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Sviben I, Glavaš M, Erben A, Bachelart T, Pavlović Saftić D, Piantanida I, Basarić N. Dipeptides Containing Pyrene and Modified Photochemically Reactive Tyrosine: Noncovalent and Covalent Binding to Polynucleotides. Molecules 2023; 28:7533. [PMID: 38005255 PMCID: PMC10672942 DOI: 10.3390/molecules28227533] [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: 10/05/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Dipeptides 1 and 2 were synthesized from unnatural amino acids containing pyrene as a fluorescent label and polynucleotide binding unit, and modified tyrosine as a photochemically reactive unit. Photophysical properties of the peptides were investigated by steady-state and time-resolved fluorescence. Both peptides are fluorescent (Φf = 0.3-0.4) and do not show a tendency to form pyrene excimers in the concentration range < 10-5 M, which is important for their application in the fluorescent labeling of polynucleotides. Furthermore, both peptides are photochemically reactive and undergo deamination delivering quinone methides (QMs) (ΦR = 0.01-0.02), as indicated from the preparative photomethanolysis study of the corresponding N-Boc protected derivatives 7 and 8. Both peptides form stable complexes with polynucleotides (log Ka > 6) by noncovalent interactions and similar affinities, binding to minor grooves, preferably to the AT reach regions. Peptide 2 with a longer spacer between the fluorophore and the photo-activable unit undergoes a more efficient deamination reaction, based on the comparison with the N-Boc protected derivatives. Upon light excitation of the complex 2·oligoAT10, the photo-generation of QM initiates the alkylation, which results in the fluorescent labeling of the oligonucleotide. This study demonstrated, as a proof of principle, that small molecules can combine dual forms of fluorescent labeling of polynucleotides, whereby initial addition of the dye rapidly forms a reversible high-affinity noncovalent complex with ds-DNA/RNA, which can be, upon irradiation by light, converted to the irreversible (covalent) form. Such a dual labeling ability of a dye could have many applications in biomedicinal sciences.
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Affiliation(s)
| | | | | | | | | | - Ivo Piantanida
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (I.S.); (M.G.); (A.E.); (T.B.); (D.P.S.)
| | - Nikola Basarić
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (I.S.); (M.G.); (A.E.); (T.B.); (D.P.S.)
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2
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Mirzakhanian A, Khoury M, Trujillo DE, Kim B, Ca D, Minehan T. DNA major versus minor groove occupancy of monomeric and dimeric crystal violet derivatives. Toward structural correlations. Bioorg Med Chem 2023; 94:117438. [PMID: 37757605 DOI: 10.1016/j.bmc.2023.117438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/05/2023] [Accepted: 08/07/2023] [Indexed: 09/29/2023]
Abstract
Six monomeric (1a-1f) and five dimeric (2a-2e) derivatives of the triphenylmethane dye crystal violet (CV) have been prepared. Evaluation of the binding of these compounds to CT DNA by competitive fluorescent intercalator displacement (FID) assays, viscosity experiments, and UV and CD spectroscopy suggest that monomeric derivative 1a and dimeric derivative 2d likely associate with the major groove of DNA, while dimeric derivatives 2a and 2e likely associate with the minor groove of DNA. Additional evidence for the groove occupancy assignments of these derivatives was obtained from ITC experiments and from differential inhibition of DNA cleavage by the major groove binding restriction enzyme BamHI, as revealed by agarose gel electrophoresis. The data indicate that major groove ligands may be optimally constructed from dye units containing a sterically bulky 3,5-dimethyl-N,N-dimethylaniline group; furthermore, the groove-selectivity of olefin-tethered dimer 2d suggests that stereoelectronic interactions (n → π*) between the ligand and DNA are also an important design consideration in the crafting of major-groove binding ligands.
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Affiliation(s)
- Aren Mirzakhanian
- Department of Chemistry and Biochemistry, California State University, Northridge, 18111 Nordhoff Street, Northridge, CA 91330, USA
| | - Michael Khoury
- Department of Chemistry and Biochemistry, California State University, Northridge, 18111 Nordhoff Street, Northridge, CA 91330, USA
| | - Donald E Trujillo
- Department of Chemistry and Biochemistry, California State University, Northridge, 18111 Nordhoff Street, Northridge, CA 91330, USA
| | - Byoula Kim
- Department of Chemistry and Biochemistry, California State University, Northridge, 18111 Nordhoff Street, Northridge, CA 91330, USA
| | - Donnie Ca
- Department of Chemistry and Biochemistry, California State University, Northridge, 18111 Nordhoff Street, Northridge, CA 91330, USA
| | - Thomas Minehan
- Department of Chemistry and Biochemistry, California State University, Northridge, 18111 Nordhoff Street, Northridge, CA 91330, USA.
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3
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Kwok JG, Yuan Z, Arora PS. An Encodable Scaffold for Sequence-Specific Recognition of Duplex RNA. Angew Chem Int Ed Engl 2023; 62:e202308650. [PMID: 37548640 PMCID: PMC10528708 DOI: 10.1002/anie.202308650] [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: 06/19/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/08/2023]
Abstract
RNA, unlike DNA, folds into a multitude of secondary and tertiary structures. This structural diversity has impeded the development of ligands that can sequence-specifically target this biomolecule. We sought to develop ligands for double-stranded RNA (dsRNA) segments, which are ubiquitous in RNA tertiary structure. The major groove of double-stranded DNA is sequence-specifically recognized by a range of dimeric helical transcription factors, including the basic leucine zippers (bZIP) and basic helix-loop-helix (bHLH) proteins; however, such simple structural motifs are not prevalent in RNA-binding proteins. We interrogated the high-resolution structures of DNA and RNA to identify requirements for a helix fork motif to occupy dsRNA major grooves akin to dsDNA. Our analysis suggested that the rigidity and angle of approach of dimeric helices in bZIP/bHLH motifs are not ideal for the binding of dsRNA major grooves. This investigation revealed that the replacement of the leucine zipper motifs in bHLH proteins with synthetic crosslinkers would allow recognition of dsRNA. We show that a model bHLH DNA-binding motif does not bind dsRNA but can be reengineered as an RNA ligand. Based on this hypothesis, we rationally designed a miniature synthetic crosslinked helix fork (CHF) as a generalizable proteomimetic scaffold for targeting dsRNA. We evaluated several CHF constructs against a set of RNA and DNA hairpins to probe the specificity of the designed construct. Our studies reveal a new class of proteomimetics as an encodable platform for sequence-specific recognition of dsRNA.
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Affiliation(s)
- Jonathan G. Kwok
- Department of Chemistry, New York University, 29 Washington Place, New York, NY10003
| | - Zhi Yuan
- Department of Chemistry, New York University, 29 Washington Place, New York, NY10003
| | - Paramjit S. Arora
- Department of Chemistry, New York University, 29 Washington Place, New York, NY10003
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4
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El Hage K, Ribaudo G, Lagardère L, Ongaro A, Kahn PH, Demange L, Piquemal JP, Zagotto G, Gresh N. Targeting the Major Groove of the Palindromic d(GGCGCC) 2 Sequence by Oligopeptide Derivatives of Anthraquinone Intercalators. J Chem Inf Model 2022; 62:6649-6666. [PMID: 35895094 DOI: 10.1021/acs.jcim.2c00337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
GC-rich sequences are recurring motifs in oncogenes and retroviruses and could be targeted by noncovalent major-groove therapeutic ligands. We considered the palindromic sequence d(G1G2C3G4C5C6)2, and designed several oligopeptide derivatives of the anticancer intercalator mitoxantrone. The stability of their complexes with an 18-mer oligonucleotide encompassing this sequence in its center was validated using polarizable molecular dynamics. We report the most salient structural features of two novel compounds, having a dialkylammonium group as a side chain on both arms. The anthraquinone ring is intercalated in the central d(CpG)2 sequence with its long axis perpendicular to that of the two base pairs. On each strand, this enables each ammonium group to bind in-register to O6/N7 of the two facing G bases upstream. We subsequently designed tris-intercalating derivatives, each dialkylammonium substituted with a connector to an N9-aminoacridine intercalator extending our target range from a six- to a ten-base-pair palindromic sequence, d(C1G2G3G4C5G6C7C8C9G10)2. The structural features of the complex of the most promising derivative are reported. The present design strategy paves the way for designing intercalator-oligopeptide derivatives with even higher selectivity, targeting an increased number of DNA bases, going beyond ten.
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Affiliation(s)
- Krystel El Hage
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91000 Evry, France
| | - Giovanni Ribaudo
- Dipartimento di Medicina Molecolare e Traslazionale, Universita degli Studi di Brescia, 25123 Brescia, Italy
| | - Louis Lagardère
- LCT, UMR7616 CNRS, Sorbonne Université Paris, 75005 Paris, France
| | - Alberto Ongaro
- Dipartimento di Medicina Molecolare e Traslazionale, Universita degli Studi di Brescia, 25123 Brescia, Italy
| | | | - Luc Demange
- Université Paris Cité, CiTCoM, UMR 8038 CNRS, 75006 Paris, France
| | - Jean-Philip Piquemal
- LCT, UMR7616 CNRS, Sorbonne Université Paris, 75005 Paris, France.,The University of Texas at Austin, Department of Biomedical Engineering, Austin, Texas 78705, United States
| | - Giuseppe Zagotto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo, 35131 Padova, Italy
| | - Nohad Gresh
- LCT, UMR7616 CNRS, Sorbonne Université Paris, 75005 Paris, France
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5
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Balazy M, Fausto A, Voskanian C, Chavez B, Panesar H, Minehan TG. Dimeric and trimeric derivatives of the azinomycin B chromophore show enhanced DNA binding. Org Biomol Chem 2018; 15:4522-4526. [PMID: 28513737 DOI: 10.1039/c7ob00944e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
To explore the utility of the azinomycin B chromophore as a platform for the development of major-groove binding small molecules, we have prepared a series of 3-methoxy-5-methylnaphthalene derivatives containing diamine, triamine, and carbohydrate linker moieties. All bis- and tris-azinomycin derivatives are intercalators that display submicromolar binding affinities for calf-thymus DNA, as revealed by viscometry measurements and fluorescent intercalator displacement (FID) assays, respectively. Although the tightest binding ligand 1d (Ka = 2.42 × 107 M-1) has similar affinities for sequence diverse polynucleotides, competition binding studies with methylated phage DNA and known major and minor groove binding small molecules suggest that the tether moiety linking the naphthalene chromophores may occupy the major groove of DNA.
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Affiliation(s)
- Milena Balazy
- Department of Chemistry and Biochemistry, California State University, Northridge, 18111 Nordhoff Street, Northridge, CA 91330, USA.
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6
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Ou Z, Qian Y, Gao Y, Wang Y, Yang G, Li Y, Jiang K, Wang X. Photophysical, G-quadruplex DNA binding and cytotoxic properties of terpyridine complexes with a naphthalimide ligand. RSC Adv 2016. [DOI: 10.1039/c6ra01441k] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The complex3inhibits A549 cells selectively over non-cancerous NIH3T3 cells, which may correlate with its selective G-quadruplex binding and nuclear location.
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Affiliation(s)
- Zhize Ou
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
| | - Yimeng Qian
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
| | - Yunyan Gao
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
| | - Yunqing Wang
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
| | - Guoqiang Yang
- CAS Key Laboratory of Photochemistry
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- People's Republic of China
| | - Yi Li
- Key Laboratory of Photochemical Convesion and Optoelectronic Material
- Technical Institute of Physics and Chemistry
- Chinese Academy of Sciences
- Beijing
- People's Republic of China
| | - Kaiyue Jiang
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
| | - Xin Wang
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
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7
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Panesar HK, Solano J, Minehan TG. Synthesis and DNA binding profile of N-mono- and N,N'-disubstituted indolo[3,2-b]carbazoles. Org Biomol Chem 2015; 13:2879-83. [PMID: 25633133 PMCID: PMC4339310 DOI: 10.1039/c4ob02566k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of N-monosubstituted and N,N'-disubstituted derivatives of the indolo[3,2-b]carbazole chromophore have been prepared, and their binding affinity for duplex DNA has been evaluated by ultraviolet and fluorescence spectroscopies. It has been found that indolo[3,2-b]carbazoles bearing basic N-alkyl substituents are intercalators that bind DNA with affinities in the micromolar and submicromolar range and a preference for associating with sequences of mixed composition and purine-pyrimidine steps.
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Affiliation(s)
- Harmanpreet Kaur Panesar
- Department of Chemistry and Biochemistry, California State University, Northridge, 18111 Nordhoff Street, Northridge, CA 91330, USA.
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8
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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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9
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Banerjee S, Veale EB, Phelan CM, Murphy SA, Tocci GM, Gillespie LJ, Frimannsson DO, Kelly JM, Gunnlaugsson T. Recent advances in the development of 1,8-naphthalimide based DNA targeting binders, anticancer and fluorescent cellular imaging agents. Chem Soc Rev 2013; 42:1601-18. [DOI: 10.1039/c2cs35467e] [Citation(s) in RCA: 492] [Impact Index Per Article: 44.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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10
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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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11
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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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12
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Rettig M, Langel W, Kamal A, Weisz K. NMR structural studies on the covalent DNA binding of a pyrrolobenzodiazepine–naphthalimide conjugate. Org Biomol Chem 2010; 8:3179-87. [DOI: 10.1039/c001893g] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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13
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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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14
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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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15
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Biron E, Voyer N. Towards sequence selective DNA binding: design, synthesis and DNA binding studies of novel bis-porphyrin peptidic nanostructures. Org Biomol Chem 2008; 6:2507-15. [DOI: 10.1039/b803281e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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16
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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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17
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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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18
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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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19
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Kaiser M, Sainlos M, Lehn JM, Bombard S, Teulade-Fichou MP. Aminoglycoside-Quinacridine Conjugates: Towards Recognition of the P6.1 Element of Telomerase RNA. Chembiochem 2006; 7:321-9. [PMID: 16408312 DOI: 10.1002/cbic.200500354] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A modular synthesis has been developed which allows easy and rapid attachment of one or two aminoglycoside units to a quinacridine intercalator, thereby leading to monomeric and dimeric conjugates. Melting temperature (Tm) experiments show that the tobramycin dimeric conjugate TD1 exhibits strong binding to the P6.1 element of human telomerase RNA. By contrast, tobramycin alone is much less efficient and the monomeric compound TM1 elicits a poor binding ability. Monitoring of the interaction by an electrophoretic mobility shift assay shows a 1:1 stoichiometry for the binding of the dimeric compound to the hairpin structure and confirms the lower affinity for a control duplex. Protection experiments with RNase T1 indicate interaction of the drug both in the stem and in the loop of the hairpin. Taken together, the data suggest a binding of TD1 inside the hairpin at the stem-loop junction. The same trends are observed with paromomycin and kanamycin analogues but with a lower affinity.
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Affiliation(s)
- Markus Kaiser
- Laboratoire de Chimie des Interactions Moléculaires, CNRS UPR 285, Collège de France
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20
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Tam VK, Liu Q, Tor Y. Extended ethidium bromide analogue as a triple helix intercalator: synthesis, photophysical properties and nucleic acids binding. Chem Commun (Camb) 2006:2684-6. [PMID: 16786087 DOI: 10.1039/b604281c] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ethidium bromide has been extended by fusing an additional aromatic ring resulting in a larger intercalator with increased affinity for poly r(A) x r(U), poly d(A) x d(T) and triple helices when compared to the parent heterocycle.
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Affiliation(s)
- Victor K Tam
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
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21
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Levine LA, Morgan CM, Ohr K, Williams ME. Tetraplatinated Artificial Oligopeptides Afford High Affinity Intercalation into dsDNA. J Am Chem Soc 2005; 127:16764-5. [PMID: 16316204 DOI: 10.1021/ja055162f] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This paper reports the binding of an artificial tetrapeptide to which are tethered four Pt(II) complexes (i.e., [Pt(tpy)(py)]48+) with a 12 base pair duplex DNA oligonucleotide. Isothermal Titration Calorimetry reveals that two tetrametallic peptides stoichiometrically bind to each DNA duplex with a binding constant, KB, of 1.7 x 106 M-1, with a change in free energy of -8.5 kcal/mol. This KB represents an affinity 2 orders of magnitude greater than that of the monometallic analogue [Pt(tpy)(pic)]2+ for the same dsDNA sequence. The metalated peptides bind by intercalation into the DNA, partially unwinding the helix while stabilizing the structure, causing an increase in the dsDNA melting temperature of 25 degrees C.
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Affiliation(s)
- Lauren A Levine
- Department of Chemistry, The Pennsylvania State University, University Park, 16802, USA
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22
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Abstract
Many important biological processes, from the interferon antiviral response to the generation of microRNA regulators of translation, involve duplex RNA. Small molecules capable of binding duplex RNA structures with high affinity and selectivity will be useful in regulating these processes and, as such, are valuable research tools and potentially therapeutic. In this paper, the synthesis and duplex RNA-binding properties of EDTA.Fe-modified peptide-intercalator conjugates (PICs) are described. Peptide appendages at the 4- and 9-positions of the planar acridine ring system render these PICs threading intercalators, directing the substituents into both grooves of double helical RNA simultaneously. Directed hydroxyl radical cleavage experiments conducted with varying RNA stem-loop structures indicate a preferred binding polarity with the N- and C-termini of the PIC in the minor and major grooves, respectively. However, this binding polarity is shown to be dependent on both the structure of the PIC and the RNA secondary structure adjacent to the intercalation site. Definition of the minimal RNA structure required for binding to one of these PICs led to the identification of an intercalation site in a pre-microRNA from Caenorhabditis elegans. Results presented will guide both rational design and combinatorial approaches for the generation of new RNA binding PICs and will continue to facilitate the identification of naturally occurring RNA targets for these small molecules.
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Affiliation(s)
- Barry D Gooch
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, USA
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23
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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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24
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Krishnamurthy M, Gooch BD, Beal PA. Peptide quinoline conjugates: a new class of RNA-binding molecules. Org Lett 2004; 6:63-6. [PMID: 14703351 DOI: 10.1021/ol036094+] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] A synthesis of 4,8-disubstituted 2-phenylquinoline amino acids is reported with the incorporation of one example into a peptide by solid-phase synthesis. The phenylquinoline-containing peptide binds an RNA target with nanomolar affinity (K(D) = 208 nM). The strategy can be used to prepare a variety of 2-substituted quinoline amino acids for alteration of affinity in intercalator peptides. Since quinolones represent an important class of antibacterials, these compounds may be useful in the discovery of new antibacterial agents.
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25
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Gallego J. Sequence-dependent nucleotide dynamics revealed by intercalated ring rotation in DNA-bisnaphthalimide complexes. Nucleic Acids Res 2004; 32:3607-14. [PMID: 15240833 PMCID: PMC484180 DOI: 10.1093/nar/gkh693] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Bisnaphthalimide intercalators are anti-tumour agents composed of two planar rings linked by a flexible diazanonylene chain. The intercalated rings of three bisnaphthalimide analogues complexed to DNA are found here to undergo 180 degrees rotating motions that do not affect the diazanonylene linker atoms bound to the major groove. These ring rotations are detected by NMR spectroscopy in a broad range of sequence contexts and duplex lengths. A comparative analysis of the frequency and activation energies of such excited states in different complexes and conditions indicates that these motions (i) are unrelated to drug dissociation; (ii) are a consequence of concerted, sequence-dependent nucleotide movements taking place on the millisecond time scale; and (iii) may occur inside the DNA duplexes. The rotation frequencies range from 2 to 25 s(-1) at 25 degrees C, depending on DNA composition and the size of the rotating rings. The detected nucleotide dynamics are likely to play an important role in the binding kinetics of the numerous proteins and drugs that require base unstacking when interacting with DNA.
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Affiliation(s)
- José Gallego
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.
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26
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Pljevaljcić G, Schmidt F, Weinhold E. Sequence-specific Methyltransferase-Induced Labeling of DNA (SMILing DNA). Chembiochem 2004; 5:265-9. [PMID: 14997517 DOI: 10.1002/cbic.200300739] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A new concept for sequence-specific labeling of DNA by using chemically modified cofactors for DNA methyltransferases is presented. Replacement of the amino acid side chain of the natural cofactor S-adenosyl-L-methionine with an aziridine group leads to a cofactor suitable for DNA methyltransferase-catalyzed sequence-specific coupling with DNA. Sequence-specifically fluorescently labeled plasmid DNA was obtained by using the DNA methyltransferase from Thermus aquaticus (M.TaqI) as catalyst and attaching a fluorophore to the aziridine cofactor. First results suggest that all classes of DNA methyltransferases with different recognition sequences can be used. In addition, this novel method for DNA labeling should be applicable to a wide variety of reporter groups.
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Affiliation(s)
- Goran Pljevaljcić
- The Scripps Research Institute, Department of Molecular Biology, MB19, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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27
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Carlson CB, Stephens OM, Beal PA. Recognition of double-stranded RNA by proteins and small molecules. Biopolymers 2003; 70:86-102. [PMID: 12925995 DOI: 10.1002/bip.10413] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Molecular recognition of double-stranded RNA (dsRNA) is a key event for numerous biological pathways including the trafficking, editing, and maturation of cellular RNA, the interferon antiviral response, and RNA interference. Over the past several years, our laboratory has studied proteins and small molecules that bind dsRNA with the goal of understanding and controlling the binding selectivity. In this review, we discuss members of the dsRBM class of proteins that bind dsRNA. The dsRBM is an approximately 70 amino acid sequence motif found in a variety of dsRNA-binding proteins. Recent results have led to a new appreciation of the ability of these proteins to bind selectivity to certain sites on dsRNA. This property is discussed in light of the RNA selectivity observed in the function of two proteins that contain dsRBMs, the RNA-dependent protein kinase (PKR) and an adenosine deaminase that acts on dsRNA (ADAR2). In addition, we introduce peptide-acridine conjugates (PACs), small molecules designed to control dsRBM-RNA interactions. These intercalating molecules bear variable peptide appendages at opposite edges of an acridine heterocycle. This design imparts the potential to exploit differences in groove characteristics and/or base-pair dynamics at binding sites to achieve selective binding.
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Affiliation(s)
- Coby B Carlson
- University of Utah, Department of Chemistry, 315 South 1400 East, Room 2020, Salt Lake City, UT 84112, USA
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28
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Carlson CB, Vuyisich M, Gooch BD, Beal PA. Preferred RNA binding sites for a threading intercalator revealed by in vitro evolution. CHEMISTRY & BIOLOGY 2003; 10:663-72. [PMID: 12890540 DOI: 10.1016/s1074-5521(03)00147-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In pursuit of small molecules capable of controlling the function of RNA targets, we have explored the RNA binding properties of peptide-acridine conjugates (PACs). In vitro evolution (SELEX) was used to isolate RNAs capable of binding the PAC Ser-Val-Acr-Arg, where Acr is an acridine amino acid. The PAC binds RNA aptamers selectively and with a high degree of discrimination over DNA. PAC binding sites contain the base-paired 5'-CpG-3' sequence, a known acridine intercalation site. However, RNA structure flanking this sequence causes binding affinities to vary over 30-fold. The preferred site (K(D) = 20 nM) contains a base-paired 5'-CpG-3' step flanked on the 5' side by a 4 nt internal loop and the 3' side by a bulged U. Several viral 5'- and 3'-UTR RNA sequences that likely form binding sites for this PAC are identified.
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Affiliation(s)
- Coby B Carlson
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
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29
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Carrasco C, Helissey P, Haroun M, Baldeyrou B, Lansiaux A, Colson P, Houssier C, Giorgi-Renault S, Bailly C. Design of a composite ethidium-netropsin-anilinoacridine molecule for DNA recognition. Chembiochem 2003; 4:50-61. [PMID: 12512076 DOI: 10.1002/cbic.200390014] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Control of gene expression is a cherished goal of cancer chemotherapy. Small ligand molecules able to bind tightly to DNA in a well-defined configuration are being actively searched for. With this goal in mind, we have designed and synthesized the trifunctional molecule R-132, which combines a bispyrrole skeleton for minor groove DNA recognition and two different chromophores, anilinoacridine and ethidium. The affinity and mode of binding of R-132 to DNA were studied by a combination of complementary biochemical and biophysical techniques, which included absorption and fluorescence spectroscopy and circular and linear dichroism. A surface plasmon resonance biosensor analysis was also performed to quantify the kinetic parameters of the drug-DNA interaction process. Altogether, the results demonstrate that the three moieties of the hybrid molecule are engaged in the interaction process, thus validating the rational design strategy. At the biological level, R-132 stabilizes topoisomerase-II-DNA covalent complexes and displays potent cytotoxic activities, which are attributable to its DNA-binding properties. R-132 easily enters and accumulates in cell nuclei, as evidenced by confocal microscopy. R-132 therefore provides a novel lead compound for the design of gene-targeted anticancer agents.
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Affiliation(s)
- Carolina Carrasco
- INSERM U-524 et Laboratoire de Pharmacologie Antitumorale du Centre Oscar Lambret, IRCL, Place de Verdun, 59045 Lille, France
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30
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Guelev V, Sorey S, Hoffman DW, Iverson BL. Changing DNA grooves--a 1,4,5,8-naphthalene tetracarboxylic diimide bis-intercalator with the linker (beta-Ala)(3)-Lys in the minor groove. J Am Chem Soc 2002; 124:2864-5. [PMID: 11902864 DOI: 10.1021/ja016834e] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have been investigating a modular, threading DNA polyintercalator design based upon the 1,4,5,8-naphthalene tetracarboxylic diimide (NDI) intercalating unit. Previously, we have reported the NMR analysis of a bis-intercalator-DNA complex in which the peptide linker between NDI units was found to occupy the DNA major groove (Guelev, Lee, Sorey, Hoffman, Iverson, Chem. Biol. 2001, 8, 415-425). Here we describe the NMR analysis of a complex between a related bis-intercalator known to display altered DNA sequence specificity. In this case, the linker resides in the DNA minor groove. We have thus shown that within this set of sequence specific bis-intercalators, both DNA grooves can be accessed, setting the stage for longer threading polyintercalators designed to have linkers occupying both grooves in an alternating fashion.
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Affiliation(s)
- Vladimir Guelev
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, TX 78722, USA
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31
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Guelev VM, Cubberley MS, Murr MM, Lokey RS, Iverson BL. Design, synthesis, and characterization of polyintercalating ligands. Methods Enzymol 2001; 340:556-70. [PMID: 11494870 DOI: 10.1016/s0076-6879(01)40442-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Affiliation(s)
- V M Guelev
- Department of Chemistry and Biochemistry, University of Texas, Austin, Texas 78712, USA
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