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Probst M, Aeschimann W, Chau TTH, Langenegger SM, Stocker A, Häner R. Structural insight into DNA-assembled oligochromophores: crystallographic analysis of pyrene- and phenanthrene-modified DNA in complex with BpuJI endonuclease. Nucleic Acids Res 2016; 44:7079-89. [PMID: 27422870 PMCID: PMC5009758 DOI: 10.1093/nar/gkw644] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 07/07/2016] [Accepted: 07/08/2016] [Indexed: 01/13/2023] Open
Abstract
The use of the DNA duplex as a supramolecular scaffold is an established approach for the assembly of chromophore aggregates. In the absence of detailed structural insight, the characterization of thus assembled oligochromophores is, today, largely based on solution-phase spectroscopy. Here, we describe the crystal structures of three DNA-organized chromophore aggregates. DNA hybrids containing non-nucleosidic pyrene and phenanthrene building blocks were co-crystallized with the recently described binding domain of the restriction enzyme BpuJI. Crystal structures of these complexes were determined at 2.7, 1.9 and 1.6 Å resolutions. The structures reveal aromatic stacking interactions between pyrene and/or phenanthrene units within the framework of the B-DNA duplex. In hybrids containing a single modification in each DNA strand near the end of the duplex, the two polyaromatic hydrocarbons are engaged in a face-to-face stacking orientation. Due to crystal packing and steric effects, the terminal GC base pair is disrupted in all three crystal structures, which results in a non-perfect stacking arrangement of the aromatic chromophores in two of the structures. In a hybrid containing a total of three pyrenes, crystal lattice induced end-to-end stacking of individual DNA duplexes leads to the formation of an extended aromatic π-stack containing four co-axially arranged pyrenes. The aromatic planes of the stacked pyrenes are oriented in a parallel way. The study demonstrates the value of co-crystallization of chemically modified DNA with the recombinant binding domain of the restriction enzyme BpuJI for obtaining detailed structural insight into DNA-assembled oligochromophores.
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Affiliation(s)
- Markus Probst
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Walter Aeschimann
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Thi T H Chau
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Simon M Langenegger
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Achim Stocker
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Robert Häner
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
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Takada T, Tanimizu Y, Nakamura M, Yamana K. Preparation of fluorescent nucleic acids generating unique emission by primer extension reaction using pyrene-labeled deoxyuridine triphosphate derivatives. ACTA ACUST UNITED AC 2014. [DOI: 10.5857/rcp.2014.3.4.76] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Abstract
Formation of the so far elusive chrysene excimer in solution is achieved by using DNA as a supramolecular scaffold.
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Affiliation(s)
- Oleg Khorev
- Department of Chemistry and Biochemistry
- University of Bern
- CH-3012 Bern, Switzerland
| | - Caroline D. Bösch
- Department of Chemistry and Biochemistry
- University of Bern
- CH-3012 Bern, Switzerland
| | - Markus Probst
- Department of Chemistry and Biochemistry
- University of Bern
- CH-3012 Bern, Switzerland
| | - Robert Häner
- Department of Chemistry and Biochemistry
- University of Bern
- CH-3012 Bern, Switzerland
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Nussbaumer AL, Samain F, Malinovskii VL, Häner R. Supramolecular polymerization of oligopyrenotides--control by single, natural nucleotides. Org Biomol Chem 2012; 10:4891-8. [PMID: 22610059 DOI: 10.1039/c2ob25320h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Amphiphilic heptapyrenotides (Py(7)) assemble into supramolecular polymers. Here we present a comprehensive spectroscopic study of aggregates and co-aggregates of the non-chiral Py(7) and its mono- or di-substituted nucleotide analogs (Py(7)-N and N-Py(7)-N'). The data show that the formation of supramolecular polymers from oligopyrenotides is highly sensitive to the nature of the attached, chiral auxiliary. A single natural nucleotide may be sufficient for the fine tuning of the aggregates' properties by changing the mechanism of aggregation from an isodesmic to a nucleation-elongation process, which results in a high degree of amplification of chirality in the formed supramolecular polymers. Watson-Crick complementarity does not play a significant role, since co-aggregates of oligomers modified with complementary nucleotides show no signs of supramolecular polymerization. Depending on the nucleotide, the helical sense of the polymers is shifted to an M-helix or a P-helix. The findings demonstrate the value of oligopyrenotides as oligomeric building blocks for the generation of optically active supramolecular polymers.
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Affiliation(s)
- Alina L Nussbaumer
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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Malinovskii VL, Nussbaumer AL, Häner R. Oligopyrenotides: chiral nanoscale templates for chromophore assembly. Angew Chem Int Ed Engl 2012; 51:4905-8. [PMID: 22492542 DOI: 10.1002/anie.201201352] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Indexed: 01/29/2023]
Abstract
Getting organized: DNA-like supramolecular polymers formed of short oligopyrenotides serve as a helical scaffold for the molecular assembly of ligands. The cationic porphyrin meso-tetrakis(1-methylpyridin-4-yl)porphyrin interacts with the helical polymers in a similar way as with poly(dA:dT).
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Malinovskii VL, Nussbaumer AL, Häner R. Oligopyrenotides: Chiral Nanoscale Templates for Chromophore Assembly. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201201352] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Probst M, Wenger D, Biner SM, Häner R. The DNA three-way junction as a mould for tripartite chromophore assembly. Org Biomol Chem 2012; 10:755-9. [DOI: 10.1039/c1ob06400b] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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8
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Adeyemi OO, Malinovskii VL, Biner SM, Calzaferri G, Häner R. Photon harvesting by excimer-forming multichromophores. Chem Commun (Camb) 2012; 48:9589-91. [DOI: 10.1039/c2cc34183b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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9
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Nakamura M, Fukuda M, Takada T, Yamana K. Highly ordered pyrene π-stacks on an RNA duplex display static excimer fluorescence. Org Biomol Chem 2012; 10:9620-6. [DOI: 10.1039/c2ob26773j] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Garo F, Häner R. A DNA-based light-harvesting antenna. Angew Chem Int Ed Engl 2011; 51:916-9. [PMID: 22162263 DOI: 10.1002/anie.201103295] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 10/18/2011] [Indexed: 12/20/2022]
Affiliation(s)
- Florian Garo
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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Nussbaumer AL, Studer D, Malinovskii VL, Häner R. Amplification of Chirality by Supramolecular Polymerization of Pyrene Oligomers. Angew Chem Int Ed Engl 2011; 50:5490-4. [DOI: 10.1002/anie.201100677] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Indexed: 12/20/2022]
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13
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Nussbaumer AL, Studer D, Malinovskii VL, Häner R. Amplification of Chirality by Supramolecular Polymerization of Pyrene Oligomers. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201100677] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Biner SM, Kummer D, Malinovskii VL, Häner R. Signal control by self-assembly of fluorophores in a molecular beacon—a model study. Org Biomol Chem 2011; 9:2628-33. [DOI: 10.1039/c0ob01132k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Seela F, Ingale SA. "Double click" reaction on 7-deazaguanine DNA: synthesis and excimer fluorescence of nucleosides and oligonucleotides with branched side chains decorated with proximal pyrenes. J Org Chem 2010; 75:284-95. [PMID: 20000692 DOI: 10.1021/jo902300e] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The 7-tripropargylamine-7-deaza-2'-deoxyguanosine (2) containing two terminal triple bonds in the side chain was synthesized by the Sonogashira cross-coupling reaction from the corresponding 7-iodo nucleoside 1b. This was protected at the 2-amino group with an iso-butyryl residue, affording the protected intermediate 5. Then, compound 5 was converted to the 5'-O-DMT derivative 6, which on phosphitylation afforded the phosphoramidite 7. This was employed in solid-phase synthesis of a series of oligonucleotides. T(m) measurements demonstrate that a covalently attached tripropargylamine side chain increases duplex stability. Both terminal triple bonds of nucleoside 2 and corresponding oligonucleotides were functionalized by the Cu(I)-mediated 1,3-dipolar cycloaddition "double click reaction" with 1-azidomethyl pyrene 3, decorating the side chain with two proximal pyrenes. While the monomeric tripropargylamine nucleoside with two proximal pyrenes (4) shows strong excimer fluorescence, the ss-oligonucleotide containing 4 does not. This was also observed for ds-oligonucleotides when the complementary strand was unmodified. However, duplex DNA bearing pyrene residues in both strands exhibits strong excimer fluorescence when each strand contains two pyrene residues linked to the tripropargylamine moiety. This pyrene-pyrene interstrand interaction occurs when the pyrene modification sites of the duplex are separated by two base pairs which bring the fluorescent dyes in a proximal position. Molecular modeling indicates that only two out of four pyrene residues are interacting forming the exciplex while the other two do not communicate.
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Affiliation(s)
- Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.
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Häner R, Biner S, Langenegger S, Meng T, Malinovskii V. A Highly Sensitive, Excimer-Controlled Molecular Beacon. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200905829] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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17
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Häner R, Biner S, Langenegger S, Meng T, Malinovskii V. A Highly Sensitive, Excimer-Controlled Molecular Beacon. Angew Chem Int Ed Engl 2010; 49:1227-30. [DOI: 10.1002/anie.200905829] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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