1
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Brandner L, Müller TJJ. Multicomponent synthesis of chromophores – The one-pot approach to functional π-systems. Front Chem 2023; 11:1124209. [PMID: 37007054 PMCID: PMC10065161 DOI: 10.3389/fchem.2023.1124209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/26/2023] [Indexed: 03/19/2023] Open
Abstract
Multicomponent reactions, conducted in a domino, sequential or consecutive fashion, have not only considerably enhanced synthetic efficiency as one-pot methodology, but they have also become an enabling tool for interdisciplinary research. The highly diversity-oriented nature of the synthetic concept allows accessing huge structural and functional space. Already some decades ago this has been recognized for life sciences, in particular, lead finding and exploration in pharma and agricultural chemistry. The quest for novel functional materials has also opened the field for diversity-oriented syntheses of functional π-systems, i.e. dyes for photonic and electronic applications based on their electronic properties. This review summarizes recent developments in MCR syntheses of functional chromophores highlighting syntheses following either the framework forming scaffold approach by establishing connectivity between chromophores or the chromogenic chromophore approach by de novo formation of chromophore of interest. Both approaches warrant rapid access to molecular functional π-systems, i.e. chromophores, fluorophores, and electrophores for various applications.
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2
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Gebhard J, Hirsch L, Schwechheimer C, Wagenknecht HA. Hybridization-Sensitive Fluorescent Probes for DNA and RNA by a Modular "Click" Approach. Bioconjug Chem 2022; 33:1634-1642. [PMID: 35995426 PMCID: PMC9501807 DOI: 10.1021/acs.bioconjchem.2c00241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Fluorescent DNA probes were prepared in a modular approach
using
the “click” post-synthetic modification strategy. The
new glycol-based module and DNA building block place just two carbons
between the phosphodiester bridges and anchor the dye by an additional
alkyne group. This creates a stereocenter in the middle of this artificial
nucleoside substitute. Both enantiomers and a variety of photostable
cyanine–styryl dyes as well as thiazole orange derivatives
were screened as “clicked” conjugates in different surrounding
DNA sequences. The combination of the (S)-configured
DNA anchor and the cyanylated cyanine–styryl dye shows the
highest fluorescence light-up effect of 9.2 and a brightness of approximately
11,000 M–1 cm–1. This hybridization
sensitivity and fluorescence readout were further developed utilizing
electron transfer and energy transfer processes. The combination of
the hybridization-sensitive DNA building block with the nucleotide
of 5-nitroindole as an electron acceptor and a quencher increases
the light-up effect to 20 with the DNA target and to 15 with the RNA
target. The fluorescence readout could significantly be enhanced to
values between 50 and 360 by the use of energy transfer to a second
DNA probe with commercially available dyes, like Cy3.5, Cy5, and Atto590,
as energy acceptors at the 5′-end. The latter binary probes
shift the fluorescent readout from the range of 500–550 nm
to the range of 610–670 nm. The optical properties make these
fluorescent DNA probes potentially useful for RNA imaging. Due to
the strong light-up effect, they will not require washing procedures
and will thus be suitable for live-cell imaging.
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Affiliation(s)
- Julian Gebhard
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 7631 Karlsruhe, Germany
| | - Lara Hirsch
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 7631 Karlsruhe, Germany
| | - Christian Schwechheimer
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 7631 Karlsruhe, Germany
| | - Hans-Achim Wagenknecht
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 7631 Karlsruhe, Germany
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3
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Ochs M, Mayer B, Müller TJJ. Unimolecular Exciplexes by Ugi Four-Component Reaction. Front Chem 2019; 7:717. [PMID: 31737597 PMCID: PMC6838752 DOI: 10.3389/fchem.2019.00717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 10/10/2019] [Indexed: 12/28/2022] Open
Abstract
Exciplex or excited complex emission is an excited state process, arising from considerable charge transfer of an excited energy donor to an acceptor, which can be identified by the occurrence of a redshifted emission band that is absent in the individual constituents. Particularly interesting are exciplexes that are formed by intramolecular excited state interaction, which are inherently concentration independent. Based upon our previous experience in the Ugi-4CR syntheses of donor-acceptor conjugates capable of photo-induced intramolecular electron transfer (PIET), that is, generation of light-induced charge separation, we now disclose the diversity-oriented approach on unimolecular exciplex emitters and their reference systems by Ugi-4CR. The photophysics is studied by absorption and emission spectroscopy and accompanied by density functional theory (DFT) and time-dependent density functional theory (TDDFT) calculations.
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Affiliation(s)
- Maria Ochs
- Institut für Organische Chemie and Makromolekulare Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
- Ernst-Berl Institut für Technische and Makromolekulare Chemie, Technische Universität Darmstadt, Darmstadt, Germany
| | - Bernhard Mayer
- Institut für Organische Chemie and Makromolekulare Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Thomas J. J. Müller
- Institut für Organische Chemie and Makromolekulare Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
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4
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Vecchioni S, Capece MC, Toomey E, Nguyen L, Ray A, Greenberg A, Fujishima K, Urbina J, Paulino-Lima IG, Pinheiro V, Shih J, Wessel G, Wind SJ, Rothschild L. Construction and characterization of metal ion-containing DNA nanowires for synthetic biology and nanotechnology. Sci Rep 2019; 9:6942. [PMID: 31061396 PMCID: PMC6502794 DOI: 10.1038/s41598-019-43316-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/25/2019] [Indexed: 12/28/2022] Open
Abstract
DNA is an attractive candidate for integration into nanoelectronics as a biological nanowire due to its linear geometry, definable base sequence, easy, inexpensive and non-toxic replication and self-assembling properties. Recently we discovered that by intercalating Ag+ in polycytosine-mismatch oligonucleotides, the resulting C-Ag+-C duplexes are able to conduct charge efficiently. To map the functionality and biostability of this system, we built and characterized internally-functionalized DNA nanowires through non-canonical, Ag+-mediated base pairing in duplexes containing cytosine-cytosine mismatches. We assessed the thermal and chemical stability of ion-coordinated duplexes in aqueous solutions and conclude that the C-Ag+-C bond forms DNA duplexes with replicable geometry, predictable thermodynamics, and tunable length. We demonstrated continuous ion chain formation in oligonucleotides of 11-50 nucleotides (nt), and enzyme ligation of mixed strands up to six times that length. This construction is feasible without detectable silver nanocluster contaminants. Functional gene parts for the synthesis of DNA- and RNA-based, C-Ag+-C duplexes in a cell-free system have been constructed in an Escherichia coli expression plasmid and added to the open-source BioBrick Registry, paving the way to realizing the promise of inexpensive industrial production. With appropriate design constraints, this conductive variant of DNA demonstrates promise for use in synthetic biological constructs as a dynamic nucleic acid component and contributes molecular electronic functionality to DNA that is not already found in nature. We propose a viable route to fabricating stable DNA nanowires in cell-free and synthetic biological systems for the production of self-assembling nanoelectronic architectures.
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Affiliation(s)
- Simon Vecchioni
- Department of Biomedical Engineering, Columbia University, New York, NY, 10027, USA.
| | - Mark C Capece
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Emily Toomey
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Le Nguyen
- School of Engineering, Brown University, Providence, RI, 02912, USA
| | - Austin Ray
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Alissa Greenberg
- Department of History, Stanford University, Stanford, CA, 94305, USA
| | - Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Jesica Urbina
- Geology, Minerals, Energy, & Geophysics Science Center, U.S. Geological Survey, Menlo Park, CA, 94025, USA
- Planetary Science Branch, NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - Ivan G Paulino-Lima
- Blue Marble Space Institute of Science, NASA Ames Research Center, Planetary Systems Branch, Moffett Field, CA, 94035-0001, USA
| | - Vitor Pinheiro
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Joseph Shih
- Department of Natural Sciences and Mathematics, University of Saint Mary, Leavenworth, KS, 66048, USA
| | - Gary Wessel
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, 02912, USA
| | - Shalom J Wind
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY, 10027, USA
| | - Lynn Rothschild
- Planetary Science Branch, NASA Ames Research Center, Moffett Field, CA, 94035, USA.
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, 02912, USA.
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5
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Müller TJJ. Multi-component synthesis of fluorophores via catalytic generation of alkynoyl intermediates. DRUG DISCOVERY TODAY. TECHNOLOGIES 2018; 29:19-26. [PMID: 30471669 DOI: 10.1016/j.ddtec.2018.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 06/08/2018] [Indexed: 06/09/2023]
Abstract
This account summarizes recent developments of aggregation-induced emissive and emission solvatochromic fluorophores by multicomponent reactions. Key intermediates are catalytically generated alkynoyl derivatives that are directly transformed into luminophores in a one-pot fashion. The conciseness in combination with ready access to tailored chromophore libraries makes this synthetic methodological concept superior over classical multistep syntheses.
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Affiliation(s)
- Thomas J J Müller
- Institut für Organische Chemie und Makromolekulare Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany.
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6
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Whitfield CJ, Little RC, Khan K, Ijiro K, Connolly BA, Tuite EM, Pike AR. Self-Priming Enzymatic Fabrication of Multiply Modified DNA. Chemistry 2018; 24:15267-15274. [PMID: 29931815 DOI: 10.1002/chem.201801976] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/19/2018] [Indexed: 12/15/2022]
Abstract
The self-priming synthesis of multiply modified DNA by the extension of repeating unit duplex "oligoseeds" provides a source of versatile DNA. Sterically-demanding nucleotides 5-Br-dUTP, 7-deaza-7-I-dATP, 6-S-dGTP, 5-I-dCTP as well as 5-(octadiynyl)-dCTP were incorporated into two extending oligoseeds; [GATC]5 /[GATC]5 and [A4 G]4 /[CT4 ]4 . The products contained modifications on one or both strands of DNA, demonstrating their recognition by the polymerase as both template (reading) and substrate (writing). Nucleobase modifications that lie in the major groove were reliably read and written by the polymerase during the extension reaction, even when bulky or in contiguous sequences. Repeat sequence DNA over 500 bp long, bearing four different modified units was produced by this method. The number, position and type of modification, as well as the overall length of the DNA can be controlled to yield designer DNA that offers sequence-determined sites for further chemical adaptations, targeted small molecule binding studies, or sensing and sequencing applications.
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Affiliation(s)
- Colette J Whitfield
- Chemistry-School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Rachel C Little
- Chemistry-School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Kasid Khan
- Chemistry-School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Kuniharu Ijiro
- Research Institute for Electronic Science, Hokkaido University, Sapporo, 001-0021, Japan
| | - Bernard A Connolly
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Eimer M Tuite
- Chemistry-School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Andrew R Pike
- Chemistry-School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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7
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Schönhaber J, D'Souza DM, Glißmann T, Mayer B, Janiak C, Rominger F, Frank W, Müller TJJ. Domino Insertion-Coupling Synthesis of Solid-State Luminescent Propynylidene Indolones. Chemistry 2018; 24:14712-14723. [DOI: 10.1002/chem.201802237] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 07/10/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Jan Schönhaber
- Institut für Organische Chemie und Makromolekulare Chemie; Heinrich-Heine-Universität Düsseldorf; Universitätsstraße 1 40225 Düsseldorf Germany
| | - Daniel M. D'Souza
- Organisch-Chemisches Institut; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 270 69198 Heidelberg Germany
| | - Tobias Glißmann
- Institut für Organische Chemie und Makromolekulare Chemie; Heinrich-Heine-Universität Düsseldorf; Universitätsstraße 1 40225 Düsseldorf Germany
| | - Bernhard Mayer
- Institut für Organische Chemie und Makromolekulare Chemie; Heinrich-Heine-Universität Düsseldorf; Universitätsstraße 1 40225 Düsseldorf Germany
| | - Christoph Janiak
- Institut für Anorganische Chemie und Strukturchemie; Heinrich-Heine-Universität Düsseldorf; Universitätsstraße 1 40225 Düsseldorf Germany
| | - Frank Rominger
- Organisch-Chemisches Institut; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 270 69198 Heidelberg Germany
| | - Walter Frank
- Institut für Anorganische Chemie und Strukturchemie; Heinrich-Heine-Universität Düsseldorf; Universitätsstraße 1 40225 Düsseldorf Germany
| | - Thomas J. J. Müller
- Institut für Organische Chemie und Makromolekulare Chemie; Heinrich-Heine-Universität Düsseldorf; Universitätsstraße 1 40225 Düsseldorf Germany
- Organisch-Chemisches Institut; Ruprecht-Karls-Universität Heidelberg; Im Neuenheimer Feld 270 69198 Heidelberg Germany
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8
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Merkt FK, Müller TJJ. Solid State and Aggregation Induced Emissive Chromophores by Multi-component Syntheses. Isr J Chem 2018. [DOI: 10.1002/ijch.201800058] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Franziska K. Merkt
- Institut für Organische Chemie und Makromolekulare Chemie; Heinrich-Heine-Universität Düsseldorf; Universitätsstrasse 1 D-40225 Düsseldorf Germany
| | - Thomas J. J. Müller
- Institut für Organische Chemie und Makromolekulare Chemie; Heinrich-Heine-Universität Düsseldorf; Universitätsstrasse 1 D-40225 Düsseldorf Germany
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9
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Hallé F, Fin A, Rovira AR, Tor Y. Emissive Synthetic Cofactors: Enzymatic Interconversions of tz A Analogues of ATP, NAD + , NADH, NADP + , and NADPH. Angew Chem Int Ed Engl 2018; 57:1087-1090. [PMID: 29228460 PMCID: PMC5771816 DOI: 10.1002/anie.201711935] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Indexed: 12/11/2022]
Abstract
A series of enzymatic transformations, which generate visibly emissive isofunctional cofactors based on an isothiazolo[4,3-d]pyrimidine analogue of adenosine (tz A), was developed. Nicotinamide adenylyl transferase condenses nicotinamide mononucleotide and tz ATP to yield Ntz AD+ , which can be enzymatically phosphorylated by NAD+ kinase and ATP or tz ATP to the corresponding Ntz ADP+ . The latter can be engaged in NADP-specific coupled enzymatic transformations involving conversion to Ntz ADPH by glucose-6-phosphate dehydrogenase and reoxidation to Ntz ADP+ by glutathione reductase. The Ntz ADP+ /Ntz ADPH cycle can be monitored in real time by fluorescence spectroscopy.
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Affiliation(s)
- François Hallé
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Andrea Fin
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Alexander R Rovira
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
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10
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Emissive Synthetic Cofactors: Enzymatic Interconversions of tz
A Analogues of ATP, NAD+
, NADH, NADP+
, and NADPH. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201711935] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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11
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Affiliation(s)
- Thomas J. J. Müller
- Institut für Organische Chemie und Makromolekulare Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
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12
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Bag SS, Das SK, Pradhan MK, Jana S. Hybridization accompanying FRET event in labeled natural nucleoside-unnatural nucleoside containing chimeric DNA duplexes. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 162:669-673. [PMID: 27498231 DOI: 10.1016/j.jphotobiol.2016.07.043] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 07/30/2016] [Indexed: 01/05/2023]
Abstract
Förster resonance energy transfer (FRET) is a highly efficient strategy in illuminating the structures, structural changes and dynamics of DNA, proteins and other biomolecules and thus is being widely utilized in studying such phenomena, in designing molecular/biomolecular probes for monitoring the hybridization event of two single stranded DNA to form duplex, in gene detection and in many other sensory applications in chemistry, biology and material sciences. Moreover, FRET can give information about the positional status of chromophores within the associated biomolecules with much more accuracy than other methods can yield. Toward this end, we want to report here the ability of fluorescent unnatural nucleoside, triazolylphenanthrene ((TPhen)BDo) to show FRET interaction upon hybridization with fluorescently labeled natural nucleosides, (Per)U or (OxoPy)U or (Per)U, forming two stable chimeric DNA duplexes. The pairing selectivity and the thermal duplex stability of the chimeric duplexes are higher than any of the duplexes with natural nucleoside formed. The hybridization results in a Förster resonance energy transfer (FRET) from donor triazolylphenanthrene of (TPhen)BDo to acceptor oxopyrene of (OxoPy)U and/or to perylene chromophore of (Per)U, respectively, in two chimeric DNA duplexes. Therefore, we have established the FRET process in two chimeric DNA duplexes wherein a fluorescently labeled natural nucleoside ((OxoPy)U or (Per)U) paired against an unnatural nucleoside ((TPhen)BDo) without sacrificing the duplex stability and B-DNA conformation. The hybridization accompanying FRET event in these classes of interacting fluorophores is new. Moreover, there is no report of such designed system of chimeric DNA duplex. Our observed phenomenon and the design can potentially be exploited in designing more of such efficient FRET pairs for useful application in the detection and analysis of biomolecular interactions and in material science application.
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Affiliation(s)
- Subhendu Sekhar Bag
- Bio-organic Chemistry Laboratory, Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
| | - Suman K Das
- Bio-organic Chemistry Laboratory, Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Manoj Kumar Pradhan
- Bio-organic Chemistry Laboratory, Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Subhashis Jana
- Bio-organic Chemistry Laboratory, Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
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13
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Moni L, Gers-Panther CF, Anselmo M, Müller TJJ, Riva R. Highly Convergent Synthesis of Intensively Blue Emissive Furo[2,3-c
]isoquinolines by a Palladium-Catalyzed Cyclization Cascade of Unsaturated Ugi Products. Chemistry 2016; 22:2020-2031. [DOI: 10.1002/chem.201504335] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Lisa Moni
- Dipartimento di Chimica e Chimica Industriale; University of Genova; Via Dodecaneso 31 16146 Genova Italy
| | - Charlotte F. Gers-Panther
- Institut für Organische Chemie und Makromoleculare Chemie; Heinrich-Heine-Universität Düsseldorf; Universitätsstraße 1 40225 Düsseldorf Germany
| | - Manuel Anselmo
- Dipartimento di Chimica e Chimica Industriale; University of Genova; Via Dodecaneso 31 16146 Genova Italy
| | - Thomas J. J. Müller
- Institut für Organische Chemie und Makromoleculare Chemie; Heinrich-Heine-Universität Düsseldorf; Universitätsstraße 1 40225 Düsseldorf Germany
| | - Renata Riva
- Dipartimento di Chimica e Chimica Industriale; University of Genova; Via Dodecaneso 31 16146 Genova Italy
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14
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Mata G, Schmidt OP, Luedtke NW. A fluorescent surrogate of thymidine in duplex DNA. Chem Commun (Camb) 2016; 52:4718-21. [DOI: 10.1039/c5cc09552b] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
DMAT is a new fluorescent thymidine mimic composed of 2′-deoxyuridine fused to dimethylaniline.
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Affiliation(s)
- Guillaume Mata
- Department of Chemistry
- University of Zurich
- CH-8057 Zurich
- Switzerland
| | - Olivia P. Schmidt
- Department of Chemistry
- University of Zurich
- CH-8057 Zurich
- Switzerland
| | - Nathan W. Luedtke
- Department of Chemistry
- University of Zurich
- CH-8057 Zurich
- Switzerland
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15
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Foller Larsen A, Dumat B, Wranne MS, Lawson CP, Preus S, Bood M, Gradén H, Marcus Wilhelmsson L, Grøtli M. Development of bright fluorescent quadracyclic adenine analogues: TDDFT-calculation supported rational design. Sci Rep 2015; 5:12653. [PMID: 26227585 PMCID: PMC4530663 DOI: 10.1038/srep12653] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 07/06/2015] [Indexed: 02/01/2023] Open
Abstract
Fluorescent base analogues (FBAs) comprise a family of increasingly important molecules for the investigation of nucleic acid structure and dynamics. We recently reported the quantum chemical calculation supported development of four microenvironment sensitive analogues of the quadracyclic adenine (qA) scaffold, the qANs, with highly promising absorptive and fluorescence properties that were very well predicted by TDDFT calculations. Herein, we report on the efficient synthesis, experimental and theoretical characterization of nine novel quadracyclic adenine derivatives. The brightest derivative, 2-CNqA, displays a 13-fold increased brightness (εΦF = 4500) compared with the parent compound qA and has the additional benefit of being a virtually microenvironment-insensitive fluorophore, making it a suitable candidate for nucleic acid incorporation and use in quantitative FRET and anisotropy experiments. TDDFT calculations, conducted on the nine novel qAs a posteriori, successfully describe the relative fluorescence quantum yield and brightness of all qA derivatives. This observation suggests that the TDDFT-based rational design strategy may be employed for the development of bright fluorophores built up from a common scaffold to reduce the otherwise costly and time-consuming screening process usually required to obtain useful and bright FBAs.
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Affiliation(s)
- Anders Foller Larsen
- Department of Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology, S-41296 Gothenburg, Sweden
| | - Blaise Dumat
- Department of Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology, S-41296 Gothenburg, Sweden
| | - Moa S. Wranne
- Department of Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology, S-41296 Gothenburg, Sweden
| | - Christopher P. Lawson
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-41296 Gothenburg, Sweden
| | - Søren Preus
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, DK-8000, Denmark
| | - Mattias Bood
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-41296 Gothenburg, Sweden
| | | | - L. Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology, S-41296 Gothenburg, Sweden
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-41296 Gothenburg, Sweden
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16
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Lawson CP, Dierckx A, Miannay FA, Wellner E, Wilhelmsson LM, Grøtli M. Synthesis and photophysical characterisation of new fluorescent triazole adenine analogues. Org Biomol Chem 2015; 12:5158-67. [PMID: 24912077 DOI: 10.1039/c4ob00904e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fluorescent nucleic acid base analogues are powerful probes of DNA structure. Here we describe the synthesis and photo-physical characterisation of a series of 2-(4-amino-5-(1H-1,2,3-triazol-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl) and 2-(4-amino-3-(1H-1,2,3-triazol-4-yl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl) analogues via Sonogashira cross-coupling and [3 + 2]-cycloaddition reactions as the key steps in the synthesis. Compounds with a nitrogen atom in position 8 showed an approximately ten-fold increase in quantum yield and decreased Stokes shift compared to analogues with a carbon atom in position 8. Furthermore, the analogues containing nitrogen in the 8-position showed a more red-shifted and structured absorption as opposed to those which have a carbon incorporated in the same position. Compared to the previously characterised C8-triazole modified adenine, the emissive potential was significantly lower (tenfold or more) for this new family of triazoles-adenine compounds. However, three of the compounds have photophysical properties which will make them interesting to monitor inside DNA.
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Affiliation(s)
- Christopher P Lawson
- Department of Chemistry, Medicinal Chemistry, University of Gothenburg, S-41296 Gothenburg, Sweden.
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Moni L, Denissen M, Valentini G, Müller TJJ, Riva R. Diversity-oriented synthesis of intensively blue emissive 3-hydroxyisoquinolines by sequential Ugi four-component reaction/reductive Heck cyclization. Chemistry 2014; 21:753-62. [PMID: 25369792 DOI: 10.1002/chem.201404209] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Indexed: 11/09/2022]
Abstract
A convergent approach to highly functionalized 3-hydroxyisoquinolines is reported. The key steps are an Ugi multicomponent reaction and a subsequent intramolecular reductive Heck reaction; these can also be performed as a one-pot procedure. The structures display very interesting properties as blue-fluorescence emitters. Photophysical studies on the absorption and static fluorescence indicate that the substitution pattern on the pyridyl part influences the optical properties only to a minor extent, unless the amide substituent becomes sterically demanding and leads to significant nonradiative deactivation. The donor substitution on the benzo core considerably enhances the fluorescence quantum yields and trimethoxy substitution causes a pronounced redshift of the emission bands. Protonation of the isoquinolyl nitrogen atom causes efficient static quenching of the fluorescence.
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Affiliation(s)
- Lisa Moni
- Dipartimento di Chimica e Chimica Industriale, University of Genova, Via Dodecaneso 31, 16146 Genova (Italy)
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18
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Tedeschi T, Tonelli A, Sforza S, Corradini R, Marchelli R. A pyrenyl-PNA probe for DNA and RNA recognition: Fluorescence and UV absorption studies. ARTIFICIAL DNA, PNA & XNA 2014; 1:83-89. [PMID: 21686243 DOI: 10.4161/adna.1.2.13899] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Revised: 10/08/2010] [Accepted: 10/09/2010] [Indexed: 11/19/2022]
Abstract
The design and the synthesis of a PNA oligomer containing a pyrenyl residue in the backbone were performed. PNA sequence was chosen complementary to a "G rich" target sequence involved in G-quadruplex formation. The pyrenyl unit replaced a nucleobase in the middle of the PNA through covalent linkage to the backbone by a carboxymethyl unit. A systematic study on the binding properties of this probe towards DNA and RNA complementary strands was carried out by UV and fluorescence spectroscopy. UV melting curves indicated that the PNA probe binds more tightly to RNA rather than to DNA. Thermodynamic data obtained by Van't Hoff fitting of the melting curves indicated that, in the case of RNA, a more favorable interaction occurs between the pyrenyl unit and the RNA nucleobases, leading to a very favorable enthalpic contribution.The fluorescence analysis showed specific quenching of the pyrene emission associated to the formation of the full-match PNA-DNA or PNA-RNA duplexes. Again, this behavior was more evident in the case of RNA, consistently with the stronger interaction of the pyrenyl unit with the complementary strand. In order to study the sequence specificity of the pyrenyl-PNA probe (pyr-PNA), recognition experiments on mismatched DNA and RNA sequences were also performed.
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Affiliation(s)
- Tullia Tedeschi
- Department of Organic and Industrial Chemistry; University of Parma; Parma, Italy
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19
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Bay S, Makhloufi G, Janiak C, Müller TJJ. The Ugi four-component reaction as a concise modular synthetic tool for photo-induced electron transfer donor-anthraquinone dyads. Beilstein J Org Chem 2014; 10:1006-16. [PMID: 24991251 PMCID: PMC4077531 DOI: 10.3762/bjoc.10.100] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 04/03/2014] [Indexed: 12/13/2022] Open
Abstract
Phenothiazinyl and carbazolyl-donor moieties can be covalently coupled to an anthraquinone acceptor unit through an Ugi four-component reaction in a rapid, highly convergent fashion and with moderate to good yields. These novel donor–acceptor dyads are electronically decoupled in the electronic ground state according to UV–vis spectroscopy and cyclic voltammetry. However, in the excited state the inherent donor luminescence is efficiently quenched. Previously performed femtosecond spectroscopic measurements account for a rapid exergonic depopulation of the excited singlet states into a charge-separated state. Calculations of the Gibbs energy of photo-induced electron transfer from readily available UV–vis spectroscopic and cyclovoltammetric data applying the Weller approximation enables a quick evaluation of these novel donor–acceptor dyads. In addition, the X-ray structure of a phenothiazinyl–anthraquinone dyad supports short donor–acceptor distances by an intramolecular π-stacking conformation, an important assumption also implied in the calculations of the Gibbs energies according to the Weller approximation.
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Affiliation(s)
- Sarah Bay
- Heinrich-Heine Universität Düsseldorf, Institut für Organische Chemie und Makromolekulare Chemie, Universitätsstraße 1, D-40225 Düsseldorf, Germany
| | - Gamall Makhloufi
- Heinrich-Heine Universität Düsseldorf, Institut für Anorganische Chemie und Strukturchemie, Universitätsstraße 1, D-40225 Düsseldorf, Germany
| | - Christoph Janiak
- Heinrich-Heine Universität Düsseldorf, Institut für Anorganische Chemie und Strukturchemie, Universitätsstraße 1, D-40225 Düsseldorf, Germany
| | - Thomas J J Müller
- Heinrich-Heine Universität Düsseldorf, Institut für Organische Chemie und Makromolekulare Chemie, Universitätsstraße 1, D-40225 Düsseldorf, Germany
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20
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Muschelknautz C, Visse R, Nordmann J, Müller TJJ. One-pot three-component synthesis and photophysical characteristics of novel triene merocyanines. Beilstein J Org Chem 2014; 10:599-612. [PMID: 24778710 PMCID: PMC3999876 DOI: 10.3762/bjoc.10.51] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 01/28/2014] [Indexed: 01/10/2023] Open
Abstract
Novel triene merocyanines, i.e. 1-styryleth-2-enylidene and 4-(1,3,3-trimethylindolin-2-ylidene)but-2-en-1-ylideneindolones are obtained in good to excellent yields in a consecutive three-component insertion Sonogashira coupling-addition sequence. The selectivity of either series is remarkable and has its origin in the stepwise character of the terminal addition step as shown by extensive computations on the DFT level. All merocyanines display intense absorption bands in solution and the film spectra indicate J-aggregation. While 1-styryleth-2-enylideneindolones show an intense deep red emission in films, 4-(1,3,3-trimethylindolin-2-ylidene)but-2-en-1-ylideneindolones are essentially nonemissive in films or in the solid state. TD-DFT computations rationalize the charge-transfer nature of the characteristic broad long-wavelength absorptions bands.
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Affiliation(s)
- Christian Muschelknautz
- Institut für Organische Chemie und Makromolekulare Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Robin Visse
- Institut für Organische Chemie und Makromolekulare Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Jan Nordmann
- Institut für Organische Chemie und Makromolekulare Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany
| | - Thomas J J Müller
- Institut für Organische Chemie und Makromolekulare Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany
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21
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Heisig F, Gollos S, Freudenthal SJ, El-Tayeb A, Iqbal J, Müller CE. Synthesis of BODIPY derivatives substituted with various bioconjugatable linker groups: a construction kit for fluorescent labeling of receptor ligands. J Fluoresc 2013; 24:213-30. [PMID: 24052460 DOI: 10.1007/s10895-013-1289-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2013] [Accepted: 08/09/2013] [Indexed: 12/15/2022]
Abstract
The goal of the present study was to design small, functionalized green-emitting BODIPY dyes, which can readily be coupled to target molecules such as receptor ligands, or even be integrated into their pharmacophores. A simple two-step one-pot procedure starting from 2,4-dimethylpyrrole and ω-bromoalkylcarboxylic acid chlorides was used to obtain new ω-bromoalkyl-substituted BODIPY fluorophores (1a-1f) connected via alkyl spacers of different length to the 8-position of the fluorescent dye. The addition of radical inhibitors reduced the amount of side products. The ω-bromoalkyl-substituted BODIPYs were further converted to introduce various functional groups: iodo-substituted dyes were obtained by Finkelstein reaction in excellent yields; microwave-assisted reaction with methanolic ammonia led to fast and clean conversion to the amino-substituted dyes; a hydroxyl-substituted derivative was prepared by reaction with sodium ethylate, and thiol-substituted BODIPYs were obtained by reaction of 1a-1f with potassium thioacetate followed by alkaline cleavage of the thioesters. Water-soluble derivatives were prepared by introducing sulfonate groups into the 2- and 6-position of the BODIPY core. The synthesized BODIPY derivatives showed high fluorescent yields and appeared to be stable under basic, reducing and oxidative conditions. As a proof of concept, 2-thioadenosine was alkylated with bromoethyl-BODIPY 1b. The resulting fluorescent 2-substituted adenosine derivative 15 displayed selectivity for the A3 adenosine receptor (ARs) over the other AR subtypes, showed agonistic activity, and may thus become a useful tool for studying A3ARs, or a lead structure for further optimization. The new functionalized dyes may be widely used for fluorescent labeling allowing the investigation of biological targets and processes.
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Affiliation(s)
- Fabian Heisig
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University Bonn, 53121, Bonn, Germany
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22
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Consecutive three-component synthesis of film luminescent indolone merocyanines with L-amino acid ester donors. Chem Heterocycl Compd (N Y) 2013. [DOI: 10.1007/s10593-013-1320-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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23
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Bortolozzi R, Ihmels H, Thomas L, Tian M, Viola G. 9-(4-Dimethylaminophenyl)benzo[b]quinolizinium: a near-infrared fluorophore for the multicolor analysis of proteins and nucleic acids in living cells. Chemistry 2013; 19:8736-41. [PMID: 23703698 DOI: 10.1002/chem.201301164] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Indexed: 01/08/2023]
Affiliation(s)
- Roberta Bortolozzi
- Dipartimento di Salute della Donna e del Bambino, Laboratorio di Oncoematologia, University of Padova, via Giustiniani 3, I-35128 Padova, Italy
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24
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Wang G, Zhao Q, Kang X, Guan X. Probing mercury(II)-DNA interactions by nanopore stochastic sensing. J Phys Chem B 2013; 117:4763-9. [PMID: 23565989 DOI: 10.1021/jp309541h] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In this work, DNA-Hg(II) interactions were investigated by monitoring the translocation of DNA hairpins in a protein ion channel in the absence and presence of metal ions. Our experiments demonstrate that target-specific hairpin structures could be stabilized much more significantly by mercuric ions than by the stem length and the loop size of the hairpin due to the formation of Thymine-Hg(II)-Thymine complexes. In addition, the designed DNA probe allows the development of a highly sensitive nanopore sensor for Hg(2+) with a detection limit of 25 nM. Further, the sensor is specific, and other tested metal ions including Pb(2+), Cu(2+), Cd(2+), and so on with concentrations of up to 2 orders of magnitude greater than that of Hg(2+) would not interfere with the mercury detection.
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Affiliation(s)
- Guihua Wang
- Department of Biological and Chemical Sciences, Illinois Institute of Technology, 3101 South Dearborn Street, Chicago, Illinois 60616, United States
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25
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Unusual reactivity of 1-aminoanthraquinone in copper catalyzed multicomponent reaction with isatins and aryl alkynes: synthesis and photophysical properties of regioisomeric fluorescent 3-spiroheterocyclic 2-oxindoles. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.02.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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26
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Maiti S, Das K, Das PK. Label-free fluorimetric detection of histone using quaternized carbon dot–DNA nanobiohybrid. Chem Commun (Camb) 2013; 49:8851-3. [DOI: 10.1039/c3cc44492a] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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27
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Berchel M, Haelters JP, Couthon-Gourvès H, Deschamps L, Midoux P, Lehn P, Jaffrès PA. Modular Construction of Fluorescent Lipophosphoramidates by Click Chemistry. European J Org Chem 2011. [DOI: 10.1002/ejoc.201100900] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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28
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Periyaraja S, Mandal AB, Shanmugam P. Unprecedented Binary Cu(I)/Cu(II) Catalyzed One-Pot, Three-Component Synthesis and Evaluation of Luminescent Property of 2-Amino-3-iminoethenylidene-2-indolones: A New Class of Merocyanine Dye Analogues. Org Lett 2011; 13:4980-3. [DOI: 10.1021/ol2022164] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Somasundharam Periyaraja
- Council of Scientific and Industrial Research (CSIR)-Central Leather Research Institute (CLRI), Organic Chemistry Division, Chemical Laboratory, Adyar, Chennai-600020, India
| | - Asit Baran Mandal
- Council of Scientific and Industrial Research (CSIR)-Central Leather Research Institute (CLRI), Organic Chemistry Division, Chemical Laboratory, Adyar, Chennai-600020, India
| | - Ponnusamy Shanmugam
- Council of Scientific and Industrial Research (CSIR)-Central Leather Research Institute (CLRI), Organic Chemistry Division, Chemical Laboratory, Adyar, Chennai-600020, India
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29
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Dumas A, Luedtke NW. Fluorescence properties of 8-(2-pyridyl)guanine "2PyG" as compared to 2-aminopurine in DNA. Chembiochem 2011; 12:2044-51. [PMID: 21786378 DOI: 10.1002/cbic.201100214] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Indexed: 12/24/2022]
Abstract
Because of their environment-sensitive fluorescence quantum yields, base analogues such as 2-aminopurine (2AP), 6-methylisoxanthopterin (6-MI), and 3-methylisoxanthopterin (3-MI) are widely used in nucleic-acid folding and catalysis assays. Emissions from these guanine mimics are quenched by base-stacking interactions and collisions with purine residues. Fluorescent base analogues that remain highly emissive in folded nucleic acids can provide sensitive means to differentiate DNA/RNA structures by participating in energy transfer from proximal ensembles of unmodified nucleobases. The development of new, highly emissive guanine mimics capable of proper base stacking and base-pairing interactions is an important prerequisite to this approach. Here we report a comparison of the most commonly used probe, 2-aminopurine (2AP), to 8-(2-pyridyl)-2'-deoxyguanosine (2PyG). The photophysical properties of these purine derivatives are very different. 2PyG exhibits enhanced fluorescence quantum yields upon its incorporation into folded nucleic acids--approximately 50-fold brighter fluorescence intensity than 2AP in the context of duplex DNA. Due to its bright fluorescence and compatibility with proper DNA folding, 2PyG can be used to accurately quantify energy-transfer efficiencies, whereas 2AP is much less sensitive to structure-specific trends in energy transfer. When using nucleoside monomers, Stern-Volmer plots of 2AP fluorescence revealed upward curvature of F(0) /F upon titration of guanosine monophoshate (GMP), whereas 2PyG exhibited unusual downward curvature of F(0) /F that resulted in a recovery of fluorescence at high GMP concentrations. These results are consistent with the trends observed for 2PyG- and 2AP-containing oligonucleotides, and furthermore suggest that solutions containing high concentrations of GMP can, in some ways, mimic the high local nucleobase densities of folded nucleic acids.
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Affiliation(s)
- Anaëlle Dumas
- Institute of Organic Chemistry, University of Zürich, Winterthurerstrasse 190, Zürich 8057, Switzerland
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30
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Sinkeldam RW, Marcus P, Uchenik D, Tor Y. Multisensing emissive pyrimidine. Chemphyschem 2011; 12:2260-5. [PMID: 21698743 DOI: 10.1002/cphc.201100315] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2011] [Indexed: 11/10/2022]
Abstract
Fluorescent nucleoside analogs, commonly used to explore nucleic acid dynamics, recognition and damage, frequently respond to a single environmental parameter. Herein we address the development of chromophores that can simultaneously probe more than one environmental factor while having each associated with a unique spectroscopic signature. We demonstrate that an isomorphic emissive pyridine-modified 2-deoxy-uridine 1, containing multiple sensory elements, responds to changes in acidity, viscosity, and polarity. Protonation of the pyridine moiety (pK(a) 4.4) leads to enhanced emission (λ(em) =388 nm) and red-shifted absorption spectra (λ(abs) =319 nm), suggesting the formation of an intramolecular hydrogen bond with the neighboring pyrimidine carbonyl. This "locked" conformation can also be mimicked by increasing solvent viscosity, resulting in a stark enhancement of emission quantum yield. Finally, increasing solvent polarity substantially impacts the chromophore's Stokes shift [from 5.8×10(3) cm(-1) at E(T) (30)=36.4 kcal mol(-1) to 9.3 ×10(3) cm(-1) at E(T) (30)=63.1 kcal mol(-1)]. The opposite effect is seen for the impact of solvent polarity of the protonated form. The characteristic photophysical signature induced by each parameter facilitates the exploration of these environmental factors both individually and simultaneously.
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Affiliation(s)
- Renatus W Sinkeldam
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
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31
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Tonelli A, Tedeschi T, Germini A, Sforza S, Corradini R, Medici MC, Chezzi C, Marchelli R. Real time RNA transcription monitoring by Thiazole Orange (TO)-conjugated Peptide Nucleic Acid (PNA) probes: norovirus detection. MOLECULAR BIOSYSTEMS 2011; 7:1684-92. [PMID: 21399831 DOI: 10.1039/c0mb00353k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Thiazole Orange (TO)-conjugated Peptide Nucleic Acid (PNA) probes have been reported as a valuable strategy for DNA analysis; however, no investigations targeting RNA molecules and no comparisons between different derivatization approaches have been reported so far. In this work, two TO-conjugated PNAs for genogroup II noroviruses (NoV GII) detection were designed and synthesized. Both the probes target the most conserved stretch of nucleotides identified in the open reading frame 1-2 (ORF1-ORF2) junction region and differ for the dye conjugation strategy: one PNA is end-labelled with the TO molecule tethered by a linker; the other probe bears the TO molecule directly linked to the PNA backbone, replacing a conventional nucleobase. The spectroscopic properties of the two PNA probes were studied and their applicability to NoVs detection, using an isothermal assay, was investigated. Both probes showed good specificity and high fluorescence enhancement upon hybridization, especially targeting RNA molecules. Moreover, the two probes were successfully employed for NoVs detection from stool specimens in an isothermal-based amplification assay targeting RNA 'amplicons'. The probes showed to be specific even in the presence of high concentrations of non-target RNA.
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Affiliation(s)
- Alessandro Tonelli
- Department of Organic and Industrial Chemistry, University of Parma, Vle GP Usberti 17/A, 43124 Parma, Italy
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Berndl S, Herzig N, Kele P, Lachmann D, Li X, Wolfbeis OS, Wagenknecht HA. Comparison of a nucleosidic vs non-nucleosidic postsynthetic "click" modification of DNA with base-labile fluorescent probes. Bioconjug Chem 2010; 20:558-64. [PMID: 19220008 DOI: 10.1021/bc8004864] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The azides 1 and 2 bearing a phenoxazinium and a coumarin fluorophore, respectively, were applied in postsynthetic "click"-type bioconjugation and coupled to oligonucleotides modified with alkyne groups using two alternative approaches: (i) as a nucleotide modification at the 2'-position of uridine and (ii) as a nucleotide substitution using (S)-(-)-3-amino-1,2-propanediol as an acyclic linker between the phosphodiester bridges. The corresponding alkynylated phosporamidites 3 and 6 were used as DNA building blocks for the preparation of alkyne-bearing DNA duplexes. The base pairs adjacent to the site of modification and the base opposite to it were varied in the DNA sequences. The modified duplexes were investigated by UV/vis absorption spectroscopy (including melting temperatures) and fluorescence spectroscopy in order to study the different optical properties of the two chromophores and to evaluate their potential for bioanalytical applications. The sequence-selective fluorescence quenching of phenoxazinium 1 differs only slightly and does not depend on the type of modification, meaning whether it has been attached to the 2'-position of uridine or as DNA base surrogate using the acyclic glycol linker. The 2'-chromophore-modified uridine still recognizes adenine as the counterbase, and the duplexes exhibit a sufficient thermal stability that is comparable to that of unmodified duplexes. Thus, the application of the 2'-modification site of uridine is preferred in comparison to glycol-assisted DNA base surrogates. Accordingly, the coumarin dye azide 2 was attached only to the 2'-position of uridine. The significant Stokes shift of approximately 100 nm and the good quantum yields make the coumarin chromophore a powerful fluorescent label for nucleic acids.
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Affiliation(s)
- Sina Berndl
- Institute of Organic Chemistry, University of Regensburg, Regensburg, Germany
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D’Souza DM, Muschelknautz C, Rominger F, Müller TJJ. Unusual Solid-State Luminescent Push−Pull Indolones: A General One-Pot Three-component Approach. Org Lett 2010; 12:3364-7. [DOI: 10.1021/ol101165m] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniel M. D’Souza
- Institut für Organische Chemie und Makromolekulare Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany, and Organisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, D-69120 Heidelberg, Germany
| | - Christian Muschelknautz
- Institut für Organische Chemie und Makromolekulare Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany, and Organisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, D-69120 Heidelberg, Germany
| | - Frank Rominger
- Institut für Organische Chemie und Makromolekulare Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany, and Organisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, D-69120 Heidelberg, Germany
| | - Thomas J. J. Müller
- Institut für Organische Chemie und Makromolekulare Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany, and Organisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, D-69120 Heidelberg, Germany
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Gardarsson H, Sigurdsson ST. Large flanking sequence effects in single nucleotide mismatch detection using fluorescent nucleoside C(f). Bioorg Med Chem 2010; 18:6121-6. [PMID: 20638291 DOI: 10.1016/j.bmc.2010.06.060] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Revised: 06/11/2010] [Accepted: 06/16/2010] [Indexed: 01/28/2023]
Abstract
The first systematic study of flanking sequence effects on mismatch detection by a fluorescent nucleotide is described, using fluoroside C(f). Although a high degree of variance was observed in fluorescence intensity of mismatched duplexes between different flanking sequences, C(f) was able to distinguish a mismatch from the fully base-paired duplex in 13 out of 16 sequences, and even identify each mismatch in 10 of those flanking sequences. For the flanking sequences where fluoroside C(f) did not unambiguously determine its base-pairing partner, the experimental conditions were varied in an attempt to facilitate mismatch identification. No beneficial effect on the relative fluorescence intensities was achieved by changing the temperature, adding organic co-solvents or potassium iodide. In contrast, mercuric ions selectively quenched the fluorescence intensity of the C(f).T mismatch, effectively resolving the overlap of all emission spectra and thereby facilitating identification of all base-pairing partners in any flanking sequence by C(f). This is the first time mercuric ions have been used to selectively quench the fluorescence of a single mismatch. A noticeable characteristic of C(f) is that, unlike most fluorosides, the fluorescence intensity of C(f) was not quenched to a discernable degree by a flanking G-C pair.
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Preus S, Kilså K, Wilhelmsson LM, Albinsson B. Photophysical and structural properties of the fluorescent nucleobase analogues of the tricyclic cytosine (tC) family. Phys Chem Chem Phys 2010; 12:8881-92. [PMID: 20532361 DOI: 10.1039/c000625d] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Fundamental insight into the unique fluorescence and nucleobase-mimicking properties of the fluorescent nucleobase analogues of the tC family is not only vital in explaining the behaviour of these probes in nucleic acid environments, but will also be profitable in the development of new and improved fluorescent base analogues. Here, temperature-dependent fluorescence quantum yield measurements are used to successfully separate and quantify the temperature-dependent and temperature-independent non-radiative excited-state decay processes of the three nucleobase analogues tC, tC(O) and tC(nitro); all of which are derivatives of a phenothiazine or phenoxazine tricyclic framework. These results strongly suggest that the non-radiative decay process dominating the fast deactivation of tC(nitro) is an internal conversion of a different origin than the decay pathways of tC and tC(O). tC(nitro) is reported to be fluorescent only in less dipolar solvents at room temperature, which is explained by an increase in excited-state dipole moment along the main non-radiative decay pathway, a suggestion that applies in the photophysical discussion of large polycyclic nitroaromatics in general. New insight into the ground and excited-state potential energy surfaces of the isolated tC bases is obtained by means of high level DFT and TDDFT calculations. The S(0) potential energy surfaces of tC and tC(nitro) possess two global minima corresponding to geometries folded along the middle sulfur-nitrogen axis separated by an energy barrier of 0.05 eV as calculated at the B3LYP/6-311+G(2d,p) level. The ground-state potential energy surface of tC(O) is also predicted to be shallow along the bending coordinate but with an equilibrium geometry corresponding to the planar conformation of the tricyclic framework, which may explain some of the dissimilar properties of tC and tC(O) in various confined (biological) environments. The S(1) equilibrium geometries of all three base analogues are predicted to be planar. These results are discussed in the context of the tC bases positioned in double-stranded DNA scenarios.
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Affiliation(s)
- Søren Preus
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark.
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Sinkeldam RW, Greco NJ, Tor Y. Fluorescent analogs of biomolecular building blocks: design, properties, and applications. Chem Rev 2010; 110:2579-619. [PMID: 20205430 PMCID: PMC2868948 DOI: 10.1021/cr900301e] [Citation(s) in RCA: 658] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Renatus W. Sinkeldam
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0358
| | | | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0358
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Teo YN, Kool ET. Polyfluorophore excimers and exciplexes as FRET donors in DNA. Bioconjug Chem 2010; 20:2371-80. [PMID: 19916519 DOI: 10.1021/bc9003926] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe studies aimed at testing whether oligomeric exciplex and excimer fluorophores conjugated to DNA have the potential to act as donors for energy transfer by the Forster mechanism. Oligodeoxyfluorosides (ODFs) are composed of stacked, electronically interacting fluorophores replacing the bases on a DNA scaffold. The monomer chromophores in the twenty tetramer-length ODFs studied here include pyrene (Y), benzopyrene (B), perylene (E), dimethylaminostilbene (D), and a nonfluorescent spacer (S); these are conjugated in varied combinations at the 3' end of a 14mer DNA probe sequence. In the absence of an acceptor chromophore, many of the ODF-DNAs show broad, unstructured long-wavelength emission peaks characteristic of excimer and exciplex excited states, similar to what has been observed for unconjugated ODFs. Although such delocalized excited states have been widely studied, we know of no prior report of their use in FRET. We tested the ability of the twenty ODFs to donate energy to Cy5 and TAMRA dyes conjugated to a complementary strand of DNA, with these acceptors oriented either at the near or far end of the ODF-conjugated probes. Results showed that a number of the ODF fluorophores exhibited relatively efficient energy transfer characteristic of the Forster mechanism, as judged by drops in donor emission quantum yield and fluorescence lifetime, accompanied by increases in intensity of acceptor emission bands. Excimer/exciplex bands in the donors were selectively quenched while shorter-wavelength monomer emission stayed relatively constant, consistent with the notion that the delocalized excited states, rather than individual fluorophores, are the donors. Interestingly, only specific sequences of ODFs were able to act as donors, while others did not, even though their emission wavelengths were similar. The new FRET donors possess large Stokes shifts, which can be beneficial for multiple applications. In addition, all ODFs can be excited at a single wavelength; thus, ODFs may be candidates as "universal FRET donors", thus allowing multicolor FRET of multiple species to be carried out with one excitation.
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Affiliation(s)
- Yin Nah Teo
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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Borkar A, Ghosh I, Bhattacharyya D. Structure and Dynamics of Double Helical DNA in Torsion Angle Hyperspace: A Molecular Mechanics Approach. J Biomol Struct Dyn 2010; 27:695-712. [DOI: 10.1080/07391102.2010.10508582] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Preus S, Börjesson K, Kilså K, Albinsson B, Wilhelmsson LM. Characterization of nucleobase analogue FRET acceptor tCnitro. J Phys Chem B 2010; 114:1050-6. [PMID: 20039634 DOI: 10.1021/jp909471b] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The fluorescent nucleobase analogues of the tricyclic cytosine (tC) family, tC and tC(O), possess high fluorescence quantum yields and single fluorescence lifetimes, even after incorporation into double-stranded DNA, which make these base analogues particularly useful as fluorescence resonance energy transfer (FRET) probes. Recently, we reported the first all-nucleobase FRET pair consisting of tC(O) as the donor and the novel tC(nitro) as the acceptor. The rigid and well-defined position of this FRET pair inside the DNA double helix, and consequently excellent control of the orientation factor in the FRET efficiency, are very promising features for future studies of nucleic acid structures. Here, we provide the necessary spectroscopic and photophysical characterization of tC(nitro) needed in order to utilize this probe as a FRET acceptor in nucleic acids. The lowest energy absorption band from 375 to 525 nm is shown to be the result of a single in-plane polarized electronic transition oriented approximately 27 degrees from the molecular long axis. This band overlaps the emission bands of both tC and tC(O), and the Forster characteristics of these donor-acceptor pairs are calculated for double-stranded DNA scenarios. In addition, the UV-vis absorption of tC(nitro) is monitored in a broad pH range and the neutral form is found to be totally predominant under physiological conditions with a pK(a) of 11.1. The structure and electronic spectrum of tC(nitro) is further characterized by density functional theory calculations.
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Affiliation(s)
- Søren Preus
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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Delon A, Wang I, Lambert E, Mache S, Mache R, Derouard J, Motto-Ros V, Galland R. Measuring, in solution, multiple-fluorophore labeling by combining fluorescence correlation spectroscopy and photobleaching. J Phys Chem B 2010; 114:2988-96. [PMID: 20143802 DOI: 10.1021/jp910082h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Determining the number of fluorescent entities that are coupled to a given molecule (DNA, protein, etc.) is a key point of numerous biological studies, especially those based on a single molecule approach. Reliable methods are important, in this context, not only to characterize the labeling process but also to quantify interactions, for instance within molecular complexes. We combined fluorescence correlation spectroscopy (FCS) and photobleaching experiments to measure the effective number of molecules and the molecular brightness as a function of the total fluorescence count rate on solutions of cDNA (containing a few percent of C bases labeled with Alexa Fluor 647). Here, photobleaching is used as a control parameter to vary the experimental outputs (brightness and number of molecules). Assuming a Poissonian distribution of the number of fluorescent labels per cDNA, the FCS-photobleaching data could be easily fit to yield the mean number of fluorescent labels per cDNA strand (approximately = 2). This number could not be determined solely on the basis of the cDNA brightness, because of both the statistical distribution of the number of fluorescent labels and their unknown brightness when incorporated in cDNA. The statistical distribution of the number of fluorophores labeling cDNA was confirmed by analyzing the photon count distribution (with the cumulant method), which showed clearly that the brightness of cDNA strands varies from one molecule to the other. We also performed complementary continuous photobleaching experiments and found that the photobleaching decay rate of Alexa Fluor 647 in the excited state decreases by about 30% when incorporated into cDNA, while its nonradiative decay rate is increased such that the brightness of individual Alexa labels is decreased by 25% compared to free Alexa dyes.
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Affiliation(s)
- Antoine Delon
- Laboratoire de Spectrométrie Physique UMR 5588, Université de Grenoble I/CNRS, BP 87, 38402 Saint Martin d'Hères, France.
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Lachmann D, Berndl S, Wolfbeis OS, Wagenknecht HA. Synthetic incorporation of Nile Blue into DNA using 2'-deoxyriboside substitutes: Representative comparison of (R)- and (S)-aminopropanediol as an acyclic linker. Beilstein J Org Chem 2010; 6:13. [PMID: 20485595 PMCID: PMC2871008 DOI: 10.3762/bjoc.6.13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Accepted: 01/25/2010] [Indexed: 12/13/2022] Open
Abstract
The Nile Blue chromophore was incorporated into oligonucleotides using “click” chemistry for the postsynthetic modification of oligonucleotides. These were synthesized using DNA building block 3 bearing an alkyne group and reacted with the azide 4. (R)-3-amino-1,2-propanediol was applied as the linker between the phosphodiester bridges. Two sets of DNA duplexes were prepared. One set carried the chromophore in an A-T environment, the second set in a G-C environment. Both were characterized by optical spectroscopy. Sequence-dependent fluorescence quenching was applied as a sensitive tool to compare the stacking interactions with respect to the chirality of the acyclic linker attachment. The results were compared to recent results from duplexes that carried the Nile Blue label in a sequentially and structurally identical context, except for the opposite chirality of the linker ((S)-3-amino-1,2-propandiol). Only minor, negligible differences were observed. Melting temperatures, UV–vis absorption spectra together with fluorescence quenching data indicate that Nile Blue stacks perfectly between the adjacent base pairs regardless of whether it has been attached via an S- or R-configured linker. This result was supported by geometrically optimized DNA models.
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Affiliation(s)
- Daniel Lachmann
- University of Regensburg, Institute for Organic Chemistry, 93040 Regensburg, Germany
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