1
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Ogorek AN, Zhou X, Martell JD. Switchable DNA Catalysts for Proximity Labeling at Sites of Protein-Protein Interactions. J Am Chem Soc 2023; 145:16913-16923. [PMID: 37463457 DOI: 10.1021/jacs.3c05578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Proximity labeling (PL) has emerged as a powerful approach to elucidate proteomes within a defined radius around a protein of interest (POI). In PL, a catalyst is attached to the POI and tags nearby endogenous proteins, which are then isolated by affinity purification and identified by mass spectrometry. Although existing PL methods have yielded numerous biological insights, proteomes with greater spatial resolution could be obtained if PL catalysts could be activated at more specific subcellular locations, such as sites where both the POI and a chemical stimulus are present or sites of protein-protein interactions (PPIs). Here, we report DNA-based switchable PL catalysts that are attached to a POI and become activated only when a secondary molecular trigger is present. The DNA catalysts consist of a photocatalyst and a spectral quencher tethered to a DNA oligomer. They are catalytically inactive by default but undergo a conformational change in response to a specific molecular trigger, thus activating PL. We designed a system in which the DNA catalyst becomes activated on living mammalian cells specifically at sites of Her2-Her3 heterodimers and c-Met homodimers, PPIs known to increase the invasion and growth of certain cancers. While this study employs a Ru(bpy)3-type complex for tagging proteins with biotin phenol, the switchable DNA catalyst design is compatible with diverse synthetic PL photocatalysts. Furthermore, the switchable DNA PL catalysts can be constructed from conformation-switching DNA aptamers that respond to small molecules, ions, and proteins, opening future opportunities for PL in highly specific subcellular locations.
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Affiliation(s)
- Ashley N Ogorek
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Xu Zhou
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Jeffrey D Martell
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53726, United States
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2
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Pimentel EB, Peters-Clarke TM, Coon JJ, Martell JD. DNA-Scaffolded Synergistic Catalysis. J Am Chem Soc 2021; 143:21402-21409. [PMID: 34898209 PMCID: PMC9101022 DOI: 10.1021/jacs.1c10757] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We report DNA-scaffolded synergistic catalysis, a concept that combines the diverse reaction scope of synergistic catalysis with the ability of DNA to precisely preorganize abiotic groups and undergo stimuli-triggered conformational changes. As an initial demonstration of this concept, we focus on Cu-TEMPO-catalyzed aerobic alcohol oxidation, using DNA as a scaffold to hold a copper cocatalyst and an organic radical cocatalyst (TEMPO) in proximity. The DNA-scaffolded catalyst maintained a high turnover number upon dilution and exhibited 190-fold improvement in catalyst turnover number relative to the unscaffolded cocatalysts. By incorporating the cocatalysts into a DNA hairpin-containing scaffold, we demonstrate that the rate of the synergistic catalytic reaction can be controlled through a reversible DNA conformational change that alters the distance between the cocatalysts. This work demonstrates the compatibility of synergistic catalytic reactions with DNA scaffolding, opening future avenues in reaction discovery, sensing, responsive materials, and chemical biology.
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Affiliation(s)
- Edward B. Pimentel
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | | | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA, Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA, National Center for Quantitative Biology of Complex Systems, Madison, WI, 53706, USA, Morgridge Institute for Research, Madison, WI, 53515, USA
| | - Jeffrey D. Martell
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53705, USA,
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3
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Liu W, Watson EE, Winssinger N. Photocatalysis in Chemical Biology: Extending the Scope of Optochemical Control and Towards New Frontiers in Semisynthetic Bioconjugates and Biocatalysis. Helv Chim Acta 2021. [DOI: 10.1002/hlca.202100179] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Weilong Liu
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Science University of Geneva 30 quai Ernest Ansermet CH-1211 Geneva Switzerland
| | - Emma E. Watson
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Science University of Geneva 30 quai Ernest Ansermet CH-1211 Geneva Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry NCCR Chemical Biology Faculty of Science University of Geneva 30 quai Ernest Ansermet CH-1211 Geneva Switzerland
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4
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Altrichter Y, Schöller J, Seitz O. Toward conditional control of Smac mimetic activity by RNA-templated reduction of azidopeptides on PNA or 2'-OMe-RNA. Biopolymers 2021; 112:e23466. [PMID: 34287823 DOI: 10.1002/bip.23466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 11/06/2022]
Abstract
Oligonucleotide templated reactions can be used to control the activity of functional molecules based on the presence of a specific trigger sequence. We report an RNA-controlled reaction system to conditionally restore the N-terminal amino group and thus binding affinity of azide-modified Smac mimetic compounds (SMCs) for their target protein X-linked Inhibitor of Apoptosis Protein (XIAP). Two templated reactions were compared: Staudinger reduction with phosphines and a photocatalytic reaction with Ru(bpy)2 (mcbpy). The latter proved faster and more efficient, especially for the activation of a bivalent SMC, which requires two consecutive reduction steps. The templated reaction proceeds with turnover when 2'-OMe-RNA probes are used, but is significantly more efficient with PNA, catalyzing a reaction in the presence of low, substoichiometric amounts (1%-3%, 10 nM) of target RNA.
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Affiliation(s)
- Yannic Altrichter
- Department of Chemistry, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Justus Schöller
- Department of Chemistry, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Oliver Seitz
- Department of Chemistry, Humboldt-Universität zu Berlin, Berlin, Germany
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5
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Interrogating biological systems using visible-light-powered catalysis. Nat Rev Chem 2021; 5:322-337. [PMID: 37117838 DOI: 10.1038/s41570-021-00265-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2021] [Indexed: 12/12/2022]
Abstract
Light-powered catalysis has found broad utility as a chemical transformation strategy, with widespread impact on energy, environment, drug discovery and human health. A noteworthy application impacting human health is light-induced sensitization of cofactors for photodynamic therapy in cancer treatment. The clinical adoption of this photosensitization approach has inspired the search for other photochemical methods, such as photoredox catalysis, to influence biological discovery. Over the past decade, light-mediated catalysis has enabled the discovery of valuable synthetic transformations, propelling it to become a highly utilized chemical synthesis strategy. The reaction components required to achieve a photoredox reaction are identical to photosensitization (catalyst, light source and substrate), making it ideally suited for probing biological environments. In this Review, we discuss the therapeutic application of photosensitization and advancements made in developing next-generation catalysts. We then highlight emerging uses of photoredox catalytic methods for protein bioconjugation and probing complex cellular environments in living cells.
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6
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Koo B, Yoo H, Choi HJ, Kim M, Kim C, Kim KT. Visible Light Photochemical Reactions for Nucleic Acid-Based Technologies. Molecules 2021; 26:556. [PMID: 33494512 PMCID: PMC7865461 DOI: 10.3390/molecules26030556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/18/2021] [Accepted: 01/18/2021] [Indexed: 12/16/2022] Open
Abstract
The expanding scope of chemical reactions applied to nucleic acids has diversified the design of nucleic acid-based technologies that are essential to medicinal chemistry and chemical biology. Among chemical reactions, visible light photochemical reaction is considered a promising tool that can be used for the manipulations of nucleic acids owing to its advantages, such as mild reaction conditions and ease of the reaction process. Of late, inspired by the development of visible light-absorbing molecules and photocatalysts, visible light-driven photochemical reactions have been used to conduct various molecular manipulations, such as the cleavage or ligation of nucleic acids and other molecules as well as the synthesis of functional molecules. In this review, we describe the recent developments (from 2010) in visible light photochemical reactions involving nucleic acids and their applications in the design of nucleic acid-based technologies including DNA photocleaving, DNA photoligation, nucleic acid sensors, the release of functional molecules, and DNA-encoded libraries.
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Affiliation(s)
| | | | | | - Min Kim
- Department of Chemistry, Chungbuk National University, Cheongju 28644, Korea; (B.K.); (H.Y.); (H.J.C.)
| | - Cheoljae Kim
- Department of Chemistry, Chungbuk National University, Cheongju 28644, Korea; (B.K.); (H.Y.); (H.J.C.)
| | - Ki Tae Kim
- Department of Chemistry, Chungbuk National University, Cheongju 28644, Korea; (B.K.); (H.Y.); (H.J.C.)
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7
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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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8
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Ito Y. Development of Ruthenium Complex-Conjugated Oligonucleotides. J SYN ORG CHEM JPN 2020. [DOI: 10.5059/yukigoseikyokaishi.78.898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yuta Ito
- Faculty of Pharmaceutical Sciences, Tokushima Bunri Univeristy
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9
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Dutta S, Rühle J, Schikora M, Deussner-Helfmann N, Heilemann M, Zatsepin T, Duchstein P, Zahn D, Knör G, Mokhir A. Red light-triggered photoreduction on a nucleic acid template. Chem Commun (Camb) 2020; 56:10026-10029. [PMID: 32728684 DOI: 10.1039/d0cc03086d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Conjugate Sn(iv)(pyropheophorbide a)dichloride-(peptide nucleic acid) catalyzes reduction of azobenzene derivatives in the presence of complementary nucleic acid (NA) upon irridiation with red light (660 nm). This is the first red light-induced NA-templated photoreduction. It is highly sensitive to single mismatches in the NA-template and can detect down to 5 nM NAs.
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Affiliation(s)
- Subrata Dutta
- Department of Chemistry and Pharmacy, Organic Chemistry II, Friedrich-Alexander-University of Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany.
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10
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Ruthenium(II)-cored supramolecular organic framework-mediated recyclable visible light photoreduction of azides to amines and cascade formation of lactams. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2019.03.056] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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11
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Zozulia O, Bachmann T, Mokhir A. Red Light Triggered Fluorogenic Reaction with Picomolar Sensitivity Toward Nucleic Acids. Bioconjug Chem 2019; 30:2023-2031. [PMID: 31195795 DOI: 10.1021/acs.bioconjchem.9b00299] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We have previously reported on a red light triggered, singlet oxygen-mediated fluorogenic reaction that is templated in a highly sequence specific fashion by nucleic acids (S. Dutta, A. Fulop, A. Mokhir, Bioconjgate Chem. 2013, 24 (9), 1533-1542). Up to the present date, it has remained a single templated reaction responsive to nontoxic >650 nm light. However, it is operative only in the presence of relatively high (>2 nM) concentrations of templates that dramatically limit its applicability in nucleic acid detection. In the current work, we established that an inefficient intermolecular electron transfer involved in reduction of the 1,4-endoperoxide intermediate, formed in the rate-limiting reaction step, is responsible for inhibition of the reaction at low reagent concentrations. We suggested the solution of the problem which includes a combination of a cleavable (9-alkoxyanthracene) moiety with a two-electron donating fragment in one molecule. This approach enables the efficient intramolecular electron transfer to the endoperoxide intermediate in the critical reaction step. Due to the intramolecular character of the latter process, it is practically independent of concentration of the reagents. The reaction based on the improved cleavable moiety was found to be >200-fold more sensitive than the previously reported one. It is fast, sequence specific, and compatible with live cells. Accounting for short reactions times (<30 min), nontoxic trigger (red light), excellent sensitivity, and sequence specificity, this is presently the best reported photochemical templated reaction compatible with live cells.
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Affiliation(s)
- Oleksii Zozulia
- Friedrich-Alexander University Erlangen-Nürnberg (FAU) , Department of Chemistry and Pharmacy, Organic Chemistry Chair II , Nikolaus-Fiebiger-Strasse 10 , 91058 Erlangen , Germany
| | - Tobias Bachmann
- Friedrich-Alexander University Erlangen-Nürnberg (FAU) , Department of Chemistry and Pharmacy, Organic Chemistry Chair II , Nikolaus-Fiebiger-Strasse 10 , 91058 Erlangen , Germany
| | - Andriy Mokhir
- Friedrich-Alexander University Erlangen-Nürnberg (FAU) , Department of Chemistry and Pharmacy, Organic Chemistry Chair II , Nikolaus-Fiebiger-Strasse 10 , 91058 Erlangen , Germany
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12
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Angerani S, Winssinger N. Visible Light Photoredox Catalysis Using Ruthenium Complexes in Chemical Biology. Chemistry 2019; 25:6661-6672. [PMID: 30689234 DOI: 10.1002/chem.201806024] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Indexed: 12/24/2022]
Abstract
The development of bioorthogonal reactions have had a transformative impact in chemical biology and the quest to expand this toolbox continues. Herein we review recent applications of ruthenium-catalyzed photoredox reactions used in chemical biology.
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Affiliation(s)
- Simona Angerani
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 Quai Ernest-Ansermet, 1205, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 Quai Ernest-Ansermet, 1205, Geneva, Switzerland
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13
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Anzola M, Winssinger N. Turn On of a Ruthenium(II) Photocatalyst by DNA-Templated Ligation. Chemistry 2018; 25:334-342. [PMID: 30451338 DOI: 10.1002/chem.201804283] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Indexed: 01/05/2023]
Abstract
Here, the synthesis of a RuII photocatalyst by light-directed oligonucleotide-templated ligation reaction is described. The photocatalyst was found to have tremendous potential for signal amplification with >15000 turnovers measured in 9 hours. A templated reaction was used to turn on the activity of this ruthenium(II) photocatalyst in response to a specific DNA sequence. The photocatalysis of the ruthenium(II) complex was harnessed to uncage a new precipitating dye that is highly fluorescent and photostable in the solid state. This reaction was used to discriminate between different DNA analytes based on localization of the precipitate as well as for in cellulo miRNA detection. Finally, a bipyridine ligand functionalized with two different peptide nucleic acid (PNA) sequences was shown to enable template-mediated ligation (turn on of the ruthenium(II) photocatalysis) and recruitment of substrate for templated photocatalysis.
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Affiliation(s)
- Marcello Anzola
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 Quai Ernest-Ansermet, 1205, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 Quai Ernest-Ansermet, 1205, Geneva, Switzerland
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14
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Ukale DU, Lönnberg T. 2,6‐Dimercuriphenol as a Bifacial Dinuclear Organometallic Nucleobase. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201809398] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
| | - Tuomas Lönnberg
- Department of ChemistryUniversity of Turku Vatselankatu 2 20014 Turku Finland
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15
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Ukale DU, Lönnberg T. 2,6-Dimercuriphenol as a Bifacial Dinuclear Organometallic Nucleobase. Angew Chem Int Ed Engl 2018; 57:16171-16175. [PMID: 30358071 DOI: 10.1002/anie.201809398] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/11/2018] [Indexed: 11/07/2022]
Abstract
A C-nucleoside having 2,6-dimercuriphenol as the base moiety has been synthesized and incorporated into an oligonucleotide. NMR and UV melting experiments revealed the ability of this bifacial organometallic nucleobase surrogate to form stable dinuclear HgII -mediated base triples with adenine, cytosine, and thymine (or uracil) in solution as well as within a triple-helical oligonucleotide. A single HgII -mediated base triple between 2,6-dimercuriphenol and two thymines increased both Hoogsteen and Watson-Crick melting temperatures of a 15-mer pyrimidine⋅purine*pyrimidine triple helix by more than 10 °C relative to an unmodified triple helix of the same length. This novel binding mode could be exploited in targeting certain pathogenic nucleic acids as well as in DNA nanotechnology.
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Affiliation(s)
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014, Turku, Finland
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16
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Luciferase-induced photoreductive uncaging of small-molecule effectors. Nat Commun 2018; 9:3539. [PMID: 30166547 PMCID: PMC6117273 DOI: 10.1038/s41467-018-05916-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 08/03/2018] [Indexed: 12/14/2022] Open
Abstract
Bioluminescence resonance energy transfer (BRET) is extensively used to study dynamic systems and has been utilized in sensors for studying protein proximity, metabolites, and drug concentrations. Herein, we demonstrate that BRET can activate a ruthenium-based photocatalyst which performs bioorthogonal reactions. BRET from luciferase to the ruthenium photocatalyst is used to uncage effector molecules with up to 64 turnovers of the catalyst, achieving concentrations >0.6 μM effector with 10 nM luciferase construct. Using a BRET sensor, we further demonstrate that the catalysis can be modulated in response to an analyte, analogous to allosterically controlled enzymes. The BRET-induced reaction is used to uncage small-molecule drugs (ibrutinib and duocarmycin) at biologically effective concentrations in cellulo. Bioluminescence resonance energy transfer (BRET) has been mostly employed in imaging applications. Here the authors use BRET to activate a ruthenium-based photocatalyst and perform a bioorthogonal chemical reaction, which can be used to uncage small molecule drugs in a cellular context.
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17
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Hibino M, Aiba Y, Watanabe Y, Shoji O. Peptide Nucleic Acid Conjugated with Ruthenium-Complex Stabilizing Double-Duplex Invasion Complex Even under Physiological Conditions. Chembiochem 2018; 19:1601-1604. [PMID: 29797750 DOI: 10.1002/cbic.201800256] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Indexed: 02/03/2023]
Abstract
Peptide nucleic acid (PNA) can form a stable duplex with DNA, and, accordingly, directly recognize double-stranded DNA through the formation of a double-duplex invasion complex, wherein a pair of complementary PNA strands form two PNA/DNA duplexes. Because invasion does not require prior denaturation of DNA, PNA holds great potential for in cellulo or in vivo applications. To broaden the applicability of PNA invasion, we developed a new conjugate of PNA with a ruthenium complex. This Ru-PNA conjugate exhibits higher DNA-binding affinity, which results in enhanced invasion efficiency, even under physiological conditions.
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Affiliation(s)
- Masaki Hibino
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-Cho Chikusa-Ku, Nagoya, Aichi, 464-8602, Japan
| | - Yuichiro Aiba
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-Cho Chikusa-Ku, Nagoya, Aichi, 464-8602, Japan
| | - Yoshihito Watanabe
- Research Center for Materials Science, Nagoya University, Furo-Cho Chikusa-Ku, Nagoya, Aichi, 464-8602, Japan
| | - Osami Shoji
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-Cho Chikusa-Ku, Nagoya, Aichi, 464-8602, Japan
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18
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Werther P, Möhler JS, Wombacher R. A Bifunctional Fluorogenic Rhodamine Probe for Proximity-Induced Bioorthogonal Chemistry. Chemistry 2017; 23:18216-18224. [DOI: 10.1002/chem.201703607] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Indexed: 01/10/2023]
Affiliation(s)
- Philipp Werther
- Institut für Pharmazie und Molekulare Biotechnologie; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Jasper S. Möhler
- Institut für Pharmazie und Molekulare Biotechnologie; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Richard Wombacher
- Institut für Pharmazie und Molekulare Biotechnologie; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 364 69120 Heidelberg Germany
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19
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Speckmeier E, Zeitler K. Desyl and Phenacyl as Versatile, Photocatalytically Cleavable Protecting Groups: A Classic Approach in a Different (Visible) Light. ACS Catal 2017. [DOI: 10.1021/acscatal.7b02117] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Elisabeth Speckmeier
- Institut für Organische
Chemie, Universität Leipzig, Johannisallee 29, D-04103 Leipzig, Germany
| | - Kirsten Zeitler
- Institut für Organische
Chemie, Universität Leipzig, Johannisallee 29, D-04103 Leipzig, Germany
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20
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Abstract
Nucleic acid directed bioorthogonal reactions offer the fascinating opportunity to unveil and redirect a plethora of intracellular mechanisms. Nano- to picomolar amounts of specific RNA molecules serve as templates and catalyze the selective formation of molecules that 1) exert biological effects, or 2) provide measurable signals for RNA detection. Turnover of reactants on the template is a valuable asset when concentrations of RNA templates are low. The idea is to use RNA-templated reactions to fully control the biodistribution of drugs and to push the detection limits of DNA or RNA analytes to extraordinary sensitivities. Herein we review recent and instructive examples of conditional synthesis or release of compounds for in cellulo protein interference and intracellular nucleic acid imaging.
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Affiliation(s)
- Margherita Di Pisa
- Department of ChemistryHumboldt University BerlinBrook-Taylor Strasse 212489BerlinGermany
| | - Oliver Seitz
- Department of ChemistryHumboldt University BerlinBrook-Taylor Strasse 212489BerlinGermany
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21
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Velema WA, Kool ET. Fluorogenic Templated Reaction Cascades for RNA Detection. J Am Chem Soc 2017; 139:5405-5411. [PMID: 28345912 DOI: 10.1021/jacs.7b00466] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nucleic acids detection is essential to the study of biological processes and to diagnosis of pathological states. Although PCR is highly effective in vitro, methods that can function without prior sample preparation, thermal cycling, or enzymes are of interest due to their simplicity. Most current non-PCR detection methods rely on linear signal amplification, which hinders the detection of small amounts of genetic material. To address this limitation, we tested a new strategy for attaining higher-order signal amplification, in which a target sequence templates a chemical ligation, and the product of this reaction is in turn detected with a second templated reaction. The method is nonenzymatic, isothermal, and fluorogenic, allowing the direct detection of nucleic acids in complex matrices. Using this approach, as little as 500 attomoles (10 pM) could be detected with single nucleotide resolution. In a test of selectivity, single nucleotide substitutions and deletions could successfully be detected, including a deletion that is associated with tetracycline resistance in Helicobacter pylori. Compatibility with biological matrices was demonstrated by the direct detection of rRNA in bacterial lysate. Imaging and detection of target sequences on a solid support further illustrates the potential of the new approach for high-throughput analysis.
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Affiliation(s)
- Willem A Velema
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Eric T Kool
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
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22
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Karimi M, Zangabad PS, Baghaee-Ravari S, Ghazadeh M, Mirshekari H, Hamblin MR. Smart Nanostructures for Cargo Delivery: Uncaging and Activating by Light. J Am Chem Soc 2017; 139:4584-4610. [PMID: 28192672 PMCID: PMC5475407 DOI: 10.1021/jacs.6b08313] [Citation(s) in RCA: 256] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nanotechnology has begun to play a remarkable role in various fields of science and technology. In biomedical applications, nanoparticles have opened new horizons, especially for biosensing, targeted delivery of therapeutics, and so forth. Among drug delivery systems (DDSs), smart nanocarriers that respond to specific stimuli in their environment represent a growing field. Nanoplatforms that can be activated by an external application of light can be used for a wide variety of photoactivated therapies, especially light-triggered DDSs, relying on photoisomerization, photo-cross-linking/un-cross-linking, photoreduction, and so forth. In addition, light activation has potential in photodynamic therapy, photothermal therapy, radiotherapy, protected delivery of bioactive moieties, anticancer drug delivery systems, and theranostics (i.e., real-time monitoring and tracking combined with a therapeutic action to different diseases sites and organs). Combinations of these approaches can lead to enhanced and synergistic therapies, employing light as a trigger or for activation. Nonlinear light absorption mechanisms such as two-photon absorption and photon upconversion have been employed in the design of light-responsive DDSs. The integration of a light stimulus into dual/multiresponsive nanocarriers can provide spatiotemporal controlled delivery and release of therapeutic agents, targeted and controlled nanosystems, combined delivery of two or more agents, their on-demand release under specific conditions, and so forth. Overall, light-activated nanomedicines and DDSs are expected to provide more effective therapies against serious diseases such as cancers, inflammation, infections, and cardiovascular disease with reduced side effects and will open new doors toward the treatment of patients worldwide.
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Affiliation(s)
- Mahdi Karimi
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Parham Sahandi Zangabad
- Advanced Nanobiotechnology and Nanomedicine Research Group (ANNRG), Iran University of Medical Sciences, Tehran, Iran
- Research Center for Pharmaceutical Nanotechnology (RCPN), Tabriz University of Medical Science (TUOMS), Tabriz, Iran
- Department of Materials Science and Engineering, Sharif University of Technology, 11365-9466 Tehran, Iran
- Nanomedicine Research Association (NRA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Soodeh Baghaee-Ravari
- Joint School of Nanoscience and Nanoengineering, University of North Carolina at Greensboro, Greensboro, North Carolina 27401, United States
| | - Mehdi Ghazadeh
- Joint School of Nanoscience and Nanoengineering, University of North Carolina at Greensboro, Greensboro, North Carolina 27401, United States
| | - Hamid Mirshekari
- Advanced Nanobiotechnology and Nanomedicine Research Group (ANNRG), Iran University of Medical Sciences, Tehran, Iran
| | - Michael R. Hamblin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
- Department of Dermatology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, Massachusetts 02139, United States
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23
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Chang D, Lindberg E, Winssinger N. Critical Analysis of Rate Constants and Turnover Frequency in Nucleic Acid-Templated Reactions: Reaching Terminal Velocity. J Am Chem Soc 2017; 139:1444-1447. [DOI: 10.1021/jacs.6b12764] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dalu Chang
- Department of Organic Chemistry,
NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest-Ansermet, 1205 Geneva, Switzerland
| | - Eric Lindberg
- Department of Organic Chemistry,
NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest-Ansermet, 1205 Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry,
NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest-Ansermet, 1205 Geneva, Switzerland
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24
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Barluenga S, Winssinger N. PNA as a Biosupramolecular Tag for Programmable Assemblies and Reactions. Acc Chem Res 2015; 48:1319-31. [PMID: 25947113 DOI: 10.1021/acs.accounts.5b00109] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The programmability of oligonucleotide hybridization offers an attractive platform for the design of assemblies with emergent properties or functions. Developments in DNA nanotechnologies have transformed our thinking about the applications of nucleic acids. Progress from designed assemblies to functional outputs will continue to benefit from functionalities added to the nucleic acids that can participate in reactions or interactions beyond hybridization. In that respect, peptide nucleic acids (PNAs) are interesting because they combine the hybridization properties of DNA with the modularity of peptides. In fact, PNAs form more stable duplexes with DNA or RNA than the corresponding natural homoduplexes. The high stability achieved with shorter oligomers (an 8-mer is sufficient for a stable duplex at room temperature) typically results in very high sequence fidelity in the hybridization with negligible impact of the ionic strength of the buffer due to the lack of electrostatic repulsion between the duplex strands. The simple peptidic backbone of PNA has been shown to be tolerant of modifications with substitutions that further enhance the duplex stability while providing opportunities for functionalization. Moreover, the metabolic stability of PNAs facilitates their integration into systems that interface with biology. Over the past decade, there has been a growing interest in using PNAs as biosupramolecular tags to program assemblies and reactions. A series of robust templated reactions have been developed with functionalized PNA. These reactions can be used to translate DNA templates into functional polymers of unprecedented complexity, fluorescent outputs, or bioactive small molecules. Furthermore, cellular nucleic acids (mRNA or miRNA) have been harnessed to promote assemblies and reactions in live cells. The tolerance of PNA synthesis also lends itself to the encoding of small molecules that can be further assembled on the basis of their nucleic acid sequences. It is now well-established that hybridization-based assemblies displaying two or more ligands can interact synergistically with a target biomolecule. These assemblies have now been shown to be functional in vivo. Similarly, PNA-tagged macromolecules have been used to prepare bioactive assemblies and three-dimensional nanostructures. Several technologies based on DNA-templated synthesis of sequence-defined polymers or DNA-templated display of ligands have been shown to be compatible with reiterative cycles of selection/amplification starting with large libraries of DNA templates, bringing the power of in vitro evolution to synthetic molecules and offering the possibility of exploring uncharted molecular diversity space with unprecedented scope and speed.
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Affiliation(s)
- Sofia Barluenga
- Department of Organic Chemistry,
NCCR Chemical Biology, University of Geneva, 30 quai Ernest Ansermet, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry,
NCCR Chemical Biology, University of Geneva, 30 quai Ernest Ansermet, Geneva, Switzerland
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25
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Biomolecule-compatible chemical bond-formation and bond-cleavage reactions induced by visible light. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2014.12.034] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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26
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Yan L, Zhou J, Zheng Y, Gamson AS, Roembke BT, Nakayama S, Sintim HO. Isothermal amplified detection of DNA and RNA. MOLECULAR BIOSYSTEMS 2014; 10:970-1003. [PMID: 24643211 DOI: 10.1039/c3mb70304e] [Citation(s) in RCA: 282] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review highlights various methods that can be used for a sensitive detection of nucleic acids without using thermal cycling procedures, as is done in PCR or LCR. Topics included are nucleic acid sequence-based amplification (NASBA), strand displacement amplification (SDA), loop-mediated amplification (LAMP), Invader assay, rolling circle amplification (RCA), signal mediated amplification of RNA technology (SMART), helicase-dependent amplification (HDA), recombinase polymerase amplification (RPA), nicking endonuclease signal amplification (NESA) and nicking endonuclease assisted nanoparticle activation (NENNA), exonuclease-aided target recycling, Junction or Y-probes, split DNAZyme and deoxyribozyme amplification strategies, template-directed chemical reactions that lead to amplified signals, non-covalent DNA catalytic reactions, hybridization chain reactions (HCR) and detection via the self-assembly of DNA probes to give supramolecular structures. The majority of these isothermal amplification methods can detect DNA or RNA in complex biological matrices and have great potential for use at point-of-care.
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Affiliation(s)
- Lei Yan
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA.
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27
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Patzke V, McCaskill JS, von Kiedrowski G. DNA mit 3′-5′-Disulfid-Verknüpfung - schnelle chemische Ligation durch isosteren Ersatz. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201310644] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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28
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Patzke V, McCaskill JS, von Kiedrowski G. DNA with 3'-5'-disulfide links--rapid chemical ligation through isosteric replacement. Angew Chem Int Ed Engl 2014; 53:4222-6. [PMID: 24623660 DOI: 10.1002/anie.201310644] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Revised: 01/28/2014] [Indexed: 11/11/2022]
Abstract
Efforts to chemically ligate oligonucleotides, without resorting to biochemical enzymes, have led to a multitude of synthetic analogues, and have extended oligomer ligation to reactions of novel oligonucleotides, peptides, and hybrids such as PNA.1 Key requirements for potential diagnostic tools not based on PCR include a fast templated chemical DNA ligation method that exhibits high pairing selectivity, and a sensitive detection method. Here we report on a solid-phase synthesis of oligonucleotides containing 5'- or 3'-mercapto-dideoxynucleotides and their chemical ligations, yielding 3'-5'-disulfide bonds as a replacement for 3'-5'-phosphodiester units. Employing a system designed for fluorescence monitoring, we demonstrate one of the fastest ligation reactions with half-lives on the order of seconds. The nontemplated ligation reaction is efficiently suppressed by the choice of DNA modification and the 3'-5' orientation of the activation site. The influence of temperature on the templated reaction is shown.
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Affiliation(s)
- Volker Patzke
- Lehrstuhl für Bioorganische Chemie, Ruhr-Universität Bochum, 44780 Bochum (Germany).
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29
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Schikora M, Dutta S, Mokhir A. Nucleic acid-specific photoactivation of oligodeoxyribonucleotides labeled with deuterated dihydro-N,N,N',N'-tetramethylrhodamine using green light. Histochem Cell Biol 2014; 142:103-11. [PMID: 24496596 DOI: 10.1007/s00418-014-1187-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/21/2014] [Indexed: 11/29/2022]
Abstract
We developed a simple protocol for high-yielding synthesis of conjugates of a deuterated dihydro-N,N,N',N'-tetramethylrhodamine (F*) with oligodeoxyribonucleotides and a 2'-OMe RNA (a representative nuclease-resistant, chemically modified oligonucleotide) using easily accessible starting materials including NaBD4 and conjugates of oligonucleotides with N,N,N',N'-tetramethylrhodamine (F). These compounds were found to be stable in air and insensitive to light at 525, 635 and 650 nm, whereas slow activation occurs upon their exposure to 470 nm light. However, at the conditions of the templated reaction, in the presence of a target nucleic acid and a photocatalyst based on the eosin structure, the F* is oxidized forming fluorescent F. This reaction is >30-fold faster than the background reaction in the absence of the template. Moreover, the presence of a single mismatch in the target nucleic acid slows down the templated reaction by eightfold. These activatable dyes can potentially find applications as nucleic acid-specific probes for super-resolution imaging in live cells.
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Affiliation(s)
- Margot Schikora
- Department of Chemistry and Pharmacy, Organic Chemistry II, Friedrich-Alexander-University of Erlangen-Nuremberg, Henkestr. 42, 91054, Erlangen, Germany
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30
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Vázquez O, Seitz O. Templated native chemical ligation: peptide chemistry beyond protein synthesis. J Pept Sci 2014; 20:78-86. [PMID: 24395765 DOI: 10.1002/psc.2602] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 11/22/2013] [Accepted: 11/22/2013] [Indexed: 12/11/2022]
Abstract
Native chemical ligation (NCL) is a powerful method for the convergent synthesis of proteins and peptides. In its original format, NCL between a peptide containing a C-terminal thioester and another peptide offering an N-terminal cysteine has been used to enable protein synthesis of unprotected peptide fragments. However, the applications of NCL extend beyond the scope of protein synthesis. For instance, NCL can be put under the control of template molecules. In such a scenario, NCL enables the design of conditional reaction systems in which, peptide bond formation occurs only when a specific third party molecule is present. In this review, we will show how templates can be used to control the reactivity and chemoselectivity of NCL reactions. We highlight peptide and nucleic-acid-templated NCL reactions and discuss potential applications in nucleic acid diagnosis, origin-of-life studies and gene-expression-specific therapies.
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Affiliation(s)
- Olalla Vázquez
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, D-12489, Berlin, Germany
| | - Oliver Seitz
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, D-12489, Berlin, Germany
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31
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Michaelis J, Roloff A, Seitz O. Amplification by nucleic acid-templated reactions. Org Biomol Chem 2014; 12:2821-33. [DOI: 10.1039/c4ob00096j] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Nucleic acid-templated reactions that proceed with turnover provide a means for signal amplification, which facilitates the use and detection of biologically occurring DNA/RNA molecules.
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Affiliation(s)
- Julia Michaelis
- Institut für Chemie der Humboldt-Universität zu Berlin
- 12489-Berlin, Germany
| | - Alexander Roloff
- Institut für Chemie der Humboldt-Universität zu Berlin
- 12489-Berlin, Germany
| | - Oliver Seitz
- Institut für Chemie der Humboldt-Universität zu Berlin
- 12489-Berlin, Germany
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32
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Affiliation(s)
- Krishna N. Ganesh
- Indian Institute of Science Education and Research, Division of Chemistry, 900, NCL Innovation Park, Dr Homi Bhabha Road, Pune, Maharashtra India
| | - Yamuna Krishnan
- National Centre for Biological Sciences,
Biophysics, Biochemistry and Bioinformatics, TIFR,
GKVK Campus, Bellary Road, Bangalore 560065, Karnataka, India
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33
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Boutorine AS, Novopashina DS, Krasheninina OA, Nozeret K, Venyaminova AG. Fluorescent probes for nucleic Acid visualization in fixed and live cells. Molecules 2013; 18:15357-97. [PMID: 24335616 PMCID: PMC6270009 DOI: 10.3390/molecules181215357] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 11/20/2013] [Accepted: 12/05/2013] [Indexed: 12/13/2022] Open
Abstract
This review analyses the literature concerning non-fluorescent and fluorescent probes for nucleic acid imaging in fixed and living cells from the point of view of their suitability for imaging intracellular native RNA and DNA. Attention is mainly paid to fluorescent probes for fluorescence microscopy imaging. Requirements for the target-binding part and the fluorophore making up the probe are formulated. In the case of native double-stranded DNA, structure-specific and sequence-specific probes are discussed. Among the latest, three classes of dsDNA-targeting molecules are described: (i) sequence-specific peptides and proteins; (ii) triplex-forming oligonucleotides and (iii) polyamide oligo(N-methylpyrrole/N-methylimidazole) minor groove binders. Polyamides seem to be the most promising targeting agents for fluorescent probe design, however, some technical problems remain to be solved, such as the relatively low sequence specificity and the high background fluorescence inside the cells. Several examples of fluorescent probe applications for DNA imaging in fixed and living cells are cited. In the case of intracellular RNA, only modified oligonucleotides can provide such sequence-specific imaging. Several approaches for designing fluorescent probes are considered: linear fluorescent probes based on modified oligonucleotide analogs, molecular beacons, binary fluorescent probes and template-directed reactions with fluorescence probe formation, FRET donor-acceptor pairs, pyrene excimers, aptamers and others. The suitability of all these methods for living cell applications is discussed.
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Affiliation(s)
- Alexandre S. Boutorine
- Muséum National d’Histoire Naturelle, CNRS, UMR 7196, INSERM, U565, 57 rue Cuvier, B.P. 26, Paris Cedex 05, F-75231, France; E-Mail:
| | - Darya S. Novopashina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
| | - Olga A. Krasheninina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova Str., 2, Novosibirsk 630090, Russia
| | - Karine Nozeret
- Muséum National d’Histoire Naturelle, CNRS, UMR 7196, INSERM, U565, 57 rue Cuvier, B.P. 26, Paris Cedex 05, F-75231, France; E-Mail:
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
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34
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Saneyoshi H, Shimada N, Maruyama A, Ito Y, Abe H. Polycation-assisted DNA detection by reduction triggered fluorescence amplification probe. Bioorg Med Chem Lett 2013; 23:6851-3. [DOI: 10.1016/j.bmcl.2013.10.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 09/28/2013] [Accepted: 10/02/2013] [Indexed: 10/26/2022]
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35
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Roloff A, Seitz O. Reducing product inhibition in nucleic acid-templated ligation reactions: DNA-templated cycligation. Chembiochem 2013; 14:2322-8. [PMID: 24243697 DOI: 10.1002/cbic.201300516] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Indexed: 01/19/2023]
Abstract
Programmable interactions allow nucleic acid molecules to template chemical reactions by increasing the effective molarities of appended reactive groups. DNA/RNA-triggered reactions can proceed, in principle, with turnover in the template. The amplification provided by the formation of many product molecules per template is a valuable asset when the availability of the DNA or RNA target is limited. However, turnover is usually impeded by reaction products that block access to the template. Product inhibition is most severe in ligation reactions, where products after ligation have dramatically increased template affinities. We introduce a potentially generic approach to reduce product inhibition in nucleic acid-programmed ligation reactions. A DNA-triggered ligation-cyclization sequence ("cycligation") of bifunctional peptide nucleic acid (PNA) conjugates affords cyclic ligation products. Melting experiments revealed that product cyclization is accompanied by a pronounced decrease in template affinity compared to linear ligation products. The reaction system relies upon haloacetylated PNA-thioesters and isocysteinyl-PNA-cysteine conjugates, which were ligated on a DNA template according to a native chemical ligation mechanism. Dissociation of the resulting linear product-template duplex (induced by, for example, thermal cycling) enabled product cyclization through sulfur-halide substitution. Both ligation and cyclization are fast reactions (ligation: 86 % yield after 20 min, cyclization: quantitative after 5 min). Under thermocycling conditions, the DNA template was able to trigger the formation of new product molecules when fresh reactants were added. Furthermore, cycligation produced 2-3 times more product than a conventional ligation reaction with substoichiometric template loads (0.25-0.01 equiv). We believe that cyclization of products from DNA-templated reactions could ultimately afford systems that completely overcome product inhibition.
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Affiliation(s)
- Alexander Roloff
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489-Berlin (Germany)
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36
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Shibata A, Uzawa T, Nakashima Y, Ito M, Nakano Y, Shuto S, Ito Y, Abe H. Very rapid DNA-templated reaction for efficient signal amplification and its steady-state kinetic analysis of the turnover cycle. J Am Chem Soc 2013; 135:14172-8. [PMID: 24015779 DOI: 10.1021/ja404743m] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oligonucleotide-templated reactions are powerful tools for the detection of nucleic acid sequences. One of the major scientific challenges associated with this technique is the rational design of non-enzyme-mediated catalytic templated reactions capable of multiple turnovers that provide high levels of signal amplification. Herein, we report the development of a nucleophilic aromatic substitution reaction-triggered fluorescent probe. The probe underwent a rapid templated reaction without any of the undesired background reactions. The fluorogenic reaction conducted in the presence of a template provided a 223-fold increase in fluorescence after 30 s compared with the nontemplated reaction. The probe provided an efficient level of signal amplification that ultimately enabled particularly sensitive levels of detection. Assuming a simple model for the templated reactions, it was possible to estimate the rate constants of the chemical reaction in the presence and in the absence of the template. From these kinetic analyses, it was possible to confirm that an efficient turnover cycle had been achieved, on the basis of the dramatic enhancement in the rate of the chemical reaction considered to be the rate-determining step. With maximized turnover efficiency, it was demonstrated that the probe could offer a high turnover number of 1500 times to enable sensitive levels of detection with a detection limit of 0.5 pM in the catalytic templated reactions.
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Affiliation(s)
- Aya Shibata
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute , 2-1, Hirosawa, Wako-Shi, Saitama 351-0198, Japan
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37
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Saneyoshi H, Ito Y, Abe H. Long-lived luminogenic probe for detection of RNA in a crude solution of living bacterial cells. J Am Chem Soc 2013; 135:13632-5. [PMID: 24010717 DOI: 10.1021/ja406724k] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A pre-type sensitizer for a lanthanide complex on an oligonucleotide was successfully converted to a perfect final structure in a target DNA/RNA-templated reaction, without any chemical reagent or enzyme, under neutral conditions. The final form of the lanthanide-oligonucleotide provided a long-lived luminescence signal, appropriate for time-gated luminescence analysis and signal amplification. Target DNA/RNA-assisted time-gated luminescence analysis is a powerful tool for elimination of autofluorescence and detection of target RNA in living bacterial cells.
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Affiliation(s)
- Hisao Saneyoshi
- Nano Medical Engineering Laboratory, RIKEN , 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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38
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Dutta S, Fülöp A, Mokhir A. Fluorogenic, Catalytic, Photochemical Reaction for Amplified Detection of Nucleic Acids. Bioconjug Chem 2013; 24:1533-42. [DOI: 10.1021/bc400152n] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Subrata Dutta
- Institute of Organic Chemistry
II, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestr. 42, 91054 Erlangen, Germany
| | - Annabelle Fülöp
- Institute of Organic Chemistry
II, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestr. 42, 91054 Erlangen, Germany
| | - Andriy Mokhir
- Institute of Organic Chemistry
II, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestr. 42, 91054 Erlangen, Germany
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39
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Sasmal PK, Streu CN, Meggers E. Metal complex catalysis in living biological systems. Chem Commun (Camb) 2013; 49:1581-7. [PMID: 23250079 DOI: 10.1039/c2cc37832a] [Citation(s) in RCA: 169] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This feature article discusses synthetic metal complexes that are capable of catalyzing chemical transformations in living organisms. Photodynamic therapy exemplifies what is probably the most established artificial catalytic process exploited in medicine, namely the photosensitized catalytic generation of cell-damaging singlet oxygen. Different redox catalysts have been designed over the last two decades to target a variety of redox alterations in cancer and other diseases. For example, pentaazamacrocyclic manganese(ii) complexes catalyze the dismutation of superoxide to O(2) and H(2)O(2)in vivo and thus reduce oxidative stress in analogy to the native enzyme superoxide dismutase. Recently, piano-stool ruthenium and iridium complexes were reported to influence cellular redox homeostasis indirectly by catalytic glutathione oxidation and catalytic transfer hydrogenation using the coenzyme NADH, respectively. Over the last few years, significant progress has been made towards the application of non-biological reactions in living systems, ranging from the organoruthenium-catalyzed cleavage of allylcarbamates and a gold-catalyzed intramolecular hydroarylation to palladium-catalyzed Suzuki-Miyaura and Sonogashira cross-couplings within the cytoplasm or on the surface of living cells. The design of bioorthogonal catalyst/substrate pairs, which can passively diffuse into cells, combines the advantages of small molecules with catalysis and promises to provide exciting new tools for future chemical biology studies.
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Affiliation(s)
- Pijus K Sasmal
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße, 35043 Marburg, Germany
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40
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Gorska K, Winssinger N. Reactions templated by nucleic acids: more ways to translate oligonucleotide-based instructions into emerging function. Angew Chem Int Ed Engl 2013; 52:6820-43. [PMID: 23794204 DOI: 10.1002/anie.201208460] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Indexed: 12/30/2022]
Abstract
The programmability of oligonucleotide recognition offers an attractive platform to direct the assembly of reactive partners that can engage in chemical reactions. Recently, significant progress has been made in both the breadth of chemical transformations and in the functional output of the reaction. Herein we summarize these recent progresses and illustrate their applications to translate oligonucleotide instructions into functional materials and novel architectures (conductive polymers, nanopatterns, novel oligonucleotide junctions); into fluorescent or bioactive molecule using cellular RNA; to interrogate secondary structures or oligonucelic acids; or a synthetic oligomer.
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Affiliation(s)
- Katarzyna Gorska
- Institut de Science et Ingénierie Supramoléculaires (ISIS-UMR 7006), Universite de Strasbourg-CNRS, 8 allée Gaspard Monge, 67000 Strasbourg, France
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Gorska K, Winssinger N. Reaktionen an Nucleinsäuretemplaten: mehr Methoden zur Übersetzung Oligonucleotid-basierter Informationen in neue Funktionen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208460] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Sadhu KK, Winssinger N. Detection of miRNA in live cells by using templated RuII-catalyzed unmasking of a fluorophore. Chemistry 2013; 19:8182-9. [PMID: 23633397 DOI: 10.1002/chem.201300060] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Indexed: 12/21/2022]
Abstract
Reactions templated by cellular nucleic acids are attractive for nucleic acid sensing or responsive systems. Herein we report the use of a photocatalyzed reductive cleavage of an immolative linker to unmask a rhodamine fluorophore, and its application to miRNA imaging. The reaction was found to proceed with a very high turnover (>4000) and provided reliable detection down to 5 pM of template by using γ-serine-modified peptide nucleic acid (PNA) probes. The reaction was used for the selective detection of miR-21 in BT474 cells and miR-31 in HeLa cells following irradiation for 30 min. The probes were introduced by using reversible permeation with streptolysin-O (SLO) or a transfection technique.
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Affiliation(s)
- Kalyan K Sadhu
- Institut de Science et Ingénierie Supramoléculaires (ISIS-UMR 7006), Université de Strasbourg, CNRS, 8 allée Gaspard Monge, 67000 Strasbourg, France
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Sadhu KK, Röthlingshöfer M, Winssinger N. DNA as a Platform to Program Assemblies with Emerging Functions in Chemical Biology. Isr J Chem 2013. [DOI: 10.1002/ijch.201200100] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Kalyan K. Sadhu
- Institut de Science et Ingénierie Supramoléculaires (ISIS – UMR 7006), Université de Strasbourg – CNRS, 8 allée Gaspard Monge, F67000 Strasbourg (France)
| | - Manuel Röthlingshöfer
- Institut de Science et Ingénierie Supramoléculaires (ISIS – UMR 7006), Université de Strasbourg – CNRS, 8 allée Gaspard Monge, F67000 Strasbourg (France)
| | - Nicolas Winssinger
- Institut de Science et Ingénierie Supramoléculaires (ISIS – UMR 7006), Université de Strasbourg – CNRS, 8 allée Gaspard Monge, F67000 Strasbourg (France)
- Department of Organic Chemistry, University of Geneva, 30 quai Ernest Ansermet, CH‐1211 Geneva 4 (Switzerland) phone: +41‐22‐379‐61‐05 fax: +41‐22‐379‐32‐15
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Stoop M, Désiron C, Leumann CJ. Nucleic acid sensing by an orthogonal reporter system based on homo-DNA. ARTIFICIAL DNA, PNA & XNA 2013; 4:28-33. [PMID: 23507698 PMCID: PMC3654727 DOI: 10.4161/adna.24227] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We have developed an assay for single strand DNA or RNA detection which is based on the homo-DNA templated Staudinger reduction of the profluorophore rhodamine-azide. The assay is based on a three component system, consisting of a homo-DNA/DNA hybrid probe, a set of homo-DNA reporter strands and the target DNA or RNA. We present two different formats of the assay (Omega probe and linear probe) in which the linear probe was found to perform best with catalytic turnover of the reporter strands (TON: 8) and a match/mismatch discrimination of up to 19. The advantage of this system is that the reporting (homo-DNA) and sensing (DNA) domain are decoupled from each other since the two pairing systems are bioorthogonal. This allows independent optimization of either domain which may lead to higher selectivity in in vivo imaging.
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Affiliation(s)
- Matthias Stoop
- University of Bern, Department of Chemistry and Biochemistry, Bern, Switzerland
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Gislason K, Sigurdsson ST. Rigid 5'-6-locked phenanthroline-derived nucleosides chelated to ruthenium and europium ions. Bioorg Med Chem Lett 2013. [PMID: 23177784 DOI: 10.1016/j.bmcl.2012.10.104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We describe complexes of ruthenium and europium with rigid, 5'-6-locked 1,10-phenanthroline-containing nucleosides. Both nucleosides were synthesized from condensation of 5-amino-2'-deoxycytidine with the corresponding diketone. The ruthenium nucleoside displayed fluorescence characteristic of polypyridine ruthenium complexes with a maximum at 616 nm and a quantum yield of 0.011. Binding of europium to the 1,10-phenanthroline-2,9-diacid moiety of the lanthanide binding nucleoside showed formation of a 1:1 complex with emission at 570-630 nm, whose emission was enhanced by addition of two phenanthroline ligands. The lanthanide-binding nucleoside was incorporated into DNA oligonucleotides and shown to selectively bind one equivalent of europium ions.
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Affiliation(s)
- Kristmann Gislason
- University of Iceland, Department of Chemistry, Science Institute, Dunhaga 3, 107 Reykjavik, Iceland
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46
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Detection of pre-mRNA splicing in vitro by an RNA-templated fluorogenic reaction. Bioorg Med Chem Lett 2012; 22:7248-51. [DOI: 10.1016/j.bmcl.2012.09.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Revised: 09/10/2012] [Accepted: 09/11/2012] [Indexed: 11/19/2022]
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47
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Sadhu KK, Eierhoff T, Römer W, Winssinger N. Photoreductive uncaging of fluorophore in response to protein oligomers by templated reaction in vitro and in cellulo. J Am Chem Soc 2012. [PMID: 23186060 DOI: 10.1021/ja310171s] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The photoreduction of azide-based immolative linker by Ru(II) conjugates to uncage rhodamine was achieved using different oligomeric protein templates. The generality of the approach was validated with three sets of ligand having varying affinity to their target (biotin, desthiobiotin and raloxifene). The reaction rates of the templated reaction was found to be at least 30-fold faster than the untemplated reaction providing a clear fluorescent signal in response to the protein oligomer within 30 min. The templated reaction was found to also proceed in cellulo and could be used to identify acetyl coenzyme A carboxylase (ACC) in Pseudomonas aeruginosa and human cell lines as well the and estrogen receptor (ER).
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Affiliation(s)
- Kalyan K Sadhu
- Institut de Science et Ingénierie Supramoléculaires (ISIS-UMR 7006), Université de Strasbourg-CNRS, 8 allée Gaspard Monge, F67000 Strasbourg, France
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Prusty DK, Kwak M, Wildeman J, Herrmann A. Modular assembly of a Pd catalyst within a DNA scaffold for the amplified colorimetric and fluorimetric detection of nucleic acids. Angew Chem Int Ed Engl 2012; 51:11894-8. [PMID: 23076826 PMCID: PMC3533772 DOI: 10.1002/anie.201206006] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Indexed: 11/10/2022]
Affiliation(s)
- Deepak K Prusty
- University of Groningen, Zernike Institute for Advanced Materials, Department of Polymer Chemistry, Nijenborgh 4, 9747 AG Groningen, Netherlands
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Prusty DK, Kwak M, Wildeman J, Herrmann A. Modular Assembly of a Pd Catalyst within a DNA Scaffold for the Amplified Colorimetric and Fluorimetric Detection of Nucleic Acids. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201206006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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50
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Photochemically relevant DNA-based molecular systems enabling chemical and signal transductions and their analytical applications. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2012. [DOI: 10.1016/j.jphotochemrev.2012.03.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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