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Saha A, Kizaki S, Han JH, Yu Z, Sugiyama H. UVA irradiation of BrU-substituted DNA in the presence of Hoechst 33258. Bioorg Med Chem 2018; 26:37-40. [PMID: 29170027 DOI: 10.1016/j.bmc.2017.11.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/02/2017] [Accepted: 11/04/2017] [Indexed: 01/15/2023]
Abstract
Given that our knowledge of DNA repair is limited because of the complexity of the DNA system, a technique called UVA micro-irradiation has been developed that can be used to visualize the recruitment of DNA repair proteins at double-strand break (DSB) sites. Interestingly, Hoechst 33258 was used under micro-irradiation to sensitize 5-bromouracil (BrU)-labelled DNA, causing efficient DSBs. However, the molecular basis of DSB formation under UVA micro-irradiation remains unknown. Herein, we investigated the mechanism of DSB formation under UVA micro-irradiation conditions. Our results suggest that the generation of a uracil-5-yl radical through electron transfer from Hoechst 33258 to BrU caused DNA cleavage preferentially at self-complementary 5'-AABrUBrU-3' sequences to induce DSB. We also investigated the DNA cleavage in the context of the nucleosome to gain a better understanding of UVA micro-irradiation in a cell-like model. We found that DNA cleavage occurred in both core and linker DNA regions although its efficiency reduced in core DNA.
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Affiliation(s)
- Abhijit Saha
- Department of Science, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Seiichiro Kizaki
- Department of Science, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Ji Hoon Han
- Department of Science, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Zutao Yu
- Department of Science, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Science, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan; Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida Ushinomiya-cho, Sakyo, Kyoto 606-8502, Japan.
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Kashanian S, Khodaei MM, Roshanfekr H, Peyman H. DNA interaction of [Cu(dmp)(phen-dion)] (dmp=4,7 and 2,9 dimethyl phenanthroline, phen-dion=1,10-phenanthroline-5,6-dion) complexes and DNA-based electrochemical biosensor using chitosan-carbon nanotubes composite film. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 114:642-649. [PMID: 23811151 DOI: 10.1016/j.saa.2013.05.091] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 05/22/2013] [Accepted: 05/24/2013] [Indexed: 06/02/2023]
Abstract
The interaction of two new water-soluble [Cu(4,7-dmp)(phen-dione)Cl]Cl (1) and [Cu(2,9-dmp)(phen-dione)Cl]Cl (2) which dmp is dimethyl-1,10-phenanthroline and phen-dion represents 1,10-phenanthroline-5,6-dion, with DNA in solution and immobilized DNA on a chitosan-carbon nanotubes composite modified glassy carbon electrode were investigated by cyclic voltammetry and UV-Vis spectroscopy techniques. In solution interactions, spectroscopic and electrochemical evidences indicate outside binding of these complexes. To clarify the binding mode of complexes, it was done competition studies with Hoechst and Neutral red as groove binder and intercalative probes, respectively. All these results indicating that, these two complexes (1) and (2) interact with DNA via groove binding and partially intercalative modes, respectively. The electrochemical characterization experiments showed that the nanocomposite film of chitosan-carbon nanotubes could effectively immobilize DNA and greatly improve the electron-transfer reactions of the electroactive molecules that latter finding is the result of strong interactions between captured DNA and Cu complexes. This result indicates that these complexes could be noble candidates as hybridization indicators in further studies. At the end, these new complexes showed excellent antitumor activity against K562 (human chronic myeloid leukemia) cell lines.
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Affiliation(s)
- Soheila Kashanian
- Faulty of Chemistry, Sensor and Biosensor Research Center (SBRC) & Nanoscience and Nanotechnology Research Center (NNRC), Razi University, Kermanshah, Iran.
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Ju XH, Wang WJ, Qiu L, Xiao HM. Ab Initioand DFT Studies on the Structure, Infrared Spectrum, and Thermodynamic Properties of Hoechst 33258. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200500063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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He G, Vasilieva E, Bashkin JK, Dupureur CM. Mapping small DNA ligand hydroxyl radical footprinting and affinity cleavage products for capillary electrophoresis. Anal Biochem 2013; 439:99-101. [PMID: 23608054 PMCID: PMC3713177 DOI: 10.1016/j.ab.2013.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 04/08/2013] [Accepted: 04/10/2013] [Indexed: 12/17/2022]
Abstract
The mapping of DNA footprints and affinity cleavage sites for small DNA ligands is affected by the choice of sequencing chemistry and end label, and the potential for indexing errors can be significant when mapping small ligand-DNA interactions. Described here is a mechanism for avoiding such errors based on a summary of standard labeling, cleavage, and indexing chemistries and a comparison among them for analysis of these interactions by capillary electrophoresis. The length dependence of the difference between Sanger and Maxam-Gilbert indexing is examined for a number of duplexes of mixed sequence.
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Affiliation(s)
- Gaofei He
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121
| | - Elena Vasilieva
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121
| | - James K. Bashkin
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121
| | - Cynthia M. Dupureur
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121
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Role of structure-proteins in the porphyrin-DNA interaction. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2009; 96:207-15. [PMID: 19604705 DOI: 10.1016/j.jphotobiol.2009.06.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Revised: 06/17/2009] [Accepted: 06/18/2009] [Indexed: 11/22/2022]
Abstract
We studied the complexation of meso-tetrakis(4-N-methylpyridyl)porphyrin (TMPyP) with HeLa nucleosomes and compared it to our earlier results on T7 phage nucleoprotein complex (NP) and isolated DNA. To identify binding modes and relative concentrations of the bound TMPyP forms, the porphyrin absorption spectra were analyzed at various base pair/porphyrin ratios. Spectral decomposition and circular dichroism measurements proved that the two main binding modes of TMPyP, i.e., external binding and intercalation occur also in the nucleosomes. The DNA superstructure maintained by the proteins decreases its accessibility for TMPyP similarly in both nucleoproteins. A difference is observed between the partitioning of the two binding modes: in the case of nucleosome the ratio of intercalation to groove-binding is changed from 60/40 to 40/60 as determined for T7 NP and for isolated DNA-s. Using UV and CD melting studies, we revealed that TMPyP destabilizes the DNA-protein interaction in the nucleosomes but not in the T7 phage. Lastly, photoinduced reaction of bound TMPyP caused alterations in DNA structures and DNA-protein interactions within both nucleoprotein complexes; the nucleosomes were found to be more sensitive to the photoreaction.
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Tawar U, Bansal S, Shrimal S, Singh M, Tandon V. Nuclear condensation and free radical scavenging: a dual mechanism of bisbenzimidazoles to modulate radiation damage to DNA. Mol Cell Biochem 2007; 305:221-33. [PMID: 17619948 DOI: 10.1007/s11010-007-9546-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2007] [Accepted: 06/21/2007] [Indexed: 10/23/2022]
Abstract
The complexing of histones with DNA and the resulting condensation of chromatin protects mammalian cell, from radiation-induced strand breakage. In the present study, benzimidazoles DMA and TBZ showed marked radioprotection through drug-induced compaction of chromatin and direct quenching of free radicals generated by radiation. The mammalian cells were incubated with 100 microM concentration of DMA and TBZ and irradiated at 5 Gy; both the ligands showed nuclei condensation suggesting a probable mechanism to protect DNA from radiation damage. The bisubstituted analogs of Hoechst 33342 are found to be better free radical scavengers and protect DNA against radiation-induced damage at a lower concentration than the parent molecule. Both the ligands also quenched free radicals in isolated free radical system suggesting their dual mode of action against radiation-induced damage to DNA. Molecules binding to the chromatin alter gene expression, whereas in this study both the ligands have not shown any profound effect on the nucleosome assembly and gene expression in vitro and in vivo. Both ligands afford a 2-fold protection by altering DNA structure as well as through direct free radical quenching in bulk solution in comparison to the parent ligand, which acts only through quenching of free radicals.
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Affiliation(s)
- Urmila Tawar
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, 110007, India
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Dawson S, Malkinson JP, Paumier D, Searcey M. Bisintercalator natural products with potential therapeutic applications: isolation, structure determination, synthetic and biological studies. Nat Prod Rep 2007; 24:109-26. [PMID: 17268609 DOI: 10.1039/b516347c] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Echinomycin is the prototypical bisintercalator, a molecule that binds to DNA by inserting two planar chromophores between the base-pairs of duplex DNA, placing its cyclic depsipeptide backbone in the minor groove. As such, it has been the focus of an extensive number of investigations into its biological activity, nucleic acid binding and, to some extent, its structure-activity relationships. However, echinomycin is also the parent member of an extended family of natural products that interact with DNA by a similar mechanism of bisintercalation. The structural variety in these compounds leads to changes in sequence selectivity and and biological activity, particularly as anti-tumour and anti-viral agents. One of the more recently identified marine natural products that is moving close to clinical development is thiocoraline, and it therefore seems timely to review the various bisintercalator natural products.
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Affiliation(s)
- Simon Dawson
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University of London, 29-39 Brunswick Square, London, WC1N 1AX, UK
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Tsujita S, Tanada M, Kataoka T, Sasaki S. Equilibrium shift by target DNA substrates for determination of DNA binding ligands. Bioorg Med Chem Lett 2006; 17:68-72. [PMID: 17046249 DOI: 10.1016/j.bmcl.2006.09.089] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2006] [Revised: 09/14/2006] [Accepted: 09/29/2006] [Indexed: 11/17/2022]
Abstract
An equilibrium containing the thiol derivative of Hoechst33258 (Ht-SH), glutathione (G-SH), and the corresponding homo and hetero disulfides was shifted by the addition of the duplex DNA. It was shown from the analysis of the components that the hetero disulfide Ht-SS-G increased by binding with the DNA (CA14) with an A(3)T(3) binding motif for the structure of Hoechst33258, and that the different equilibrium shift was observed in the presence of CT14 with no A(3)T(3) binding motif.
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Affiliation(s)
- Saori Tsujita
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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Tanada M, Tsujita S, Kataoka T, Sasaki S. Cu2+-Mediated Assembly of the Minor Groove Binders on the DNA Template with Sequence Selectivity. Org Lett 2006; 8:2475-8. [PMID: 16737292 DOI: 10.1021/ol060632b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The ligands (Bpy-H, 5) have been designed to connect the Hoechst33258 skeleton for DNA binding and 2,2'-bipyridine for Cu(2+) complexation. It has been revealed that the new Hoechst ligand long Bpy-H (5L) having a long linker exhibits Cu(2+)-mediated assembly on the DNA template having two A(3)T(3) sites in a selective manner depending on the length of the linker of the ligand as well as on the distance between the two A(3)T(3) sites of DNA. [reaction: see text]
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Affiliation(s)
- Mikimasa Tanada
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
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May LG, Madine MA, Waring MJ. Echinomycin inhibits chromosomal DNA replication and embryonic development in vertebrates. Nucleic Acids Res 2004; 32:65-72. [PMID: 14704344 PMCID: PMC373276 DOI: 10.1093/nar/gkh166] [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: 11/13/2022] Open
Abstract
Echinomycin, a member of the quinoxaline family of antibiotics, is known to be a strong inhibitor of RNA synthesis which has been attributed to its ability to bind to double-helical DNA. Here we study the effect of echinomycin upon DNA replication using egg extracts and embryos from Xenopus laevis as well as cultured human cells. Evidence is presented that echinomycin interferes with chromatin decondensation, nuclear assembly and DNA replication. In the absence of transcription and translation, the drug specifically blocks DNA replication in both Xenopus sperm chromatin and HeLa cell nuclei in vitro. By contrast, replication of single-stranded DNA is not inhibited indicating that echinomycin acts by interacting with the DNA and not the replication elongation proteins of chromatin. The addition of the antibiotic to HeLa cells and X.laevis embryos results in anaphase bridges and cell death. Importantly, in X.laevis embryos injected with echinomycin at the two-cell stage the drug specifically inhibits the cell cycle prior to the onset of transcription, suggesting that quinoxaline antibiotics could exert anti- proliferative effects by inhibition of chromosomal DNA replication.
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Affiliation(s)
- Laurence G May
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
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Wang S, Peng T, Yang CF. Investigation on the interaction of DNA and electroactive ligands using a rapid electrochemical method. JOURNAL OF BIOCHEMICAL AND BIOPHYSICAL METHODS 2003; 55:191-204. [PMID: 12706904 DOI: 10.1016/s0165-022x(02)00181-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A rapid method for investigation of the interaction of DNA and electroactive ligands based on an electrochemical equation for irreversible processes is presented. The binding constant (K) and the size of binding site (s) are simultaneously obtained from the dependence of the current on the amount of added DNA in voltammetry. A non-intercalative binder (Hoechst 33258) and two DNA-intercalators (mitoxantrone (MXT) and actinomycin D (AMD)) were examined in experiments. It was found that the binding constant of Hoechst 33258, mitoxantrone and actinomycin D, were 2.1 x 10(8), 8.9 x 10(9) and 9.1 x 10(9) cm(3) mol(-1); and the size of their binding sites were 4, 3 and 8, respectively. The study provides a convenient and sensitive approach for estimating affinity parameters and outlining the interaction between DNA and electroactive targeting compounds.
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Affiliation(s)
- Sufen Wang
- Department of Chemistry, Xixi Campus, Zhejiang University, Hangzhou 310028, China
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