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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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2
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Zhang L, Xie X, Djokovic N, Nikolic K, Kosenkov D, Abendroth F, Vázquez O. Reversible Control of RNA Splicing by Photoswitchable Small Molecules. J Am Chem Soc 2023. [PMID: 37276581 DOI: 10.1021/jacs.3c03275] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Dynamics are intrinsic to both RNA function and structure. Yet, the available means to precisely provide RNA-based processes with spatiotemporal resolution are scarce. Here, our work pioneers a reversible approach to regulate RNA splicing within primary patient-derived cells by synthetic photoswitches. Our small molecule enables conditional real-time control at mRNA and protein levels. NMR experiments, together with theoretical calculations, photochemical characterization, fluorescence polarization measurements, and living cell-based assays, confirmed light-dependent exon inclusion as well as an increase in the target functional protein. Therefore, we first demonstrated the potential of photopharmacology modulation in splicing, tweaking the current optochemical toolkit. The timeliness on the consolidation of RNA research as the driving force toward therapeutical innovation holds the promise that our approach will contribute to redrawing the vision of RNA.
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Affiliation(s)
- Lei Zhang
- Department of Chemistry, University of Marburg, Marburg, D-35043, Germany
| | - Xiulan Xie
- Department of Chemistry, University of Marburg, Marburg, D-35043, Germany
| | - Nemanja Djokovic
- Department of Pharmaceutical Chemistry, University of Belgrade, Belgrade, 11000, Serbia
| | - Katarina Nikolic
- Department of Pharmaceutical Chemistry, University of Belgrade, Belgrade, 11000, Serbia
| | - Dmitri Kosenkov
- Department of Chemistry and Physics, Monmouth University, West Long Branch, New Jersey 07764, United States
| | - Frank Abendroth
- Department of Chemistry, University of Marburg, Marburg, D-35043, Germany
| | - Olalla Vázquez
- Department of Chemistry, University of Marburg, Marburg, D-35043, Germany
- Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, Marburg, D-35043, Germany
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3
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Ishii S, Murayama K, Sada K, Asanuma H, Kakugo A. Unexpected Dissociation of Photoresponsive UV-ON DNA Carrying p-tert-Butyl Azobenzene under UV Light Irradiation. CHEM LETT 2022. [DOI: 10.1246/cl.210788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Satsuki Ishii
- Graduate School of Chemical Sciences & Engineering, Hokkaido University, Kita 10 Nishi 8, Sapporo, 060-0810, Japan
| | - Keiji Murayama
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Aichi, 464-8603, Japan
| | - Kazuki Sada
- Graduate School of Chemical Sciences & Engineering, Hokkaido University, Kita 10 Nishi 8, Sapporo, 060-0810, Japan
- Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Sapporo, 060-0810, Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Aichi, 464-8603, Japan
| | - Akira Kakugo
- Graduate School of Chemical Sciences & Engineering, Hokkaido University, Kita 10 Nishi 8, Sapporo, 060-0810, Japan
- Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Sapporo, 060-0810, Japan
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4
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Wang C, O'Hagan MP, Li Z, Zhang J, Ma X, Tian H, Willner I. Photoresponsive DNA materials and their applications. Chem Soc Rev 2022; 51:720-760. [PMID: 34985085 DOI: 10.1039/d1cs00688f] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Photoresponsive nucleic acids attract growing interest as functional constituents in materials science. Integration of photoisomerizable units into DNA strands provides an ideal handle for the reversible reconfiguration of nucleic acid architectures by light irradiation, triggering changes in the chemical and structural properties of the nanostructures that can be exploited in the development of photoresponsive functional devices such as machines, origami structures and ion channels, as well as environmentally adaptable 'smart' materials including nanoparticle aggregates and hydrogels. Moreover, photoresponsive DNA components allow control over the composition of dynamic supramolecular ensembles that mimic native networks. Beyond this, the modification of nucleic acids with photosensitizer functionality enables these biopolymers to act as scaffolds for spatial organization of electron transfer reactions mimicking natural photosynthesis. This review provides a comprehensive overview of these exciting developments in the design of photoresponsive DNA materials, and showcases a range of applications in catalysis, sensing and drug delivery/release. The key challenges facing the development of the field in the coming years are addressed, and exciting emergent research directions are identified.
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Affiliation(s)
- Chen Wang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Michael P O'Hagan
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Ziyuan Li
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Junji Zhang
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Xiang Ma
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - He Tian
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Itamar Willner
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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5
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Barbosa N, Sagresti L, Brancato G. Photoinduced azobenzene-modified DNA dehybridization: insights into local and cooperativity effects from a molecular dynamics study. Phys Chem Chem Phys 2021; 23:25170-25179. [PMID: 34730143 DOI: 10.1039/d1cp04032d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photoresponsive azobenzene-modified DNA (RNA) has become a very fruitful material for nanotechnology due to the capability of switching on and off hybridization (i.e., duplex formation) in smart nanostructures. This nanomaterial exploits the well-known azobenzene trans/cis photo-isomerization. In fact, it has been found that DNA tethered with trans-azobenzene shows normal nucleic acid recognition and hybridization, while the cis form destabilizes the duplex configuration, eventually leading to DNA unzipping. However, while the working principle of the light-triggered DNA dehybridization is apparent, specific details of this mechanism still remain elusive to experiments. Previous in silico studies successfully addressed some aspects (e.g., local structural effects, thermal stability, and early events of azobenzene photoisomerization) of this challenging molecular process characterized by timescales spanning several orders of magnitude, from picoseconds (i.e., azobenzene photoisomerization) to micro- and milli-seconds (i.e., complete strand detachment). In this work, inspired by a recent report by Asanuma and coworkers, we focus on the local and cooperativity effects played by multiple azobenzene units on a 10-mer azobenzene-modified DNA duplex. Using molecular dynamics (MD) simulations, we investigated nine systems equipped with a variable number (from 1 to 7) of photoswitch units and different configurations, focusing our analysis on the initial events (from few ps to hundreds of ns) characterizing DNA destabilization upon trans-to-cis isomerization, such as hydrogen bonding breakage and base pair misalignment. Results highlight, on one hand, the local effects of single azobenzene units on DNA duplex structure and, on the other hand, the cooperative role that multiple photoswitches show in enhancing and accelerating DNA dehybridization following trans-to-cis conversion, in agreement with previously reported data and observations.
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Affiliation(s)
- Nuno Barbosa
- Scuola Normale Superiore and CSGI, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.
| | - Luca Sagresti
- Scuola Normale Superiore and CSGI, Piazza dei Cavalieri 7, I-56126 Pisa, Italy. .,Istituto Nazionale di Fisica Nucleare, Largo Pontecorvo 3, I-56100 Pisa, Italy
| | - Giuseppe Brancato
- Scuola Normale Superiore and CSGI, Piazza dei Cavalieri 7, I-56126 Pisa, Italy. .,Istituto Nazionale di Fisica Nucleare, Largo Pontecorvo 3, I-56100 Pisa, Italy
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6
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Volarić J, Szymanski W, Simeth NA, Feringa BL. Molecular photoswitches in aqueous environments. Chem Soc Rev 2021; 50:12377-12449. [PMID: 34590636 PMCID: PMC8591629 DOI: 10.1039/d0cs00547a] [Citation(s) in RCA: 129] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Indexed: 12/17/2022]
Abstract
Molecular photoswitches enable dynamic control of processes with high spatiotemporal precision, using light as external stimulus, and hence are ideal tools for different research areas spanning from chemical biology to smart materials. Photoswitches are typically organic molecules that feature extended aromatic systems to make them responsive to (visible) light. However, this renders them inherently lipophilic, while water-solubility is of crucial importance to apply photoswitchable organic molecules in biological systems, like in the rapidly emerging field of photopharmacology. Several strategies for solubilizing organic molecules in water are known, but there are not yet clear rules for applying them to photoswitchable molecules. Importantly, rendering photoswitches water-soluble has a serious impact on both their photophysical and biological properties, which must be taken into consideration when designing new systems. Altogether, these aspects pose considerable challenges for successfully applying molecular photoswitches in aqueous systems, and in particular in biologically relevant media. In this review, we focus on fully water-soluble photoswitches, such as those used in biological environments, in both in vitro and in vivo studies. We discuss the design principles and prospects for water-soluble photoswitches to inspire and enable their future applications.
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Affiliation(s)
- Jana Volarić
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
| | - Wiktor Szymanski
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
- Department of Radiology, Medical Imaging Center, University of Groningen, University Medical Centre Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Nadja A Simeth
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
- Institute for Organic and Biomolecular Chemistry, University of Göttingen, Tammannstr. 2, 37077 Göttingen, Germany
| | - Ben L Feringa
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
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8
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Leistner AL, Kirchner S, Karcher J, Bantle T, Schulte ML, Gödtel P, Fengler C, Pianowski ZL. Fluorinated Azobenzenes Switchable with Red Light. Chemistry 2021; 27:8094-8099. [PMID: 33769596 PMCID: PMC8252058 DOI: 10.1002/chem.202005486] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Indexed: 02/06/2023]
Abstract
Molecular photoswitches triggered with red or NIR light are optimal for photomodulation of complex biological systems, including efficient penetration of the human body for therapeutic purposes ("therapeutic window"). Yet, they are rarely reported, and even more rarely functional under aqueous conditions. In this work, fluorinated azobenzenes are shown to exhibit efficient E→Z photoisomerization with red light (PSS660nm >75 % Z) upon conjugation with unsaturated substituents. Initially demonstrated for aldehyde groups, this effect was also observed in a more complex structure by incorporating the chromophore into a cyclic dipeptide with propensity for self-assembly. Under physiological conditions, the latter molecule formed a supramolecular material that reversibly changed its viscosity upon irradiation with red light. Our observation can lead to design of new photopharmacology agents or phototriggered materials for in vivo use.
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Affiliation(s)
- Anna-Lena Leistner
- Institut für Organische Chemie, Karlsruher Institut für Technologie, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Susanne Kirchner
- Institut für Organische Chemie, Karlsruher Institut für Technologie, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Johannes Karcher
- Institut für Organische Chemie, Karlsruher Institut für Technologie, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Tobias Bantle
- Institut für Organische Chemie, Karlsruher Institut für Technologie, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Mariam L Schulte
- Institut für Organische Chemie, Karlsruher Institut für Technologie, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Peter Gödtel
- Institut für Organische Chemie, Karlsruher Institut für Technologie, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Christian Fengler
- Institut für Technische Chemie und Polymerchemie, Karlsruher Institut für Technologie (KIT), Engesserstraße 18, 76128, Karlsruhe, Germany
| | - Zbigniew L Pianowski
- Institut für Organische Chemie, Karlsruher Institut für Technologie, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
- Institute of Biological and Chemical Systems - FMS, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
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9
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Hammill ML, Desaulniers JP. Synthesis of Azobenzene Derivative Phosphoramidites for Incorporation into Oligonucleotides. ACTA ACUST UNITED AC 2021; 81:e107. [PMID: 32383810 DOI: 10.1002/cpnc.107] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This article contains the detailed synthesis and characterization protocols of azobenzene containing siRNAs, which have photoswitchable properties effectively controlled with light. First, the azobenzene scaffolds are synthesized via reduction of nitrophenyl alcohols in the presence of zinc. Next, the hydroxyl group of azobenzene derivatives are protected with a dimethoxytrityl (DMT) group, followed by phosphitylation with 2-cyanoethyl-N,N-diisopropylchlorophosphoramidite. These phosphoramidite monomers are compatible with automated solid-phase oligonucleotide synthesis to generate azobenzene-containing oligonucleotides. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Synthesis of 4,4'-bis(hydroxymethyl)-azobenzene phosphoramidite Basic Protocol 2: Synthesis of 4,4'-bis(hydroxyethyl)-azobenzene phosphoramidite Basic Protocol 3: Synthesis, purification and characterization of oligonucleotides containing azobenzene derivatives.
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Affiliation(s)
- Matthew L Hammill
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario, Canada
| | - Jean-Paul Desaulniers
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario, Canada
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10
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Kolmar T, Büllmann SM, Sarter C, Höfer K, Jäschke A. Development of High-Performance Pyrimidine Nucleoside and Oligonucleotide Diarylethene Photoswitches. Angew Chem Int Ed Engl 2021; 60:8164-8173. [PMID: 33476096 PMCID: PMC8049081 DOI: 10.1002/anie.202014878] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 01/05/2021] [Indexed: 01/17/2023]
Abstract
Nucleosidic and oligonucleotidic diarylethenes (DAEs) are an emerging class of photochromes with high application potential. However, their further development is hampered by the poor understanding of how the chemical structure modulates the photochromic properties. Here we synthesized 26 systematically varied deoxyuridine- and deoxycytidine-derived DAEs and analyzed reaction quantum yields, composition of the photostationary states, thermal and photochemical stability, and reversibility. This analysis identified two high-performance photoswitches with near-quantitative, fully reversible back-and-forth switching and no detectable thermal or photochemical deterioration. When incorporated into an oligonucleotide with the sequence of a promotor, the nucleotides maintained their photochromism and allowed the modulation of the transcription activity of T7 RNA polymerase with an up to 2.4-fold turn-off factor, demonstrating the potential for optochemical control of biological processes.
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Affiliation(s)
- Theresa Kolmar
- Institute of Pharmacy and Molecular BiotechnologyHeidelberg UniversityIm Neuenheimer Feld 36469120HeidelbergGermany
| | - Simon M. Büllmann
- Institute of Pharmacy and Molecular BiotechnologyHeidelberg UniversityIm Neuenheimer Feld 36469120HeidelbergGermany
| | - Christopher Sarter
- Institute of Pharmacy and Molecular BiotechnologyHeidelberg UniversityIm Neuenheimer Feld 36469120HeidelbergGermany
| | - Katharina Höfer
- Institute of Pharmacy and Molecular BiotechnologyHeidelberg UniversityIm Neuenheimer Feld 36469120HeidelbergGermany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular BiotechnologyHeidelberg UniversityIm Neuenheimer Feld 36469120HeidelbergGermany
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11
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Kolmar T, Büllmann SM, Sarter C, Höfer K, Jäschke A. Development of High‐Performance Pyrimidine Nucleoside and Oligonucleotide Diarylethene Photoswitches. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014878] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Theresa Kolmar
- 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
| | - Christopher Sarter
- Institute of Pharmacy and Molecular Biotechnology Heidelberg University Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Katharina Höfer
- 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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12
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Yin YD, Zhang L, Leng XZ, Gu ZY. Harnessing biological nanopore technology to track chemical changes. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.116091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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13
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Hammill ML, Islam G, Desaulniers JP. Controlling Gene-Silencing with Azobenzene-Containing siRNAs (siRNAzos). ACTA ACUST UNITED AC 2020; 83:e119. [PMID: 33175468 DOI: 10.1002/cpnc.119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
This article contains the detailed biophysical characterization, biological testing, and photo-switching protocols of azobenzene containing siRNAs (siRNAzos), which have photoswitchable properties that can be controlled with light. First, the siRNAzos are characterized by annealing the sense and anti-sense strands together and then measuring the circular dichroism (CD) profile, and the melting temperatures (Tm ) of the duplexes. Second, the biological testing of the siRNAzos in cell culture is done to determine their gene silencing efficacy. Finally, their gene-silencing activities are measured after exposure to ultraviolet (UV) light in order to inactivate the siRNAzo, and then broadband visible light, which re-activates the siRNAzo. This inactivation/reactivation protocol can be done in real time, and is reversible and robust and can be performed multiple times on the same sample if desired. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Bio-physical characterization of siRNAzo duplexes Basic Protocol 2: Evaluation of azobenzene gene-silencing using Firefly Luciferase Basic Protocol 3: Evaluation of azobenzene gene-silencing using reverse transcriptase-polymerase chain reaction (RT-PCR).
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Affiliation(s)
- Matthew L Hammill
- University of Ontario Institute of Technology, Faculty of Science, Oshawa, Ontario, Canada
| | - Golam Islam
- University of Ontario Institute of Technology, Faculty of Science, Oshawa, Ontario, Canada
| | - Jean-Paul Desaulniers
- University of Ontario Institute of Technology, Faculty of Science, Oshawa, Ontario, Canada
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14
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Grebenovsky N, Hermanns V, Heckel A. Photoswitchable 2‐Phenyldiazenyl‐Purines and their Influence on DNA Hybridization. CHEMPHOTOCHEM 2020. [DOI: 10.1002/cptc.202000162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Nikolai Grebenovsky
- Institute for Organic Chemistry and Chemical Biology Goethe-University Frankfurt Max-von-Laue-Straße 7 D 60438 Frankfurt am Main Germany
| | - Volker Hermanns
- Institute for Organic Chemistry and Chemical Biology Goethe-University Frankfurt Max-von-Laue-Straße 7 D 60438 Frankfurt am Main Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology Goethe-University Frankfurt Max-von-Laue-Straße 7 D 60438 Frankfurt am Main Germany
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15
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Wu Z, Zhang L. Photoregulation between small DNAs and reversible photochromic molecules. Biomater Sci 2019; 7:4944-4962. [PMID: 31650136 DOI: 10.1039/c9bm01305a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Oligonucleotides are widely used biological materials in the fields of biomedicine, nanotechnology, and materials science. Due to the demands for the photoregulation of DNA activities, scientists are placing more and more research interest in the interactions between reversible photochromic molecules and DNAs. Photochromic molecules can work as switches for regulating the DNAs' behavior under light irradiation; meanwhile, DNAs also exert influence over the photochromic molecules. The photochromic molecules can be attached to DNAs either by covalent bonds or by noncovalent forces, which results in different regulative functions. Azobenzenes, spiropyrans, diarylethenes, and stilbene-like compounds are important photochromic molecules working as photoswitches. By summarizing their interactions with oligonucleotides, this review intends to facilitate the relevant research on oligonucleotides/photochromic molecules in the biological and medicinal fields and in materials science.
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Affiliation(s)
- Zhongtao Wu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No. 53 Zhengzhou Rd, Qingdao, 266042, PR China.
| | - Lei Zhang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No. 53 Zhengzhou Rd, Qingdao, 266042, PR China.
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16
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Grebenovsky N, Luma L, Müller P, Heckel A. Introducing LNAzo: More Rigidity for Improved Photocontrol of Oligonucleotide Hybridization. Chemistry 2019; 25:12298-12302. [PMID: 31386225 DOI: 10.1002/chem.201903240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/05/2019] [Indexed: 12/15/2022]
Abstract
Oligonucleotide-based therapeutics have made rapid progress in clinical treatment of a variety of disease indications. Since most therapeutic oligonucleotides serve more than just one function and tend to have a prolonged lifetime, spatio-temporal control of these functions would be desirable. Photoswitches like azobenzene have proven themselves as useful tools in this matter. Upon irradiation, the photoisomerization of the azobenzene moiety causes destabilization in adjacent base pairs, leading to a decreased hybridization affinity. Since the way the azobenzene is incorporated in the oligonucleotide is of utmost importance, we synthesized locked azobenzene C-nucleosides and compared their photocontrol capabilities to established azobenzene C-nucleosides in oligonucleotide test-sequences by means of fluorescence-, UV/Vis-, and CD-spectroscopy.
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Affiliation(s)
- Nikolai Grebenovsky
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
| | - Larita Luma
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
| | - Patricia Müller
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt am Main, Germany
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17
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Sarter C, Dey S, Jäschke A. Photoswitchable Oligonucleotides Containing Different Diarylethene-Modified Nucleotides. ACS OMEGA 2019; 4:12125-12129. [PMID: 31460326 PMCID: PMC6682051 DOI: 10.1021/acsomega.9b01070] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 06/18/2019] [Indexed: 06/10/2023]
Abstract
Diarylethenes are a well-studied class of photoswitches and have often been linked to partner molecules to render them photoresponsive. Earlier, our lab developed a new type of diarylethenes in which the purine or pyrimidine base of a nucleoside or oligonucleotide serves as one of the two aryl residues of the photochromic system. Here, we report the synthesis of three different diarylethene-deoxyuridine phosphoramidites and their site-specific incorporation into oligodeoxynucleotides by solid-phase synthesis. Various DNA sequences carrying single or multiple, identical or different photoswitchable moieties are synthesized with high yield and purity. Upon UV irradiation, these DNA strands form a colored closed-ring isomer. The combination of different diarylethenes within one strand leads to an additive absorption spectrum. The photochromic DNA oligonucleotides are thermostable and photoreversible.
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18
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Zhang TS, Li ZW, Fang Q, Barbatti M, Fang WH, Cui G. Stereoselective Excited-State Isomerization and Decay Paths in cis-Cyclobiazobenzene. J Phys Chem A 2019; 123:6144-6151. [DOI: 10.1021/acs.jpca.9b04372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Teng-Shuo Zhang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Zi-Wen Li
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Qiu Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | | | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
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19
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Murayama K, Yamano Y, Asanuma H. 8-Pyrenylvinyl Adenine Controls Reversible Duplex Formation between Serinol Nucleic Acid and RNA by [2 + 2] Photocycloaddition. J Am Chem Soc 2019; 141:9485-9489. [DOI: 10.1021/jacs.9b03267] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Keiji Murayama
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Yuuhei Yamano
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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20
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Asanuma H, Ishikawa T, Yamano Y, Murayama K, Liang X. cis
‐On/
trans
‐Off of DNA Hybridization with Alkylthio‐azobenzene on L‐Threoninol Responding to Visible Light. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201900060] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Hiroyuki Asanuma
- Department of Biomolecular Engineering Graduate School of Engineering, Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Teruchika Ishikawa
- Department of Biomolecular Engineering Graduate School of Engineering, Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Yuuhei Yamano
- Department of Biomolecular Engineering Graduate School of Engineering, Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Keiji Murayama
- Department of Biomolecular Engineering Graduate School of Engineering, Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Xingguo Liang
- College of Food Science and Engineering Ocean University of China, Qingdao 266003 P. R. China
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21
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Heinrich B, Bouazoune K, Wojcik M, Bakowsky U, Vázquez O. ortho-Fluoroazobenzene derivatives as DNA intercalators for photocontrol of DNA and nucleosome binding by visible light. Org Biomol Chem 2019; 17:1827-1833. [PMID: 30604825 DOI: 10.1039/c8ob02343c] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We report a high-affinity photoswitchable DNA binder, which displays different nucleosome-binding capacities upon visible-light irradiation. Both photochemical and DNA-recognition properties were examined by UV-Vis, HPLC, CD spectroscopy, NMR, FID assays, EMSA and DLS. Our probe sets the basis for developing new optoepigenetic tools for conditional modulation of nucleosomal DNA accessibility.
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Affiliation(s)
- Benedikt Heinrich
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35043, Marburg, Germany.
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22
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Pianowski ZL. Recent Implementations of Molecular Photoswitches into Smart Materials and Biological Systems. Chemistry 2019; 25:5128-5144. [PMID: 30614091 DOI: 10.1002/chem.201805814] [Citation(s) in RCA: 182] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/30/2018] [Indexed: 12/11/2022]
Abstract
Light is a nearly ideal stimulus for molecular systems. It delivers information encoded in the form of wavelengths and their intensities with high precision in space and time. Light is a mild trigger that does not permanently contaminate targeted samples. Its energy can be reversibly transformed into molecular motion, polarity, or flexibility changes. This leads to sophisticated functions at the supramolecular and macroscopic levels, from light-triggered nanomaterials to photocontrol over biological systems. New methods and molecular adapters of light are reported almost daily. Recently reported applications of photoresponsive systems, particularly azobenzenes, spiropyrans, diarylethenes, and indigoids, for smart materials and photocontrol of biological setups are described herein with the aim to demonstrate that the 21st century has become the Age of Enlightenment-"Le siècle des Lumières"-in molecular sciences.
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Affiliation(s)
- Zbigniew L Pianowski
- Institut für Organische Chemie, Karlsruher Institut für Technologie, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany.,Institut für Toxikologie und Genetik, Karlsruher Institut für Technologie, Campus Nord, Hermann-von-Helmholtz Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
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23
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Abstract
Pseudouridine (1) was synthesized by functional group interconversions of the Heck adduct11from 2,4-dimethoxy-5-iodopyrimidine (8) and ribofuranoid glycal4.
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Affiliation(s)
- Cheng-Ping Yu
- Department of Chemistry
- National Taiwan Normal University
- Taipei 11677
- Taiwan
| | - Hsin-Yun Chang
- Department of Chemistry
- National Taiwan Normal University
- Taipei 11677
- Taiwan
| | - Tun-Cheng Chien
- Department of Chemistry
- National Taiwan Normal University
- Taipei 11677
- Taiwan
- Faculty of Pharmacy
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24
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Keyhani S, Goldau T, Blümler A, Heckel A, Schwalbe H. Chemo-Enzymatic Synthesis of Position-Specifically Modified RNA for Biophysical Studies including Light Control and NMR Spectroscopy. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807125] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sara Keyhani
- Institute for Organic Chemistry and Chemical Biology; Center for Biomolecular Magnetic Resonance; Goethe University Frankfurt am Main; Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
- Institute for Organic Chemistry and Chemical Biology; Goethe University Frankfurt am Main; Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
| | - Thomas Goldau
- Institute for Organic Chemistry and Chemical Biology; Goethe University Frankfurt am Main; Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
| | - Anja Blümler
- Institute for Organic Chemistry and Chemical Biology; Goethe University Frankfurt am Main; Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology; Goethe University Frankfurt am Main; Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology; Center for Biomolecular Magnetic Resonance; Goethe University Frankfurt am Main; Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
- Institute for Organic Chemistry and Chemical Biology; Goethe University Frankfurt am Main; Max-von-Laue-Strasse 7 60438 Frankfurt/Main Germany
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25
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Keyhani S, Goldau T, Blümler A, Heckel A, Schwalbe H. Chemo-Enzymatic Synthesis of Position-Specifically Modified RNA for Biophysical Studies including Light Control and NMR Spectroscopy. Angew Chem Int Ed Engl 2018; 57:12017-12021. [PMID: 30007102 DOI: 10.1002/anie.201807125] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Indexed: 02/04/2023]
Abstract
The investigation of non-coding RNAs requires RNAs containing modifications at every possible position within the oligonucleotide. Here, we present the chemo-enzymatic RNA synthesis containing photoactivatable or 13 C,15 N-labelled nucleosides. All four ribonucleotides containing ortho-nitrophenylethyl (NPE) photocages, photoswitchable azobenzene C-nucleotides and 13 C,15 N-labelled nucleotides were incorporated position-specifically in high yields. We applied this approach for the synthesis of light-inducible 2'dG-sensing riboswitch variants and detected ligand-induced structural reorganization upon irradiation by NMR spectroscopy. This chemo-enzymatic method opens the possibility to incorporate a wide range of modifications at any desired position of RNAs of any lengths beyond the limits of solid-phase synthesis.
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Affiliation(s)
- Sara Keyhani
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany.,Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany
| | - Thomas Goldau
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany
| | - Anja Blümler
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany.,Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438, Frankfurt/Main, Germany
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26
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Mondal P, Granucci G, Rastädter D, Persico M, Burghardt I. Azobenzene as a photoregulator covalently attached to RNA: a quantum mechanics/molecular mechanics-surface hopping dynamics study. Chem Sci 2018; 9:4671-4681. [PMID: 29899961 PMCID: PMC5969502 DOI: 10.1039/c8sc00072g] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 04/25/2018] [Indexed: 12/21/2022] Open
Abstract
Azobenzene covalently attached to RNA undergoes trans-to-cis photo-switching on a time scale of ∼15 picoseconds – 30 times slower than in vacuo.
The photoregulation of nucleic acids by azobenzene photoswitches has recently attracted considerable interest in the context of emerging biotechnological applications. To understand the mechanism of photoinduced isomerisation and conformational control in these complex biological environments, we employ a Quantum Mechanics/Molecular Mechanics (QM/MM) approach in conjunction with nonadiabatic Surface Hopping (SH) dynamics. Two representative RNA–azobenzene complexes are investigated, both of which contain the azobenzene chromophore covalently attached to an RNA double strand via a β-deoxyribose linker. Due to the pronounced constraints of the local RNA environment, it is found that trans-to-cis isomerization is slowed down to a time scale of ∼10–15 picoseconds, in contrast to 500 femtoseconds in vacuo, with a quantum yield reduced by a factor of two. By contrast, cis-to-trans isomerization remains in a sub-picosecond regime. A volume-conserving isomerization mechanism is found, similarly to the pedal-like mechanism previously identified for azobenzene in solution phase. Strikingly, the chiral RNA environment induces opposite right-handed and left-handed helicities of the ground-state cis-azobenzene chromophore in the two RNA–azobenzene complexes, along with an almost completely chirality conserving photochemical pathway for these helical enantiomers.
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Affiliation(s)
- Padmabati Mondal
- Institute of Physical and Theoretical Chemistry , Goethe University Frankfurt , Max-von-Laue-Str. 7 , 60438 Frankfurt , Germany . ;
| | - Giovanni Granucci
- Dipartimento di Chimica e Chimica Industriale , Università di Pisa , v. Moruzzi 13 , I-56124 Pisa , Italy .
| | - Dominique Rastädter
- Institute of Physical and Theoretical Chemistry , Goethe University Frankfurt , Max-von-Laue-Str. 7 , 60438 Frankfurt , Germany . ;
| | - Maurizio Persico
- Dipartimento di Chimica e Chimica Industriale , Università di Pisa , v. Moruzzi 13 , I-56124 Pisa , Italy .
| | - Irene Burghardt
- Institute of Physical and Theoretical Chemistry , Goethe University Frankfurt , Max-von-Laue-Str. 7 , 60438 Frankfurt , Germany . ;
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27
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Lubbe AS, Szymanski W, Feringa BL. Recent developments in reversible photoregulation of oligonucleotide structure and function. Chem Soc Rev 2018; 46:1052-1079. [PMID: 28128377 DOI: 10.1039/c6cs00461j] [Citation(s) in RCA: 206] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
There is a growing interest in the photoregulation of biological functions, due to the high level of spatiotemporal precision achievable with light. Additionally, light is non-invasive and waste-free. In particular, the photoregulation of oligonucleotide structure and function is a rapidly developing study field with relevance to biological, physical and material sciences. Molecular photoswitches have been incorporated in oligonucleotides for 20 years, and the field has currently grown beyond fundamental studies on photochemistry of the switches and DNA duplex stability, and is moving towards applications in chemical biology, nanotechnology and material science. Moreover, the currently emerging field of photopharmacology indicates the relevance of photocontrol in future medicine. In recent years, a large number of publications has appeared on photoregulation of DNA and RNA structure and function. New strategies are evaluated and novel, exciting applications are shown. In this comprehensive review, the key strategies for photoswitch inclusion in oligonucleotides are presented and illustrated with recent examples. Additionally the applications that have emerged in recent years are discussed, including gene regulation, drug delivery and materials design. Finally, we identify the challenges that the field currently faces and look forward to future applications.
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Affiliation(s)
- Anouk S Lubbe
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
| | - Wiktor Szymanski
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands. and Department of Radiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands.
| | - Ben L Feringa
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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28
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Wu D, Wang YT, Fang WH, Cui G, Thiel W. QM/MM Studies on Photoisomerization Dynamics of Azobenzene Chromophore Tethered to a DNA Duplex: Local Unpaired Nucleobase Plays a Crucial Role. Chem Asian J 2018; 13:780-784. [PMID: 29446260 DOI: 10.1002/asia.201800006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 02/07/2018] [Indexed: 01/10/2023]
Abstract
The photoresponsive azobenzene-tethered DNAs have received growing experimental attention because of their potential applications in biotechnology and nanotechnology; however, little is known about the initial photoisomerization of azobenzene in these systems. Herein we have employed quantum mechanics/molecular mechanics (QM/MM) methods to explore the photoisomerization dynamics of an azobenzene-tethered DNA duplex. We find that in the S1 state the trans-cis photoisomerization path is much steeper in DNA than in vacuo, which makes the photoisomerization much faster in the DNA environment. This acceleration is primarily caused by complex steric interactions between azobenzene and the nearby unpaired thymine nucleobase, which also change the photoisomerization mechanism of azobenzene in the DNA duplex.
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Affiliation(s)
- Dan Wu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Ya-Ting Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
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29
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Hu ZL, Li ZY, Ying YL, Zhang J, Cao C, Long YT, Tian H. Real-Time and Accurate Identification of Single Oligonucleotide Photoisomers via an Aerolysin Nanopore. Anal Chem 2018. [PMID: 29516718 DOI: 10.1021/acs.analchem.8b00096] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Identification of the configuration for the photoresponsive oligonucleotide plays an important role in the ingenious design of DNA nanomolecules and nanodevices. Due to the limited resolution and sensitivity of present methods, it remains a challenge to determine the accurate configuration of photoresponsive oligonucleotides, much less a precise description of their photoconversion process. Here, we used an aerolysin (AeL) nanopore-based confined space for real-time determination and quantification of the absolute cis/ trans configuration of each azobenzene-modified oligonucleotide (Azo-ODN) with a single molecule resolution. The two completely separated current distributions with narrow peak widths at half height (<0.62 pA) are assigned to cis/ trans-Azo-ODN isomers, respectively. Due to the high current sensitivity, each isomer of Azo-ODN could be undoubtedly identified, which gives the accurate photostationary conversion values of 82.7% for trans-to- cis under UV irradiation and 82.5% for cis-to- trans under vis irradiation. Further real-time kinetic evaluation reveals that the photoresponsive rate constants of Azo-ODN from trans-to- cis and cis-to -trans are 0.43 and 0.20 min-1, respectively. This study will promote the sophisticated design of photoresponsive ODN to achieve an efficient and applicable photocontrollable process.
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Affiliation(s)
- Zheng-Li Hu
- Key Laboratory for Advanced Materials and School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai , 200237 , P. R. China
| | - Zi-Yuan Li
- Key Laboratory for Advanced Materials and School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai , 200237 , P. R. China
| | - Yi-Lun Ying
- Key Laboratory for Advanced Materials and School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai , 200237 , P. R. China
| | - Junji Zhang
- Key Laboratory for Advanced Materials and School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai , 200237 , P. R. China
| | - Chan Cao
- Key Laboratory for Advanced Materials and School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai , 200237 , P. R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials and School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai , 200237 , P. R. China
| | - He Tian
- Key Laboratory for Advanced Materials and School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai , 200237 , P. R. China
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30
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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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31
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Grebenovsky N, Goldau T, Bolte M, Heckel A. Light Regulation of DNA Minicircle Dimerization by Utilizing Azobenzene C
-Nucleosides. Chemistry 2018; 24:3425-3428. [DOI: 10.1002/chem.201706003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Indexed: 01/05/2023]
Affiliation(s)
- Nikolai Grebenovsky
- Institute of Organic Chemistry and Chemical Biology; J. W. Goethe University Frankfurt; Max-von-Laue-Straße 7 D-60438 Frankfurt am Main Germany
| | - Thomas Goldau
- Institute of Organic Chemistry and Chemical Biology; J. W. Goethe University Frankfurt; Max-von-Laue-Straße 7 D-60438 Frankfurt am Main Germany
| | - Michael Bolte
- Institute for Inorganic Chemistry; J. W. Goethe University Frankfurt; Max-von-Laue-Straße 7 D-60438 Frankfurt am Main Germany
| | - Alexander Heckel
- Institute of Organic Chemistry and Chemical Biology; J. W. Goethe University Frankfurt; Max-von-Laue-Straße 7 D-60438 Frankfurt am Main Germany
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32
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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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33
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Adam V, Prusty DK, Centola M, Škugor M, Hannam JS, Valero J, Klöckner B, Famulok M. Expanding the Toolbox of Photoswitches for DNA Nanotechnology Using Arylazopyrazoles. Chemistry 2018; 24:1062-1066. [DOI: 10.1002/chem.201705500] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Volker Adam
- LIMES Chemical Biology Unit; Universität Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Germany
| | - Deepak K. Prusty
- Max-Planck-Fellowship Group Chemical Biology; Center of Advanced European Studies and Research; Ludwig-Erhard-Allee 2 53175 Bonn Germany
| | - Mathias Centola
- LIMES Chemical Biology Unit; Universität Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Germany
| | - Marko Škugor
- LIMES Chemical Biology Unit; Universität Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Germany
| | - Jeffrey S. Hannam
- LIMES Chemical Biology Unit; Universität Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Germany
| | - Julián Valero
- Max-Planck-Fellowship Group Chemical Biology; Center of Advanced European Studies and Research; Ludwig-Erhard-Allee 2 53175 Bonn Germany
| | - Bernhard Klöckner
- Kekulé Institut für Organische Chemie und Biochemie; Gerhard-Domagk-Str.1 53121 Bonn Germany
| | - Michael Famulok
- LIMES Chemical Biology Unit; Universität Bonn; Gerhard-Domagk-Straße 1 53121 Bonn Germany
- Max-Planck-Fellowship Group Chemical Biology; Center of Advanced European Studies and Research; Ludwig-Erhard-Allee 2 53175 Bonn Germany
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34
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Vulcano R, Pengo P, Velari S, Wouters J, De Vita A, Tecilla P, Bonifazi D. Toward Fractioning of Isomers through Binding-Induced Acceleration of Azobenzene Switching. J Am Chem Soc 2017; 139:18271-18280. [PMID: 29064236 DOI: 10.1021/jacs.7b09568] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The E/Z isomerization process of a uracil-azobenzene derivative in which the nucleobase is conjugated to a phenyldiazene tail is studied in view of its ability to form triply H-bonded complexes with a suitably complementary 2,6-diacetylamino-4-pyridine ligand. UV-vis and 1H NMR investigations of the photochemical and thermal isomerization kinetics show that the thermal Z → E interconversion is 4-fold accelerated upon formation of the H-bonded complex. DFT calculations show that the formation of triple H-bonds triggers a significant elongation of the N═N double bond, caused by an increase of its πg* antibonding character. This results in a reduction of the N═N torsional barrier and thus in accelerated thermal Z → E isomerization. Combined with light-controlled E → Z isomerization, this enables controllable fractional tuning of the two configurational isomers.
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Affiliation(s)
- Rosaria Vulcano
- Department of Chemistry, University of Namur (UNamur) , Rue de Bruxelles 61, Namur, 5000, Belgium
| | | | | | - Johan Wouters
- Department of Chemistry, University of Namur (UNamur) , Rue de Bruxelles 61, Namur, 5000, Belgium
| | - Alessandro De Vita
- Department of Physics, King's College London , Strand, London WC2R 2LS, United Kingdom
| | | | - Davide Bonifazi
- Department of Chemistry, University of Namur (UNamur) , Rue de Bruxelles 61, Namur, 5000, Belgium.,School of Chemistry, Cardiff University , Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
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35
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Procházková E, Čechová L, Kind J, Janeba Z, Thiele CM, Dračínský M. Photoswitchable Intramolecular Hydrogen Bonds in 5-Phenylazopyrimidines Revealed By In Situ Irradiation NMR Spectroscopy. Chemistry 2017; 24:492-498. [DOI: 10.1002/chem.201705146] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Eliška Procházková
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 16610 Prague 6 Czech Republic
| | - Lucie Čechová
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 16610 Prague 6 Czech Republic
| | - Jonas Kind
- Clemens-Schöpf Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss Strasse 16 64287 Darmstadt Germany
| | - Zlatko Janeba
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 16610 Prague 6 Czech Republic
| | - Christina M. Thiele
- Clemens-Schöpf Institut für Organische Chemie und Biochemie; Technische Universität Darmstadt; Alarich-Weiss Strasse 16 64287 Darmstadt Germany
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 16610 Prague 6 Czech Republic
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36
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Hammill ML, Isaacs-Trépanier C, Desaulniers JP. siRNAzos: A New Class of Azobenzene-Containing siRNAs that Can Photochemically Regulate Gene Expression. ChemistrySelect 2017. [DOI: 10.1002/slct.201702322] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Matthew L. Hammill
- Faculty of Science; University of Ontario Institute of Technology; Oshawa ON L1H 7 K4 Canada
| | | | - Jean-Paul Desaulniers
- Faculty of Science; University of Ontario Institute of Technology; Oshawa ON L1H 7 K4 Canada
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37
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Jaumann EA, Steinwand S, Klenik S, Plackmeyer J, Bats JW, Wachtveitl J, Prisner TF. A combined optical and EPR spectroscopy study: azobenzene-based biradicals as reversible molecular photoswitches. Phys Chem Chem Phys 2017. [PMID: 28639638 DOI: 10.1039/c7cp02088k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Azobenzene compounds are known as versatile examples for photoswitchable systems because of their isomeric cis- and trans-configurations. The switching between these isomers can be reversibly controlled by light excitation. In this study we characterize two members of this class by joining the azobenzene moiety with each two paramagnetic nitroxide spin labels. Two different linkers were chosen to tune the molecular properties. The combined approach using optical and EPR spectroscopy proved the reversibility of photoexcitation and high fatigue resistance. Furthermore, depending on the nature of the linker, PELDOR distance measurements monitored clearly the photo-induced structural changes of the azobenzene unit. Thus, a powerful concept is presented resulting from the combination of these two complementary spectroscopic techniques.
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Affiliation(s)
- Eva A Jaumann
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 7, D-60438 Frankfurt, Germany.
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38
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Kink F, Collado MP, Wiedbrauk S, Mayer P, Dube H. Bistable Photoswitching of Hemithioindigo with Green and Red Light: Entry Point to Advanced Molecular Digital Information Processing. Chemistry 2017; 23:6237-6243. [DOI: 10.1002/chem.201700826] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Florian Kink
- Department of Chemistry and Pharmacy and Munich Center for Integrated Protein Science CIPSM; Ludwig-Maximilians-Universität München; Butenandtstr. 5-13 81377 Munich Germany
| | - Marina Polo Collado
- Department of Chemistry and Pharmacy and Munich Center for Integrated Protein Science CIPSM; Ludwig-Maximilians-Universität München; Butenandtstr. 5-13 81377 Munich Germany
| | - Sandra Wiedbrauk
- Department of Chemistry and Pharmacy and Munich Center for Integrated Protein Science CIPSM; Ludwig-Maximilians-Universität München; Butenandtstr. 5-13 81377 Munich Germany
| | - Peter Mayer
- Department of Chemistry and Pharmacy and Munich Center for Integrated Protein Science CIPSM; Ludwig-Maximilians-Universität München; Butenandtstr. 5-13 81377 Munich Germany
| | - Henry Dube
- Department of Chemistry and Pharmacy and Munich Center for Integrated Protein Science CIPSM; Ludwig-Maximilians-Universität München; Butenandtstr. 5-13 81377 Munich Germany
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39
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Meng FN, Li ZY, Ying YL, Liu SC, Zhang J, Long YT. Structural stability of the photo-responsive DNA duplexes containing one azobenzene via a confined pore. Chem Commun (Camb) 2017; 53:9462-9465. [DOI: 10.1039/c7cc04599a] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Herein, the structural stability of single azobenzene modified DNA duplexes, including the trans form and cis form, has been examined separately based on their distinguishable unzipping kinetics from the mixture by an α-hemolysin nanopore.
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Affiliation(s)
- Fu-Na Meng
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering
- Shanghai
- China
| | - Zi-Yuan Li
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering
- Shanghai
- China
| | - Yi-Lun Ying
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering
- Shanghai
- China
| | - Shao-Chuang Liu
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering
- Shanghai
- China
| | - Junji Zhang
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering
- Shanghai
- China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering
- Shanghai
- China
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40
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Murayama K, Asanuma H. Effect of Methyl Group on Acyclic Serinol Scaffold for Tethering Dyes on the DNA Duplex Stability. Chembiochem 2016; 18:142-149. [DOI: 10.1002/cbic.201600558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Keiji Murayama
- Graduate School of Engineering; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8603 Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8603 Japan
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41
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Pianowski ZL, Karcher J, Schneider K. Photoresponsive self-healing supramolecular hydrogels for light-induced release of DNA and doxorubicin. Chem Commun (Camb) 2016; 52:3143-6. [PMID: 26804160 DOI: 10.1039/c5cc09633b] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
An azobenzene-containing cyclic dipeptide PAP-DKP-Lys is a photoresponsive low-MW hydrogelator. The gelation process can be triggered with temperature, pH, light, and ionic strength. The resulting self-healing gels can encapsulate dsDNA or an anticancer drug doxorubicin, and release them in a light-dependent manner.
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Affiliation(s)
- Zbigniew L Pianowski
- Institut für Organische Chemie, Karlsruher Institut für Technologie, Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany and Institut für Toxikologie und Genetik, Karlsruher Institut für Technologie, Herman-von-Helmholtz Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany.
| | - Johannes Karcher
- Institut für Organische Chemie, Karlsruher Institut für Technologie, Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
| | - Knut Schneider
- Institut für Organische Chemie, Karlsruher Institut für Technologie, Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
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42
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Guentner M, Uhl E, Mayer P, Dube H. Photocontrol of Polar Aromatic Interactions by a Bis-Hemithioindigo Based Helical Receptor. Chemistry 2016; 22:16433-16436. [DOI: 10.1002/chem.201604237] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Manuel Guentner
- Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstr. 5-13 81377 Munich Germany
| | - Edgar Uhl
- Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstr. 5-13 81377 Munich Germany
| | - Peter Mayer
- Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstr. 5-13 81377 Munich Germany
| | - Henry Dube
- Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstr. 5-13 81377 Munich Germany
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43
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Steinwand S, Yu Z, Hecht S, Wachtveitl J. Ultrafast Dynamics of Photoisomerization and Subsequent Unfolding of an Oligoazobenzene Foldamer. J Am Chem Soc 2016; 138:12997-13005. [DOI: 10.1021/jacs.6b07720] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Sabrina Steinwand
- Institute
of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 7, D-60438 Frankfurt, Germany
| | - Zhilin Yu
- Department of Chemistry & IRIS Adlershof, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany
| | - Stefan Hecht
- Department of Chemistry & IRIS Adlershof, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany
| | - Josef Wachtveitl
- Institute
of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 7, D-60438 Frankfurt, Germany
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44
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Wiedbrauk S, Maerz B, Samoylova E, Reiner A, Trommer F, Mayer P, Zinth W, Dube H. Twisted Hemithioindigo Photoswitches: Solvent Polarity Determines the Type of Light-Induced Rotations. J Am Chem Soc 2016; 138:12219-27. [DOI: 10.1021/jacs.6b05981] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Sandra Wiedbrauk
- Department
für Chemie, Ludwig-Maximilians-Universität München, D-81377 Munich, Germany
| | - Benjamin Maerz
- Institut
für Biomolekulare Optik, Ludwig-Maximilians-Universität München, D-80538 Munich, Germany
| | - Elena Samoylova
- Institut
für Biomolekulare Optik, Ludwig-Maximilians-Universität München, D-80538 Munich, Germany
| | - Anne Reiner
- Institut
für Biomolekulare Optik, Ludwig-Maximilians-Universität München, D-80538 Munich, Germany
| | - Florian Trommer
- Institut
für Biomolekulare Optik, Ludwig-Maximilians-Universität München, D-80538 Munich, Germany
| | - Peter Mayer
- Department
für Chemie, Ludwig-Maximilians-Universität München, D-81377 Munich, Germany
| | - Wolfgang Zinth
- Institut
für Biomolekulare Optik, Ludwig-Maximilians-Universität München, D-80538 Munich, Germany
| | - Henry Dube
- Department
für Chemie, Ludwig-Maximilians-Universität München, D-81377 Munich, Germany
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45
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Kingsland A, Samai S, Yan Y, Ginger DS, Maibaum L. Local Density Fluctuations Predict Photoisomerization Quantum Yield of Azobenzene-Modified DNA. J Phys Chem Lett 2016; 7:3027-3031. [PMID: 27428569 DOI: 10.1021/acs.jpclett.6b00956] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Azobenzene incorporated into DNA has a photoisomerization quantum yield that depends on the DNA sequence near the azobenzene attachment site. We use Molecular Dynamics computer simulations to elucidate which physical properties of the modified DNA determine the quantum yield. We show for a wide range of DNA sequences that the photoisomerization quantum yield is strongly correlated with the variance of the number of atoms in close proximity to the outer phenyl ring of the azobenzene group. We infer that quantum yield is controlled by the availability of fluctuations that enable the conformational change. We demonstrate that these simulations can be used as a qualitative predictive tool by calculating the quantum yield for several novel DNA sequences, and confirming these predictions using UV-vis spectroscopy. Our results will be useful for the development of a wide range of applications of photoresponsive DNA nanotechnology.
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Affiliation(s)
- Addie Kingsland
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Soumyadyuti Samai
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Yunqi Yan
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - David S Ginger
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Lutz Maibaum
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
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46
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Doi T, Kawai H, Murayama K, Kashida H, Asanuma H. Visible-Light-Triggered Cross-Linking of DNA Duplexes by Reversible [2+2] Photocycloaddition of Styrylpyrene. Chemistry 2016; 22:10533-8. [DOI: 10.1002/chem.201602006] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Tetsuya Doi
- Graduate School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Hayato Kawai
- Graduate School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Keiji Murayama
- Graduate School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Hiromu Kashida
- Graduate School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
- PRESTO (Japan) Science and Technology Agency; 4-1-8 Honcho, Kawaguchi Saitama 332-0012 Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering; Nagoya University; Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
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47
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Freeman NS, Moore CE, Wilhelmsson LM, Tor Y. Chromophoric Nucleoside Analogues: Synthesis and Characterization of 6-Aminouracil-Based Nucleodyes. J Org Chem 2016; 81:4530-9. [PMID: 27128151 PMCID: PMC5493935 DOI: 10.1021/acs.joc.6b00310] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Nucleodyes, visibly colored chromophoric nucleoside analogues, are reported. Design criteria are outlined and the syntheses of cytidine and uridine azo dye analogues derived from 6-aminouracil are described. Structural analysis shows that the nucleodyes are sound structural analogues of their native nucleoside counterparts, and photophysical studies demonstrate that the nucleodyes are sensitive to microenvironmental changes. Quantum chemical calculations are presented as a valuable complementary tool for the design of strongly absorbing nucleodyes, which overlap with the emission of known fluorophores. Förster critical distance (R0) calculations determine that the nucleodyes make good FRET pairs with both 2-aminopurine (2AP) and pyrrolocytosine (PyC). Additionally, unique tautomerization features exhibited by 5-(4-nitrophenylazo)-6-oxocytidine (8) are visualized by an extraordinary crystal structure.
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Affiliation(s)
- Noam S. Freeman
- Department of Chemistry and Biochemistry, University of
California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United
States
| | - Curtis E. Moore
- Department of Chemistry and Biochemistry, University of
California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United
States
| | - L. Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering/Chemistry
and Biochemistry, Chalmers University of Technology, Gothenburg 41296, Sweden
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of
California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United
States
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48
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Sarter C, Heimes M, Jäschke A. The role of alkyl substituents in deazaadenine-based diarylethene photoswitches. Beilstein J Org Chem 2016; 12:1103-10. [PMID: 27340498 PMCID: PMC4901873 DOI: 10.3762/bjoc.12.106] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 05/13/2016] [Indexed: 12/11/2022] Open
Abstract
Diarylethenes are an important class of reversible photoswitches and often claimed to require two alkyl substituents at the carbon atoms between which the bond is formed or broken in the electrocyclic rearrangement. Here we probe this claim by the synthesis and characterization of four pairs of deazaadenine-based diarylethene photoswitches with either one or two methyl groups at these positions. Depending on the substitution pattern, diarylethenes with one alkyl group can exhibit significant photochromism, but they generally show poor stability towards extended UV irradiation, low thermal stability, and decreased fatigue resistance. The results obtained provide an important direction for the design of new efficient DNA photoswitches for the application in bionanotechnology and synthetic biology.
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Affiliation(s)
- Christopher Sarter
- Institut für Pharmazie und Molekulare Biotechnologie, Universität Heidelberg, 69120 Heidelberg, Germany
| | - Michael Heimes
- Institut für Pharmazie und Molekulare Biotechnologie, Universität Heidelberg, 69120 Heidelberg, Germany
| | - Andres Jäschke
- Institut für Pharmazie und Molekulare Biotechnologie, Universität Heidelberg, 69120 Heidelberg, Germany
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49
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Morihiro K, Hasegawa O, Mori S, Tsunoda S, Obika S. C5-azobenzene-functionalized locked nucleic acid uridine: isomerization properties, hybridization ability, and enzymatic stability. Org Biomol Chem 2016; 13:5209-14. [PMID: 25853508 DOI: 10.1039/c5ob00477b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Oligonucleotides (ONs) modified with a locked nucleic acid (LNA) are widely used in the fields of therapeutics, diagnosis, and nanotechnology. There have been significant efforts towards developing LNA analogues bearing modified bridges to improve their hybridization ability, nuclease resistance, and pharmacokinetic profiles. Moreover, nucleobase modifications of LNA are useful strategies for the functionalization of ONs. Modifications of the C5-position of pyrimidine nucleobases are particularly interesting because they enable predictable positioning of functional groups in the major groove of the duplex. Here we report the synthesis of C5-azobenzene-functionalized LNA uridine (LNA-U(Az)) and properties of LNA-U(Az)-modified ONs, including isomerization properties, hybridization ability, and enzyme stability. LNA-U(Az) in ON is photo-isomerized effectively and reversibly by irradiation at 365 nm (trans to cis) and 450 nm (cis to trans). LNA-U(Az)-modified ONs show RNA-selective hybridization ability despite the large hydrophobic azobenzene moiety extending into the major groove of the duplex. The enzymatic stability of LNA-U(Az)-modified ONs is higher than that of natural and LNA-modified ONs with or without photo-irradiation. Our results indicate that LNA-U(Az) holds promise for RNA targeting and photo-switchable technologies.
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Affiliation(s)
- K Morihiro
- National Institute of Biomedical Innovation (NIBIO), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan.
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50
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Wu J, Yu F, Zhang Z, Chen Y, Du J. Highly sensitive self-complementary DNA nanoswitches triggered by polyelectrolytes. NANOSCALE 2016; 8:464-470. [PMID: 26627445 DOI: 10.1039/c5nr05193b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Dimerization of two homologous strands of genomic DNA/RNA is an essential feature of retroviral replication. Herein we show that a cationic comb-type copolymer (CCC), poly(L-lysine)-graft-dextran, accelerates the dimerization of self-complementary stem-loop DNA, frequently found in functional DNA/RNA molecules, such as aptamers. Furthermore, an anionic polymer poly(sodium vinylsulfonate) (PVS) dissociates CCC from the duplex shortly within a few seconds. Then single stem-loop DNA spontaneously transforms from its dimer. Thus we can easily control the dimer and stem-loop DNA by switching on/off CCC activity. Both polyelectrolytes and DNA concentrations are in the nanomole per liter range. The polyelectrolyte-assisted transconformation and sequences design strategy ensures the reversible state control with rapid response and effective switching under physiologically relevant conditions. A further application of this sensitive assembly is to construct an aptamer-type drug delivery system, bind or release functional molecules responding to its transconformation.
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Affiliation(s)
- Jincai Wu
- College of Materials and Chemistry Engineering, Hainan University, Haikou 570228, China.
| | - Feng Yu
- College of Materials and Chemistry Engineering, Hainan University, Haikou 570228, China.
| | - Zheng Zhang
- College of Materials and Chemistry Engineering, Hainan University, Haikou 570228, China.
| | - Yong Chen
- College of Materials and Chemistry Engineering, Hainan University, Haikou 570228, China.
| | - Jie Du
- College of Materials and Chemistry Engineering, Hainan University, Haikou 570228, China.
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