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Dömötör O, Teixeira RG, Spengler G, Avecilla F, Marques F, Lenis-Rojas OA, Matos CP, de Almeida RFM, Enyedy ÉA, Tomaz AI. Ruthenium(II) polypyridyl complexes with benzothiophene and benzimidazole derivatives: Synthesis, antitumor activity, solution studies and biospeciation. J Inorg Biochem 2023; 238:112058. [PMID: 36375357 DOI: 10.1016/j.jinorgbio.2022.112058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 11/08/2022]
Abstract
With the aim to incorporate pharmacophore motifs into the Ru(II)-polypyridyl framework, compounds [Ru(II)(1,10-phenantroline)2(2-(2-pyridyl)benzo[b]thiophene)](CF3SO3)2 (1) and [Ru(II)(1,10-phenantroline)2(2-(2-pyridyl)benzimidazole)](CF3SO3)2 (2) were prepared, characterized and tested for their antitumor potential. The solid-state structure of the compounds was confirmed by single-crystal X-ray diffraction analysis. The solution behavior of both complexes was investigated, namely their solubility, stability, and lipophilicity in physiological mimetic conditions, as well as an eventual uptake by passive diffusion. In vitro anticancer activity of the complexes on ovarian and different colon cancer cells and apoptosis induction by the complexes were studied. A slow transformation process was observed for complex 1 in aqueous solution when exposed to sunlight, while complex 2 undergoes deprotonation (pKa = 7.59). The lipophilicity of this latter complex depends strongly on the pH and ionic strength. In contrast, 1 is rather hydrophilic under various conditions. Complex 1 was highly cytotoxic on Colo-205 human colon (IC50 = 7.87 μM) and A2780 ovarian (IC50 = 2.2 μM) adenocarcinoma cell lines, while 2 displayed moderate anticancer activity (30.9 μM and 18.0 μM, respectively). The complexes induced late apoptosis and necrosis. Only a weak binding of the complexes to human serum albumin, the main transport protein in blood serum, was found. However, a more significant binding to calf thymus DNA was observed in UV-visible titrations and fluorometric dye displacement studies. Detailed analysis of fluorescence lifetime data collected for the latter systems reveals not only the partial intercalation of the complexes, but goes beyond the usual simplified interpretations.
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Affiliation(s)
- Orsolya Dömötör
- Department of Inorganic and Analytical Chemistry, Interdisciplinary Excellence Centre, University of Szeged, Dóm tér 7, H-6720 Szeged, Hungary; MTA-SZTE Lendület Functional Metal Complexes Research Group, University of Szeged, Dóm tér 7, H-6720 Szeged, Hungary.
| | - Ricardo G Teixeira
- Centro de Química Estrutural, Institute of Molecular Sciences, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1049-016 Lisboa, Portugal
| | - Gabriella Spengler
- MTA-SZTE Lendület Functional Metal Complexes Research Group, University of Szeged, Dóm tér 7, H-6720 Szeged, Hungary; Department of Medical Microbiology, Albert Szent-Györgyi Health Center and Albert Szent-Györgyi Medical School, University of Szeged, Semmelweis u. 6, H-6725 Szeged, Hungary
| | - Fernando Avecilla
- Universidade da Coruña, Grupo NanoToxGen, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Química, Facultade de Ciencias, Campus de A Coruña, 15071A Coruña, Spain
| | - Fernanda Marques
- Centro de Ciências e Tecnologias Nucleares and Departamento de Ciências e Engenharia Nucleares, Instituto Superior Técnico, Universidade de Lisboa, EN 10 (km 139,7), 2695-066 Bobadela, Loures, Portugal
| | - Oscar A Lenis-Rojas
- Centro de Química Estrutural, Institute of Molecular Sciences, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1049-016 Lisboa, Portugal
| | - Cristina P Matos
- Centro de Química Estrutural, Institute of Molecular Sciences, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1049-016 Lisboa, Portugal
| | - Rodrigo F M de Almeida
- Centro de Química Estrutural, Institute of Molecular Sciences, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1049-016 Lisboa, Portugal
| | - Éva A Enyedy
- Department of Inorganic and Analytical Chemistry, Interdisciplinary Excellence Centre, University of Szeged, Dóm tér 7, H-6720 Szeged, Hungary; MTA-SZTE Lendület Functional Metal Complexes Research Group, University of Szeged, Dóm tér 7, H-6720 Szeged, Hungary
| | - Ana Isabel Tomaz
- Centro de Química Estrutural, Institute of Molecular Sciences, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1049-016 Lisboa, Portugal.
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Pósa V, Hajdu B, Tóth G, Dömötör O, Kowol CR, Keppler BK, Spengler G, Gyurcsik B, Enyedy ÉA. The coordination modes of (thio)semicarbazone copper(II) complexes strongly modulate the solution chemical properties and mechanism of anticancer activity. J Inorg Biochem 2022; 231:111786. [DOI: 10.1016/j.jinorgbio.2022.111786] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/24/2022] [Accepted: 02/27/2022] [Indexed: 12/27/2022]
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3
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Burns JR, Wood JW, Stulz E. A Porphyrin-DNA Chiroptical Molecular Ruler With Base Pair Resolution. Front Chem 2020; 8:113. [PMID: 32175308 PMCID: PMC7054460 DOI: 10.3389/fchem.2020.00113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/06/2020] [Indexed: 11/13/2022] Open
Abstract
DNA-based molecular rulers enable scientists to determine important parameters across biology, from the measurement of protein binding interactions, to the study of membrane dynamics in cells. However, existing rulers can suffer from poor nanometre resolution due to the flexible nature of linkers used to tether to the DNA framework. We aimed to overcome this problem using zinc and free-base porphyrin chromophores attached via short and rigid acetylene linkers. This connectivity enables the distance and angle between the porphyrins to be fine-tuned along the DNA scaffold. The porphyrins undergo favorable energy transfer and chiral exciton coupling interactions to act as highly sensitive molecular ruler probes. To validate the system, we monitored the detection of small changes in DNA structure upon intercalation of ethidium bromide. CD spectroscopy showed the porphyrins undergo highly sensitive changes in excitation coupling to facilitate base pair resolution of the novel system.
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Affiliation(s)
- Jonathan R Burns
- Department of Chemistry, University College London, London, United Kingdom
| | - James W Wood
- School of Chemistry & Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Eugen Stulz
- School of Chemistry & Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
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4
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Asadollahi K, Riazi G, Rabbani Chadegani A, Rafiee S. DNA-binding mode transition of tau in the presence of Zinc ions. J Biomol Struct Dyn 2017. [PMID: 28636842 DOI: 10.1080/07391102.2017.1343684] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Kazem Asadollahi
- a Institute of Biochemistry and Biophysics (IBB), University of Tehran , Tehran , Iran
| | - Gholamhossein Riazi
- a Institute of Biochemistry and Biophysics (IBB), University of Tehran , Tehran , Iran
| | | | - Saharnaz Rafiee
- a Institute of Biochemistry and Biophysics (IBB), University of Tehran , Tehran , Iran
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Jamison JM, Krabill K, Allen KA, Stuart SH, Tsai CC. RNA–Intercalating Agent Interactions: in vitro Antiviral Activity Studies. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029000100601] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Twenty intercalating agents were tested to examine the effects of intercalating dye-induced perturbations upon the antiviral activity of poly (adenylate–uridylate) [poly (A-U)]. Neither poly (A-U) alone nor each intercalative dye was an efficacious antiviral agent. When poly (A-U) was combined with major groove intercalating dyes (acridine orange or proflavine), no synergism was observed. When poly (A-U) was combined with minor groove intercalating dyes [ethidium (EB), propidium (PI), adriamycin (ADR) or daunomycin (DMN)] or minor/major groove intercalating dyes [9-aminoacridine (9-AA), N2-methyl-9-hydroxy-ellipticine (NMHE) or N2,N6-dimethyl-9-hydroxy-ellipticine (DMHE)] the 50% effective doses (ED50) of the poly (A-U), 9-AA, ADR, DMHE, DMN, EB, NMHE and PI decreased 18-, 22-, 60-, 274-, 61-, 154-, 113- and 299-fold, respectively. When poly (A-U) was combined individually with 11 dyes whose mode of intercalation was not known, the ED50 of ametantrone (HAQ), chloroquine (CHL), mitoxantrone (DHAQ) and quinine (QUI) decreased 125-, 65-, 251- and 32-fold, respectively. These results suggest that the four dyes may intercalate into poly (A-U) from the minor groove. Ten (ADR, CHL, DMN, DHAQ, DMHE, EB, HAQ, NMHE, PI, QUI) of the 20 dyes evaluated exhibited significant synergism with poly (A-U), as quantified by the fractional inhibitory concentration index. Interferon (IFN) neutralization assays demonstrated that the IFN-inducing capability of the dye/poly (A-U) combinations approximated the sum of the capabilities of the poly (A-U) and the dyes employed. These results suggest that the majority of the dyes tested potentiate the antiviral activity of poly (A-U) without affecting the amount of IFN induced.
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Affiliation(s)
- J. M. Jamison
- Department of Chemistry, Kent State University, Kent, OH 44242, USA
- Department of Microbiology and Immunology, Northeastern Ohio Universities College of Medicine, Rootstown, OH 44272, USA
| | - K. Krabill
- Department of Chemistry, Kent State University, Kent, OH 44242, USA
- Department of Microbiology and Immunology, Northeastern Ohio Universities College of Medicine, Rootstown, OH 44272, USA
| | - K. A. Allen
- Department of Microbiology and Immunology, Northeastern Ohio Universities College of Medicine, Rootstown, OH 44272, USA
| | - S. H. Stuart
- Department of Microbiology and Immunology, Northeastern Ohio Universities College of Medicine, Rootstown, OH 44272, USA
| | - C.-C. Tsai
- Department of Chemistry, Kent State University, Kent, OH 44242, USA
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Guo Y, Brecht E, Aznavour K, Nix JC, Xiao Y, Wang H, George SJ, Bau R, Keable S, Peters JW, Adams MWW, Jenney F, Sturhahn W, Alp EE, Zhao J, Yoda Y, Cramer SP. Nuclear resonance vibrational spectroscopy (NRVS) of rubredoxin and MoFe protein crystals. ACTA ACUST UNITED AC 2012; 222:77-90. [PMID: 26052177 DOI: 10.1007/s10751-012-0643-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We have applied 57Fe nuclear resonance vibrational spectroscopy (NRVS) for the first time to study the dynamics of Fe centers in Fe-S protein crystals, including oxidized wild type rubredoxin crystals from Pyrococcus furiosus, and the MoFe protein of nitrogenase from Azotobacter vinelandii. Thanks to the NRVS selection rule, selectively probed vibrational modes have been observed in both oriented rubredoxin and MoFe protein crystals. The NRVS work was complemented by extended X-ray absorption fine structure spectroscopy (EXAFS) measurements on oxidized wild type rubredoxin crystals from Pyrococcus furiosus. The EXAFS spectra revealed the Fe-S bond length difference in oxidized Pf Rd protein, which is qualitatively consistent with the X-ray crystal structure.
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Affiliation(s)
- Yisong Guo
- Department of Applied Science, University of California, Davis, CA 95616
| | - Eric Brecht
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
| | - Kristen Aznavour
- Department of Chemistry, University of Southern California, Los Angeles, CA 90033
| | - Jay C Nix
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Yuming Xiao
- Department of Applied Science, University of California, Davis, CA 95616
| | - Hongxin Wang
- Department of Applied Science, University of California, Davis, CA 95616 ; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Simon J George
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Robert Bau
- Department of Chemistry, University of Southern California, Los Angeles, CA 90033
| | - Stephen Keable
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
| | - John W Peters
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
| | | | - Francis Jenney
- Georgia Campus, Philadelphia College of Osteopathic Medicine, Suwanee, GA 30024
| | - Wolfgang Sturhahn
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439
| | - Ercan E Alp
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439
| | - Jiyong Zhao
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439
| | - Yoshitaka Yoda
- JASRI, SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Stephen P Cramer
- Department of Applied Science, University of California, Davis, CA 95616 ; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 ; Department of Chemistry, University of California, Davis, CA 95616
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Nandi S, Routh P, Layek RK, Nandi AK. Ethidium Bromide-Adsorbed Graphene Templates as a Platform for Preferential Sensing of DNA. Biomacromolecules 2012; 13:3181-8. [DOI: 10.1021/bm3009632] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sudipta Nandi
- Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700 032, India
| | - Parimal Routh
- Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700 032, India
| | - Rama K. Layek
- Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700 032, India
| | - Arun K. Nandi
- Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700 032, India
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del Mundo IMA, Siters KE, Fountain MA, Morrow JR. Structural basis for bifunctional zinc(II) macrocyclic complex recognition of thymine bulges in DNA. Inorg Chem 2012; 51:5444-57. [PMID: 22507054 DOI: 10.1021/ic3004245] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The zinc(II) complex of 1-(4-quinoylyl)methyl-1,4,7,10-tetraazacyclododecane (cy4q) binds selectively to thymine bulges in DNA and to a uracil bulge in RNA. Binding constants are in the low-micromolar range for thymine bulges in the stems of hairpins, for a thymine bulge in a DNA duplex, and for a uracil bulge in an RNA hairpin. Binding studies of Zn(cy4q) to a series of hairpins containing thymine bulges with different flanking bases showed that the complex had a moderate selectivity for thymine bulges with neighboring purines. The dissociation constants of the most strongly bound Zn(cy4q)-DNA thymine bulge adducts were 100-fold tighter than similar sequences with fully complementary stems or than bulges containing cytosine, guanine, or adenine. In order to probe the role of the pendent group, three additional zinc(II) complexes containing 1,4,7,10-tetraazacyclododecane (cyclen) with aromatic pendent groups were studied for binding to DNA including 1-(2-quinolyl)methyl-1,4,7,10-tetraazacyclododecane (cy2q), 1-(4-biphenyl)methyl-1,4,7,10-tetraazacyclododecane (cybp), and 5-(1,4,7,10-tetraazacyclododecan-1-ylsulfonyl)-N,N-dimethylnaphthalen-1-amine (dsc). The Zn(cybp) complex binds with moderate affinity but little selectivity to DNA hairpins with thymine bulges and to DNA lacking bulges. Similarly, Zn(dsc) binds weakly both to thymine bulges and hairpins with fully complementary stems. The zinc(II) complex of cy2q has the 2-quinolyl moiety bound to the Zn(II) center, as shown by (1)H NMR spectroscopy and pH-potentiometric titrations. As a consequence, only weak (500 μM) binding is observed to DNA with no appreciable selectivity. An NMR structure of a thymine-bulge-containing hairpin shows that the thymine is extrahelical but rotated toward the major groove. NMR data for Zn(cy4q) bound to DNA containing a thymine bulge is consistent with binding of the zinc(II) complex to the thymine N3(-) and stacking of the quinoline on top of the thymine. The thymine-bulge bound zinc(II) complex is pointed into the major groove, and there are interactions with the guanine positioned 5' to the thymine bulge.
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Affiliation(s)
- Imee Marie A del Mundo
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260, USA
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Hamoir G, Sonveaux E. 3′-5′ Cyclic Oligothymidylic Acids: Conformation and Complexation of Intercalating Agents. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/bscb.19931020506] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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10
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Firth WJ, Watkins CL, Graves DE, Yielding LW. Synthesis and characterization of ethidium analogs: Emphasis on amino and azido substituents. J Heterocycl Chem 2009. [DOI: 10.1002/jhet.5570200347] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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11
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Molecular recognition of plant DNA: does it differ from conventional animal DNA? Int J Biol Macromol 2009; 44:133-7. [PMID: 19059281 DOI: 10.1016/j.ijbiomac.2008.11.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Revised: 10/07/2008] [Accepted: 11/05/2008] [Indexed: 11/20/2022]
Abstract
The recognition mechanism of DNA with small drugs/ligands is an important field of research from pharmacological point of view. Such studies are ample with DNAs extracted from animal cells, but are rare for those extracted from plant cells. However, such a study is strongly demanding for the formulation of pesticides and other agrochemicals. In this contribution, for the first time, we report the interaction of two well-known DNA binder ethidium bromide (EB) and Hoechst 33258 (H33258) with two genomic DNAs extracted from the leaves of Ricinus communis L. (castor bean) and Mangifera indica (mango) using steady-state and picosecond-resolved fluorescence spectroscopy. The purity of the extracted DNAs is confirmed from gel electrophoresis and optical absorption studies. As evidenced from the circular dichroism (CD) measurements the DNAs retain physiologically relevant B forms. The well-known DNA intercalator EB has been found to show an additional electrostatic mode of binding with the DNAs, which is not present in the conventional animal DNAs. The binding affinity of EB is found to be even weaker for the DNA extracted from M. indica compared to that in R. communis L. On the other hand, the binding affinity of H33258 with the plant DNAs is found to be comparable to that of animal DNAs. The difference in interaction could be rationalized from the possible differences in the base sequences.
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Moretti R, Ansari AZ. Expanding the specificity of DNA targeting by harnessing cooperative assembly. Biochimie 2008; 90:1015-25. [PMID: 18343232 DOI: 10.1016/j.biochi.2008.02.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2008] [Accepted: 02/18/2008] [Indexed: 12/24/2022]
Abstract
The precise control of developmental and regulatory processes in the cell requires accurate recognition of specific DNA sites. For genomes as large as that of humans, single-molecule-DNA binders have difficulties accurately and specifically recognizing the intended targets. Natural transcription factors overcome these difficulties by forming non-covalent complexes on the DNA with other transcription factors. These cooperative complexes overcome the difficulties of single-molecule transcription factors, allowing specific, combinatorial control of a range of transcriptional targets. Artificial transcription factors have been designed to take advantage of this technique of cooperative assembly, facilitating future studies in whole genome targeting. In contrast to a simple model of component independence, cooperative complexes as a whole often display slightly altered DNA specificity from what would be expected from the analysis of their separate components. The true sequence specificity of cooperative complexes, and thus their presumed in vivo targets, have to be experimentally probed. A number of techniques, such as the cognate site identity array, now allow for rapid, high-throughput determination of the specificity of cooperative complexes.
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Affiliation(s)
- Rocco Moretti
- Department of Biochemistry, The Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706, USA
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Sarkar R, Pal SK. Interaction of Hoechst 33258 and Ethidium with Histone1−DNA Condensates. Biomacromolecules 2007; 8:3332-9. [PMID: 17902690 DOI: 10.1021/bm700690p] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report structural and dynamical aspects of DNAs from various sources including synthetic oligonucleotides in bulk buffer and as a complex with histone1 (H1). High-resolution transmission electron microscopic (HRTEM) studies reveal the structural change of the DNAs upon complexation with H1 leading to formation of compact-globular and hollow-toroidal particles. In order to explore the functionality of ligand binding of the DNAs and their complexes with H1, we have used two biologically common fluorescent probes Hoechst 33258 (H33258) and Ethidium (EB) as model ligands. Picosecond resolved fluorescence and polarization gated anisotropy studies examined that the minor groove binding of H33258 to the genomic DNA-H1 complex remains almost unaltered. However, the intercalative interaction of EB with the DNA in the complex is severely perturbed compared to that with the DNA in bulk buffer. Time-dependent solvochromic effect of the probe H33258 further elucidates the dynamical solvation, which is reflective of the overall environmental relaxation of the DNAs upon condensation by H1. We have also performed circular dichroism (CD) studies on the DNAs and their complexes with H1, which reveal the change in conformation of the DNAs in the complexes. Our studies in the ligand-binding mechanisms of the DNA-H1 complex are important to understand the mechanism of drug binding to linker DNA in condensed chromatin.
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Affiliation(s)
- Rupa Sarkar
- Unit for Nano Science & Technology, Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Salt Lake, Kolkata, India
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14
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Sergeyev DS, Zarytova VF. Interaction of bleomycin and its oligonucleotide derivatives with nucleic acids. RUSSIAN CHEMICAL REVIEWS 2007. [DOI: 10.1070/rc1996v065n04abeh000216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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15
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Cosa G, Focsaneanu KS, McLean JRN, McNamee JP, Scaiano JC. Photophysical Properties of Fluorescent DNA-dyes Bound to Single- and Double-stranded DNA in Aqueous Buffered Solution¶. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2001)0730585ppofdd2.0.co2] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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16
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KONAKAHARA T, KOMATSU H, SAKAI N, GOLD B. Computational Analysis of Molecular Recognition in DNA Base-Sequence and Groove by Methidium Chloride Using Molecular Mechanics Calculation. ACTA ACUST UNITED AC 2007. [DOI: 10.2477/jccj.6.27] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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17
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Cosa G, Focsaneanu KS, McLean JR, McNamee JP, Scaiano JC. Photophysical properties of fluorescent DNA-dyes bound to single- and double-stranded DNA in aqueous buffered solution. Photochem Photobiol 2001; 73:585-99. [PMID: 11421063 DOI: 10.1562/0031-8655(2001)073<0585:ppofdd>2.0.co;2] [Citation(s) in RCA: 243] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The absorption and fluorescence spectra, fluorescence quantum yields, lifetimes and time-resolved fluorescence spectra are reported for nine different fluorescent DNA-dyes. The work was initiated in search of a quantitative method to detect the ratio of single-to-double stranded DNA (ssDNA/dsDNA) in solution based on the photophysics of dye-DNA complexes; the result is a comprehensive study providing a vast amount of information for users of DNA strains. The dyes examined were the bisbenzimide or indole-derived stains (Hoechst 33342, Hoechst 33258 and 4',6-diamidino-2-phenylindole), phenanthridinium stains (ethidium bromide and propidium iodide) and cyanine dyes (PicoGreen, YOYO-1 iodide, SYBR Green I and SYBR Gold). All were evaluated under the same experimental conditions in terms of ionic strength, pH and dye-DNA ratio. Among the photophysical properties evaluated only fluorescence lifetimes for the cyanine stilbene dyes allowed a convenient differentiation between ssDNA and dsDNA. The bisbenzimide dyes showed multiexponential decays when bound to either form of DNA, making lifetime-based analysis cumbersome with inherent errors. These dyes also presented biexponential decay when free in aqueous buffered solutions at different pH. A mechanism for their deactivation is proposed based on two different conformers decaying with different kinetics. The phenanthridinium dyes showed monoexponential decays with ssDNA and dsDNA, but there was no discrimination between them. High dye-DNA ratios (e.g. 1:1) resulted in multiexponential decays for cyanine dyes, resulting from energy transfer or self-quenching deactivation. Shifts in both absorption and fluorescence maxima for both ssDNA and dsDNA DNA-cyanine dye complexes were small. Broadening of dye-ssDNA absorption and fluorescence bands for the cyanine dyes relative to dye-dsDNA bands was detected and attributed to higher degrees of rotational freedom in the former.
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Affiliation(s)
- G Cosa
- Department of Chemistry, University of Ottawa, 10 Marie-Curie, Ottawa, Ontario, Canada K1N 6N5
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18
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Affiliation(s)
- Tzyh‐Chyang Tang
- Department of Chemistry, National Sun Yat‐Sen University, Kaohsiung 80424, Taiwan
| | - Hsuan‐Jung Huang
- Department of Chemistry, National Sun Yat‐Sen University, Kaohsiung 80424, Taiwan
- Permanent address: Department of Pharmacology, Chia Nan College of Pharmacy and Science, Tainan 71710, Taiwan
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19
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Barr RG. Ethidium bromide binding to unstructured and structured 2' GMP. J Biomol Struct Dyn 1995; 13:339-49. [PMID: 8579792 DOI: 10.1080/07391102.1995.10508844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
For disordered 2' GMP and 5' GMP the ethidium cation (Etd) was found to form 1:1 and 2:1 Eth:nucleotide complex. For alkali metal solution self-structured 2'GMP and 5'GMP Etd was found to form 1:1 and 2:1 Etd: order nucleotide complex. The best computer fit was obtained for a structured nucleotide stoichiometry of Na4(2'GMP)8. Binding constants for the Etd:disordered 2'GMP complexes were determined to be (1.6 +/- 0.1) x 10(4)M(-1) and 6.3 +/- 0.5 M(-1) at O degrees C and (1.1 +/- 0.2) x 10(4) M(-1) and 18 +/- 11M(-1) for 5'GMP at 5 degrees C for the 1:1 and 1:2 complex, respectively. For the 1:1 and 1:2 2'GMP:Etd species the enthalpies were determined to be -19.8 +/- 1.0 kcal/mole and 0.1 +/- 0.3 kcal/mole, respectively, and the entropies were -53.3 +/- 6.6 eu and 3.9 +/- 1.6 eu, respectively. Binding constants for the Etd: structured 2'GMP complex, assuming a complex with stoichoimetry (Na+)4 (2'GMP)8 for the structured unit, were determined to be (1.9 +/- 0.1) x 10(4)M(-1) and 5.8 +/- 0.6) x 10(2)M(-1), respectively at 0 degrees C.
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Affiliation(s)
- R G Barr
- Department of Radiology, St. Elizabeth Hospital Medical Center, Youngstown, Ohio 44501-1790, USA
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Triebel H, Bär H, Walter A, Burckhardt G, Zimmer C. Modulation of DNA supercoiling by interaction with netropsin and other minor groove binders. J Biomol Struct Dyn 1994; 11:1085-105. [PMID: 7524538 DOI: 10.1080/07391102.1994.10508054] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The assay of DNA unwinding by ethidium, followed by sedimentation velocity techniques, was applied to complexes of supercoiled plasmid DNA with different non-intercalating drugs which strongly and sequence-specifically bind to DNA. Compared with the behaviour of naked DNA, most of the complexes exhibit an increase in the critical EB/nucleotide binding ratio associated with the principal minimum in the sedimentation profile. Using netropsin (Nt) as the paradigm of the minor groove binders investigated, the drug-induced alterations in various structural parameters of both the relaxed and supercoiled form of DNA are described. Whereas winding number, helical repeat (both being defined with reference to a surface normal), and linking number of the superhelical DNA remain constant in our experiments, its twist number, surface twist, number of superhelical turns as well as the absolute values of linking number difference, superhelix density, and writhing number increase on binding of Nt. Correspondingly, compared with the naked relaxed DNA a higher linking number (or twist number, or winding number), a higher average duplex winding angle and a lower helical repeat have to be assigned to the relaxed Nt-DNA complex. The various minor groove binders investigated were found to differ considerably in their efficiency to alter the structure of supercoiled DNA.
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Affiliation(s)
- H Triebel
- Institut für Molekularbiologie der Friedrich-Schiller-Universität Jena
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21
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Snyder JG, Hartman NG, D'Estantoit BL, Kennard O, Remeta DP, Breslauer KJ. Binding of actinomycin D to DNA: evidence for a nonclassical high-affinity binding mode that does not require GpC sites. Proc Natl Acad Sci U S A 1989; 86:3968-72. [PMID: 2726760 PMCID: PMC287369 DOI: 10.1073/pnas.86.11.3968] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We have employed a combination of temperature-dependent UV absorption spectroscopy, circular dichroism, and batch calorimetry to characterize the binding of actinomycin D to a series of oligomeric DNA duplexes. We find the duplex [d(CGTCGACG)]2 to be unique in its ability to bind actinomycin D strongly despite the absence of a classic GpC site. We present evidence that this non-GpC-containing duplex binds two actinomycin D molecules in an apparently cooperative manner to form a complex that exhibits aberrant spectroscopic and calorimetric behavior. We propose that these observations are consistent with actinomycin D exhibiting a high-affinity, sequence-dependent DNA-binding mode distinct from its classic binding to isolated GpC sites.
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Affiliation(s)
- J G Snyder
- University Chemical Laboratory, Cambridge, United Kingdom
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22
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Wu PG, Song L, Clendenning JB, Fujimoto BS, Benight AS, Schurr JM. Interaction of chloroquine with linear and supercoiled DNAs. Effect on the torsional dynamics, rigidity, and twist energy parameter. Biochemistry 1988; 27:8128-44. [PMID: 3233199 DOI: 10.1021/bi00421a023] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The magnitude and uniformity of the torsion elastic constant (alpha) of linear pBR322 DNA and supercoiled pBR322 DNAs with high-twist (sigma = -0.083) and normal-twist (sigma = -0.48) are measured in 0.1 M NaCl as a function of added chloroquine/base-pair ratio (chl/bp) by studying the fluorescence polarization anisotrophy (FPA) of intercalated ethidium dye. The time-resolved FPA is measured by using a picosecond dye laser for excitation and time-correlated single-photon counting detection. A general theory is developed for the binding of ligands that unwind superhelical DNAs, and the simultaneous binding of two different intercalators is treated in detail. The equilibrium constant (K) for binding chloroquine to linear pBR322 DNA and the number (r) of bound chloroquines per base pair are determined from the relative amplitude ratio of the slow (normally intercalated) and fast (free) components in the decay of the (probe) ethidium fluorescence intensity as a function of chl/bp. For chloroquine binding to supercoiled pBR322 DNAs, the intrinsic binding constant is assumed to be the same as for the linear DNA, but the twist energy parameter ET (N times the free energy to change the linking number from 0 to 1 in units of kBT) is regarded as adjustable. Using the best-fit ET, the binding ratios r are calculated for each chl/bp ratio. Twist energy parameters are also determined for ethidium binding to these supercoiled DNAs by competitive dialysis. For chloroquine binding, we obtain ET = 360 and 460 respectively for the normal-twist and high-twist supercoiled DNAs. For ethidium binding the corresponding values are ET = 280 +/- 70 and 347 +/- 50. Like other dye-binding values, these are substantially lower than those obtained by ligation methods. In the absence of chloroquine, the torsion constants of all three DNAs are virtually identical, alpha = (5.0 +/- 0.4) x 10(-12) dyn.cm. For linear pBR322 DNA, the magnitude and uniformity of alpha remain unaltered by intercalated chloroquine up to r = 0.19. This finding argues that the FPA is not significantly relaxed by diffusion of any kinks or solitons. If alpha d denotes the torsion constant between a dye and a base pair and alpha 0 that between two base pairs, then our data imply that alpha d/alpha 0 lies in the range 0.65-1.64, with a most probable value of 1.0.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- P G Wu
- Department of Chemistry, University of Washington, Seattle 98195
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23
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Cheng CC. Structural aspects of antineoplastic agents--a new approach. PROGRESS IN MEDICINAL CHEMISTRY 1988; 25:35-83. [PMID: 3076970 DOI: 10.1016/s0079-6468(08)70277-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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24
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Babayan Y, Manzini G, Xodo LE, Quadrifoglio F. Base specificity in the interaction of ethidium with synthetic polyribonucleotides. Nucleic Acids Res 1987; 15:5803-12. [PMID: 2441360 PMCID: PMC306024 DOI: 10.1093/nar/15.14.5803] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Base specificity in the interaction of ethidium with double stranded synthetic RNA homopolymers has been studied by means of spectroscopic (UV-visible absorption and fluorescence), microcalorimetric and dilatometric techniques. The results show a strong base specificity in this interaction, the association constant with poly A:poly U being more than three order of magnitude higher than with poly O:poly C. The interaction is mainly enthalpy driven, the differences in affinity being essentially entropic in origin. These evidences along with the dilatometric data suggest that the observed base specificity may arise from the different extent of water release upon intercalation.
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25
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Study of structures of complexes of proflavine with dinucleotides in aqueous solution by the1H NMR method. J STRUCT CHEM+ 1987. [DOI: 10.1007/bf00755201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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26
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Abstract
The formation of complexes between the self-complementary ribo-dinucleoside monophosphate CpG and ethidium ion is observed by use of an ethidium ion selective electrode. The ratio of total CpG to total ethidium was varied from 50:1 to .4:1, with CpG concentrations ranging from 0.2 to 1.1 mM. Scatchard plots show that the system is strongly cooperative with respect to ethidium ion; cooperativity with respect to dinucleoside has been previously reported (Krugh, T.R., Wittlin, F.N., and Cramer, S.P. (1975) Biopolymers 14,197-210). Cooperative behavior with respect to ethidium ion implies the existence of complexes containing at least two molecules of ethidium ion in combination with one or more CpG molecules.
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27
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Nandi R, Maiti M. Binding of sanguinarine to deoxyribonucleic acids of differing base composition. Biochem Pharmacol 1985; 34:321-4. [PMID: 3970714 DOI: 10.1016/0006-2952(85)90038-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The binding of the alkaloid sanguinarine to natural DNAs of differing GC content has been studied by spectrophotometry and viscometry techniques. Binding parameters determined from spectrophotometric measurements by Scatchard analysis, according to an excluded-site model, indicate a very high specificity of sanguinarine binding to GC rich DNA. In the strong binding region, the increase of contour length of DNA depends strongly on its base composition, being larger with GC rich DNA than with AT rich DNA. It is concluded that the alkaloid binds preferentially to the GC pairs in DNA template.
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Newlin DD, Miller KJ, Pilch DF. Interactions of molecules with nucleic acids. VII. Intercalation and T.A specificity of daunomycin in DNA. Biopolymers 1984; 23:139-58. [PMID: 6696975 DOI: 10.1002/bip.360230111] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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31
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Dougherty G, Pilbrow JR. Physico-chemical probes of intercalation. THE INTERNATIONAL JOURNAL OF BIOCHEMISTRY 1984; 16:1179-92. [PMID: 6397369 DOI: 10.1016/0020-711x(84)90215-5] [Citation(s) in RCA: 83] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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32
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Mantooth D, Georghiou S. Complex formation between ethidium bromide and the nucleotides AMP and GMP. Photochem Photobiol 1983; 38:623-6. [PMID: 6316377 DOI: 10.1111/j.1751-1097.1983.tb03393.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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33
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Abstract
Fluorescence and absorbance methods were used to study the interaction of daunomycin with four deoxypolynucleotides. The binding may be described by the neighbor-exclusion model for binding ratios greater than 0.05, with intrinsic binding constants decreasing in the order poly[d(A-T)] X poly[d(A-T)] greater than poly[d(G-C)] X poly[d(G-C)] greater than poly(dG) X poly(dC) greater than poly(dA) X poly(dT). The exclusion parameter was found to be approximately 2 for the A-T-containing polynucleotides, 4 for the alternating G-C polymer, and nearly 10 for poly(dG) X poly(dC). Poly(dA) X poly(dT) showed positive cooperativity at low binding ratios. Thermal denaturation studies provided quantitative support for the measured binding parameters; the delta Tm values measured may be correlated primarily with the differences seen in the exclusion parameter. Sedimentation velocity experiments on daunomycin-deoxypolynucleotide complexes show an unusual nonlinear dependence of Sapp on the binding ratio for poly[d(A-T)] X poly[d(A-T)], poly[d(G-C)] X poly[d(G-C)], and poly(dA) X poly(dT), indicative of either a nonstandard conformational change accompanying intercalation or cooperative drug binding.
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34
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Winkle SA, Rosenberg LS, Krugh TR. On the cooperative and noncooperative binding of ethidium to DNA. Nucleic Acids Res 1982; 10:8211-23. [PMID: 7162990 PMCID: PMC327080 DOI: 10.1093/nar/10.24.8211] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The equilibrium binding of ethidium bromide to native DNAs and to poly(dG-dC) X poly(dG-dC) has been studied by both phase partition and direct spectrophotometric techniques. The binding isotherms obtained from both experimental techniques show that ethidium binds in a cooperative manner to E. coli DNA. On the other hand, no evidence of cooperative binding was observed in the binding isotherms obtained with calf thymus, C. perfringens, M. lysodeikticus, or poly(dG-dC) X (dG-dC) under the experimental conditions used (0.1 M NaCl).
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35
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Hurley I, Osei-Gyimah P, Archer S, Scholes CP, Lerman LS. Torsional motion and elasticity of the deoxyribonucleic acid double helix and its nucleosomal complexes. Biochemistry 1982; 21:4999-509. [PMID: 6291596 DOI: 10.1021/bi00263a025] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Torsional thermal oscillations of the DNA double helix within the electron paramagnetic resonance (EPR) time scale (10(-10)-10(-3) s) as indicated by a rigid, intercalating probe are much smaller in the spacer segment between nucleosomes in chromatin than in long, free DNA molecules. Still smaller DNA oscillation is indicated in intact nuclei and yet smaller if the nuclei have been treated with glutaraldehyde. The values of EPR measurements are not affected by the loading density of probe. If the probe were capable of substantial oscillations or movement different from that of the helix, those oscillations would be expected to dominate the spectra when movement of the helix is restrained. We conclude that the correlation time for torsional movement of free DNA inferred from EPR spectra is characteristic of the double helix and that there is no significant independent motion of the probe. The correlation time for the DNA double helix in molecules longer than approximately 500 base pairs is close to 30 ns, corresponding to an elastic constant of 1.5 X 10(-19) ergs cm for deformation by twisting. The motions observed in chromatin are consistent with a model in which spheres of 50-60-A radius are connected by simple elastic rods with the length of spacer DNA and the same elastic constant. The spin-labeled ethidium probe has been characterized in detail by nuclear magnetic resonance, infrared, fluorescence, and visible light spectroscopy. The binding equilibria are consistent with the hypothesis that strongly immobilized probe molecules are preferentially bound to spacer DNA.
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36
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Dougherty G. A comparison of the base-pair specificities of three phenanthridine drugs using solution spectroscopy. THE INTERNATIONAL JOURNAL OF BIOCHEMISTRY 1982; 14:493-504. [PMID: 7106349 DOI: 10.1016/0020-711x(82)90117-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
1. The absorption spectrum of three phenanthridine drugs (ethidium, dimidium and prothidium bromide) bound to natural DNAs of differing G-C content were obtained using a novel mixing scheme and analysed according to the excluded site binding model. 2. Ethidium bromide shows a strong G-C specificity at low binding ratios. especially at low ionic concentration. 3. Dimidium bromide shows a less strong G-C specificity. 4. For both drugs, the binding site size reflects a situation close to nearest-neighbour exclusion. 5. Prothidium shows no specificity in its binding. The binding modes are different than for the other two phenanthridines, and it is suggested that the primary mode is "sideways" intercalation.
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37
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Baldini G, Doglia S, Dolci S, Sassi G. Fluorescence-determined preferential binding of quinacrine to DNA. Biophys J 1981; 36:465-77. [PMID: 7326321 PMCID: PMC1327640 DOI: 10.1016/s0006-3495(81)84746-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Quinacrine complexes with native DNA (Calf thymus, Micrococcus lysodeikticus, Escherichia coli, Bacillus subtilis, and Colstridium perfringens) and synthetic polynucleotides (poly(dA) . poly(dT), poly[d(A-T)] . poly[d(A-T)], poly(dG) . poly(dC) and poly[d(G-C)] . poly[d(G-C)]) has been investigated in solution at 0.1 M NaCl, 0.05 M Tris HCl, 0.001 M EDTA, pH 7.5, at 20 degrees C. Fluorescence excitation spectra of complexes with dye concentration D = 5-30 microM and DNA phosphate concentration P = 400 microM have been examined from 300 to 500 nm, while collecting the emission above 520 nm. The amounts of free and bound quinacrine in the dye-DNA complexes have been determined by means of equilibrium dialysis experiments. Different affinities have been found for the various DNAs and their values have been examined with a model that assumes that the binding constants associated with alternating purine and pyrimidine sequences are larger than those relative to nonalternating ones. Among the alternating nearest neighbor base sequences, the Pyr(3'-5')Pur sequences, i.e., C-G, T-G, C-A and T-A seem to bind quinacrine stronger than the remaining sequences. In particular the three sites, where a G . C base pair is involved, are found to display higher affinities. Good agreement is found with recent calculations on the energetics of intercalation sites in DNA. The analysis of the equilibrium shows also that the strength of the excitation spectrum of bound dye depends strongly upon the ratio of bound quinacrine to DNA. This effect can be attributed to dye-dye energy transfer along DNA.
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38
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Bernier JL, Henichart JP, Catteau JP. ESR study of intercalation: quantitative evaluation of drug-DNA binding through competition with a spin-labeled 9-aminoacridine. Anal Biochem 1981; 117:12-7. [PMID: 6274226 DOI: 10.1016/0003-2697(81)90683-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Abstract
We report equilibrium dialysis studies of the binding of ethidium to a variety of double-helical synthetic polynucleotides containing A.U (or T) and I.C base pairs. The results are interpreted in terms of the neighbor exclusion model of drug binding, with allowance both for cooperativity of binding and for a structural switch of the helix to a different form which binds the drug more effectively. Both DNA and the alternating copolymers examined [poly[d(A-T)] and poly[d(I-C)]] showed high affinity (10(4)--10(5) M-1) in 1 M salt. Homopolynucleotides showed a more complicated pattern of affinities: poly(rA).poly(rU), poly(rA).poly(dT), and poly(dA).poly(rU) showed high affinity, whereas poly(dA).poly(dT), poly(rI).poly(rC), and poly(dI).poly(dC) showed low affinity (less than or equal to 10(3) M-1). The neighbor exclusion range was inferred to be two base pairs for DNA or B family helices and three for RNA or A family helices. Generally, polynucleotides showed some cooperativity in their ethidium binding. The data reveal a switch of poly[d(I-C)] to a form able to bind ethidium more effectively.
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41
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Stabilities of nearest-neighbor doublets in double-helical DNA determined by fitting calculated melting profiles to observed profiles. Biopolymers 1981. [DOI: 10.1002/bip.1981.360200513] [Citation(s) in RCA: 195] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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42
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Graves DE, Watkins CL, Yielding LW. Ethidium bromide and its photoreactive analogues: spectroscopic analysis of deoxyribonucleic acid binding properties. Biochemistry 1981; 20:1887-92. [PMID: 7225364 DOI: 10.1021/bi00510a026] [Citation(s) in RCA: 64] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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43
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Borissova OF, Krichevskaya AA, Samarina OP. Structural investigation of nuclear RNP particles containing pre-mRNA by different fluorescence techniques. Nucleic Acids Res 1981; 9:663-81. [PMID: 7220348 PMCID: PMC327229 DOI: 10.1093/nar/9.3.663] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Ethidium bromide (EB) adsorption isotherms on 30S nuclear RNP particles isolated from liver nuclei has revealed 6% of double-stranded regions in pre-mRNA (dsRNA). It has been established by measurements of the EB fluorescence polarization that the bulk of dsRNA regions in RNP is rigidly attached to RNP. They are longer than 45 degree A. The increase of NaCl concentration from 0.1 up to 0.4 M causes a significant loosening of dsRNA-protein bonds. As a result the dsRNA segments become more flexible. Measurements of energy transfer from fluorescamine (covalently bound to the protein) to EB (adsorbed on dsRNA) have yielded information about dsRNA location. The fact that absorbtion of exciting light by fluorescamine causes pronounced increase of EB fluorescence is consistent with the idea that helical regions of RNA are located outside the RNP particles.
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Young PR, Kallenbach NR. Binding of 9-aminoacridine to deoxydinucleoside phosphates of defined sequence: preferences and stereochemistry. J Mol Biol 1981; 145:785-813. [PMID: 7265221 DOI: 10.1016/0022-2836(81)90315-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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45
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Miller KJ, Brodzinsky R, Hall S. Interactions of molecules with nucleic acids. IV. Binding energies and conformations of acridine and phenanthridine compounds in the two principal and in several unconstrained dimer-duplex intercalation sites. Biopolymers 1980; 19:2091-122. [PMID: 7437502 DOI: 10.1002/bip.1980.360191111] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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46
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Dean PM, Wakelin LP. The docking manoeuvre at a drug receptor: a quantum mechanical study of intercalative attack of ethidium and its carboxylated derivative on a DNA fragment. Philos Trans R Soc Lond B Biol Sci 1979; 287:571-604. [PMID: 42936 DOI: 10.1098/rstb.1979.0084] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Various semi-empirical quantum mechanical methods have been used to investigate the docking manoeuvre of ethidium and of its carboxylated derivative at the (dC-dG) • (dC-dG) receptor. The objective of the work was to determine whether the drug attacks the receptor in a random orientation or is pre-aligned for effective docking. An analogy was made between the interaction and two docking space vehicles. Charge distributions were computed for the intercalative site and the drug molecules; from these distributions it was possible to map, in three-dimensional space, the molecular electrostatic potential surrounding the receptor. Perturbation of the receptor fields by an approaching drug molecule showed field neutralization and a shifting local minimum as docking proceeds. Most of the electrostatic potential surrounding the receptor was shown to be derived from the two ionized phosphate groups. The orientation of the drug molecule was studied in a simplified anionic field constructed to reproduce that of the receptor phosphates. Rotation of ethidium and
p
-carboxyphenylethidium round the Eulerian axes in this simulated anionic field showed up distinct preferences for orientation of drug molecules in the vicinity of the receptor. Probability distributions for rotational populations demonstrated clearly that the receptor induces an orientation in the approaching ligand. The energy involved in modification of the alignment could be attributed to electrostatic interactions over large separation distances and to induced electron delocalization as the drug approaches closer to the receptor. This partition of the energy was considered further by monitoring electron migration in the drug molecules and analysis of dipole moment fluctuations. Orientation restrictions reflect entropy changes in the association reaction; these are discussed with respect to their importance in determination of reaction kinetics, and in two established models for drug- receptor interaction, namely, the ‘lock and key’ and ‘zipper’ mechanisms.
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47
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Ornstein RL, Rein R. Energetic and structural aspects of ethidium cation intercalation into DNA minihelices. Biopolymers 1979; 18:2821-47. [PMID: 508904 DOI: 10.1002/bip.1979.360181112] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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48
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Broyde S, Hingerty B. Conformational origin of the pyrimidine (3'-5') purine base sequence preference for intercalation into RNAs. Biopolymers 1979; 18:2905-10. [PMID: 508906 DOI: 10.1002/bip.1979.360181117] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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50
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Yielding LW, Graves DE, Brown BR, Yielding KL. Covalent binding of ethidium azide analogs to Salmonella DNA in vivo: competition by ethidium bromide. Biochem Biophys Res Commun 1979; 87:424-32. [PMID: 444231 DOI: 10.1016/0006-291x(79)91813-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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