14220 Prague 4 , Czech Republic .
| | - Libor Krásný
- Dept. of Molecular Genetics of Bacteria , Institute of Microbiology , Czech Academy of Sciences , CZ-14220 Prague 4 , Czech Republic .
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo nam. 2 , 16610 Prague 6 , Czech Republic . .,Department of Organic Chemistry , Faculty of Science , Charles University in Prague , Hlavova 8 , CZ-12843 Prague 2 , Czech Republic
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33
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Boháčová S, Ludvíková L, Poštová Slavětínská L, Vaníková Z, Klán P, Hocek M. Protected 5-(hydroxymethyl)uracil nucleotides bearing visible-light photocleavable groups as building blocks for polymerase synthesis of photocaged DNA. Org Biomol Chem 2019; 16:1527-1535. [PMID: 29431832 DOI: 10.1039/c8ob00160j] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nucleosides, nucleotides and 2'-deoxyribonucleoside triphosphates (dNTPs) containing 5-(hydroxymethyl)uracil protected with photocleavable groups (2-nitrobenzyl-, 6-nitropiperonyl or 9-anthrylmethyl) were prepared and tested as building blocks for the polymerase synthesis of photocaged oligonucleotides and DNA. Photodeprotection (photorelease) reactions were studied in detail on model nucleoside monophosphates and their photoreaction quantum yields were determined. Photocaged dNTPs were then tested and used as substrates for DNA polymerases in primer extension or PCR. DNA probes containing photocaged or free 5-hydroxymethylU in the recognition sequence of restriction endonucleases were prepared and used for the study of photorelease of caged DNA by UV or visible light at different wavelengths. The nitropiperonyl-protected nucleotide was found to be a superior building block because the corresponding dNTP is a good substrate for DNA polymerases, and the protecting group is efficiently cleavable by irradiation by UV or visible light (up to 425 nm).
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Affiliation(s)
- Soňa Boháčová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic.
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34
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Frisch H, Bloesser FR, Barner‐Kowollik C. Controlling Chain Coupling and Single‐Chain Ligation by Two Colours of Visible Light. Angew Chem Int Ed Engl 2019; 58:3604-3609. [DOI: 10.1002/anie.201811541] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Hendrik Frisch
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) 2 George Street Brisbane QLD 4000 Australia
| | - Fabian R. Bloesser
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) 2 George Street Brisbane QLD 4000 Australia
| | - Christopher Barner‐Kowollik
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) 2 George Street Brisbane QLD 4000 Australia
- Macromolecular Architectures Institut für Technische Chemie und Polymerchemie Karlsruhe Institute of Technology (KIT) Engesserstr. 18 76131 Karlsruhe Germany
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35
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Frisch H, Bloesser FR, Barner‐Kowollik C. Kontrolle über Kettenvernetzung und Einzelkettenverknüpfung durch zwei Farben des sichtbaren Lichts. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201811541] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Hendrik Frisch
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) 2 George Street Brisbane QLD 4000 Australien
| | - Fabian R. Bloesser
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) 2 George Street Brisbane QLD 4000 Australien
| | - Christopher Barner‐Kowollik
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) 2 George Street Brisbane QLD 4000 Australien
- Macromolecular Architectures Institut für Technische Chemie und Polymerchemie Karlsruhe Institute of Technology (KIT) Engesserstraße 18 76131 Karlsruhe Deutschland
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36
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Huang F, Zhang J, Li T, Duan R, Xia F, Willner I. Two-Photon Lithographic Patterning of DNA-Coated Single-Microparticle Surfaces. NANO LETTERS 2019; 19:618-625. [PMID: 30585496 DOI: 10.1021/acs.nanolett.8b04975] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The spatially defined functionalization of microparticles with asymmetric shape-controlled nucleic acid patterns is a major challenge in materials science. The asymmetric patterning of microparticles is important to allow the controlled fabrication of crystalline lattices or controlled aggregates of microparticles. We present the combination of two-photon lithography and photocleavable o-nitrobenzylphosphate ester nucleic acid coating-modified microparticles as a versatile means to asymmetrically pattern single microparticle surfaces. The two-photon patterning of microparticles with predesigned nucleic acid structures of different sizes (700 nm to 2.8 μm) and shapes (circles, rings, triangles, and squares) are demonstrated. In addition, complex patterned domains consisting of two different asymmetric nucleic acid domains are fabricated by the controlled Z-positioning of the microparticles in respect to the two-photon irradiation sources. In addition, the two-photon lithographic patterning of the photocleavable DNA coating allows the generation of functional nucleic acid domains for the photostimulated activation of the catalytic hybridization assembly (CHA) of branched nucleic acid structures on single microparticles.
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Affiliation(s)
- Fujian Huang
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry , China University of Geosciences , Wuhan 430074 , China
| | - Juan Zhang
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry , China University of Geosciences , Wuhan 430074 , China
| | - Tao Li
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry , China University of Geosciences , Wuhan 430074 , China
| | - Ruilin Duan
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry , China University of Geosciences , Wuhan 430074 , China
| | - Fan Xia
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry , China University of Geosciences , Wuhan 430074 , China
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering , Huazhong University of Science and Technology , Wuhan 430074 , China
| | - Itamar Willner
- Institute of Chemistry, Center for Nanoscience and Nanotechnology , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
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37
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Yang L, Kim HB, Sul JY, Yeldell SB, Eberwine JH, Dmochowski IJ. Efficient Synthesis of Light-Triggered Circular Antisense Oligonucleotides Targeting Cellular Protein Expression. Chembiochem 2018; 19:1250-1254. [PMID: 29479781 PMCID: PMC6248878 DOI: 10.1002/cbic.201800012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Indexed: 02/06/2023]
Abstract
Light-activated ("caged") antisense oligonucleotides are powerful molecules for regulating gene expression at submicron spatial resolution through the focal modulation of endogenous cellular processes. Cyclized caged oligos are particularly promising structures because of their inherent stability and similarity to naturally occurring circular DNA and RNA molecules. Here, we introduce an efficient route for cyclizing an antisense oligodeoxynucleotide incorporating a photocleavable linker. Oligo cyclization was achieved for several sequences in nearly quantitative yields through intramolecular copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC). Caging stability and light activation were characterized by FRET efficiency, denaturing gel assay, and melting temperature measurements. Finally, a cyclized caged oligo was designed to target gfap, and it gave a tenfold reduction in glial fibrillary acidic protein upon photoactivation in astrocytes.
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Affiliation(s)
- Linlin Yang
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA, 19104-6323, USA
| | - Hyun Bum Kim
- Department of Pharmacology, University of Pennsylvania, 38 John Morgan Building, 3620 Hamilton Walk, Philadelphia, PA, 19104-6084, USA
| | - Jai-Yoon Sul
- Department of Pharmacology, University of Pennsylvania, 38 John Morgan Building, 3620 Hamilton Walk, Philadelphia, PA, 19104-6084, USA
| | - Sean B Yeldell
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA, 19104-6323, USA
| | - James H Eberwine
- Department of Pharmacology, University of Pennsylvania, 38 John Morgan Building, 3620 Hamilton Walk, Philadelphia, PA, 19104-6084, USA
| | - Ivan J Dmochowski
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA, 19104-6323, USA
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38
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Marschner DE, Frisch H, Offenloch JT, Tuten BT, Becer CR, Walther A, Goldmann AS, Tzvetkova P, Barner-Kowollik C. Visible Light [2 + 2] Cycloadditions for Reversible Polymer Ligation. Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b00613] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- David E. Marschner
- School of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology (QUT), 2 George Street, Brisbane, QLD 4000, Australia
- Macromolecular Architectures, Institut für Technische Chemie und Polymerchemie, Karlsruhe Institute of Technology (KIT), Engesserstr. 18, 76131 Karlsruhe, Germany
| | - Hendrik Frisch
- School of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology (QUT), 2 George Street, Brisbane, QLD 4000, Australia
| | - Janin T. Offenloch
- Macromolecular Architectures, Institut für Technische Chemie und Polymerchemie, Karlsruhe Institute of Technology (KIT), Engesserstr. 18, 76131 Karlsruhe, Germany
| | - Bryan T. Tuten
- School of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology (QUT), 2 George Street, Brisbane, QLD 4000, Australia
| | - C. Remzi Becer
- Polymer Chemistry Laboratory, School of Engineering and Materials Science, Queen Mary University of London (QMUL), E1 4NS London, United Kingdom
| | - Andreas Walther
- Institute for Macromolecular Chemistry, Stefan-Meier-Straße 31, University of Freiburg, 79104 Freiburg, Germany
| | - Anja S. Goldmann
- School of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology (QUT), 2 George Street, Brisbane, QLD 4000, Australia
- Macromolecular Architectures, Institut für Technische Chemie und Polymerchemie, Karlsruhe Institute of Technology (KIT), Engesserstr. 18, 76131 Karlsruhe, Germany
| | - Pavleta Tzvetkova
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 − Magnetic Resonance, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Christopher Barner-Kowollik
- School of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology (QUT), 2 George Street, Brisbane, QLD 4000, Australia
- Macromolecular Architectures, Institut für Technische Chemie und Polymerchemie, Karlsruhe Institute of Technology (KIT), Engesserstr. 18, 76131 Karlsruhe, Germany
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39
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Bowden S, Joseph C, Tang S, Cannon J, Francis E, Zhou M, Baker JR, Choi SK. Oritavancin Retains a High Affinity for a Vancomycin-Resistant Cell-Wall Precursor via Its Bivalent Motifs of Interaction. Biochemistry 2018; 57:2723-2732. [PMID: 29651842 DOI: 10.1021/acs.biochem.8b00187] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Despite its potent antibacterial activities against drug-resistant Gram-positive pathogens, oritavancin remains partially understood with respect to its primary mode of hydrogen bond interaction with a cell-wall peptide regarding the role of its lipophilic 4'-chlorobiphenyl moiety. Here we report a surface plasmon resonance (SPR) study performed in two cell-wall model surfaces, each prepared by immobilization with a vancomycin-susceptible Lys-d-Ala-d-Ala or vancomycin-resistant Lys-d-Ala-d-Lac peptide. Analysis of binding kinetics performed on the peptide surface showed that oritavancin bound ∼100-1000-fold more tightly than vancomycin on each model surface. Ligand competition experiments conducted by SPR and fluorescence spectroscopy provided evidence that such affinity enhancement can be attributed to its 4'-chlorobiphenyl moiety, possibly through a hydrophobic interaction that led to a gain of free energy with a contribution from enthalpy as suggested by a variable-temperature SPR experiment. On the basis of these findings, we propose a model for the bivalent motifs of interaction of oritavancin with cell-wall peptides, by which the drug molecule can retain a strong interaction even with the vancomycin-resistant peptide. In summary, this study advances our understanding of oritavancin and offers new insight into the significance of bivalent motifs in the design of glycopeptide antibiotics.
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40
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Hammer CA, Falahati K, Jakob A, Klimek R, Burghardt I, Heckel A, Wachtveitl J. Sensitized Two-Photon Activation of Coumarin Photocages. J Phys Chem Lett 2018; 9:1448-1453. [PMID: 29498870 DOI: 10.1021/acs.jpclett.7b03364] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Here we report the design of a new coumarin-based photolabile protecting group with enhanced two-photon absorption. Two-photon excited fluorescence (TPEF), color-tuned ultrafast transient absorption spectroscopy and infrared (IR) measurements are employed to photochemically characterize the newly designed ATTO 390-DEACM-cargo triad. Increased two-photon cross-section values of the novel cage in comparison to the widely used protecting group DEACM ([7-(diethylamino)coumarin-4-yl]methyl) are extracted from TPEF experiments. Femtosecond pump-probe experiments reveal a fast intramolecular charge transfer, a finding that is confirmed by quantum chemical calculations. Uncaging of glutamate is monitored in IR measurements by photodecarboxylation of the carbamate linker between the photolabile protecting group and the glutamate, showing the full functionality of the novel two-photon activatable photocage.
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41
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Liu JW, Wang YM, Zhang CH, Duan LY, Li Z, Yu RQ, Jiang JH. Tumor-Targeted Graphitic Carbon Nitride Nanoassembly for Activatable Two-Photon Fluorescence Imaging. Anal Chem 2018. [DOI: 10.1021/acs.analchem.7b05192] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Jin-Wen Liu
- Institute of Chemical Biology and Nanomedicine,
State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, People’s Republic of China
| | - Yu-Min Wang
- Institute of Chemical Biology and Nanomedicine,
State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, People’s Republic of China
| | - Chong-Hua Zhang
- Institute of Chemical Biology and Nanomedicine,
State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, People’s Republic of China
| | - Lu-Ying Duan
- Institute of Chemical Biology and Nanomedicine,
State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, People’s Republic of China
| | - Zheng Li
- Institute of Chemical Biology and Nanomedicine,
State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, People’s Republic of China
| | - Ru-Qin Yu
- Institute of Chemical Biology and Nanomedicine,
State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, People’s Republic of China
| | - Jian-Hui Jiang
- Institute of Chemical Biology and Nanomedicine,
State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, People’s Republic of China
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42
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Ankenbruck N, Courtney T, Naro Y, Deiters A. Optochemical Control of Biological Processes in Cells and Animals. Angew Chem Int Ed Engl 2018; 57:2768-2798. [PMID: 28521066 PMCID: PMC6026863 DOI: 10.1002/anie.201700171] [Citation(s) in RCA: 293] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 05/06/2017] [Indexed: 12/13/2022]
Abstract
Biological processes are naturally regulated with high spatial and temporal control, as is perhaps most evident in metazoan embryogenesis. Chemical tools have been extensively utilized in cell and developmental biology to investigate cellular processes, and conditional control methods have expanded applications of these technologies toward resolving complex biological questions. Light represents an excellent external trigger since it can be controlled with very high spatial and temporal precision. To this end, several optically regulated tools have been developed and applied to living systems. In this review we discuss recent developments of optochemical tools, including small molecules, peptides, proteins, and nucleic acids that can be irreversibly or reversibly controlled through light irradiation, with a focus on applications in cells and animals.
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Affiliation(s)
- Nicholas Ankenbruck
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - Taylor Courtney
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA
| | - Yuta Naro
- 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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43
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Goegan B, Terzi F, Bolze F, Cambridge S, Specht A. Synthesis and Characterization of Photoactivatable Doxycycline Analogues Bearing Two-Photon-Sensitive Photoremovable Groups Suitable for Light-Induced Gene Expression. Chembiochem 2018; 19:1341-1348. [DOI: 10.1002/cbic.201700628] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Bastien Goegan
- Laboratoire de Conception et Application de Molécules Bioactives; UMR 7199; CNRS; Faculté de Pharmacie; Université de Strasbourg; 74 Route du Rhin 67400 Illkirch France
| | - Firat Terzi
- University of Heidelberg; Department of Functional Neuroanatomy; Im Neuenheimer Feld 307 69120 Heidelberg Germany
| | - Frédéric Bolze
- Laboratoire de Conception et Application de Molécules Bioactives; UMR 7199; CNRS; Faculté de Pharmacie; Université de Strasbourg; 74 Route du Rhin 67400 Illkirch France
| | - Sidney Cambridge
- University of Heidelberg; Department of Functional Neuroanatomy; Im Neuenheimer Feld 307 69120 Heidelberg Germany
| | - Alexandre Specht
- Laboratoire de Conception et Application de Molécules Bioactives; UMR 7199; CNRS; Faculté de Pharmacie; Université de Strasbourg; 74 Route du Rhin 67400 Illkirch France
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Becker Y, Unger E, Fichte MAH, Gacek DA, Dreuw A, Wachtveitl J, Walla PJ, Heckel A. A red-shifted two-photon-only caging group for three-dimensional photorelease. Chem Sci 2018; 9:2797-2802. [PMID: 29732066 PMCID: PMC5914290 DOI: 10.1039/c7sc05182d] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 02/08/2018] [Indexed: 12/27/2022] Open
Abstract
Based on nitrodibenzofuran (NDBF) a new photocage with higher two-photon action cross section and red-shifted absorption was developed. Due to calculations, a dimethylamino functionality (DMA) was added at ring position 7. The uncaging of nucleobases after two-photon excitation (2PE) could be visualized via double-strand displacement in a hydrogel. With this assay we achieved three-dimensional photorelease of DMA-NDBF-protected DNA orthogonal to NDBF-protected strands. While being an excellent 2P-cage, DMA-NDBF is surprisingly stable under visible-light one-photon excitation (1PE). This case of excitation-specific photochemistry enhances the scope of orthogonal photoregulation.
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Affiliation(s)
- Yvonne Becker
- Goethe University Frankfurt , Institute for Organic Chemistry and Chemical Biology , Max-von-Laue-Str. 7 , 60438 Frankfurt , Germany .
| | - Erik Unger
- Goethe University Frankfurt , Institute for Organic Chemistry and Chemical Biology , Max-von-Laue-Str. 7 , 60438 Frankfurt , Germany .
| | - Manuela A H Fichte
- Goethe University Frankfurt , Institute for Organic Chemistry and Chemical Biology , Max-von-Laue-Str. 7 , 60438 Frankfurt , Germany .
| | - Daniel A Gacek
- Technical University Braunschweig , Institute for Physical and Theoretical Chemistry , Gaußstr. 17 , 38106 Braunschweig , Germany
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing (IWR) , Theoretical and Computational Chemistry , Im Neuenheimer Feld 205A , 69120 Heidelberg , Germany
| | - Josef Wachtveitl
- Goethe University Frankfurt , Institute for Physical and Theoretical Chemistry , Max-von-Laue-Str. 7 , 60438 Frankfurt , Germany
| | - Peter J Walla
- Technical University Braunschweig , Institute for Physical and Theoretical Chemistry , Gaußstr. 17 , 38106 Braunschweig , Germany
| | - Alexander Heckel
- Goethe University Frankfurt , Institute for Organic Chemistry and Chemical Biology , Max-von-Laue-Str. 7 , 60438 Frankfurt , Germany .
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Ankenbruck N, Courtney T, Naro Y, Deiters A. Optochemische Steuerung biologischer Vorgänge in Zellen und Tieren. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201700171] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Nicholas Ankenbruck
- Department of Chemistry University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
| | - Taylor Courtney
- Department of Chemistry University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
| | - Yuta Naro
- 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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Frisch H, Marschner DE, Goldmann AS, Barner‐Kowollik C. Wellenlängengesteuerte dynamische kovalente Chemie. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201709991] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Hendrik Frisch
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) 2 George Street QLD 4000 Brisbane Australien
| | - David E. Marschner
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) 2 George Street QLD 4000 Brisbane Australien
- Macromolecular Architectures Institut für Technische Chemie und Polymerchemie Karlsruher Institute of Technology (KIT) Engesserstraße 18 76131 Karlsruhe Deutschland
| | - Anja S. Goldmann
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) 2 George Street QLD 4000 Brisbane Australien
- Macromolecular Architectures Institut für Technische Chemie und Polymerchemie Karlsruher Institute of Technology (KIT) Engesserstraße 18 76131 Karlsruhe Deutschland
| | - Christopher Barner‐Kowollik
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) 2 George Street QLD 4000 Brisbane Australien
- Macromolecular Architectures Institut für Technische Chemie und Polymerchemie Karlsruher Institute of Technology (KIT) Engesserstraße 18 76131 Karlsruhe Deutschland
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47
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Frisch H, Marschner DE, Goldmann AS, Barner‐Kowollik C. Wavelength‐Gated Dynamic Covalent Chemistry. Angew Chem Int Ed Engl 2018; 57:2036-2045. [DOI: 10.1002/anie.201709991] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Hendrik Frisch
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) 2 George Street QLD 4000 Brisbane Australia
| | - David E. Marschner
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) 2 George Street QLD 4000 Brisbane Australia
- Macromolecular Architectures Institut für Technische Chemie und Polymerchemie Karlsruhe Institute of Technology (KIT) Engesserstrasse 18 76131 Karlsruhe Germany
| | - Anja S. Goldmann
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) 2 George Street QLD 4000 Brisbane Australia
- Macromolecular Architectures Institut für Technische Chemie und Polymerchemie Karlsruhe Institute of Technology (KIT) Engesserstrasse 18 76131 Karlsruhe Germany
| | - Christopher Barner‐Kowollik
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) 2 George Street QLD 4000 Brisbane Australia
- Macromolecular Architectures Institut für Technische Chemie und Polymerchemie Karlsruhe Institute of Technology (KIT) Engesserstrasse 18 76131 Karlsruhe Germany
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48
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Boháčová S, Vaníková Z, Poštová Slavětínská L, Hocek M. Protected 2′-deoxyribonucleoside triphosphate building blocks for the photocaging of epigenetic 5-(hydroxymethyl)cytosine in DNA. Org Biomol Chem 2018; 16:5427-5432. [DOI: 10.1039/c8ob01106k] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
2′-Deoxyribonucleoside triphosphates containing 5-(hydroxymethyl)cytosine protected with photocleavable groups were prepared and studied as substrates for the enzymatic synthesis of DNA containing a photocaged epigenetic 5hmC base.
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Affiliation(s)
- Soňa Boháčová
- Institute of Organic Chemistry and Biochemistry
- Czech Academy of Sciences
- CZ-16610 Prague 6
- Czech Republic
| | - Zuzana Vaníková
- Institute of Organic Chemistry and Biochemistry
- Czech Academy of Sciences
- CZ-16610 Prague 6
- Czech Republic
- Department of Organic Chemistry
| | - Lenka Poštová Slavětínská
- Institute of Organic Chemistry and Biochemistry
- Czech Academy of Sciences
- CZ-16610 Prague 6
- Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry
- Czech Academy of Sciences
- CZ-16610 Prague 6
- Czech Republic
- Department of Organic Chemistry
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49
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Dunkel P, Petit M, Dhimane H, Blanchard-Desce M, Ogden D, Dalko PI. Quinoline-Derived Two-Photon-Sensitive Octupolar Probes. ChemistryOpen 2017; 6:660-667. [PMID: 29046861 PMCID: PMC5641908 DOI: 10.1002/open.201700097] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Indexed: 01/05/2023] Open
Abstract
A systematic study on quinoline‐derived light sensitive probes, having third‐order rotational symmetry is presented. The electronically linked octupolar structures show considerably improved linear and nonlinear photophysical properties under one‐ and two‐photon irradiation conditions compared to the corresponding monomers. Photolysis of the three acetate derivatives shows strong structure dependency: whereas irradiation of the 6‐ and 7‐aminoquinoline derivatives resulted in fast intramolecular cyclization and only trace amounts of fragmentation products, the 8‐aminoquinoline derivative afforded clean and selective photolysis, with a sequential release of their acetate groups (δu[730]=0.67 GM).
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Affiliation(s)
- Petra Dunkel
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques Université Paris Descartes 45, rue des Saints-Pères 75270 Paris Cedex 06 France
| | - Morgane Petit
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques Université Paris Descartes 45, rue des Saints-Pères 75270 Paris Cedex 06 France
| | - Hamid Dhimane
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques Université Paris Descartes 45, rue des Saints-Pères 75270 Paris Cedex 06 France
| | - Mireille Blanchard-Desce
- Université de Bordeaux ISM (CNRS UMR5255) Bâtiment A12, 351, Cours de la Libération 33405 Talence Cedex France
| | - David Ogden
- Laboratoire de Physiologie Cérébrale Université Paris Descartes 45, rue des Saints-Pères 75270 Paris Cedex 06 France
| | - Peter I Dalko
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques Université Paris Descartes 45, rue des Saints-Pères 75270 Paris Cedex 06 France
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50
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Weyel XMM, Fichte MAH, Heckel A. A Two-Photon-Photocleavable Linker for Triggering Light-Induced Strand Breaks in Oligonucleotides. ACS Chem Biol 2017; 12:2183-2190. [PMID: 28678467 DOI: 10.1021/acschembio.7b00367] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We synthesized a two-photon-sensitive photocleavable linker based on the 7-diethylaminocoumarin structure and introduced it successfully into DNA strands. First, we demonstrated the inducibility of strand scissions upon irradiation at 365 nm. To verify and visualize the two-photon activity, we used a fluorescence assay based on a DNA strand displacement immobilized in a hydrogel. Additionally, we investigated its use in a new class of DNA decoys that are able to catch and release nuclear factor κB (NF-κB) by using light as an external trigger signal. In cell culture we were able to show the regulation of NF-κB-controlled transcription of green fluorescent protein.
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Affiliation(s)
- Xenia M M Weyel
- Institute of Organic Chemistry and Chemical Biology, Goethe-University Frankfurt , Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
| | - Manuela A H Fichte
- Institute of Organic Chemistry and Chemical Biology, Goethe-University Frankfurt , Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
| | - Alexander Heckel
- Institute of Organic Chemistry and Chemical Biology, Goethe-University Frankfurt , Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
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