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Müller M, Neitz H, Höbartner C, Helten H. BN-Phenanthrene- and BN-Pyrene-Based Fluorescent Uridine Analogues. Org Lett 2024; 26:1051-1055. [PMID: 38285916 DOI: 10.1021/acs.orglett.3c04226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Two unprecedented fluorescent nucleosides that feature BN-doped polycyclic aromatic hydrocarbons are presented. One of them, having a BN-modified phenanthrene moiety incorporated, shows blue fluorescence but suffers from poor stability under aqueous conditions. The other nucleoside comprises an internally BN-doped pyrene as the chromophore. It shows green fluorescence in various solvents and is stable under aqueous and alkaline conditions.
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Affiliation(s)
- Michael Müller
- Julius-Maximilians-Universität Würzburg, Institute of Inorganic Chemistry, Am Hubland, 97074 Würzburg, Germany
- Julius-Maximilians-Universität Würzburg, Institute for Sustainable Chemistry & Catalysis with Boron (ICB), Am Hubland, 97074 Würzburg, Germany
| | - Hermann Neitz
- Julius-Maximilians-Universität Würzburg, Institute of Organic Chemistry, Am Hubland, 97074 Würzburg, Germany
| | - Claudia Höbartner
- Julius-Maximilians-Universität Würzburg, Institute of Organic Chemistry, Am Hubland, 97074 Würzburg, Germany
- Julius-Maximilians-Universität Würzburg, Center for Nanosystems Chemistry (CNC), Theodor-Boveri-Weg, 97074 Würzburg, Germany
| | - Holger Helten
- Julius-Maximilians-Universität Würzburg, Institute of Inorganic Chemistry, Am Hubland, 97074 Würzburg, Germany
- Julius-Maximilians-Universität Würzburg, Institute for Sustainable Chemistry & Catalysis with Boron (ICB), Am Hubland, 97074 Würzburg, Germany
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Smietana M, Müller S. Stimuli-Responsive Boronate Formation to Control Nucleic Acid-Based Functional Architectures. Chempluschem 2024; 89:e202300613. [PMID: 38033190 DOI: 10.1002/cplu.202300613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/02/2023]
Abstract
Boronate esters, formed by the reaction of an oligonucleotide bearing a 5'-boronic acid moiety with the 3'-terminal cis-diol of another oligonucleotide, support the assembly of functional nucleic acid architectures. Reversible formation of boronate esters occurs in templated fashion and has been shown to restore the activity of split DNA and RNA enzymes as well as a split fluorescent light-up aptamer. Apart from their suitability for the design and application of split nucleic acid enzymes and aptamers in the field of biosensing, boronate esters may have played an important role in early life as surrogates of the natural phosphodiester bond. Their formation is reversible and thus fulfills an important requirement for biological self-assembly. Here we discuss the general concept of stimuli-dependent boronate formation and its application in biomolecules with implications for future research.
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Affiliation(s)
- Michael Smietana
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM Pôle Chimie Balard, 34095, Montpellier, France
| | - Sabine Müller
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Straße 4, 17489, Greifswald, Germany
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Bremer J, Richter C, Schwalbe H, Richert C. Synthesis of a Peptidoyl RNA Hairpin via a Combination of Solid-Phase and Template-Directed Chain Assembly. Chembiochem 2022; 23:e202200352. [PMID: 35867587 PMCID: PMC9542650 DOI: 10.1002/cbic.202200352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 07/21/2022] [Indexed: 12/02/2022]
Abstract
Peptidoyl RNAs are the products of ribosome‐free, single‐nucleotide translation. They contain a peptide in the backbone of the oligoribonucleotide and are interesting from a synthetic and a bioorganic point of view. A synthesis of a stabilized version of peptidoyl RNA, with an amide bond between the C‐terminus of a peptide and a 3′‐amino‐2′,3′‐dideoxynucleoside in the RNA chain was developed. The preferred synthetic route used an N‐Teoc‐protected aminonucleoside support and involved a solution‐phase coupling of the amino‐terminal oligonucleotide to a dipeptido dinucleotide. Exploratory UV‐melting and NMR analysis of the hairpin 5′‐UUGGCGAAAGCdC‐LeuLeu‐AA‐3′ indicated that the peptide‐linked RNA segments do not fold in a cooperative fashion. The synthetic access to doubly RNA‐linked peptides on a scale sufficient for structural biology opens the door to the exploration of their structural and biochemical properties.
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Affiliation(s)
- Jennifer Bremer
- University of Stuttgart: Universitat Stuttgart, Chemistry, GERMANY
| | - Christian Richter
- Universität Frankfurt am Main: Goethe-Universitat Frankfurt am Main, Chemistry, GERMANY
| | - Harald Schwalbe
- Universität Frankfurt am Main: Goethe-Universitat Frankfurt am Main, Chemistry, GERMANY
| | - Clemens Richert
- Universität Stuttgart, Institut für Organische Chemie, Pfaffenwaldring 55, 70569, Stuttgart, GERMANY
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Maverick MA, Gaillard M, Vasseur J, Debart F, Smietana M. Direct Access to Unique C‐5’‐Acyl Modified Nucleosides through Liebeskind–Srogl Cross‐Coupling Reaction. European J Org Chem 2022. [DOI: 10.1002/ejoc.202101061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Mary Anne Maverick
- Institut des Biomolécules Max Mousseron Université de Montpellier CNRS ENSCM 1919, route de Mende 34293 Montpellier
| | - Marie Gaillard
- Institut des Biomolécules Max Mousseron Université de Montpellier CNRS ENSCM 1919, route de Mende 34293 Montpellier
| | - Jean‐Jacques Vasseur
- Institut des Biomolécules Max Mousseron Université de Montpellier CNRS ENSCM 1919, route de Mende 34293 Montpellier
| | - Françoise Debart
- Institut des Biomolécules Max Mousseron Université de Montpellier CNRS ENSCM 1919, route de Mende 34293 Montpellier
| | - Michael Smietana
- Institut des Biomolécules Max Mousseron Université de Montpellier CNRS ENSCM 1919, route de Mende 34293 Montpellier
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Debiais M, Vasseur JJ, Smietana M. Applications of the Reversible Boronic Acids/Boronate Switch to Nucleic Acids. CHEM REC 2022; 22:e202200085. [PMID: 35641415 DOI: 10.1002/tcr.202200085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/16/2022] [Indexed: 11/09/2022]
Abstract
Over the last decades, boron and nucleic acids chemistries have gained a lot of attention for biological, medicinal and analytical applications. Our laboratory has a long-standing interest in both chemistries and owing to the ability of boronic acids to react with cis-diol function in aqueous media we developed over the years a variety of applications ranging from molecular recognition and sensing to the development of reversible dynamic systems in which the natural phosphodiester linkage was replaced by a boronate. In this account, we summarize research results from our group from our preliminary studies on molecular recognition of ribonucleosides to the dynamic assembly of functional DNAzymes. In particular, the various parameters influencing the dynamic nature of these reversible covalent bonds able to respond to external stimuli are discussed. Finally, current challenges and opportunities for boron-based nucleic acids are also addressed.
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Affiliation(s)
- Mégane Debiais
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 1919 route de Mende, 34095, Montpellier, France
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 1919 route de Mende, 34095, Montpellier, France
| | - Michael Smietana
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 1919 route de Mende, 34095, Montpellier, France
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Debiais M, Gimenez Molina A, Müller S, Vasseur JJ, Barvik I, Baraguey C, Smietana M. Design and NMR characterization of reversible head-to-tail boronate-linked macrocyclic nucleic acids. Org Biomol Chem 2022; 20:2889-2895. [PMID: 35319560 DOI: 10.1039/d2ob00232a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Inspired by the ability of boronic acids to bind with compounds containing diol moieties, we envisioned the formation in solution of boronate ester-based macrocycles by the head-to-tail assembly of a nucleosidic precursor that contains both a boronic acid and the natural 2',3'-diol of ribose. DOSY NMR spectroscopy experiments in water and anhydrous DMF revealed the dynamic assembly of this precursor into dimeric and trimeric macrocycles in a concentration-dependent fashion as well as the reversibility of the self-assembly process. NMR experimental values and quantum mechanics calculations provided further insight into the sugar pucker conformation profile of these macrocycles.
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Affiliation(s)
- Mégane Debiais
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 1919 route de Mende, 34095 Montpellier, France.
| | - Alejandro Gimenez Molina
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 1919 route de Mende, 34095 Montpellier, France.
| | - Sabine Müller
- University Greifswald, Institute for Biochemistry, Greifswald, Germany
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 1919 route de Mende, 34095 Montpellier, France.
| | - Ivan Barvik
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, Prague 2, 121 16, Czech Republic
| | - Carine Baraguey
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 1919 route de Mende, 34095 Montpellier, France.
| | - Michael Smietana
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 1919 route de Mende, 34095 Montpellier, France.
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Debiais M, Lelievre A, Vasseur J, Müller S, Smietana M. Boronic Acid-Mediated Activity Control of Split 10-23 DNAzymes. Chemistry 2021; 27:1138-1144. [PMID: 33058268 PMCID: PMC7839725 DOI: 10.1002/chem.202004227] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Indexed: 12/11/2022]
Abstract
The 10-23 DNAzyme is an artificially developed Mg2+ -dependent catalytic oligonucleotide that can cleave an RNA substrate in a sequence-specific fashion. In this study, new split 10-23 DNAzymes made of two nonfunctional fragments, one of which carries a boronic acid group at its 5' end, while the other has a ribonucleotide at its 3' end, were designed. Herein it is demonstrated that the addition of Mg2+ ions leads to assembly of the fragments, which in turn induces the formation of a new boronate internucleoside linkage that restores the DNAzyme activity. A systematic evaluation identified the best-performing system. The results highlight key features for efficient control of DNAzyme activity through the formation of boronate linkages.
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Affiliation(s)
- Mégane Debiais
- Institut des Biomolécules Max MousseronUniversité de MontpellierCNRSENSCMPlace Eugène Bataillon34095MontpellierFrance
| | - Amandine Lelievre
- University GreifswaldInstitute for BiochemistryFelix-Hausdorff-Strasse 417487GreifswaldGermany
| | - Jean‐Jacques Vasseur
- Institut des Biomolécules Max MousseronUniversité de MontpellierCNRSENSCMPlace Eugène Bataillon34095MontpellierFrance
| | - Sabine Müller
- University GreifswaldInstitute for BiochemistryFelix-Hausdorff-Strasse 417487GreifswaldGermany
| | - Michael Smietana
- Institut des Biomolécules Max MousseronUniversité de MontpellierCNRSENSCMPlace Eugène Bataillon34095MontpellierFrance
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Clavé G, Dursun E, Vasseur JJ, Smietana M. An Entry of the Chemoselective Sulfo-Click Reaction into the Sphere of Nucleic Acids. Org Lett 2020; 22:1914-1918. [DOI: 10.1021/acs.orglett.0c00265] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Guillaume Clavé
- Institut des Biomolécules Max Mousseron, Univ. Montpellier, CNRS, ENSCM, 34090 Montpellier, France
| | - Enes Dursun
- Institut des Biomolécules Max Mousseron, Univ. Montpellier, CNRS, ENSCM, 34090 Montpellier, France
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron, Univ. Montpellier, CNRS, ENSCM, 34090 Montpellier, France
| | - Michael Smietana
- Institut des Biomolécules Max Mousseron, Univ. Montpellier, CNRS, ENSCM, 34090 Montpellier, France
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Pandith A, Kim HY, Shin T, Seo YJ. Unprecedented green-emissive boranyl-hydrazone supramolecular assemblies and their in vitro diagnostic applications. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2019; 197:111553. [PMID: 31326845 DOI: 10.1016/j.jphotobiol.2019.111553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/29/2019] [Accepted: 07/09/2019] [Indexed: 06/10/2023]
Abstract
This paper describes a novel symmetric N,N'-diethylsalicylaldehyde boranyl hydrazone (1) and its in situ-generated assemblies displaying opto-analytical capabilities for the diagnosis of nucleic acids under physiological conditions. The sensing capabilities of these unprecedented supramolecular assemblies were characterized using UV-Vis spectroscopy, fluorescence spectroscopy, 1D and 2D NMR spectroscopy, dynamic light scattering, and zeta potential measurements. Model compounds lacking boranyl units (2, 3) were prepared to correlate and evaluate the sensing mechanism. The rationally designed probe 1 displays unusual aggregation-induced emissive (AIE) properties, with an average particle size of 1096 nm exhibiting green emission upon excitation at 377 nm in pH-7.2 TRIZMA buffer. A selective switch on response toward organic PO43- accompanied through specific nano-aggregations patterns and sizes, thereby causing a significant red-shift through AIE. Exploiting such switch on in green channel behavior has allowed the monitoring of DNase I activities and polymerase chain reactions.
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Affiliation(s)
- Anup Pandith
- Department of Chemistry, Chonbuk National University, Jeonju 54398, Republic of Korea
| | - Hye-Yeon Kim
- Department of Chemistry, Chonbuk National University, Jeonju 54398, Republic of Korea
| | - Taeho Shin
- Department of Chemistry, Chonbuk National University, Jeonju 54398, Republic of Korea
| | - Young Jun Seo
- Department of Chemistry, Chonbuk National University, Jeonju 54398, Republic of Korea; Department of Bioactive Materials, Chonbuk National University, Jeonju 54398, Republic of Korea.
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