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Krebs J, Brändler L, Krummenacher I, Friedrich A, Braunschweig H, Finze M, Curchod BFE, Marder TB. Synthesis, Photophysical and Electronic Properties of a D-π-A Julolidine-Like Pyrenyl-o-Carborane. Chemistry 2024; 30:e202401704. [PMID: 38758081 DOI: 10.1002/chem.202401704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/17/2024] [Accepted: 05/17/2024] [Indexed: 05/18/2024]
Abstract
We synthesized 2-(1-1,2-dicarbadodecaboranyl(12))-6,6,12,12-tetramethyl-7,8,11,12-tetrahydro-6H,10H-phenaleno[1,9-fg]pyrido[3,2,1-ij]quinoline (4), a julolidine-like pyrenyl-o-carborane, with pyrene substituted at the 2,7-positions on the HOMO/LUMO nodal plane. Using solid state molecular structures, photophysical data, cyclic voltammetry, DFT and LR-TDDFT calculations, we compare o-carborane and B(Mes)2 (Mes=2,4,6-Me3C6H2) as acceptor groups. Whereas the π-acceptor strength of B(Mes)2 is sufficient to drop the pyrene LUMO+1 below the LUMO, the carborane does not do this. We confirm the π-donor strength of the julolidine-like moiety, however, which raises the pyrene HOMO-1 above the HOMO. In contrast to the analogous pyrene-2-yl-o-carborane, 2-(1-1,2-dicarbadodecaboranyl(12))-pyrene VI, which exhibits dual fluorescence, because the rate of internal conversion between locally-excited (LE) and charge transfer (CT) (from the pyrene to the carborane) states is faster than the radiative decay rate, leading to a thermodynamic equilibrium between the 2 states, 4 shows only single fluorescence, as the CT state involving the carborane as the acceptor moiety in not kinetically accessible, so a more localized CT emission involving the julolidine-like pyrene moiety is observed.
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Affiliation(s)
- Johannes Krebs
- Institute for Inorganic Chemistry and Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Lisa Brändler
- Institute for Inorganic Chemistry and Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Ivo Krummenacher
- Institute for Inorganic Chemistry and Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Alexandra Friedrich
- Institute for Inorganic Chemistry and Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Holger Braunschweig
- Institute for Inorganic Chemistry and Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Maik Finze
- Institute for Inorganic Chemistry and Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Basile F E Curchod
- Centre for Computational Chemistry, School of Chemistry, Cantock's Close, University of Bristol, Bristol, BS8 1TS, United Kingdom
| | - Todd B Marder
- Institute for Inorganic Chemistry and Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
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2
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Tan L, Zheng X, Shi J, Qin T, Ji L. 4,9- and 4,10-Substituted pyrenes: synthesis, successful isolation, and optoelectronic properties. Org Biomol Chem 2024; 22:1676-1685. [PMID: 38299623 DOI: 10.1039/d3ob01936e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
We report herein a way to prepare and purify optoelectronic functional 4,9- and 4,10-substituted pyrene isomers. By tuning the size of substituents, the designed 4,9- and 4,10-isomers can be successfully isolated by recycling preparative size-exclusion chromatography (SEC) and/or repeated recrystallization. The structure and purity of the isolated compounds 1-5 have been confirmed by 1H NMR, 13C NMR, and HRMS. The photophysical and electrochemical properties of compounds 1-5 have been studied in detail both experimentally and theoretically. The lowest transitions of these pyrenes, 1-5, are allowed, with moderate to high fluorescence quantum yields and radiative decay rates around 108 s-1. The differences between the electrochemical and photophysical properties of 4,9-, 4,10-, 1,6-, and 2,7-substituted isomers are compared and concluded.
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Affiliation(s)
- Leibo Tan
- Key laboratory of Flexible Electronics of Zhejiang Provience, Ningbo Institute of Northwestern Polytechnical University, 218 Qingyi Road, Ningbo, 315103, China.
- Institute of Flexible Electronics, Northwestern Polytechnical University, 127 West Youyi Road, 710027 Xi'an, China
| | - Xiuli Zheng
- Qilu Pharmaceutical Co. Ltd, No. 23999, Gongye Bei Road, Jinan 250100, China
| | - Junqing Shi
- Key laboratory of Flexible Electronics of Zhejiang Provience, Ningbo Institute of Northwestern Polytechnical University, 218 Qingyi Road, Ningbo, 315103, China.
- Institute of Flexible Electronics, Northwestern Polytechnical University, 127 West Youyi Road, 710027 Xi'an, China
| | - Tianshi Qin
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (NanjingTech), Nanjing, Jiangsu 211816, China.
| | - Lei Ji
- Key laboratory of Flexible Electronics of Zhejiang Provience, Ningbo Institute of Northwestern Polytechnical University, 218 Qingyi Road, Ningbo, 315103, China.
- Institute of Flexible Electronics, Northwestern Polytechnical University, 127 West Youyi Road, 710027 Xi'an, China
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Nikšić-Franjić I, Colasson B, Reinaud O, Višnjevac A, Piantanida I, Pavlović Saftić D. Novel pyrene-calix[4]arene derivatives as highly sensitive sensors for nucleotides, DNA and RNA. RSC Adv 2023; 13:27423-27433. [PMID: 37711378 PMCID: PMC10498358 DOI: 10.1039/d3ra05696a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 09/07/2023] [Indexed: 09/16/2023] Open
Abstract
Covalent functionalization of a calix[4]arene with one or two pyrene arms at one rim and two imidazoles at the opposite rim of the macrocyclic basket, yields fluorescent conjugates characterized by intramolecular pyrene-calixarene exciplex emission of a mono-pyrene conjugate, whereas the bis-pyrene derivative exhibits pyrene excimer fluorescence. The pyrene emission in these novel compounds is shown to be sensitive to non-covalent interactions with both mono- and polynucleotides. Pyrene-calixarene conjugates, acting as host molecules, strongly interact with nucleotides, as monitored by moderate emission quenching, reaching 0.1 μM affinities, comparable to some of the most effective supramolecular sensors for nucleotides. These compounds are efficiently inserted into ds-DNA/RNA grooves, with a high, 0.1-1 μM affinity, not influencing significantly any of the ds-polynucleotide native properties, whereby complete emission quenching allows the detection of DNA at nM concentration.
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Affiliation(s)
- Ivana Nikšić-Franjić
- Division of Physical Chemistry, Laboratory for Chemical and Biological Crystallography, Ruđer Bošković Institute Bijenička cesta 54 10000 Zagreb Croatia
| | - Benoit Colasson
- Université de Paris - Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, CNRS UMR 8601 45 rue des Saints Pères 75006 Paris France
| | - Olivia Reinaud
- Université de Paris - Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, CNRS UMR 8601 45 rue des Saints Pères 75006 Paris France
| | - Aleksandar Višnjevac
- Division of Physical Chemistry, Laboratory for Chemical and Biological Crystallography, Ruđer Bošković Institute Bijenička cesta 54 10000 Zagreb Croatia
| | - Ivo Piantanida
- Division of Organic Chemistry and Biochemistry, Laboratory for Biomolecular Interactions and Spectroscopy, Ruđer Bošković Institute Bijenička cesta 54 10000 Zagreb Croatia
| | - Dijana Pavlović Saftić
- Division of Organic Chemistry and Biochemistry, Laboratory for Biomolecular Interactions and Spectroscopy, Ruđer Bošković Institute Bijenička cesta 54 10000 Zagreb Croatia
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4
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Opačak S, Pernar Kovač M, Brozovic A, Piantanida I, Kirin SI. Turn-on fluorescence of ruthenium pyrene complexes in response to bovine serum albumin. Dalton Trans 2023; 52:11698-11704. [PMID: 37555301 DOI: 10.1039/d3dt02289g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Two novel pyrene triphenylphosphine ruthenium conjugates act as fluorescent turn-on beacons for serum albumin, being non-fluorescent in aqueous media but exhibiting strong emission upon binding to BSA. The selective cytotoxicity of the compounds against tumour cells is enhanced upon irradiation by UV-light, paving the way for application in photodynamic therapy under two-photon excitation.
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Affiliation(s)
- Saša Opačak
- Ruđer Boškovic Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia.
| | | | - Anamaria Brozovic
- Ruđer Boškovic Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia.
| | - Ivo Piantanida
- Ruđer Boškovic Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia.
| | - Srećko I Kirin
- Ruđer Boškovic Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia.
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5
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Kole GK, Košćak M, Amar A, Majhen D, Božinović K, Brkljaca Z, Ferger M, Michail E, Lorenzen S, Friedrich A, Krummenacher I, Moos M, Braunschweig H, Boucekkine A, Lambert C, Halet J, Piantanida I, Müller‐Buschbaum K, Marder TB. Methyl Viologens of Bis-(4'-Pyridylethynyl)Arenes - Structures, Photophysical and Electrochemical Studies, and their Potential Application in Biology. Chemistry 2022; 28:e202200753. [PMID: 35502627 PMCID: PMC9400870 DOI: 10.1002/chem.202200753] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Indexed: 12/20/2022]
Abstract
A series of bis-(4'-pyridylethynyl)arenes (arene=benzene, tetrafluorobenzene, and anthracene) were synthesized and their bis-N-methylpyridinium compounds were investigated as a class of π-extended methyl viologens. Their structures were determined by single crystal X-ray diffraction, and their photophysical and electrochemical properties (cyclic voltammetry), as well as their interactions with DNA/RNA were investigated. The dications showed bathochromic shifts in emission compared to the neutral compounds. The neutral compounds showed very small Stokes shifts, which are a little larger for the dications. All of the compounds showed very short fluorescence lifetimes (<4 ns). The neutral compound with an anthracene core has a quantum yield of almost unity. With stronger acceptors, the analogous bis-N-methylpyridinium compound showed a larger two-photon absorption cross-section than its neutral precursor. All of the dicationic compounds interact with DNA/RNA; while the compounds with benzene and tetrafluorobenzene cores bind in the grooves, the one with an anthracene core intercalates as a consequence of its large, condensed aromatic linker moiety, and it aggregates within the polynucleotide when in excess over DNA/RNA. Moreover, all cationic compounds showed highly specific CD spectra upon binding to ds-DNA/RNA, attributed to the rare case of forcing the planar, achiral molecule into a chiral rotamer, and negligible toxicity toward human cell lines at ≤10 μM concentrations. The anthracene-analogue exhibited intracellular accumulation within lysosomes, preventing its interaction with cellular DNA/RNA. However, cytotoxicity was evident at 1 μM concentration upon exposure to light, due to singlet oxygen generation within cells. These multi-faceted features, in combination with its two-photon absorption properties, suggest it to be a promising lead compound for development of novel light-activated theranostic agents.
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Affiliation(s)
- Goutam Kumar Kole
- Institut für Anorganische Chemie, andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
- Department of ChemistryCollege of Engineering and TechnologySRM Institute of Science and Technology, SRM NagarKattankulathurTamil Nadu603203India
| | | | - Anissa Amar
- Laboratoire de Physique et Chimie QuantiquesUniversité Mouloud MammeriTizi Ouzou15000 Tizi-OuzouAlgeria
| | | | | | | | - Matthias Ferger
- Institut für Anorganische Chemie, andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Evripidis Michail
- Institut für Organische ChemieJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Sabine Lorenzen
- Institut für Anorganische Chemie, andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Alexandra Friedrich
- Institut für Anorganische Chemie, andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Ivo Krummenacher
- Institut für Anorganische Chemie, andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Michael Moos
- Institut für Organische ChemieJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Holger Braunschweig
- Institut für Anorganische Chemie, andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Abdou Boucekkine
- Univ Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, Institut des Sciences Chimiques de Rennes UMR 622635000RennesFrance
| | - Christoph Lambert
- Institut für Organische ChemieJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Jean‐François Halet
- Univ Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, Institut des Sciences Chimiques de Rennes UMR 622635000RennesFrance
- CNRS-Saint-Gobain-NIMSIRL 3629Laboratory for Innovative Key Materials and Structures (LINK)National Institute for Materials Science (NIMS)Tsukuba305-0044Japan
| | | | - Klaus Müller‐Buschbaum
- Institut für Anorganische und Analytische ChemieJustus-Liebig-Universität GießenHeinrich-Buff-Ring 1735392GießenGermany
| | - Todd B. Marder
- Institut für Anorganische Chemie, andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
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6
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Semikolenova OA, Golyshev VM, Kim BH, Venyaminova AG, Novopashina DS. New Two-Component Pyrene Probes Based on Oligo(2'-O-Methylribonucleotides) for microRNA Detection. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021020230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Kole GK, Merz J, Amar A, Fontaine B, Boucekkine A, Nitsch J, Lorenzen S, Friedrich A, Krummenacher I, Košćak M, Braunschweig H, Piantanida I, Halet J, Müller‐Buschbaum K, Marder TB. 2- and 2,7-Substituted para-N-Methylpyridinium Pyrenes: Syntheses, Molecular and Electronic Structures, Photophysical, Electrochemical, and Spectroelectrochemical Properties and Binding to Double-Stranded (ds) DNA. Chemistry 2021; 27:2837-2853. [PMID: 33231335 PMCID: PMC7898908 DOI: 10.1002/chem.202004748] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Indexed: 11/10/2022]
Abstract
Two N-methylpyridinium compounds and analogous N-protonated salts of 2- and 2,7-substituted 4-pyridyl-pyrene compounds were synthesised and their crystal structures, photophysical properties both in solution and in the solid state, electrochemical and spectroelectrochemical properties were studied. Upon methylation or protonation, the emission maxima are significantly bathochromically shifted compared to the neutral compounds, although the absorption maxima remain almost unchanged. As a result, the cationic compounds show very large apparent Stokes shifts of up to 7200 cm-1 . The N-methylpyridinium compounds have a single reduction at ca. -1.5 V vs. Fc/Fc+ in MeCN. While the reduction process was reversible for the 2,7-disubstituted compound, it was irreversible for the mono-substituted one. Experimental findings are complemented by DFT and TD-DFT calculations. Furthermore, the N-methylpyridinium compounds show strong interactions with calf thymus (ct)-DNA, presumably by intercalation, which paves the way for further applications of these multi-functional compounds as potential DNA-bioactive agents.
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Affiliation(s)
- Goutam Kumar Kole
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
- Department of ChemistryCollege of Engineering and TechnologySRM Institute of Science and TechnologySRM NagarKattankulathurTamil Nadu603203India
| | - Julia Merz
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Anissa Amar
- Département de ChimieFaculté des SciencesUniversité Mouloud Mammeri15000Tizi-OuzouAlgeria
| | - Bruno Fontaine
- Univ RennesEcole Nationale Supérieure de Chimie de RennesCNRSInstitut des Sciences Chimiques de Rennes UMR 622635000RennesFrance
| | - Abdou Boucekkine
- Univ RennesEcole Nationale Supérieure de Chimie de RennesCNRSInstitut des Sciences Chimiques de Rennes UMR 622635000RennesFrance
| | - Jörn Nitsch
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Sabine Lorenzen
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Alexandra Friedrich
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Ivo Krummenacher
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Marta Košćak
- Division of Organic Chemistry and BiochemistryRuđer Bošković Institute10000ZagrebCroatia
| | - Holger Braunschweig
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Ivo Piantanida
- Division of Organic Chemistry and BiochemistryRuđer Bošković Institute10000ZagrebCroatia
| | - Jean‐François Halet
- Univ RennesEcole Nationale Supérieure de Chimie de RennesCNRSInstitut des Sciences Chimiques de Rennes UMR 622635000RennesFrance
| | - Klaus Müller‐Buschbaum
- Institut für Anorganische und Analytische ChemieJustus-Liebig-Universität GießenHeinrich-Buff-Ring 1735392GießenGermany
| | - Todd B. Marder
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
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8
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Merz J, Dietz M, Vonhausen Y, Wöber F, Friedrich A, Sieh D, Krummenacher I, Braunschweig H, Moos M, Holzapfel M, Lambert C, Marder TB. Synthesis, Photophysical and Electronic Properties of New Red-to-NIR Emitting Donor-Acceptor Pyrene Derivatives. Chemistry 2020; 26:438-453. [PMID: 31593316 PMCID: PMC6973242 DOI: 10.1002/chem.201904219] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Indexed: 02/03/2023]
Abstract
We synthesized new pyrene derivatives with strong bis(para-methoxyphenyl)amine donors at the 2,7-positions and n-azaacene acceptors at the K-region of pyrene. The compounds possess a strong intramolecular charge transfer, leading to unusual properties such as emission in the red to NIR region (700 nm), which has not been reported before for monomeric pyrenes. Detailed photophysical studies reveal very long intrinsic lifetimes of >100 ns for the new compounds, which is typical for 2,7-substituted pyrenes but not for K-region substituted pyrenes. The incorporation of strong donors and acceptors leads to very low reduction and oxidation potentials, and spectroelectrochemical studies show that the compounds are on the borderline between localized Robin-Day class-II and delocalized Robin-Day class-III species.
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Affiliation(s)
- Julia Merz
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with Boron (ICB)Julius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Maximilian Dietz
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with Boron (ICB)Julius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Yvonne Vonhausen
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with Boron (ICB)Julius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Frederik Wöber
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with Boron (ICB)Julius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Alexandra Friedrich
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with Boron (ICB)Julius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Daniel Sieh
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with Boron (ICB)Julius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Ivo Krummenacher
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with Boron (ICB)Julius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Holger Braunschweig
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with Boron (ICB)Julius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Michael Moos
- Institut für Organische ChemieJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Marco Holzapfel
- Institut für Organische ChemieJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Christoph Lambert
- Institut für Organische ChemieJulius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
| | - Todd B. Marder
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with Boron (ICB)Julius-Maximilians-Universität WürzburgAm Hubland97074WürzburgGermany
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9
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Hari Y, Osawa T, Yamashita S, Nakanishi A, Ito Y. Synthesis and Hybridization Properties of Oligonucleotides Including 2’-N-Alkoxycarbonyl-2’-amino-LNA Derivatives. HETEROCYCLES 2019. [DOI: 10.3987/com-18-s(f)46] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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10
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Krasheninina OA, Novopashina DS, Apartsin EK, Venyaminova AG. Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides. Molecules 2017; 22:E2108. [PMID: 29189716 PMCID: PMC6150046 DOI: 10.3390/molecules22122108] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 11/28/2017] [Accepted: 11/28/2017] [Indexed: 12/17/2022] Open
Abstract
In this review, we summarize the recent advances in the use of pyrene-modified oligonucleotides as a platform for functional nucleic acid-based constructs. Pyrene is of special interest for the development of nucleic acid-based tools due to its unique fluorescent properties (sensitivity of fluorescence to the microenvironment, ability to form excimers and exciplexes, long fluorescence lifetime, high quantum yield), ability to intercalate into the nucleic acid duplex, to act as a π-π-stacking (including anchoring) moiety, and others. These properties of pyrene have been used to construct novel sensitive fluorescent probes for the sequence-specific detection of nucleic acids and the discrimination of single nucleotide polymorphisms (SNPs), aptamer-based biosensors, agents for binding of double-stranded DNAs, and building blocks for supramolecular complexes. Special attention is paid to the influence of the design of pyrene-modified oligonucleotides on their properties, i.e., the structure-function relationships. The perspectives for the applications of pyrene-modified oligonucleotides in biomolecular studies, diagnostics, and nanotechnology are discussed.
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Affiliation(s)
- Olga A Krasheninina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Darya S Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Evgeny K Apartsin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Alya G Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
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11
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Astakhova K, Golovin AV, Prokhorenko IA, Ustinov AV, Stepanova IA, Zatsepin TS, Korshun VA. Design of 2′-phenylethynylpyrene excimer forming DNA/RNA probes for homogeneous SNP detection: The attachment manner matters. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.04.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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12
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Oligodeoxynucleotides containing 2'-amino-LNA nucleotides as constrained morpholino phosphoramidate and phosphorodiamidate monomers. Bioorg Med Chem Lett 2017; 27:3173-3176. [PMID: 28552336 DOI: 10.1016/j.bmcl.2017.05.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 05/05/2017] [Accepted: 05/07/2017] [Indexed: 11/23/2022]
Abstract
Incorporation in a 2'→5' direction of a phosphorodiamidite 2'-amino-LNA-T nucleotide as the morpholino phosphoramidate and N,N-dimethylamino phosphorodiamidate monomers into six oligonucleotides is reported. Thermal denaturation studies showed that the novel 2'-amino-LNA-based morpholino monomers exert a destabilizing effects on duplexes formed with complementary DNA and RNA.
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13
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Substitution of Metallocenes with [2.2]Paracyclophane to Enable Confocal Microscopy Imaging in Living Cells. Eur J Inorg Chem 2016. [DOI: 10.1002/ejic.201600281] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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14
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Chistov AA, Kutyakov SV, Ustinov AV, Aparin IO, Glybin AV, Mikhura IV, Korshun VA. 2-Ethynylperylene and improved synthesis of 3-ethynylperylene. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.01.067] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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15
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Reuss AJ, Grünewald C, Braun M, Engels JW, Wachtveitl J. The Three Possible 2-(Pyrenylethynyl) Adenosines: Rotameric Energy Barriers Govern the Photodynamics of These Structural Isomers. Chemphyschem 2016; 17:1369-76. [PMID: 26635201 DOI: 10.1002/cphc.201500958] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Indexed: 01/22/2023]
Abstract
This article presents a comprehensive study of the photophysics of 2-(2-pyrenylethynyl) adenosine and 2-(4-pyrenylethynyl) adenosine, which are structural isomers of the well-established fluorescent RNA label 2-(1-pyrenylethynyl) adenosine. We performed steady-state and ultrafast transient absorption spectroscopy studies along with time-resolved fluorescence emission experiments in different solvents to work out the interplay of locally excited and charge-transfer states. We found the ultrafast photodynamics to be crucial for the fluorescence decay behavior, which extends up to tens of nanoseconds and is partially multi-exponential. These features in the ultrafast dynamics are indicative of the rotational energy barriers in the first excited state.
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Affiliation(s)
- Andreas J Reuss
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Christian Grünewald
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Markus Braun
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Joachim W Engels
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany.
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16
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Kaura M, Hrdlicka PJ. Locked nucleic acid (LNA) induced effect on the hybridization and fluorescence properties of oligodeoxyribonucleotides modified with nucleobase-functionalized DNA monomers. Org Biomol Chem 2015; 13:7236-47. [PMID: 26055658 DOI: 10.1039/c5ob00860c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
LNA and nucleobase-modified DNA monomers are two types of building blocks that are used extensively in oligonucleotide chemistry. However, there are only very few reports in which these two monomer families are used alongside each other. In the present study we set out to characterize the biophysical properties of oligodeoxyribonucleotides in which C5-modified 2'-deoxyuridine or C8-modified 2'-deoxyadenosine monomers are flanked by LNA nucleotides. We hypothesized that the LNA monomers would alter the sugar rings of the modified DNA monomers toward more RNA-like North-type conformations for maximal DNA/RNA affinity and specificity. Indeed, the incorporation of LNA monomers almost invariably results in increased target affinity and specificity relative to the corresponding LNA-free ONs, but the magnitude of the stabilization varies greatly. Introduction of LNA nucleotides as direct neighbors into C5-pyrene-functionalized pyrimidine DNA monomers yields oligonucleotide probes with more desirable photophysical properties as compared to the corresponding LNA-free probes, including more intense fluorescence emission upon target binding and improved discrimination of single nucleotide polymorphisms (SNPs). These hybrid oligonucleotides are therefore promising probes for diagnostic applications.
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Affiliation(s)
- Mamta Kaura
- Department of Chemistry, University of Idaho, Moscow, ID 83844-2343, USA.
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17
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Ensslen P, Fritz Y, Wagenknecht HA. Mixed non-covalent assemblies of ethynyl nile red and ethynyl pyrene along oligonucleotide templates. Org Biomol Chem 2014; 13:487-92. [PMID: 25374296 DOI: 10.1039/c4ob01860e] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Ethynyl pyrene and ethynyl nile red as modifications at the 5-position of 2'-deoxyuridines self-assemble non-covalently and specifically along oligo-2'-deoxyadenosines as templates. Oligo-2'-deoxyadenosines of the lengths (dA)10-(dA)20 are able to retain nearly exactly as many ethynyl nile red units in solution as binding sites are available on these templates. In contrast, in the presence of oligo-2'-thymidines the ethynyl nile red moieties are similarly insoluble to those in the absence of any oligonucleotide and yield an aggregate. The mixed assemblies of both chromophores are highly ordered, show left-handed chirality and yield dual fluorescence. The strong excitonic coupling indicates assemblies with a high degree of order. These results show that DNA represents an important supramolecular scaffold for the templated, helical and non-covalent arrangement not only for one type of chromophore but also for mixtures of two different chromophores.
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Affiliation(s)
- Philipp Ensslen
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
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18
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Astakhova IK, Wengel J. Scaffolding along nucleic acid duplexes using 2'-amino-locked nucleic acids. Acc Chem Res 2014; 47:1768-77. [PMID: 24749544 DOI: 10.1021/ar500014g] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
CONSPECTUS: Incorporation of chemically modified nucleotide scaffolds into nucleic acids to form assemblies rich in function is an innovative area with great promise for nanotechnology and biomedical and material science applications. The intrinsic biorecognition potential of nucleic acids combined with advanced properties of the locked nucleic acids (LNAs) provide opportunities to develop new nanomaterials and devices like sensors, aptamers, and machines. In this Account, we describe recent research on preparation and investigation of the properties of LNA/DNA hybrids containing functionalized 2'-amino-LNA nucleotides. By application of different chemical reactions, modification of 2'-amino-LNA scaffolds can be efficiently performed in high yields and with various tags, postsynthetically or during the automated oligonucleotide synthesis. The choice of a synthetic method for scaffolding along 2'-amino-LNA mainly depends on the chemical nature of the modification, its price, its availability, and applications of the product. One of the most useful applications of the product LNA/DNA scaffolds containing 2'-amino-LNA is to detect complementary DNA and RNA targets. Examples of these applications include sensing of clinically important single-nucleotide polymorphisms (SNPs) and imaging of nucleic acids in vitro, in cell culture, and in vivo. According to our studies, 2'-amino-LNA scaffolds are efficient within diagnostic probes for DNA and RNA targets and as therapeutics, whereas both 2'-amino- and isomeric 2'-α-l-amino-LNA scaffolds have promising properties for stabilization and detection of DNA nanostructures. Attachment of fluorescent groups to the 2'-amino group results in very high fluorescent quantum yields of the duplexes and remarkable sensitivity of the fluorescence signal to target binding. Notably, fluorescent LNA/DNA probes bind nucleic acid targets with advantages of high affinity and specificity. Thus, molecular motion of nanodevices and programmable self-assembly of chemically modified LNA/DNA nanomaterials can be followed by bright fluorescence signaling from the functionalized LNA units. Another appealing aspect of the amino-LNA scaffolds is specific targeting of nucleic acids and proteins for therapeutic applications. 2'-Amino-LNA/DNA conjugates containing peptide and polyaromatic hydrocarbon (PAH) groups are promising in this context as well as for advanced imaging and diagnostic purposes in vivo. For imaging applications, photostability of fluorescence dyes is of crucial importance. Chemically stable and photostable fluorescent PAH molecules attached to 2'-amino functionality of the 2'-amino-LNA are potent for in vitro and in vivo imaging of DNA and RNA targets. We believe that rational evolution of the biopolymers of Nature may solve the major challenges of the future material science and biomedicine. However, this requires strong scientific progress and efficient interdisciplinary research. Examples of this Account demonstrate that among other synthetic biopolymers, synthetic nucleic acids containing functionalized 2'-amino-LNA scaffolds offer great opportunities for material science, diagnostics, and medicine of the future.
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Affiliation(s)
- I. Kira Astakhova
- Nucleic Acid Center,
Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Jesper Wengel
- Nucleic Acid Center,
Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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19
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Kumar P, Østergaard ME, Baral B, Anderson BA, Guenther DC, Kaura M, Raible DJ, Sharma PK, Hrdlicka PJ. Synthesis and biophysical properties of C5-functionalized LNA (locked nucleic acid). J Org Chem 2014; 79:5047-61. [PMID: 24825249 PMCID: PMC4049237 DOI: 10.1021/jo500614a] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Indexed: 01/07/2023]
Abstract
Oligonucleotides modified with conformationally restricted nucleotides such as locked nucleic acid (LNA) monomers are used extensively in molecular biology and medicinal chemistry to modulate gene expression at the RNA level. Major efforts have been devoted to the design of LNA derivatives that induce even higher binding affinity and specificity, greater enzymatic stability, and more desirable pharmacokinetic profiles. Most of this work has focused on modifications of LNA's oxymethylene bridge. Here, we describe an alternative approach for modulation of the properties of LNA: i.e., through functionalization of LNA nucleobases. Twelve structurally diverse C5-functionalized LNA uridine (U) phosphoramidites were synthesized and incorporated into oligodeoxyribonucleotides (ONs), which were then characterized with respect to thermal denaturation, enzymatic stability, and fluorescence properties. ONs modified with monomers that are conjugated to small alkynes display significantly improved target affinity, binding specificity, and protection against 3'-exonucleases relative to regular LNA. In contrast, ONs modified with monomers that are conjugated to bulky hydrophobic alkynes display lower target affinity yet much greater 3'-exonuclease resistance. ONs modified with C5-fluorophore-functionalized LNA-U monomers enable fluorescent discrimination of targets with single nucleotide polymorphisms (SNPs). In concert, these properties render C5-functionalized LNA as a promising class of building blocks for RNA-targeting applications and nucleic acid diagnostics.
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Affiliation(s)
- Pawan Kumar
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
- Department of Chemistry, Kurukshetra University, Kurukshetra 136119, India
| | - Michael E. Østergaard
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Bharat Baral
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Brooke A. Anderson
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Dale C. Guenther
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Mamta Kaura
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Daniel J. Raible
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Pawan K. Sharma
- Department of Chemistry, Kurukshetra University, Kurukshetra 136119, India
| | - Patrick J. Hrdlicka
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
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20
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Jørgensen AS, Gupta P, Wengel J, Astakhova IK. "Clickable" LNA/DNA probes for fluorescence sensing of nucleic acids and autoimmune antibodies. Chem Commun (Camb) 2014; 49:10751-3. [PMID: 24107917 DOI: 10.1039/c3cc45507f] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Herein we describe fluorescent oligonucleotides prepared by click chemistry between novel alkyne-modified locked nucleic acid (LNA) strands and a series of fluorescent azides for homogeneous (all-in-solution) detection of nucleic acids and autoimmune antibodies.
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Affiliation(s)
- Anna S Jørgensen
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark.
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21
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Sau SP, Madsen AS, Podbevsek P, Andersen NK, Kumar TS, Andersen S, Rathje RL, Anderson BA, Guenther DC, Karmakar S, Kumar P, Plavec J, Wengel J, Hrdlicka PJ. Identification and characterization of second-generation invader locked nucleic acids (LNAs) for mixed-sequence recognition of double-stranded DNA. J Org Chem 2013; 78:9560-70. [PMID: 24032477 PMCID: PMC3833467 DOI: 10.1021/jo4015936] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The development of synthetic agents that recognize double-stranded DNA (dsDNA) is a long-standing goal that is inspired by the promise for tools that detect, regulate, and modify genes. Progress has been made with triplex-forming oligonucleotides, peptide nucleic acids, and polyamides, but substantial efforts are currently devoted to the development of alternative strategies that overcome the limitations observed with the classic approaches. In 2005, we introduced Invader locked nucleic acids (LNAs), i.e., double-stranded probes that are activated for mixed-sequence recognition of dsDNA through modification with "+1 interstrand zippers" of 2'-N-(pyren-1-yl)methyl-2'-amino-α-l-LNA monomers. Despite promising preliminary results, progress has been slow because of the synthetic complexity of the building blocks. Here we describe a study that led to the identification of two simpler classes of Invader monomers. We compare the thermal denaturation characteristics of double-stranded probes featuring different interstrand zippers of pyrene-functionalized monomers based on 2'-amino-α-l-LNA, 2'-N-methyl-2'-amino-DNA, and RNA scaffolds. Insights from fluorescence spectroscopy, molecular modeling, and NMR spectroscopy are used to elucidate the structural factors that govern probe activation. We demonstrate that probes with +1 zippers of 2'-O-(pyren-1-yl)methyl-RNA or 2'-N-methyl-2'-N-(pyren-1-yl)methyl-2'-amino-DNA monomers recognize DNA hairpins with similar efficiency as original Invader LNAs. Access to synthetically simple monomers will accelerate the use of Invader-mediated dsDNA recognition for applications in molecular biology and nucleic acid diagnostics.
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Affiliation(s)
- Sujay P. Sau
- Department of Chemistry, University of Idaho, Moscow, ID-83844, USA
| | - Andreas S. Madsen
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, Odense, Denmark
| | | | - Nicolai K. Andersen
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, Odense, Denmark
| | - T. Santhosh Kumar
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, Odense, Denmark
| | - Sanne Andersen
- Department of Chemistry, University of Idaho, Moscow, ID-83844, USA
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, Odense, Denmark
| | - Rie L. Rathje
- Department of Chemistry, University of Idaho, Moscow, ID-83844, USA
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, Odense, Denmark
| | | | - Dale C. Guenther
- Department of Chemistry, University of Idaho, Moscow, ID-83844, USA
| | - Saswata Karmakar
- Department of Chemistry, University of Idaho, Moscow, ID-83844, USA
| | - Pawan Kumar
- Department of Chemistry, University of Idaho, Moscow, ID-83844, USA
| | - Janez Plavec
- National Institute of Chemistry, Ljubljana, Slovenia
| | - Jesper Wengel
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, Odense, Denmark
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22
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Astakhova IK, Kumar TS, Campbell MA, Ustinov AV, Korshun VA, Wengel J. Branched DNA nanostructures efficiently stabilised and monitored by novel pyrene-perylene 2'-α-L-amino-LNA FRET pairs. Chem Commun (Camb) 2013. [PMID: 23201901 DOI: 10.1039/c2cc37547h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Novel pyrene-perylene α-L-LNA FRET pairs described herein effectively detect assembly of 2- and 3-way branched DNA nanostructures prepared by postsynthetic microwave-assisted CuAAC click chemistry. The fluorescent signalling of assembly by internally positioned FRET pairs is achieved with low to no fluorescence background signal, remarkably low limit of target detection values and stabilization of the resulting nanostructures.
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Affiliation(s)
- I Kira Astakhova
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark.
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23
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Astakhova IK, Pasternak K, Campbell MA, Gupta P, Wengel J. A locked nucleic acid-based nanocrawler: designed and reversible movement detected by multicolor fluorescence. J Am Chem Soc 2013; 135:2423-6. [PMID: 23379691 DOI: 10.1021/ja311250w] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Herein we introduce a novel fluorescent LNA/DNA machine, a nanocrawler, which reversibly moves along a directionally polar complementary road controlled by affinity-enhancing locked nucleic acid (LNA) monomers and additional regulatory strands. Polyaromatic hydrocarbon (PAH) dyes attached to 2'-amino-LNA monomers are incorporated at four stations of the system, enabling simple detection of the position of the nanocrawler via a step-specific color signal. The sensing is provided by highly sensitive, chemically stable, and photostable PAH LNA interstrand communication systems, including pyrene excimer formation and pyrene-perylene interstrand Förster resonance energy transfer. We furthermore demonstrate that the nanocrawler selectively and reversibly moves along the road, followed by a bright and consistent fluorescence response for up to 10 cycles without any loss of signal.
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Affiliation(s)
- I Kira Astakhova
- Nucleic Acid Center and Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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24
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Karmakar S, Hrdlicka PJ. DNA strands with alternating incorporations of LNA and 2'- O-(pyren-1-yl)methyluridine: SNP-discriminating RNA detection probes. Chem Sci 2013; 4:3447-3454. [PMID: 23930202 DOI: 10.1039/c3sc50726b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Detection of nucleic acids using fluorophore-modified oligonucleotides forms the basis of many important applications in molecular biology, genetics and medical diagnostics. Here we demonstrate that DNA strands with central segments of alternating locked nucleic acid (LNA) and 2'-O-(pyren-1-yl)methyluridine monomers display very large and highly mismatch-sensitive increases in fluorescence emission upon RNA hybridization, whereas corresponding "LNA-free" controls do not. Absorbance spectra strongly suggest that LNA-induced conformational tuning of flanking 2'-O-(pyren-1-yl)methyluridine monomers places the reporter group in the minor groove upon RNA binding, whereby pyrene-nucleobase interactions leading to quenching of fluorescence are minimized. Accordingly, these easy-to-synthesize probes are promising SNP-discriminating RNA detection probes.
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Affiliation(s)
- Saswata Karmakar
- University of Idaho, Department of Chemistry, Moscow, ID 83844-2343, USA
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25
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Liu Z, Wang Y, Chen Y, Liu J, Fang Q, Kleeberg C, Marder TB. Ir-Catalyzed Direct Borylation at the 4-Position of Pyrene. J Org Chem 2012; 77:7124-8. [DOI: 10.1021/jo301293w] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Zhiqiang Liu
- State Key Laboratory
of Crystal
Materials, Shandong University, Jinan,
250100, China
| | - Yuanyuan Wang
- State Key Laboratory
of Crystal
Materials, Shandong University, Jinan,
250100, China
| | - Ying Chen
- State Key Laboratory
of Crystal
Materials, Shandong University, Jinan,
250100, China
| | - Jie Liu
- State Key Laboratory
of Crystal
Materials, Shandong University, Jinan,
250100, China
| | - Qi Fang
- State Key Laboratory
of Crystal
Materials, Shandong University, Jinan,
250100, China
| | - Christian Kleeberg
- Department
of Chemistry, Durham University, Durham,
DH1 3LE, United Kingdom
| | - Todd B. Marder
- Department
of Chemistry, Durham University, Durham,
DH1 3LE, United Kingdom
- Institut
für Anorganische
Chemie, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
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26
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Astakhova IK, Samokhina E, Babu BR, Wengel J. Novel (phenylethynyl)pyrene-LNA constructs for fluorescence SNP sensing in polymorphic nucleic acid targets. Chembiochem 2012; 13:1509-19. [PMID: 22761036 DOI: 10.1002/cbic.201200079] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Indexed: 01/05/2023]
Abstract
We describe fluorescent oligonucleotide probes labeled with novel (phenylethynyl)pyrene dyes attached to locked nucleic acids. Furthermore, we prove the utility of these probes for the effective detection of single-nucleotide polymorphisms in natural nucleic acids. High-affinity hybridization of the probes and excellent fluorescence responses to single-base mismatches in DNA/RNA targets are demonstrated in model dual-probe and doubly labeled probe formats. This stimulated us to develop two diagnostic systems for the homogeneous detection of a drug-resistance-causing mutation in HIV-1 protease cDNA and RNA gene fragments. Target sequences were obtained by analysis of 200 clinical samples from patients currently receiving anti-HIV/AIDS combination therapy at the Russian Federal AIDS Center. Using these fluorescent oligonucleotides, we were able to detect the target mutation despite all the challenges of the natural targets, that is, the presence of additional mutations, neighboring sequence variation, and low target concentration, which typically reduce binding and effectiveness of sensing by fluorescent oligonucleotides.
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Affiliation(s)
- Irina Kira Astakhova
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark.
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27
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Loakes D. Nucleotides and nucleic acids; oligo- and polynucleotides. ORGANOPHOSPHORUS CHEMISTRY 2012. [DOI: 10.1039/9781849734875-00169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- David Loakes
- Medical Research Council Laboratory of Molecular Biology, Hills Road Cambridge CB2 2QH UK
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28
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Crawford AG, Liu Z, Mkhalid IAI, Thibault M, Schwarz N, Alcaraz G, Steffen A, Collings JC, Batsanov AS, Howard JAK, Marder TB. Synthesis of 2‐ and 2,7‐Functionalized Pyrene Derivatives: An Application of Selective CH Borylation. Chemistry 2012; 18:5022-35. [DOI: 10.1002/chem.201103774] [Citation(s) in RCA: 158] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Indexed: 12/31/2022]
Affiliation(s)
- Andrew G. Crawford
- Department of Chemistry, Durham University, South Road, Durham, DH1 3LE (UK), Fax: (+44) 191‐384‐4737
| | - Zhiqiang Liu
- State Key Laboratory of Crystal Materials, Shandong University, 27 Shanda South Road, Jinan, 250100 (P. R. China)
| | | | - Marie‐Hélène Thibault
- Département de Chimie, Université Laval, 1045, avenue de la Médecine, Pavillon Alexandre‐Vachon, Québec, G1V 0A6 (Canada)
| | - Nicolle Schwarz
- Leibniz‐Institut für Katalyse e. V. an der Universität Rostock, Albert‐Einstein‐Strasse 29a, 18059 Rostock (Germany)
| | - Gilles Alcaraz
- Laboratoire de Chimie de Coordination du CNRS, 205 route de Narbonne, 31077 Toulouse, Cedex 04 (France)
| | - Andreas Steffen
- Department of Chemistry, Durham University, South Road, Durham, DH1 3LE (UK), Fax: (+44) 191‐384‐4737
| | - Jonathan C. Collings
- Department of Chemistry, Durham University, South Road, Durham, DH1 3LE (UK), Fax: (+44) 191‐384‐4737
| | - Andrei S. Batsanov
- Department of Chemistry, Durham University, South Road, Durham, DH1 3LE (UK), Fax: (+44) 191‐384‐4737
| | - Judith A. K. Howard
- Department of Chemistry, Durham University, South Road, Durham, DH1 3LE (UK), Fax: (+44) 191‐384‐4737
| | - Todd B. Marder
- Department of Chemistry, Durham University, South Road, Durham, DH1 3LE (UK), Fax: (+44) 191‐384‐4737
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29
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Østergaard ME, Hrdlicka PJ. Pyrene-functionalized oligonucleotides and locked nucleic acids (LNAs): tools for fundamental research, diagnostics, and nanotechnology. Chem Soc Rev 2011; 40:5771-88. [PMID: 21487621 PMCID: PMC3644995 DOI: 10.1039/c1cs15014f] [Citation(s) in RCA: 202] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Pyrene-functionalized oligonucleotides (PFOs) are increasingly explored as tools in fundamental research, diagnostics and nanotechnology. Their popularity is linked to the ability of pyrenes to function as polarity-sensitive and quenchable fluorophores, excimer-generating units, aromatic stacking moieties and nucleic acid duplex intercalators. These characteristics have enabled development of PFOs for detection of complementary DNA/RNA targets, discrimination of single nucleotide polymorphisms (SNPs), and generation of π-arrays on nucleic acid scaffolds. This critical review will highlight the physical properties and applications of PFOs that are likely to provide high degree of positional control of the chromophore in nucleic acid complexes. Particular emphasis will be placed on pyrene-functionalized Locked Nucleic Acids (LNAs) since these materials display interesting properties such as fluorescence quantum yields approaching unity and recognition of mixed-sequence double stranded DNA (144 references).
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30
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Nicolaou KC, Ellery SP, Rivas F, Saye K, Rogers E, Workinger TJ, Schallenberger M, Tawatao R, Montero A, Hessell A, Romesberg F, Carson D, Burton D. Synthesis and biological evaluation of 2',4'- and 3',4'-bridged nucleoside analogues. Bioorg Med Chem 2011; 19:5648-69. [PMID: 21840722 PMCID: PMC3348725 DOI: 10.1016/j.bmc.2011.07.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 07/12/2011] [Accepted: 07/13/2011] [Indexed: 10/18/2022]
Abstract
Most nucleosides in solution typically exist in equilibrium between two major sugar pucker forms, N-type and S-type, but bridged nucleosides can be locked into one of these conformations depending on their specific structure. While many groups have researched these bridged nucleosides for the purpose of determining their binding affinity for antisense applications, we opted to look into the potential for biological activity within these conformationally-locked structures. A small library of 2',4'- and 3',4'-bridged nucleoside analogues was synthesized, including a novel 3',4'-carbocyclic bridged system. The synthesized compounds were tested for antibacterial, antitumor, and antiviral activities, leading to the identification of nucleosides possessing such biological activities. To the best of our knowledge, these biologically active compounds represent the first example of 2',4'-bridged nucleosides to demonstrate such properties. The most potent compound, nucleoside 33, exhibited significant antiviral activity against pseudoviruses SF162 (IC(50)=7.0 μM) and HxB2 (IC(50)=2.4 μM). These findings render bridged nucleosides as credible leads for drug discovery in the anti-HIV area of research.
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Affiliation(s)
- K C Nicolaou
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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Crawford AG, Dwyer AD, Liu Z, Steffen A, Beeby A, Pålsson LO, Tozer DJ, Marder TB. Experimental and Theoretical Studies of the Photophysical Properties of 2- and 2,7-Functionalized Pyrene Derivatives. J Am Chem Soc 2011; 133:13349-62. [DOI: 10.1021/ja2006862] [Citation(s) in RCA: 242] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Andrew G. Crawford
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Austin D. Dwyer
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Zhiqiang Liu
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
- State Key Lab of Crystal Materials, Shandong University, 27 Shanda South Road, Jinan 250100, China
| | - Andreas Steffen
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Andrew Beeby
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Lars-Olof Pålsson
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - David J. Tozer
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Todd B. Marder
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
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