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Solga D, Wieske LHE, Wilcox S, Zeilinger C, Jansen-Olliges L, Cirnski K, Herrmann J, Müller R, Erdelyi M, Kirschning A. Is Simultaneous Binding to DNA and Gyrase Important for the Antibacterial Activity of Cystobactamids? Chemistry 2024; 30:e202303796. [PMID: 38217886 DOI: 10.1002/chem.202303796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/29/2023] [Accepted: 01/08/2024] [Indexed: 01/15/2024]
Abstract
Cystobactamids are aromatic oligoamides that exert their natural antibacterial properties by inhibition of bacterial gyrases. Such aromatic oligoamides were proposed to inhibit α-helix-mediated protein-protein interactions and may serve for specific recognition of DNA. Based on this suggestion, we designed new derivatives that have duplicated cystobactamid triarene units as model systems to decipher the specific binding mode of cystobactamids to double stranded DNA. Solution NMR analyses revealed that natural cystobactamids as well as their elongated analogues show an overall bent shape at their central aliphatic unit, with an average CX-CY-CZ angle of ~110 degrees. Our finding is corroborated by the target-bound structure of close analogues, as established by cryo-EM very recently. Cystobactamid CN-861-2 binds directly to the bacterial gyrase with an affinity of 9 μM, and also exhibits DNA-binding properties with specificity for AT-rich DNA. Elongation/dimerization of the triarene subunit of native cystobactamids is demonstrated to lead to an increase in DNA binding affinity. This implies that cystobactamids' gyrase inhibitory activity necessitates not just interaction with the gyrase itself, but also with DNA via their triarene unit.
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Affiliation(s)
- Danny Solga
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, 30167, Hannover, Germany
| | - Lianne H E Wieske
- Department of Chemistry - BMC, Uppsala University, Husargatan 3, SE-752 37, Uppsala, Sweden
| | - Scott Wilcox
- Department of Chemistry - BMC, Uppsala University, Husargatan 3, SE-752 37, Uppsala, Sweden
| | - Carsten Zeilinger
- Institute of Biophysics and Center of Biomolecular Drug Research (BMWZ), Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - Linda Jansen-Olliges
- Institute of Biophysics and Center of Biomolecular Drug Research (BMWZ), Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - Katarina Cirnski
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Saarland University, Campus E8.1, 66123, Saarbrücken, Germany
| | - Jennifer Herrmann
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Saarland University, Campus E8.1, 66123, Saarbrücken, Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Saarland University, Campus E8.1, 66123, Saarbrücken, Germany
| | - Mate Erdelyi
- Department of Chemistry - BMC, Uppsala University, Husargatan 3, SE-752 37, Uppsala, Sweden
| | - Andreas Kirschning
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, 30167, Hannover, Germany
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2
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Basak S, Léon JC, Ferranco A, Sharma R, Hebenbrock M, Lough A, Müller J, Kraatz HB. AgI
-Induced Switching of DNA Binding Modes via Formation of a Supramolecular Metallacycle. Chemistry 2018; 24:3729-3732. [DOI: 10.1002/chem.201800440] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Shibaji Basak
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Canada
| | - J. Christian Léon
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Germany
| | - Annaleizle Ferranco
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Canada
| | - Renu Sharma
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Canada
| | - Marian Hebenbrock
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Germany
| | - Alan Lough
- Department of Chemistry; University of Toronto; 80 St. George Street Toronto Ontario M5S 3H6 Canada
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Germany
| | - Heinz-Bernhard Kraatz
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Canada
- Department of Chemistry; University of Toronto; 80 St. George Street Toronto Ontario M5S 3H6 Canada
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3
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Pramanik B, Ahmed S, Roy R, Das BK, Singha N, Das D. A DNA-NDI Hybrid to Efficiently Detect Histone in Parts per Trillion (ppt) Level. ChemistrySelect 2017. [DOI: 10.1002/slct.201701888] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Bapan Pramanik
- Department of Chemistry; Indian Institute of Technology Guwahati; Assam India 781039
| | - Sahnawaz Ahmed
- Department of Chemistry; Indian Institute of Technology Guwahati; Assam India 781039
| | - Rupam Roy
- Department of Chemistry; Indian Institute of Technology Guwahati; Assam India 781039
| | - Basab K. Das
- Department of Chemistry; Indian Institute of Technology Guwahati; Assam India 781039
| | - Nilotpal Singha
- Department of Chemistry; Indian Institute of Technology Guwahati; Assam India 781039
| | - Debapratim Das
- Department of Chemistry; Indian Institute of Technology Guwahati; Assam India 781039
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Mao Y, Liu K, Chen L, Cao X, Yi T. A Programmed DNA Marker Based on Bis(4‐ethynyl‐1,8‐naphthalimide) and Three‐Methane‐Bridged Thiazole Orange. Chemistry 2015; 21:16623-30. [DOI: 10.1002/chem.201502874] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Indexed: 01/02/2023]
Affiliation(s)
- Yueyuan Mao
- Department of Chemistry and, Collaborative Innovation Center of Chemistry for Energy Materials, Fudan University, 220 Handan Road, Shanghai 200433 (P.R. China)
| | - Keyin Liu
- Department of Chemistry and, Collaborative Innovation Center of Chemistry for Energy Materials, Fudan University, 220 Handan Road, Shanghai 200433 (P.R. China)
| | - Liang Chen
- Department of Chemistry and, Collaborative Innovation Center of Chemistry for Energy Materials, Fudan University, 220 Handan Road, Shanghai 200433 (P.R. China)
| | - Xinhua Cao
- Department of Chemistry and, Collaborative Innovation Center of Chemistry for Energy Materials, Fudan University, 220 Handan Road, Shanghai 200433 (P.R. China)
| | - Tao Yi
- Department of Chemistry and, Collaborative Innovation Center of Chemistry for Energy Materials, Fudan University, 220 Handan Road, Shanghai 200433 (P.R. China)
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Rhoden Smith A, Iverson BL. Threading polyintercalators with extremely slow dissociation rates and extended DNA binding sites. J Am Chem Soc 2013; 135:12783-9. [PMID: 23919778 DOI: 10.1021/ja4057344] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The development of small molecules that bind DNA sequence specifically has the potential to modulate gene expression in a general way. One mode of DNA binding is intercalation, or the insertion of molecules between DNA base pairs. We have developed a modular polyintercalation system in which intercalating naphthalene diimide (NDI) units are connected by flexible linkers that alternate between the minor and major grooves of DNA when bound. We recently reported a threading tetraintercalator with a dissociation half-life of 16 days, the longest reported to date, from its preferred 14 bp binding site. Herein, three new tetraintercalator derivatives were synthesized with one, two, and three additional methylene units in the central major groove-binding linker. These molecules displayed dissociation half-lives of 57, 27, and 18 days, respectively, from the 14 bp site. The optimal major groove-binding linker was used in the design of an NDI hexaintercalator that was analyzed by gel-shift assays, DNase I footprinting, and UV-vis spectroscopy. The hexaintercalator bound its entire 22 bp binding site, the longest reported specific binding site for a synthetic, non-nucleic acid-based DNA binding molecule, but with a significantly faster dissociation rate compared to the tetraintercalators.
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Affiliation(s)
- Amy Rhoden Smith
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712, USA
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Sasikumar M, Suseela YV, Govindaraju T. Dibromohydantoin: A Convenient Brominating Reagent for 1,4,5,8-Naphthalenetetracarboxylic Dianhydride. ASIAN J ORG CHEM 2013. [DOI: 10.1002/ajoc.201300088] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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7
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Avinash MB, Govindaraju T. Amino acid derivatized arylenediimides: a versatile modular approach for functional molecular materials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2012; 24:3905-22. [PMID: 22714652 DOI: 10.1002/adma.201201544] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Indexed: 05/05/2023]
Abstract
Nature's elegant molecular designs and their assemblies with specific structure-property correlations have inspired researchers to design and develop bio-mimics for advanced functional applications. To realize such advanced molecular materials, naturally evolved amino acids are arguably the ideal auxiliaries due to their remarkable molecular/chiral recognition and distinctive sequence specific self-assembling properties. Over the years, this modular approach of derivatizing naphthalenediimides (NDIs) and perylenediimides (PDIs) with amino acids and peptides have resulted in several hitherto unknown molecular assemblies with phenomenal impact on their performance. Derivatization with versatile arylenediimides is especially interesting due to their wide spread applications in fields ranging from biomedicine to electronics. Herein some of these seminal reports of this rapidly emerging field and the design principles embraced are discussed.
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Affiliation(s)
- M B Avinash
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, India
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8
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Smith AR, Ikkanda BA, Holman GG, Iverson BL. Subtle recognition of 14-base pair DNA sequences via threading polyintercalation. Biochemistry 2012; 51:4445-52. [PMID: 22554127 PMCID: PMC3369501 DOI: 10.1021/bi300317n] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Small molecules that bind DNA in a sequence-specific manner could act as antibiotic, antiviral, or anticancer agents because of their potential ability to manipulate gene expression. Our laboratory has developed threading polyintercalators based on 1,4,5,8-naphthalene diimide (NDI) units connected in a head-to-tail fashion by flexible peptide linkers. Previously, a threading tetraintercalator composed of alternating minor-major-minor groove-binding modules was shown to bind specifically to a 14 bp DNA sequence with a dissociation half-life of 16 days [Holman, G. G., et al. (2011) Nat. Chem. 3, 875-881]. Herein are described new NDI-based tetraintercalators with a different major groove-binding module and a reversed N to C directionality of one of the minor groove-binding modules. DNase I footprinting and kinetic analyses revealed that these new tetraintercalators are able to discriminate, by as much as 30-fold, 14 bp DNA binding sites that differ by 1 or 2 bp. Relative affinities were found to correlate strongly with dissociation rates, while overall C(2) symmetry in the DNA-binding molecule appeared to contribute to enhanced association rates.
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Affiliation(s)
- Amy Rhoden Smith
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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Holman GG, Zewail-Foote M, Smith AR, Johnson KA, Iverson BL. A sequence-specific threading tetra-intercalator with an extremely slow dissociation rate constant. Nat Chem 2011; 3:875-81. [PMID: 22024884 PMCID: PMC3209807 DOI: 10.1038/nchem.1151] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Accepted: 08/17/2011] [Indexed: 12/02/2022]
Abstract
A long-lived and sequence specific ligand-DNA complex would make possible the modulation of biological processes for extended periods. We have been investigating the threading polyintercalation approach to DNA recognition in which chains of aromatic units thread back and forth repeatedly through the double helix. Here we report the preliminary sequence specificity and detailed kinetic analysis of a structurally characterized threading tetraintercalator. Specific binding on a relatively long DNA strand was observed, strongly favoring a predicted 14-base pair sequence. Kinetic studies revealed a multi-step association process and specificity was found to derive primarily from large differences in dissociation rates. Importantly, the rate-limiting dissociation rate constant of the tetraintercalator complex dissociating from its preferred binding site was extremely slow, corresponding to a 16 day half-life, making it one of the longer non-covalent complex half-lives yet measured, and, to the best of our knowledge, the longest for a DNA binding molecule.
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Affiliation(s)
- Garen G Holman
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712, USA
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10
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Doria F, di Antonio M, Benotti M, Verga D, Freccero M. Substituted heterocyclic naphthalene diimides with unexpected acidity. Synthesis, properties, and reactivity. J Org Chem 2010; 74:8616-25. [PMID: 19848382 DOI: 10.1021/jo9017342] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Naphthalene bisimides (NDIs) with a heterocyclic 1,4-dihydro-2,3-pyrazinedione moiety have been synthesized from both 2,6-dibromonaphthalene and 2,3,6,7-tetrabromonaphthalene bisanhydrides by means of a stepwise protocol including imidization, nucleophilic displacement of the bromine atoms by ethane-1,2-diamine, in situ reductive dehalogenation, and further oxidation. These heterocycles (R = n-pentyl, cyclohexyl) are yellow dyes with green emission in organic solvent, where the acid form dominates. The orange nonfluorescent conjugate base can be generated quantitatively by CH(3)COONBu(4) addition in DMSO, where it exhibits a pK(a) = 7.63. The conjugate base becomes the only detectable species (by UV-vis spectroscopy), in water solution, even under acid conditions (pH 1). In aqueous DMSO the acid/base equilibrium is a function of the DMSO/water ratio. The unexpected acidity of these heterocyclic NDIs, which justifies the reactivity with CH(2)N(2), has been rationalized by DFT computational means [PBE0/6-31+G(d,p)] in aqueous solvent (PCM models) as a result of a strong specific solvation effect, modeled by the inclusion of three water molecules.
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Affiliation(s)
- Filippo Doria
- Dipartimento di Chimica Organica, Università di Pavia, V. le Taramelli 10, 27100 Pavia, Italy
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11
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Quinone methides tethered to naphthalene diimides as selective G-quadruplex alkylating agents. J Am Chem Soc 2010; 131:13132-41. [PMID: 19694465 DOI: 10.1021/ja904876q] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have developed novel G-quadruplex (G-4) ligand/alkylating hybrid structures, tethering the naphthalene diimide moiety to quaternary ammonium salts of Mannich bases, as quinone-methide precursors, activatable by mild thermal digestion (40 degrees C). The bis-substituted naphthalene diimides were efficiently synthesized, and their reactivity as activatable bis-alkylating agents was investigated in the presence of thiols and amines in aqueous buffered solutions. The electrophilic intermediate, quinone-methide, involved in the alkylation process was trapped, in the presence of ethyl vinyl ether, in a hetero Diels-Alder [4 + 2] cycloaddition reaction, yielding a substituted 2-ethoxychroman. The DNA recognition and alkylation properties of these new derivatives were investigated by gel electrophoresis, circular dichroism, and enzymatic assays. The alkylation process occurred preferentially on the G-4 structure in comparison to other DNA conformations. By dissecting reversible recognition and alkylation events, we found that the reversible process is a prerequisite to DNA alkylation, which in turn reinforces the G-quadruplex structural rearrangement.
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12
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Chu Y, Hoffman DW, Iverson BL. A pseudocatenane structure formed between DNA and A cyclic bisintercalator. J Am Chem Soc 2009; 131:3499-508. [PMID: 19236098 PMCID: PMC2733282 DOI: 10.1021/ja805676w] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Targeting double-stranded DNA with small molecules remains an active area of basic research. Herein is described a cyclic DNA bisintercalator that is based on two naphthalene diimide (NDI) intercalating units tethered by one linking element specific for binding in the minor groove and the other linking element specific for binding in the major groove. DNase I footprinting revealed a strong preference for binding the sequence 5'-GGTACC-3'. NMR structural studies of the complex with d(CGGTACCG)(2) verified a pseudocatenane structure in which the NDI units reside four base pairs apart, with one linker segment located in the minor groove and the other in the major groove consistent with the linker designs. To the best of our knowledge, this is the first structurally well-characterized pseudocatenane complex between a sequence specific cyclic bisintercalator and intact DNA.
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Affiliation(s)
- Yongjun Chu
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712, USA
| | - David W. Hoffman
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Brent L. Iverson
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712, USA
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13
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Kim MB, Dixon DW. Hydrolysis of aliphatic naphthalene diimides: effect of charge placement in the side chains. J PHYS ORG CHEM 2008. [DOI: 10.1002/poc.1334] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Di Antonio M, Doria F, Mella M, Merli D, Profumo A, Freccero M. Novel Naphthalene Diimides as Activatable Precursors of Bisalkylating Agents, by Reduction and Base Catalysis. J Org Chem 2007; 72:8354-60. [PMID: 17892300 DOI: 10.1021/jo7014328] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mild activation of water-soluble naphthalene diimides (NDIs) as bisalkylating agents has been achieved by base catalysis and by chemical and electrochemical reductions. NDI activation by a single electron reduction represents a novelty in the field of activatable electrophiles. Under mild reduction, induced by S2O4(2-) in aqueous solution, the resulting NDI radical anion (NDI*-) undergoes a monomolecular fragmentation to yield a new transient species, where the NDI radical anion is tethered to a quinone methide moiety. The latter still retains electrophilic properties, reacting with amines, thiols, and ethyl vinyl ether. Owing to the NDI recognition properties, these results represent the first step toward selective and bioactivatable cross-linking agents.
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Affiliation(s)
- Marco Di Antonio
- Dipartimento di Chimica Organica, Università di Pavia, V.le Taramelli 10, 27100 Pavia, Italy
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Röger C, Würthner F. Core-Tetrasubstituted Naphthalene Diimides: Synthesis, Optical Properties, and Redox Characteristics. J Org Chem 2007; 72:8070-5. [PMID: 17887710 DOI: 10.1021/jo7015357] [Citation(s) in RCA: 166] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
2,3,6,7-tetrabromonaphthalene dianhydride has been synthesized by the bromination of naphthalene dianhydride with dibromoisocyanuric acid in excellent yield. The condensation of this dianhydride with 2,6-diisopropylaniline yielded the corresponding tetrabromo-substituted naphthalene diimide (NDI), which is a versatile precursor for the synthesis of core-tetrafunctionalized NDIs. Nucleophilic substitution of tetrabromo NDI with alkoxy, alkylthio, and alkylamino nucleophiles afforded a series of core-tetrasubstituted NDI chromophores that complete the series of previously reported di- and trifunctionalized NDI derivatives. The effects of electronic nature and number of core substituents on the optical and electrochemical properties of NDIs have been investigated by UV-vis and fluorescence spectroscopy and cyclic voltammetry. The absorption maxima (629-642 nm) of tetraamino NDIs are strongly bathochromically shifted compared to those of other core-functionalized NDIs.
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Affiliation(s)
- Cornelia Röger
- Universität Würzburg, Institut für Organische Chemie, Am Hubland, 97074 Würzburg, Germany
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Hvastkovs EG, Buttry DA. Electrochemical Detection of DNA Hybridization via Bis-Intercalation of a Naphthylimide-Functionalized Viologen Dimer. Anal Chem 2007; 79:6922-6. [PMID: 17696404 DOI: 10.1021/ac070358e] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The synthesis and DNA binding properties of a bis-naphthyl imide tetracationic diviologen compound NI(CH2)3V(2+)(CH2)6V(2+)(CH2)3NI (where V(2+) = 4,4'-bipyridinium and NI = naphthyl imide, NIV) are described. Binding to thiolated ssDNA and dsDNA immobilized at Au electrodes was characterized using the electrochemical response for reduction of the V(2+) state to the V+ (viologen radical cation) state. Isotherms and binding constants for this molecule to both forms of immobilized DNA were generated in this fashion. The character of the binding isotherm for dsDNA suggests bis-intercalation. Under high saline conditions, the diviologen molecule dissociated 160 times slower from dsDNA compared to ssDNA. Slow dissociation kinetics from dsDNA (kd =7.0 x 10-5 s(-1)) allow this molecule to be used as an effective DNA hybridization indicator.
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Affiliation(s)
- Eli G Hvastkovs
- Department of Chemistry (3838), University of Wyoming, 1000 East University Avenue, Laramie, Wyoming 82070, USA
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Mazzitelli CL, Chu Y, Reczek JJ, Iverson BL, Brodbelt JS. Screening of threading bis-intercalators binding to duplex DNA by electrospray ionization tandem mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:311-21. [PMID: 17098442 PMCID: PMC1853371 DOI: 10.1016/j.jasms.2006.09.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2006] [Revised: 09/21/2006] [Accepted: 09/26/2006] [Indexed: 05/11/2023]
Abstract
The DNA binding of novel threading bis-intercalators V1, trans-D1, and cis-C1, which contain two naphthalene diimide (NDI) intercalation units connected by a scaffold, was evaluated using electrospray ionization mass spectrometry (ESI-MS) and DNAse footprinting techniques. ESI-MS experiments confirmed that V1, the ligand containing the -Gly3-Lys- peptide scaffold, binds to a DNA duplex containing the 5'-GGTACC-3' specific binding site identified in previous NMR-based studies. The ligand formed complexes with a ligand/DNA binding stoichiometry of 1:1, even when there was excess ligand in solution. Trans-D1 and cis-C1 are new ligands containing a rigid spiro-tricyclic scaffold in the trans- and cis- orientations, respectively. Preliminary DNAse footprinting experiments identified possible specific binding sites of 5'-CAGTGA-5' for trans-D1 and 5'-GGTACC-3' for cis-C1. ESI-MS experiments revealed that both ligands bound to DNA duplexes containing the respective specific binding sequences, with cis-C1 exhibiting the most extensive binding based on a higher fraction of bound DNA value. Cis-C1 formed complexes with a dominant 1:1 binding stoichiometry, whereas trans-D1 was able to form 2:1 complexes at ligand/DNA molar ratios >or=1 which is suggestive of nonspecific binding. Collisional activated dissociation (CAD) experiments indicate that DNA complexes containing V1, trans-D1, and cis-C1 have a unique fragmentation pathway, which was also observed for complexes containing the commercially available bis-intercalator echinomycin, as a result of similar binding interactions, marked by intercalation in addition to hydrogen bonding by the scaffold with the DNA major or minor groove.
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Affiliation(s)
- Carolyn L Mazzitelli
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712-0165, USA
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Chu Y, Sorey S, Hoffman DW, Iverson BL. Structural Characterization of a Rigidified Threading Bisintercalator. J Am Chem Soc 2007; 129:1304-11. [PMID: 17263414 DOI: 10.1021/ja066480x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
NMR spectroscopy was used to explore the sequence-specific interaction of DNA with a new threading bisintercalator (C1) consisting of two intercalating 1,4,5,8-naphthalenetetracarboxylic diimide (NDI) units connected by a rigid, tricyclic spiro linker. A structural model of C1 complexed to d(CGGTACCG)(2) was calculated using distance constraints obtained from solution NMR data. The model was also supported by the results from residual dipolar coupling (RDC) measurements obtained using Pf1-phage as a cosolvent. According to the model, the central cyclohexane ring of the linker connecting the two NDI units lies flat in the minor groove of DNA. Linker length, hydrogen bonding, steric, and hydrophobic factors all appear to contribute to the observed sequence specificity of binding. These results serve to illustrate the versatility of threading polyintercalation given that, in a previous study, a ligand consisiting of two NDI units joined by a flexible peptide linker was shown to bind sequence specifically within the major groove of this same sequence of DNA.
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Affiliation(s)
- Yongjun Chu
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712, USA
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Zhu J, Lin JB, Xu YX, Jiang XK, Li ZT. Hydrogen bonding-mediated self-assembly of anthranilamide-based homodimers through preorganization of the amido and ureido binding sites. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.09.073] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Pengo P, Pantos GD, Otto S, Sanders JKM. Efficient and Mild Microwave-Assisted Stepwise Functionalization of Naphthalenediimide with α-Amino Acids. J Org Chem 2006; 71:7063-6. [PMID: 16930065 DOI: 10.1021/jo061195h] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Microwave dielectric heating proved to be an efficient method for the one-pot and stepwise syntheses of symmetrical and unsymmetrical naphthalenediimide derivatives of alpha-amino acids. Acid-labile side chain protecting groups are stable under the reaction conditions; protection of the alpha-carboxylic group is not required. The stepwise condensation of different amino acids resulted in high yields of unsymmetrical naphthalenediimides. The reaction proceeds without racemization and is essentially quantitative.
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Affiliation(s)
- Paolo Pengo
- University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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Chu Y, Lynch V, Iverson BL. Synthesis and DNA binding studies of bis-intercalators with a novel spiro-cyclic linker. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.03.038] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Ofir Y, Zelichenok A, Yitzchaik S. 1,4;5,8-naphthalene-tetracarboxylic diimide derivatives as model compounds for molecular layer epitaxy. ACTA ACUST UNITED AC 2006. [DOI: 10.1039/b601258b] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Zhou QZ, Jia MX, Shao XB, Wu LZ, Jiang XK, Li ZT, Chen GJ. Self-assembly of a novel series of hetero-duplexes driven by donor–acceptor interaction. Tetrahedron 2005. [DOI: 10.1016/j.tet.2005.05.039] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Lee J, Guelev V, Sorey S, Hoffman DW, Iverson BL. NMR Structural Analysis of a Modular Threading Tetraintercalator Bound to DNA. J Am Chem Soc 2004; 126:14036-42. [PMID: 15506767 DOI: 10.1021/ja046335o] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The synthesis and NMR structural studies are reported for a modular threading tetraintercalator bound to DNA. The tetraintercalator design is based on 1,4,5,8-tetracarboxylic naphthalene diimide units connected through flexible peptide linkers. Aided by an overall C(2) symmetry, NMR analysis verified a threading polyintercalation mode of binding, with linkers alternating in the order minor groove, major groove, minor groove, analogous to how a snake might climb a ladder. This study represents the first NMR analysis of a threading tetraintercalator and, as such, structurally characterizes a new topology for molecules that bind to relatively long DNA sequences with extensive access to both DNA grooves.
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Affiliation(s)
- Jeeyeon Lee
- Department of Chemistry and Biochemistry, The University of Texas, Austin, Texas 78712, USA
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Abraham B, McMasters S, Mullan MA, Kelly LA. Reactivities of Carboxyalkyl-Substituted 1,4,5,8-Naphthalene Diimides in Aqueous Solution. J Am Chem Soc 2004; 126:4293-300. [PMID: 15053619 DOI: 10.1021/ja0389265] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of water-soluble 1,4,5,8-naphthalene diimide derivatives has been prepared and their redox and photophysical properties characterized. From laser flash photolysis studies, the triplet excited state of N,N'-bis[2-(N-pyridinium)ethyl]-1,4,5,8-naphthalene diimide (NDI-pyr) was found to undergo oxidative quenching with the electron donors DABCO, tyrosine, and tryptophan as expected from thermodynamics. Interestingly, the reactivities of naphthalene diimides (NDI) possessing alpha- and beta-carboxylic acid substituents (R = -CH2COO-, -C(CH3)2COO-, and -CH2CH2COO-) were strikingly different. In these compounds, the transient produced upon 355 nm excitation did not react with the electron donors. Instead, this transient reacted rapidly (k > 10(8)-10(9) M-1 s-1) with known electron acceptors, benzyl viologen and ferricyanide. The transient spectrum of the carboxyalkyl-substituted naphthalimides observed immediately after the laser pulse was nearly identical to the one-electron-reduced form of 1,4,5,8-naphthalene diimide (produced independently using the bis-pyridinium-substituted naphthaldiimide). From our studies, we conclude that the transient produced upon nanosecond laser flash photolysis of NDI-(CH2)nCOO- is the species produced upon intramolecular electron transfer from the carboxylate moiety to the singlet excited state of NDI. In separate experiments, we verified that the singlet excited state of NDI-pyr does, indeed, react intermolecularly with acetate, alanine, and glycine. The process is further substantiated using thermodynamic driving force calculations. The results offer new prospects of the efficient photochemical production of reactive carbon-centered radicals.
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Affiliation(s)
- Bindu Abraham
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland, USA
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Carroll JB, Gray M, McMenimen KA, Hamilton DG, Rotello VM. Redox modulation of benzene triimides and diimides via noncovalent interactions. Org Lett 2003; 5:3177-80. [PMID: 12943381 DOI: 10.1021/ol034828c] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[reaction: see text] Mellitic triimides undergo three sequential one-electron reduction processes whose potentials are significantly lowered in the presence of alkyl thioureas. The two sequential reductions of benzene diimides are similarly stabilized. Calculation of the relative free energy change between the different electronic states of the imide acceptors and their corresponding alkyl thiourea complexes indicates dramatic increases in hydrogen bond strength with increasing acceptor charge density.
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Affiliation(s)
- Joseph B Carroll
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, USA
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