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Galisteo J, Navarro P, Campayo L, Yunta MJR, Gómez-Contreras F, Villa-Pulgarin JA, Sierra BG, Mollinedo F, Gonzalez J, Garcia-España E. Synthesis and cytotoxic activity of a new potential DNA bisintercalator: 1,4-Bis{3-[N-(4-chlorobenzo[g]phthalazin-1-yl)aminopropyl]}piperazine. Bioorg Med Chem 2010; 18:5301-9. [PMID: 20538470 DOI: 10.1016/j.bmc.2010.05.053] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Revised: 05/14/2010] [Accepted: 05/18/2010] [Indexed: 11/25/2022]
Abstract
The synthesis of new 1,4-bisalkylamino (2-4) and 1-alkylamino-4-chloro (5-6) substituted benzo[g]phthalazines is reported. Compounds 2-4 and 6 were prepared both in the free and heteroaromatic ring protonated forms. Bifunctional 6 contains the 1,4-bisaminopropylpiperazine chain as a linker between the two heteroaromatic units, whereas 5 is its monofunctional analogue. The in vitro antitumour activity of the synthesized compounds has been tested against human colon, breast and lung carcinoma cells, and also against human glioblastoma cells. Results obtained show that all of them are active in all cases, but bifunctional 6.2HCl is remarkably effective against the four cell lines tested, exhibiting IC50 values in the range of 10(-7) M, similar to those found for doxorubicin. The bifunctional structure of 6.2HCl enhances activity with respect to the monofunctional related compounds 5 and 7, leading to the highest activity among all the compounds tested. Molecular modelling of 6 suggests that those results could be indicative of DNA bisintercalation, which should be specially favoured in the diprotonated form 6.2HCl, a compound suitable for being studied more in depth in further biological tests. Measure of the DNA thermal melting curves show that the linear rise in Tm for bifunctional 6.2HCl is nearly twice than that one obtained for monofunctional 5, and supports the DNA-binding hypothesis.
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Affiliation(s)
- Juan Galisteo
- Instituto de Química Médica, Centro de Química Orgánica Manuel Lora-Tamayo, CSIC, c/Juan de la Cierva 3, E-28006 Madrid, Spain
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2
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Limanskaya LA, Limansky AP. S-DNA, over-supercoiled DNA with a 1.94-to 2.19-Å rise per base pair. Mol Biol 2006. [DOI: 10.1134/s0026893306010158] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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3
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Rodríguez-Ciria M, Sanz AM, Yunta MJR, Gomez-Contreras F, Navarro P, Fernandez I, Pardo M, Cano C. Synthesis and cytotoxic activity of N,N-bis-(3-[N-(4-chlorobenzo[g]-phthalazin-1-yl)]aminopropyl)-N-methylamine: a new potential DNA bisintercalator. Bioorg Med Chem 2003; 11:2143-8. [PMID: 12713823 DOI: 10.1016/s0968-0896(03)00127-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The synthesis of a new series of mono- and dinuclear 1-alkylamino-4-chlorobenzo[g]phthalazine derivatives 7-10 containing flexible polyaminic chains is reported. It has been achieved by the reaction of 1,4-dichlorobenzo[g]phthalazine with the corresponding polyamines. In vitro antitumoral activity against HT-29 human colon carcinoma cells was evaluated and showed best results for compound 10, in which two heteroaromatic units are linked by a N-methylsubstituted polyaminic chain. Molecular modelling of the complexes of 9 and 10 with DNA strongly suggests the possibility of bisintercalation, and also that the N-methyl group of 10 plays an important role in the formation of a specially stable DNA complex.
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Affiliation(s)
- Marinela Rodríguez-Ciria
- Departamento de Quimica Organica I, Facultad de Quimica, Universidad Complutense, 28040 Madrid, Spain
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4
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Davies DB, Eaton RJ, Baranovsky SF, Veselkov AN. NMR investigation of the complexation of daunomycin with deoxytetranucleotides of different base sequence in aqueous solution. J Biomol Struct Dyn 2000; 17:887-901. [PMID: 10798533 DOI: 10.1080/07391102.2000.10506577] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
500 MHz NMR spectroscopy has been used to investigate the complexation of the anthracycline antibiotic daunomycin (DAU) with self-complementary deoxytetranucleotides, 5'-d(CGCG), 5'-d(GCGC), 5'-d(TGCA), 5'-d(ACGT) and 5'-d(AGCT), of different base sequence in aqueous salt solution. 2D homonuclear 1H NMR spectroscopy (TOCSY and NOESY) and heteronuclear 1H - 31P NMR spectroscopy (HMBC) have been used for complete assignment of the non-exchangeable protons and the phosphorus resonance signals, respectively, and for a qualitative determination of the preferred binding sites of the drug. Analysis shows that DAU intercalates preferentially into the terminal sites of each of the tetranucleotides and that the aminosugar of the antibiotic is situated in the minor groove of the tetramer duplex, partly eclipsing the third base pair. A quantitative determination of the complexation of DAU with the deoxytetranucleotides has been made using the experimental concentration and temperature dependences of the drug proton chemical shifts; these have been analysed in terms of the equilibrium reaction constants, limiting proton chemical shifts and thermodynamical parameters (enthalpies deltaH, entropies deltaS) of different drug-DNA complexes (1:1, 1:2, 2:1, 2:2) in aqueous solution. It is found that DAU interacts with sites containing three adjacent base pairs but does not show any significant sequence specificity of binding with either single or double-stranded tetranucleotides, in contrast with other intercalating drugs such as proflavine, ethidium bromide and actinomycin D. The most favourable structures of the 1:2 complexes have been derived from the induced limiting proton chemical shifts of the drug in the intercalated complexes with the tetranucleotide duplex, in conjunction with 2D NOE data. It has been found that the conformational parameters of the double helix and the orientation of the DAU chromophore in the intercalated complexes depend on base sequence at the binding site of the tetramer duplexes in aqueous solution.
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Affiliation(s)
- D B Davies
- School of Biological and Chemical Sciences, Birkbeck College, University of London, UK.
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5
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Veselkov AN, Eaton RJ, Baranovskii SF, Osetrov SG, Bolotin PA, Djimant LN, Pahomov VI, Davies DB. Complexation of the antibiotic daunomycin with desoxytetraribonucleoside triphosphate 5’-d(CpGpCpG) in aqueous solution. J STRUCT CHEM+ 1999. [DOI: 10.1007/bf02903651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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6
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Taylor ER, Wiechelman K. Polarized Intercalation Site in Z-DNA. Supramol Chem 1998. [DOI: 10.1080/10610279808034965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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7
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Chen YZ, Prohofsky EW. Premelting base pair opening probability and drug binding constant of a daunomycin-poly d(GCAT).poly d(ATGC) complex. Biophys J 1994; 66:820-6. [PMID: 8011914 PMCID: PMC1275780 DOI: 10.1016/s0006-3495(94)80858-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
We calculate room temperature thermal fluctuational base pair opening probability of a daunomycin-poly d(GCAT).poly d(ATGC) complex. This system is constructed at an atomic level of detail based on x-ray analysis of a crystal structure. The base pair opening probabilities are calculated from a modified self-consistent phonon approach of anharmonic lattice dynamics theory. We find that daunomycin binding substantially enhances the thermal stability of one of the base pairs adjacent the drug because of strong hydrogen bonding between the drug and the base. The possible effect of this enhanced stability on the drug inhibition of DNA transcription and replication is discussed. We also calculate the probability of drug dissociation from the helix based on the selfconsistent calculation of the probability of the disruption of drug-base H-bonds and the unstacking probability of the drug. The calculations can be used to determine the equilibrium drug binding constant which is found to be in good agreement with observations on similar daunomycin-DNA systems.
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Affiliation(s)
- Y Z Chen
- Department of Physics, Purdue University, West Lafayette, Indiana 47907-1396
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8
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Pal MK, Yadav RC. Circular Dichroic Probe of the Competition for Drug and Dye Between Anionic Polymers DNA and Heparin. I. JOURNAL OF MACROMOLECULAR SCIENCE PART A-PURE AND APPLIED CHEMISTRY 1992. [DOI: 10.1080/10601329208054140] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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9
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Hammer BC, Russell RA, Warrener RN, Collins JG. A 19F-NMR study of 3-fluoro-4-demethoxydaunomycin intercalation complexes with the hexanucleotide d(CTGCAG)2. EUROPEAN JOURNAL OF BIOCHEMISTRY 1990; 191:307-13. [PMID: 2384081 DOI: 10.1111/j.1432-1033.1990.tb19124.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Equilibrium systems containing intercalation complexes formed between the novel anthracycline drug, 3-fluoro-4-demethoxydaunomycin (3FD), and the hexanucleotide duplex d(CTGCAG)2 have been studied by 19F-NMR spectroscopy. Solutions containing a 1:1 molar ratio of 3FD/d(CTGCAG)2 gave four 19F signals which have been assigned to each of four possible intercalation isomers for the 1:1 3FD.d(CTGCAG)2 complex, which we denote by [d(CTGCAG)2][3FD]; these were where 3FD bound between the 5'-CT-3', 5'-TG-3', 5'-GC-3' or 5'-CA-3' base sequences, with the drug sugar moiety lying in the minor groove and pointed in the 3' direction in each case. Changes in temperature and NaCl concentration affecting the equilibrium distribution of these isomers were studied and indicated that no overriding binding site preference prevailed under standard biochemical conditions. Formation of some of the 2:1 3FD.d(CTGCAG)2 complex occurred when a solution of [d(CTGCAG)2][3FD] was exposed to excess 3FD; however, this complex was unstable to gel filtration and no co-operative binding of the second 3FD molecule was observed.
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Affiliation(s)
- B C Hammer
- Department of Chemistry, University of New South Wales, Australian Defence Force Academy, Canberra
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10
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Phillips DR, Cullinane C, Trist H, White RJ. In Vitro Transcription Analysis of the Sequence Specificity of Reversible and Irreversible Complexes of Adriamycin with DNA. THE JERUSALEM SYMPOSIA ON QUANTUM CHEMISTRY AND BIOCHEMISTRY 1990. [DOI: 10.1007/978-94-011-3728-7_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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11
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Bonnett M, Taylor ER. The structure of the aflatoxin B1-DNA adduct at N7 of guanine. Theoretical intercalation and covalent adduct models. J Biomol Struct Dyn 1989; 7:127-49. [PMID: 2510767 DOI: 10.1080/07391102.1989.10507756] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Two theoretical models are proposed for the conformational structure of both intercalated and covalent adduct complexes of aflatoxin B1, designated AFB1, with N7 of guanine of DNA. The covalent adduct model requires the DNA to kink a minimum of 39 degrees about the covalent site of the C8 and N7 atoms comprising the bond of the covalent complex. The preference of AFB1 for specific G bases within a sequence of GC content followed that of experimental studies with the added feature that for binding to the third G base of a tetramer sequence from the 3'-end, the AFB1 displayed enhanced binding at the 3' site of the targeted guanosine. Binding of AFB1 to the second G base of a tetramer sequence from the 3'-end leads to preference for a 5' site of the targeted guanosine. Inhibition of AFB1's interaction with the targeted DNA in the presence of intercalated ethidium bromide is explained by these proposed models.
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Affiliation(s)
- M Bonnett
- Department of Chemistry, University of Southwestern Louisiana, Lafayette 70504-4370
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12
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Trist H, Phillips DR. In vitro transcription analysis of the role of flanking sequence on the DNA sequence specificity of adriamycin. Nucleic Acids Res 1989; 17:3673-88. [PMID: 2660099 PMCID: PMC317849 DOI: 10.1093/nar/17.10.3673] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
An in vitro transcription assay has been used to define twelve high occupancy transcriptional blockage sites in 260 bp of heterogenous DNA on three promoter-containing DNA fragments. Transcription proceeded to immediately upstream of CpA sequences in nine of these sites, and this defines the most preferred intercalation site as CpA. In almost all cases, this sequence was flanked by T on the 5' end. The consensus sequence for the highest affinity Adriamycin site is therefore 5'-TCA, with some evidence for preference of AT base pairs flanking both ends of this trinucleotide [i.e., (t)TCA(a.t)(a.t)]. In contrast, lower occupancy CpA sites were flanked on the 5' end by a GC base pair, with a preference for up to three GC base pairs on the 3' end. The low affinity consensus sequence is therefore (G.C)CA(g.c)(g.c)(g.c).
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Affiliation(s)
- H Trist
- Department of Biochemistry, La Trobe University, Victoria, Australia
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13
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Hammer BC, Russell RA, Warrener RN, Collins JG. Effects of solute conditions on the relative affinities of the oligonucleotides d(G-C)5 and d(A-T)5 for the anthracycline drug 2-fluoro-4-demethoxydaunomycin. FEBS Lett 1989; 244:227-30. [PMID: 2494065 DOI: 10.1016/0014-5793(89)81198-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
19F NMR has been used to show that changes in NaCl concentration, as well as the presence of lysine or arginine, affect the equilibrium distribution of the synthetic anthracycline 2-fluoro-4-demethoxydaunomycin (2FD) between binding sites on d(G-C)5 and d(A-T)5 in a 1:1:1 molar aqueous system: 2FD/d(G-C)5/d(A-T)5. Varying the pH between 6.2 and 7.7 had no effect. NaCl concentrations below 0.1 M led to a d(G-C)5 preference while above 0.1 M a preference for d(A-T)5 was observed. At comparable solute concentrations, use of either lysine or arginine resulted in a significant drug preference for d(G-C)5 compared to systems containing only NaCl.
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Affiliation(s)
- B C Hammer
- Department of Chemistry, University College, University of New South Wales, ACT, Australia
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14
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Hammer BC, Russell RA, Warrener RN, Collins JG. A 19F-NMR study of 2-fluoro-4-demethoxydaunomycin intercalation complexes with the decanucleotides d(G-C)5 and d(A-T)5. EUROPEAN JOURNAL OF BIOCHEMISTRY 1989; 178:683-8. [PMID: 2912727 DOI: 10.1111/j.1432-1033.1989.tb14498.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Binding configurations and equilibria of intercalation complexes formed by the novel anthracycline drug, 2-fluoro-4-demethoxydaunomycin (2FD), with the decanucleotides d(G-C)5 and d(A-T)5 have been studied by 19F-NMR spectroscopy. The 19F chemical shift of 2FD bound to d(A-T)5 was approximately 1.5 ppm downfield of that observed for 2FD bound to d(G-C)5. By mixing equimolar amounts of aqueous d(G-C)5, d(A-T)5 and 2FD, the distribution of drug between the nucleotides was followed by observing relative peak intensities and showed no G-C or A-T binding preference at room temperature. It was shown that each decanucleotide duplex bound three 2FD molecules, giving a neighbour exclusion parameter, n, of n = 3 for this drug. The stoichiometric complexes, which we denote by [d(A-T)5][2FD]3 and [d(G-C)5][2FD]3, were also purified and isolated in this study.
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Affiliation(s)
- B C Hammer
- Department of Chemistry, University College, University of New South Wales, Canberra, Australia
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15
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Molecular Mechanisms of Specificity in DNA–Antitumour Drug Interactions. ACTA ACUST UNITED AC 1989. [DOI: 10.1016/b978-0-12-013318-5.50005-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
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16
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Abstract
The DNA-sequence specificity of daunomycin was investigated by DNase I footprinting and an E. coli RNA polymerase transcription-inhibition assay. The 5'-CA sequence was identified as being the highest affinity binding site, although other modest affinity (5'-GC, CG, CT, TC, AC) and poor affinity sites (5'-AA, AT, TA) were also observed. The preference of daunomycin for 5'-CA nucleotide sequence suggests that its biological activity may arise from association with the 5'-CA-containing sequences thought to be associated with genetic regulatory elements in eukaryotes.
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Affiliation(s)
- A Skorobogaty
- Department of Chemistry, La Trobe University, Bundoora, Victoria, Australia
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17
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Chaires JB, Fox KR, Herrera JE, Britt M, Waring MJ. Site and sequence specificity of the daunomycin-DNA interaction. Biochemistry 1987; 26:8227-36. [PMID: 2831939 DOI: 10.1021/bi00399a031] [Citation(s) in RCA: 132] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The site and sequence specificity of the daunomycin-DNA interaction was examined by equilibrium binding methods, by deoxyribonuclease I footprinting studies, and by examination of the effect of the antibiotic on the cleavage of linearized pBR322 DNA by restriction endonucleases PvuI and EcoRI. These three experimental approaches provide mutually consistent results showing that daunomycin indeed recognizes specific sites along the DNA lattice. The affinity of daunomycin toward natural DNA increases with increasing GC content. The quantitative results are most readily explained by binding models in which daunomycin interacts with sites containing two adjacent GC base pairs, possibly occurring as part of a triplet recognition sequence. Deoxyribonuclease I footprinting studies utilizing the 160 base pair (bp) tyrT DNA fragment and 61 and 53 bp restriction fragments isolated from pBR322 DNA further define the sequence specificity of daunomycin binding. Specific, reproducible protection patterns were obtained for each DNA fragment at 4 degrees C. Seven protected sequences, ranging in size from 4 to 14 bp, were identified within the tyrT fragment. Relative to the overall tyrT sequence, these protected sequences were GC rich and contained a more limited and distinct distribution of di- and trinucleotides. Within all of the protected sequences, a triplet containing adjacent GC base pairs flanked by an AT base pair could be found in one or more copies. Nowhere in the tyrT fragment did that triplet occur outside a protected sequence. The same triplet occurred within seven out of nine protected sequences observed in the fragments isolated from pBR322 DNA. In the two remaining cases, three contiguous GC base pairs were found. We conclude that the preferred daunomycin triplet binding site contains adjacent GC base pairs, of variable sequence, flanked by an AT base pair. This conclusion is consistent with the results of a recent theoretical study of daunomycin sequence specificity [Chen, K.-X., Gresh, N., & Pullman, B. (1985) J. Biomol. Struct. Dyn. 3, 445-466]. Adriamycin and the beta-anomer of adriamycin produce the same qualitative pattern of protection as daunomycin with the tyrT fragment. Daunomycin inhibits the rate of digestion of pBR322 DNA by PvuI (recognition sequence 5'-CGATCG-3') to a greater extent than it does EcoRI (recognition sequence 5'-GAATTC-3'), a finding consistent with the conclusions derived from our footprinting studies. Our results, as a whole, are the clearest indication to date that daunomycin recognizes a specific DNA sequence as a preferred binding site.
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Affiliation(s)
- J B Chaires
- Department of Biochemistry, University of Mississippi Medical Center, Jackson 39216-4505
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18
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Delepierre M, Delbarre A, Langlois d'Estaintot B, Igolen J, Roques BP. 1H-NMR studies of a monointercalating drug into a d[CpGpCpG]2 minihelix. Biopolymers 1987; 26:981-1000. [PMID: 3620581 DOI: 10.1002/bip.360260702] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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19
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Chen KX, Gresh N, Pullman B. A theoretical investigation on the sequence selective binding of mitoxantrone to double-stranded tetranucleotides. Nucleic Acids Res 1986; 14:3799-812. [PMID: 3714497 PMCID: PMC339816 DOI: 10.1093/nar/14.9.3799] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Theoretical computations are performed on the comparative binding energetics of mitoxantrone (MX), a newly synthesized intercalating anthraquinone antitumor drug, to six representative double-stranded tetranucleotides: d(GCGC)2, d(CGCG)2, d(ATAT)2, d(TATA)2, d(GTGT), d(ACAC), and d(CCGG)2. The computations are performed with the SIBFA procedure, which uses empirical formulas based on ab initio SCF computations. The best binding configuration of mitoxantrone locates its two side chains in the major groove. A considerable preference is elicited for intercalation of the chromophore ring in a pyrimidine (3'-5') purine sequence rather than the isomeric purine (3'-5') pyrimidine sequence. Contrary to the situation encountered with "simple" intercalators, in which this preference is generally attributed solely to differences in the energies of unstacking necessary to generate the intercalation sites, the preference is dictated in MX to a large extent by the intermolecular interaction energy term. This result is imposed by the interactions of the side chains of MX with the oligonucleotide.
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20
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Chen KS, Gresh N, Pullman B. A theoretical investigation on the sequence selective binding of adriamycin to double-stranded polynucleotides. Nucleic Acids Res 1986; 14:2251-67. [PMID: 3960721 PMCID: PMC339656 DOI: 10.1093/nar/14.5.2251] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Theoretical computations are performed on the structural and energetical factors involved in the sequence selective binding of adriamycin (ADM) to five self-complementary double-stranded hexanucleotides. Among the two regularly alternating hexanucleotides d (TATATA)2 and d (CGCGCG)2, a stronger binding is predicted for the former. The strongest complex is computed, however, for the mixed hexanucleotide d (CGTACG)2, containing the intercalation site between two CG base pairs and an adjacent TA base pair. The overall sequence preference is the result of an intricate interplay of sequence preferences of the constituents in particular of daunosamine and the 9-OH substituent. Altogether, the selective base pair recognition by adriamycin cannot be defined in terms of the two base pairs implicated in the intercalation site alone but must be expressed in terms of a triplet of base pairs.
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21
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Chen KX, Gresh N, Pullman B. A theoretical investigation on the sequence selective binding of daunomycin to double-stranded polynucleotides. J Biomol Struct Dyn 1985; 3:445-66. [PMID: 3917031 DOI: 10.1080/07391102.1985.10508434] [Citation(s) in RCA: 73] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Theoretical computations are performed on the structural and energetical factors involved in the sequence selective binding of daunomycin (DNM) to six representative self-complementary double-stranded hexanucleotides: d(CGTACG)2,d(CGATCG)2,d(CITACI)2, d(TATATA)2, d(CGCGCG)2 and d(TACGTA)2. The conformational angles of the hexanucleotides are fixed in values found in the representative crystal structure of the d(CGTACG)2-DNM complex. The intermolecular DNM-hexanucleotide interaction energies and the conformational energy changes of DNM upon binding are computed and optimized in the framework of the SIBFA procedure, which uses empirical formulas based on ab initio SCF computations. Among the two regularly alternating hexanucleotides, d(TATATA)2 and d(CGCGCG)2, a stronger binding is predicted for the former, in agreement with experimental results obtained with poly(dA-dT).poly(dA-dT) and poly(dG-dC).poly(dG-dC). Altogether, however, among the six investigated sequences, the strongest complexes are computed for the mixed hexanucleotides d(CGATCG)2 and d(CGTACG)2, containing the intercalation site between two CG base pairs and an adjacent TA base pair. This situation may be related to the increased affinity of DNM for GC rich DNA's and to the situation in the crystal structure of the DNM-d(CGTACG)2 complex. Analysis of the intrinsic base sequence preferences expressed by the individual constituents of DNM, namely the daunosamine side chain, the chromophore ring and its two 9-hydroxyl and 9-acetoxy substituents, reveals that the overall sequence preference found is the result of a rather intricate interplay of intrinsic sequence preferences, in particular at the level of daunosamine and the 9-hydroxyl substituent.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- K X Chen
- Institut de Biologie Physico-Chimique, CNRS, Paris, France
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22
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Kelly JM, Tossi AB, McConnell DJ, OhUigin C. A study of the interactions of some polypyridylruthenium (II) complexes with DNA using fluorescence spectroscopy, topoisomerisation and thermal denaturation. Nucleic Acids Res 1985; 13:6017-34. [PMID: 4047939 PMCID: PMC321935 DOI: 10.1093/nar/13.17.6017] [Citation(s) in RCA: 756] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The nature of binding of Ru(phen) 2+ (I), Ru(bipy) 2+ (II), Ru(terpy) 2+ (III) (phen = 1,10-phenanthroline, bipy 3 = 2,2'-bipyridyl, 3 terpy = 2,2'2," - 2 terpyridyl) to DNA, poly[d(G-C)] and poly[d(A-T)] has been compared by absorption, fluorescence, DNA melting and DNA unwinding techniques. I binds intercalatively to DNA in low ionic strength solutions. Topoisomerisation shows that it unwinds DNA by 22 degrees +/- 1 per residue and that it thermally stabilizes poly[d(A-T)] in a manner closely resembling ethidium. Poly[d(A-T)] induces greater spectral changes on I than poly[d(G-C)] and a preference for A-T rich regions is indicated. I binding is very sensitive to Mg2+ concentration. In contrast to I the binding of II and III appears to be mainly electrostatic in nature, and causes no unwinding. There is no evidence for the binding of the neutral Ru(phen)2 (CN)2 or Ru(bipy)2 (CN)2 complexes. DNA is cleaved, upon visible irradiation of aerated solutions, in the presence of either I or II.
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Miller KJ, Lauer M, Caloccia W. Interactions of molecules with nucleic acids. XII. Theoretical model for the interaction of a fragment of bleomycin with DNA. Biopolymers 1985; 24:913-34. [PMID: 2411305 DOI: 10.1002/bip.360240602] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Miller KJ, Rein FH, Taylor ER, Kowalczyk PJ. Generation of nucleic acid structures and binding of molecules to DNA. Ann N Y Acad Sci 1985; 439:64-80. [PMID: 3890663 DOI: 10.1111/j.1749-6632.1985.tb25789.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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