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Lechner VM, Nappi M, Deneny PJ, Folliet S, Chu JCK, Gaunt MJ. Visible-Light-Mediated Modification and Manipulation of Biomacromolecules. Chem Rev 2021; 122:1752-1829. [PMID: 34546740 DOI: 10.1021/acs.chemrev.1c00357] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chemically modified biomacromolecules-i.e., proteins, nucleic acids, glycans, and lipids-have become crucial tools in chemical biology. They are extensively used not only to elucidate cellular processes but also in industrial applications, particularly in the context of biopharmaceuticals. In order to enable maximum scope for optimization, it is pivotal to have a diverse array of biomacromolecule modification methods at one's disposal. Chemistry has driven many significant advances in this area, and especially recently, numerous novel visible-light-induced photochemical approaches have emerged. In these reactions, light serves as an external source of energy, enabling access to highly reactive intermediates under exceedingly mild conditions and with exquisite spatiotemporal control. While UV-induced transformations on biomacromolecules date back decades, visible light has the unmistakable advantage of being considerably more biocompatible, and a spectrum of visible-light-driven methods is now available, chiefly for proteins and nucleic acids. This review will discuss modifications of native functional groups (FGs), including functionalization, labeling, and cross-linking techniques as well as the utility of oxidative degradation mediated by photochemically generated reactive oxygen species. Furthermore, transformations at non-native, bioorthogonal FGs on biomacromolecules will be addressed, including photoclick chemistry and DNA-encoded library synthesis as well as methods that allow manipulation of the activity of a biomacromolecule.
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Affiliation(s)
- Vivian M Lechner
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Manuel Nappi
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Patrick J Deneny
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Sarah Folliet
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - John C K Chu
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Matthew J Gaunt
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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2
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Morihiro K, Moriyama Y, Nemoto Y, Osumi H, Okamoto A. anti-syn Unnatural Base Pair Enables Alphabet-Expanded DNA Self-Assembly. J Am Chem Soc 2021; 143:14207-14217. [PMID: 34450012 DOI: 10.1021/jacs.1c05393] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Self-assembly properties and diversity in higher-order structures of DNA enable programmable tools to be used to construct algorithms at the molecular level. However, the utility of DNA-based programmable tools is hampered by the low orthogonality to natural nucleic acids, especially in complex molecular systems. To address this challenge, we report here the orthogonal regulation of DNA self-assembly by using an unnatural base pair (UBP) formation. Our newly designed UBP AnN:SyN is formed in combination with anti and unusual syn glycosidic conformation with high thermal stability and selectivity. Furthermore, AnC worked as a pH-sensitive artificial nucleobase, which forms a strong base pair with cytosine under a weak acidic condition (pH 6.0). The orthogonal AnN:SyN base pair functioned as a trigger for hybridization chain reaction to provide long nicked double-stranded DNA (ca. 1000 base pairs). This work represents the first example of the orthogonal DNA self-assembly that is nonreactive to natural four-letter alphabets DNA trigger and expands the types of programmable tools that work in a complex environment.
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Affiliation(s)
- Kunihiko Morihiro
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yuya Moriyama
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yui Nemoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hiraki Osumi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Akimitsu Okamoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.,Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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3
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Weinstain R, Slanina T, Kand D, Klán P. Visible-to-NIR-Light Activated Release: From Small Molecules to Nanomaterials. Chem Rev 2020; 120:13135-13272. [PMID: 33125209 PMCID: PMC7833475 DOI: 10.1021/acs.chemrev.0c00663] [Citation(s) in RCA: 253] [Impact Index Per Article: 63.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Indexed: 02/08/2023]
Abstract
Photoactivatable (alternatively, photoremovable, photoreleasable, or photocleavable) protecting groups (PPGs), also known as caged or photocaged compounds, are used to enable non-invasive spatiotemporal photochemical control over the release of species of interest. Recent years have seen the development of PPGs activatable by biologically and chemically benign visible and near-infrared (NIR) light. These long-wavelength-absorbing moieties expand the applicability of this powerful method and its accessibility to non-specialist users. This review comprehensively covers organic and transition metal-containing photoactivatable compounds (complexes) that absorb in the visible- and NIR-range to release various leaving groups and gasotransmitters (carbon monoxide, nitric oxide, and hydrogen sulfide). The text also covers visible- and NIR-light-induced photosensitized release using molecular sensitizers, quantum dots, and upconversion and second-harmonic nanoparticles, as well as release via photodynamic (photooxygenation by singlet oxygen) and photothermal effects. Release from photoactivatable polymers, micelles, vesicles, and photoswitches, along with the related emerging field of photopharmacology, is discussed at the end of the review.
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Affiliation(s)
- Roy Weinstain
- School
of Plant Sciences and Food Security, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Tomáš Slanina
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Dnyaneshwar Kand
- School
of Plant Sciences and Food Security, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Petr Klán
- Department
of Chemistry and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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4
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Chemical synthesis and biochemical characterization of cyclic oligonucleotides containing acyl groups at both 5'- and 3'-terminal positions. Bioorg Med Chem 2020; 28:115799. [PMID: 33069130 DOI: 10.1016/j.bmc.2020.115799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 11/21/2022]
Abstract
Modified oligonucleotides, whose ON-OFF switch of hybridization can be controlled by an external stimulus, are important to understanding life phenomena and efficient treatment of diseases. The ON-OFF switch can be completely controlled by chemical modification of the oligonucleotide such as cyclization. However, their chemical modifications of the previous cyclic oligonucleotides remain after the addition of an external stimulus. To overcome this problem, we carried out the first synthesis of cyclic oligonucleotides containing acyl groups at both 5'- and 3'-terminal positions, which can be hydrolyzed by intracellular esterase. The cyclic oligonucleotides were successfully synthesized via disulfide bond formation and the phosphoramidite method without base protection on polymer supports containing a silyl linker. Subsequently, we were able to introduce a functional group into the cyclic oligonucleotide using the corresponding isothiocyanate reagent. Additionally, a cyclic oligonucleotide with acyl groups was found to have a much lower binding ability than the corresponding linear oligonucleotide. Moreover, we demonstrated its structural conversion to the corresponding linear oligonucleotide with two thiol groups under reducing conditions using dithiothreitol. It was also confirmed that the two terminal acyl groups of the linear oligonucleotide were hydrolyzed by pig liver esterase. These results indicate that hybridization of cyclic acylated nucleic acid drugs with high nuclease resistance is regulated by intracellular esterase under the reducing conditions in the cell cytoplasm.
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Corrigan N, Ciftci M, Jung K, Boyer C. Gesteuerte Reaktionsorthogonalität in der Polymer‐ und Materialwissenschaft. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201912001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Nathaniel Corrigan
- Centre for Advanced Macromolecular Design and Australian Centre for Nanomedicine School of Chemical Engineering UNSW Sydney 2052 Australia
| | - Mustafa Ciftci
- Centre for Advanced Macromolecular Design and Australian Centre for Nanomedicine School of Chemical Engineering UNSW Sydney 2052 Australia
- Department of Chemistry Faculty of Engineering and Natural Science Bursa Technical University Bursa 16310 Turkey
| | - Kenward Jung
- Centre for Advanced Macromolecular Design and Australian Centre for Nanomedicine School of Chemical Engineering UNSW Sydney 2052 Australia
| | - Cyrille Boyer
- Centre for Advanced Macromolecular Design and Australian Centre for Nanomedicine School of Chemical Engineering UNSW Sydney 2052 Australia
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Corrigan N, Ciftci M, Jung K, Boyer C. Mediating Reaction Orthogonality in Polymer and Materials Science. Angew Chem Int Ed Engl 2020; 60:1748-1781. [DOI: 10.1002/anie.201912001] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Nathaniel Corrigan
- Centre for Advanced Macromolecular Design and Australian Centre for Nanomedicine School of Chemical Engineering UNSW Sydney 2052 Australia
| | - Mustafa Ciftci
- Centre for Advanced Macromolecular Design and Australian Centre for Nanomedicine School of Chemical Engineering UNSW Sydney 2052 Australia
- Department of Chemistry Faculty of Engineering and Natural Science Bursa Technical University Bursa 16310 Turkey
| | - Kenward Jung
- Centre for Advanced Macromolecular Design and Australian Centre for Nanomedicine School of Chemical Engineering UNSW Sydney 2052 Australia
| | - Cyrille Boyer
- Centre for Advanced Macromolecular Design and Australian Centre for Nanomedicine School of Chemical Engineering UNSW Sydney 2052 Australia
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Menzel JP, Feist F, Tuten B, Weil T, Blinco JP, Barner-Kowollik C. Light-Controlled Orthogonal Covalent Bond Formation at Two Different Wavelengths. Angew Chem Int Ed Engl 2019; 58:7470-7474. [PMID: 30916368 DOI: 10.1002/anie.201901275] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Indexed: 11/12/2022]
Abstract
We report light-induced reactions in a two-chromophore system capable of sequence-independent λ-orthogonal reactivity relying solely on the choice of wavelength and solvent. In a solution of water and acetonitrile, LED irradiation at λmax =285 nm leads to full conversion of 2,5-diphenyltetrazoles with N-ethylmaleimide to the pyrazoline ligation products. Simultaneously present o-methylbenzaldehyde thioethers are retained. Conversely, LED irradiation at λmax =382 nm is used to induce ligation of the o-methylbenzaldehydes in acetonitrile with N-ethylmaleimide via o-quinodimethanes, while 2,5-diphenyltetrazoles also present are retained. This unprecedented photochemical selectivity is achieved through control of the number and wavelength of incident photons as well as favorable optical properties and quantum yields of the reactants in their environment.
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Affiliation(s)
- Jan P Menzel
- School of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology (QUT), Brisbane, QLD, 4000, Australia
| | - Florian Feist
- School of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology (QUT), Brisbane, QLD, 4000, Australia.,Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Bryan Tuten
- School of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology (QUT), Brisbane, QLD, 4000, Australia
| | - Tanja Weil
- Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - James P Blinco
- School of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology (QUT), Brisbane, QLD, 4000, Australia.,Macromolecular Architectures, Institut für Technische Chemie und Polymerchemie, Karlsruhe Institute of Technology (KIT), Engesserstrasse 18, 76131, Karlsruhe, Germany
| | - Christopher Barner-Kowollik
- School of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology (QUT), Brisbane, QLD, 4000, Australia.,Macromolecular Architectures, Institut für Technische Chemie und Polymerchemie, Karlsruhe Institute of Technology (KIT), Engesserstrasse 18, 76131, Karlsruhe, Germany
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Menzel JP, Feist F, Tuten B, Weil T, Blinco JP, Barner‐Kowollik C. Lichtinduzierte orthogonale Bildung kovalenter Bindungen durch zwei Wellenlängen. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901275] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jan P. Menzel
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) Brisbane QLD 4000 Australien
| | - Florian Feist
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) Brisbane QLD 4000 Australien
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| | - Bryan Tuten
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) Brisbane QLD 4000 Australien
| | - Tanja Weil
- Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| | - James P. Blinco
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) Brisbane QLD 4000 Australien
- Macromolecular Architectures Institut für Technische Chemie und Polymerchemie Karlsruher Institut für Technologie (KIT) Engesserstraße 18 76131 Karlsruhe Deutschland
| | - Christopher Barner‐Kowollik
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QUT) Brisbane QLD 4000 Australien
- Macromolecular Architectures Institut für Technische Chemie und Polymerchemie Karlsruher Institut für Technologie (KIT) Engesserstraße 18 76131 Karlsruhe Deutschland
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9
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Kaewsomboon T, Nishizawa S, Kanamori T, Yuasa H, Ohkubo A. pH-Dependent Switching of Base Pairs Using Artificial Nucleobases with Carboxyl Groups. J Org Chem 2018; 83:1320-1327. [PMID: 29322767 DOI: 10.1021/acs.joc.7b02828] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study, we report the synthesis of modified oligonucleotides consisting of benzoic acid or isophthalic acid residues as new nucleobases. As evaluated by UV thermal denaturation analysis at different pH conditions (5.0, 6.0, 7.0, and 8.0), these modified oligonucleotides exhibited pH-dependent recognition of natural nucleobases and one is first found to be capable of base pair switching in response to a pH change. The isophthalic acid residue incorporated into the oligonucleotide on a d-threoninol backbone could preferentially bind with adenine but with guanine in response to a change in the pH conditions from pH 5 to pH 7 (or 8) without significant difference in duplex stability. These findings would be valuable for further developing pH-responsive DNA-based molecular devices.
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Affiliation(s)
- Tanasak Kaewsomboon
- Department of Life Science and Technology, Tokyo Institute of Technology , 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Shuhei Nishizawa
- Department of Life Science and Technology, Tokyo Institute of Technology , 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Takashi Kanamori
- Department of Life Science and Technology, Tokyo Institute of Technology , 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Hideya Yuasa
- Department of Life Science and Technology, Tokyo Institute of Technology , 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
| | - Akihiro Ohkubo
- Department of Life Science and Technology, Tokyo Institute of Technology , 4259 Nagatsuta, Midoriku, Yokohama 226-8501, Japan
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