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Hendrich CM, Reinschmidt M, Büllmann SM, Kolmar T, Jäschke A. Synthesis and Development of Inverse-Type Nucleoside Diarylethene Photoswitches. Chemistry 2024:e202401537. [PMID: 39045626 DOI: 10.1002/chem.202401537] [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: 04/19/2024] [Revised: 07/10/2024] [Accepted: 07/24/2024] [Indexed: 07/25/2024]
Abstract
Nucleosidic diarylethenes (DAEs) have evolved from an emerging class of photochromes into a well-established option for integrating photochromic functionalities into biological systems. However, a comprehensive understanding of how chemical structure influences their photochromic properties remains essential. While structural features, such as an inverse connection between the aryl residues and the ethene bridge, are well-documented for classical DAEs, their application to nucleosidic DAEs has been underexplored. In this study, we address this gap by developing three distinct types of inverse nucleosidic DAEs-semi-inverse thiophenes, semi-inverse uridines and inverse uridines. We successfully synthesized these compounds and conducted comprehensive analyses of their photostationary states, thermal stability, reversibility, and reaction quantum yields. Additionally, we conducted an in-depth comparison of their photochromic properties with those of their normal-type counterparts. Among the synthesized compounds, seven semi-inverse thiophenes exhibited the most promising characteristics. Notably, these compounds demonstrated excellent fatigue resistance, with up to 96 % retention of photochromic activity over 40 switching cycles, surpassing the performance of all comparable nucleosidic DAEs reported to date. These findings hold significant promise for future applications in various fields.
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Affiliation(s)
- Christoph M Hendrich
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Martin Reinschmidt
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Simon M Büllmann
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Theresa Kolmar
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
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2
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Okamura H, Yao T, Nagatsugi F. Reversible Control of Gene Expression by Guest-Modified Adenosines in a Cell-Free System via Host-Guest Interaction. J Am Chem Soc 2024; 146:18513-18523. [PMID: 38941287 PMCID: PMC11240562 DOI: 10.1021/jacs.4c04262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 06/30/2024]
Abstract
Gene expression technology has become an indispensable tool for elucidating biological processes and developing biotechnology. Cell-free gene expression (CFE) systems offer a fundamental platform for gene expression-based technology, in which the reversible and programmable control of transcription can expand its use in synthetic biology and medicine. This study shows that CFE can be controlled via the host-guest interaction of cucurbit[7]uril (CB[7]) with N6-guest-modified adenosines. These adenosine derivatives were conveniently incorporated into the DNA strand using a post-synthetic approach and formed a selective and stable base pair with complementary thymidine in DNA. Meanwhile, alternate addition of CB[7] and the exchanging guest molecule induced the reversible formation of a duplex structure through the formation and dissociation of a bulky complex on DNA. The kinetics of the reversibility was fine-tuned by changing the size of the modified guest moieties. When incorporated into a specific region of the T7 promoter sequence, the guest-modified adenosines enabled tight and reversible control of in vitro transcription and protein expression in the CFE system. This study marks the first utility of the host-guest interaction for gene expression control in the CFE system, opening new avenues for developing DNA-based technology, particularly for precise gene therapy and DNA nanotechnology.
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Affiliation(s)
- Hidenori Okamura
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
- Department
of Chemistry, Graduate School of Science, Tohoku University, Miyagi 980-8578, Japan
| | - Takeyuki Yao
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
- Department
of Chemistry, Graduate School of Science, Tohoku University, Miyagi 980-8578, Japan
| | - Fumi Nagatsugi
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
- Department
of Chemistry, Graduate School of Science, Tohoku University, Miyagi 980-8578, Japan
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3
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Bargstedt J, Reinschmidt M, Tydecks L, Kolmar T, Hendrich CM, Jäschke A. Photochromic Nucleosides and Oligonucleotides. Angew Chem Int Ed Engl 2024; 63:e202310797. [PMID: 37966433 DOI: 10.1002/anie.202310797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 11/16/2023]
Abstract
Photochromism is a reversible phenomenon wherein a material undergoes a change in color upon exposure to light. In organic photochromes, this effect often results from light-induced isomerization reactions, leading to alterations in either the spatial orientation or electronic properties of the photochrome. The incorporation of photochromic moieties into biomolecules, such as proteins or nucleic acids, has become a prevalent approach to render these biomolecules responsive to light stimuli. Utilizing light as a trigger for the manipulation of biomolecular structure and function offers numerous advantages compared to other stimuli, such as chemical or electrical treatments, due to its non-invasive nature. Consequently, light proves particularly advantageous in cellular and tissue applications. In this review, we emphasize recent advancements in the field of photochromic nucleosides and oligonucleotides. We provide an overview of the design principles of different classes of photochromes, synthetic strategies, critical analytical challenges, as well as structure-property relationships. The applications of photochromic nucleic acid derivatives encompass diverse domains, ranging from the precise photoregulation of gene expression to the controlled modulation of the three-dimensional structures of oligonucleotides and the development of DNA-based fluorescence modulators. Moreover, we present a future perspective on potential modifications and applications.
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Affiliation(s)
- Jörn Bargstedt
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Martin Reinschmidt
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Leon Tydecks
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Theresa Kolmar
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Christoph M Hendrich
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
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4
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Qiu S, Frawley AT, Leslie KG, Anderson HL. How do donor and acceptor substituents change the photophysical and photochemical behavior of dithienylethenes? The search for a water-soluble visible-light photoswitch. Chem Sci 2023; 14:9123-9135. [PMID: 37655022 PMCID: PMC10466371 DOI: 10.1039/d3sc01458d] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/28/2023] [Indexed: 09/02/2023] Open
Abstract
Dithienylethenes are a type of diarylethene and they constitute one of the most widely studied classes of photoswitch, yet there have been no systematic studies of how electron-donor or -acceptor substituents affect their properties. Here we report eight dithienylethenes bearing push-push, pull-pull and push-pull substitution patterns with different lengths of conjugation in the backbone and investigate their photophysical and photochemical properties. Donor-acceptor interactions in the closed forms of push-pull dithienylethenes shift their absorption spectra into the near-infrared region (λmax ≈ 800 nm). The push-pull systems also exhibit low quantum yields for photochemical electrocyclization, and computational studies indicate that this can be attributed to stabilization of the parallel, rather than anti-parallel, conformations. The pull-pull systems have the highest quantum yields for switching in both directions, ring-closure and ring-opening. The chloride salt of a pull-pull DTE, with alkynes on both arms, is the first water-soluble dithienylethene that can achieve >95% photostationary state distribution in both directions with visible light. It has excellent fatigue resistance: in aqueous solution on irradiation at 365 nm, the photochemical quantum yields for switching and decomposition are 0.15 and 2.6 × 10-5 respectively, i.e. decomposition is more than 5000 times slower than photoswitching. These properties make it a promising candidate for biological applications such as super-resolution microscopy and photopharmacology.
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Affiliation(s)
- Sili Qiu
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford Oxford OX1 3TA UK
| | - Andrew T Frawley
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford Oxford OX1 3TA UK
| | - Kathryn G Leslie
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford Oxford OX1 3TA UK
| | - Harry L Anderson
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford Oxford OX1 3TA UK
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5
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Büllmann SM, Kolmar T, Zorn NF, Zaumseil J, Jäschke A. A DNA-Based Two-Component Excitonic Switch Utilizing High-Performance Diarylethenes. Angew Chem Int Ed Engl 2022; 61:e202117735. [PMID: 35076154 PMCID: PMC9305942 DOI: 10.1002/anie.202117735] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Indexed: 11/13/2022]
Abstract
Nucleosidic diarylethenes (DAEs) are an emerging class of photochromes but have rarely been used in materials science. Here, we have developed doubly methylated DAEs derived from 2'-deoxyuridine with high thermal stability and fatigue resistance. These new photoswitches not only outperform their predecessors but also rival classical non-nucleosidic DAEs. To demonstrate the utility of these new DAEs, we have designed an all-optical excitonic switch consisting of two oligonucleotides: one strand containing a fluorogenic double-methylated 2'-deoxyuridine as a fluorescence donor and the other a tricyclic cytidine (tC) as acceptor, which together form a highly efficient conditional Förster-Resonance-Energy-Transfer (FRET) pair. The system was operated in liquid and solid phases and showed both strong distance- and orientation-dependent photochromic FRET. The superior ON/OFF contrast was maintained over up to 100 switching cycles, with no detectable fatigue.
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Affiliation(s)
- Simon M. Büllmann
- Institute of Pharmacy and Molecular BiotechnologyHeidelberg UniversityIm Neuenheimer Feld 36469120HeidelbergGermany
| | - Theresa Kolmar
- Institute of Pharmacy and Molecular BiotechnologyHeidelberg UniversityIm Neuenheimer Feld 36469120HeidelbergGermany
| | - Nicolas F. Zorn
- Institute for Physical ChemistryHeidelberg UniversityIm Neuenheimer Feld 25369120HeidelbergGermany
| | - Jana Zaumseil
- Institute for Physical ChemistryHeidelberg UniversityIm Neuenheimer Feld 25369120HeidelbergGermany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular BiotechnologyHeidelberg UniversityIm Neuenheimer Feld 36469120HeidelbergGermany
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6
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Büllmann SM, Kolmar T, Zorn NF, Zaumseil J, Jäschke A. Ein DNA‐basierter exzitonischer Zweikomponenten‐Schalter auf der Grundlage von Hochleistungs‐Diarylethenen. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202117735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Simon M. Büllmann
- Institut für Pharmazie und Molekulare Biotechnologie Universität Heidelberg Im Neuenheimer Feld 364 69120 Heidelberg Deutschland
| | - Theresa Kolmar
- Institut für Pharmazie und Molekulare Biotechnologie Universität Heidelberg Im Neuenheimer Feld 364 69120 Heidelberg Deutschland
| | - Nicolas F. Zorn
- Physikalisch-Chemisches Institut Universität Heidelberg Im Neuenheimer Feld 253 69120 Heidelberg Deutschland
| | - Jana Zaumseil
- Physikalisch-Chemisches Institut Universität Heidelberg Im Neuenheimer Feld 253 69120 Heidelberg Deutschland
| | - Andres Jäschke
- Institut für Pharmazie und Molekulare Biotechnologie Universität Heidelberg Im Neuenheimer Feld 364 69120 Heidelberg Deutschland
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7
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Verchozina YA, Lvov AG. Effect of incorporation of silole and phosphole heterocycles into photoswitchable diarylethenes. J Organomet Chem 2022. [DOI: 10.1016/j.jorganchem.2021.122151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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8
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Kolmar T, Becker A, Pfretzschner RA, Lelke A, Jäschke A. Development of Red-Shifted and Fluorogenic Nucleoside and Oligonucleotide Diarylethene Photoswitches. Chemistry 2021; 27:17386-17394. [PMID: 34519390 PMCID: PMC9298058 DOI: 10.1002/chem.202103133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Indexed: 12/21/2022]
Abstract
The reversible modulation of fluorescence signals by light is of high interest for applications in super‐resolution microscopy, especially on the DNA level. In this article we describe the systematic variation of the core structure in nucleoside‐based diarylethenes (DAEs), in order to generate intrinsically fluorescent photochromes. The introduction of aromatic bridging units resulted in a bathochromic shift of the visible absorption maximum of the closed‐ring form, but caused reduced thermal stability and switching efficiency. The replacement of the thiophene aryl unit by thiazol improved the thermal stability, whereas the introduction of a benzothiophene unit led to inherent and modulatable turn‐off fluorescence. This feature was further optimized by introducing a fluorescent indole nucleobase into the DAE core, resulting in an effective photoswitch with a fluorescence quantum yield of 0.0166 and a fluorescence turn‐off factor of 3.2. The site‐specific incorporation into an oligonucleotide resulted in fluorescence‐switchable DNA with high cyclization quantum yields and switching efficiency, which may facilitate future applications.
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Affiliation(s)
- Theresa Kolmar
- Institute of Pharmacy and Molecular Biotechnology, Ruprecht-Karls-Universität-Heidelberg, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Antonia Becker
- Institute of Pharmacy and Molecular Biotechnology, Ruprecht-Karls-Universität-Heidelberg, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Ronja A Pfretzschner
- Institute of Pharmacy and Molecular Biotechnology, Ruprecht-Karls-Universität-Heidelberg, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Alina Lelke
- Institute of Pharmacy and Molecular Biotechnology, Ruprecht-Karls-Universität-Heidelberg, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology, Ruprecht-Karls-Universität-Heidelberg, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
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9
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Becht S, Sen R, Büllmann SM, Dreuw A, Jäschke A. "Click-switch" - one-step conversion of organic azides into photochromic diarylethenes for the generation of light-controlled systems. Chem Sci 2021; 12:11593-11603. [PMID: 34667559 PMCID: PMC8447918 DOI: 10.1039/d1sc02526k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/27/2021] [Indexed: 01/10/2023] Open
Abstract
Diarylethenes (DAEs) are an established class of photochromic molecules, but their effective incorporation into pre-existing targets is synthetically difficult. Here we describe a new class of DAEs in which one of the aryl rings is a 1,2,3-triazole that is formed by “click” chemistry between an azide on the target and a matching alkyne–cyclopentene–thiophene component. This late-stage zero-length linking allows for tight integration of the DAE with the target, thereby increasing the chances for photomodulation of target functions. Nineteen different DAEs were synthesized and their properties investigated. All showed photochromism. Electron-withdrawing groups, and in particular −M-substituents at the triazole and/or thiophene moiety resulted in DAEs with high photo- and thermostability. Further, the chemical nature of the cyclopentene bridge had a strong influence on the behaviour upon UV light irradiation. Incorporation of perfluorinated cyclopentene led to compounds with high photo- and thermostability, but the reversible photochromic reaction was restricted to halogenated solvents. Compounds containing the perhydrogenated cyclopentene bridge, on the other hand, allowed the reversible photochromic reaction in a wide range of solvents, but had on average lower photo- and thermostabilities. The combination of the perhydrocyclopentene bridge and electron-withdrawing groups resulted in a DAE with improved photostability and no solvent restriction. Quantum chemical calculations helped to identify the photoproducts formed in halogenated as well as non-halogenated solvents. For two optimized DAE photoswitches, photostationary state composition and reaction quantum yields were determined. These data revealed efficient photochemical ring closure and opening. We envision applications of these new photochromic diarylethenes in photonics, nanotechnology, photobiology, photopharmacology and materials science. New photochromic diarylethenes are reported in which one aryl ring is a 1,2,3-triazole that is formed by “click” chemistry between an azide on the target and a matching alkyne–cyclopentene–thiophene component.![]()
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Affiliation(s)
- Steffy Becht
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Reena Sen
- Theoretical and Computational Chemistry, Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University Im Neuenheimer Feld 205A 69120 Heidelberg Germany
| | - Simon M Büllmann
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Andreas Dreuw
- Theoretical and Computational Chemistry, Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University Im Neuenheimer Feld 205A 69120 Heidelberg Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University Im Neuenheimer Feld 364 69120 Heidelberg Germany
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