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Dumat B, Larsen AF, Wilhelmsson LM. Studying Z-DNA and B- to Z-DNA transitions using a cytosine analogue FRET-pair. Nucleic Acids Res 2016; 44:e101. [PMID: 26896804 PMCID: PMC4914084 DOI: 10.1093/nar/gkw114] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 02/16/2016] [Indexed: 11/28/2022] Open
Abstract
Herein, we report on the use of a tricyclic cytosine FRET pair, incorporated into DNA with different base pair separations, to study Z-DNA and B-Z DNA junctions. With its position inside the DNA structure, the FRET pair responds to a B- to Z-DNA transition with a distinct change in FRET efficiency for each donor/acceptor configuration allowing reliable structural probing. Moreover, we show how fluorescence spectroscopy and our cytosine analogues can be used to determine rate constants for the B- to Z-DNA transition mechanism. The modified cytosines have little influence on the transition and the FRET pair is thus an easily implemented and virtually non-perturbing fluorescence tool to study Z-DNA. This nucleobase analogue FRET pair represents a valuable addition to the limited number of fluorescence methods available to study Z-DNA and we suggest it will facilitate, for example, deciphering the B- to Z-DNA transition mechanism and investigating the interaction of DNA with Z-DNA binding proteins.
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Affiliation(s)
- Blaise Dumat
- Chalmers University of Technology, Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, SE-41296 Göteborg, Sweden
| | - Anders Foller Larsen
- Chalmers University of Technology, Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, SE-41296 Göteborg, Sweden
| | - L Marcus Wilhelmsson
- Chalmers University of Technology, Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, SE-41296 Göteborg, Sweden
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Dumat B, Bood M, Wranne MS, Lawson CP, Larsen AF, Preus S, Streling J, Gradén H, Wellner E, Grøtli M, Wilhelmsson LM. Second-generation fluorescent quadracyclic adenine analogues: environment-responsive probes with enhanced brightness. Chemistry 2015; 21:4039-48. [PMID: 25641628 DOI: 10.1002/chem.201405759] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Indexed: 01/10/2023]
Abstract
Fluorescent base analogues comprise a group of increasingly important molecules for the investigation of nucleic acid structure, dynamics, and interactions with other molecules. Herein, we report on the quantum chemical calculation aided design, synthesis, and characterization of four new putative quadracyclic adenine analogues. The compounds were efficiently synthesized from a common intermediate through a two-step pathway with the Suzuki-Miyaura coupling as the key step. Two of the compounds, qAN1 and qAN4, display brightnesses (εΦF) of 1700 and 2300, respectively, in water and behave as wavelength-ratiometric pH probes under acidic conditions. The other two, qAN2 and qAN3, display lower brightnesses but exhibit polarity-sensitive dual-band emissions that could prove useful to investigate DNA structural changes induced by DNA-protein or -drug interactions. The four qANs are very promising microenvironment-sensitive fluorescent adenine analogues that display considerable brightness for such compounds.
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Affiliation(s)
- Blaise Dumat
- Department of Chemical and Chemical Engineering/, Chemistry and Biochemistry, Chalmers University of Technology, 41296 Gothenburg (Sweden)
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Abstract
The reported protocol is the first to be demonstrated to efficiently couple aryl halides to purines with predictable selectivity.
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Affiliation(s)
- Anders Foller Larsen
- Department of Physics
- Chemistry and Pharmacy
- University of Southern Denmark
- DK-5230 Odense M, Denmark
| | - Trond Ulven
- Department of Physics
- Chemistry and Pharmacy
- University of Southern Denmark
- DK-5230 Odense M, Denmark
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Nielsen MC, Larsen AF, Abdikadir FH, Ulven T. Phenanthroline-2,9-bistriazoles as selective G-quadruplex ligands. Eur J Med Chem 2013; 72:119-26. [PMID: 24361524 DOI: 10.1016/j.ejmech.2013.11.027] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 11/17/2013] [Accepted: 11/25/2013] [Indexed: 02/09/2023]
Abstract
G-quadruplex (G4) ligands are currently receiving considerable attention as potential anticancer therapeutics. A series of phenanthroline-2,9-bistriazoles carrying tethered positive end groups has been synthesized and evaluated as G4 stabilizers. The compounds were efficiently assembled by copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) in CH2Cl2 and water in the presence of a complexing agent. Characterization of the target compounds on telomeric and c-KIT G4 sequences led to the identification of guanidinium-substituted compounds as potent G4 DNA ligands with high selectivity over duplex DNA. The diisopropylguanidium ligands exhibited high selectivity for the proto-oncogenic sequence c-KIT over the human telomeric sequence in the surface plasmon resonance (SPR) assay, whereas the compounds appeared potent on both G4 structures in the FRET melting temperature assay. The phenanthroline-2,9-bistriazole ligands were thus identified as potent G4 ligands with high selectivity over duplex DNA, and preliminary results indicate that the scaffold may form basis for the development of subtype-specific G4 ligands.
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Affiliation(s)
- Mads Corvinius Nielsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Anders Foller Larsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Faisal Hussein Abdikadir
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Trond Ulven
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.
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Petersen TP, Larsen AF, Ritzén A, Ulven T. Continuous flow nucleophilic aromatic substitution with dimethylamine generated in situ by decomposition of DMF. J Org Chem 2013; 78:4190-5. [PMID: 23506299 DOI: 10.1021/jo400390t] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A safe, practical, and scalable continuous flow protocol for the in situ generation of dimethylamine from DMF followed by nucleophilic aromatic substitution of a broad range of aromatic and heteroaromatic halides is reported.
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Affiliation(s)
- Trine P Petersen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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Larsen AF, Nielsen MC, Ulven T. Tetrasubstituted Phenanthrolines as Highly Potent, Water-Soluble, and Selective G-Quadruplex Ligands. Chemistry 2012; 18:10892-902. [DOI: 10.1002/chem.201200081] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 04/29/2012] [Indexed: 11/11/2022]
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Affiliation(s)
- Anders Foller Larsen
- Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Trond Ulven
- Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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Nielsen B, Larsen AF. [How much dialysis?]. Ugeskr Laeger 1993; 155:2818-2819. [PMID: 8236556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Affiliation(s)
- B Nielsen
- Nefrologisk afdeling, Hvidovre Hospital, København
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