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Doan PH, Pitter DRG, Kocher A, Wilson JN, Goodson T. Two-Photon Spectroscopy as a New Sensitive Method for Determining the DNA Binding Mode of Fluorescent Nuclear Dyes. J Am Chem Soc 2015; 137:9198-201. [DOI: 10.1021/jacs.5b02674] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Phi H. Doan
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Demar R. G. Pitter
- Department
of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Andrea Kocher
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - James N. Wilson
- Department
of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Theodore Goodson
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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9
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Streltsov SA, Gromyko AV, Oleinikov VA, Zhuze AL. The Hoechst 33258 covalent dimer covers a total turn of the double-stranded DNA. J Biomol Struct Dyn 2007; 24:285-302. [PMID: 17054387 DOI: 10.1080/07391102.2006.10507121] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
With the goal to design ligands recognizing extended regions on dsDNA, a covalent dimer of the fluorescent dye Hoechst 33258 [bis-HT(NMe)] composed of two dye molecules linked via the phenol oxygen atoms with a (CH2)3-N+ H(CH3)-(CH2)3 fragment was constructed using computer modeling and then synthesized. Its interactions with the double-stranded DNA (dsDNA) were studied by fluorescent and UV-Vis spectroscopy and circular (CD) and linear dichroism (LD). Based on variations in the affinity to the dsDNA, it was shown that complexes of three types are formed. The first type complexes result from binding of a bis-HT(NMe) monomer in the open conformation; in this case the ligand covers the total dsDNA turn and is located in the minor groove according to the positive value of CD at 370 nm. In addition, the ability to form bis-HT(NMe)-bridges between two dsDNA molecules, i.e., each of the two bis-HT(NMe) ends binds to two different dsDNA molecules, was demonstrated for the first type complexes. Spectral characteristics (maximal absorption at 362 nm, positive sign, and maximal value of CD at 370 nm) of the first type complexes conform to those of the specific Hoechst 33258 complex with poly[d(A-T)] x poly[d(A-T]. The second type complexes correspond to the bis-HT(NMe) sandwich (as an inter- or intramolecular) binding to dsDNA with stoichiometry > or = 5 bp. Thereby, a negative LD at 360 nm and the location of bis-HT(NMe) sandwiches in the minor groove of B form dsDNA seems contradictory. Spectral characteristics (maximal positive CD at 345 nm, a dramatic decrease in fluorescence intensity and the shift of its maximum to 490 nm) of these complexes favor a suggestion that this binding correlates to the formation of nonspecific dimeric Hoechst 33258 complex with dsDNA. The third type complexes are characterized by stoichiometry of one bis-HT(NMe) molecule per approximately 2 bp and the tendency to zero of LD values at 270 and 360 nm. We assume that in these complexes bis-HT(NMe) sandwich dimers are formed on dsDNA. The complexes of this type conform to the aggregation type complex of Hoechst 33258 with dsDNA. The ability of bis-HT(NMe) to cover the whole dsDNA turn or form bridges with two dsDNA upon the formation of the first type complexes essentially distinguishes it from Hoechst 33258, which can only occupy 5 bp and does not form such bridges. This specific property of bis-HT(NMe) may support new biological activities.
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Affiliation(s)
- S A Streltsov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, Moscow 119991, Russia.
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10
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Bocian W, Kawecki R, Bednarek E, Sitkowski J, Pietrzyk A, Williamson MP, Hansen PE, Kozerski L. Multiple binding modes of the camptothecin family to DNA oligomers. Chemistry 2006; 10:5776-87. [PMID: 15472946 DOI: 10.1002/chem.200305624] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The binding constants of camptothecin, topotecan and its lactone ring-opened carboxylate derivative to DNA octamers were measured by UV and NMR spectroscopy. The self-association of topotecan (TPT) was also measured. The carboxylate form of TPT binds in the same way as the lactone, but more weakly. Titration of TPT into d(GCGATCGC)2 shows a preferred location stacked onto the terminal G1 base. However, the intermolecular NOEs cannot be reconciled with a single conformation of the complex, and suggest a model of a limited number of conformations in fast exchange. MD calculations on four pairs of starting structures with TPT stacked onto the G1-C8 base pair in different orientations were therefore performed. The use of selected experimental "docking" restraints yielded ten MD trajectories covering a wide conformational space. From a combination of calculated free energies, NOEs and chemical shifts, some of the structures produced could be eliminated, and it is concluded that the data are consistent with two major families of conformations in fast exchange. One of these is the conformation found in a crystal of a TPT/DNA/topoisomerase I ternary complex [Proc. Natl. Acad. Sci. USA 2002, 99, 15 387-15 392].
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Affiliation(s)
- Wojciech Bocian
- National Institute of Public Health, 00-725 Warszawa, Chełmska 30/34, Poland
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12
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Streltsov S, Oleinikov V, Ermishov M, Mochalov K, Sukhanova A, Nechipurenko Y, Grokhovsky S, Zhuze A, Pluot M, Nabiev I. Interaction of clinically important human DNA topoisomerase I poison, topotecan, with double-stranded DNA. Biopolymers 2003; 72:442-54. [PMID: 14587067 DOI: 10.1002/bip.10479] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Topotecan (TPT), a water-soluble derivative of camptothecin, is a potent antitumor poison of human DNA topoisomerase I (top1) that stabilizes the cleavage complex between the enzyme and DNA. The role of the recently discovered TPT affinity to DNA remains to be defined. The aim of this work is to clarify the molecular mechanisms of the TPT-DNA interaction and to propose the models of TPT-DNA complexes in solution in the absence of top1. It is shown that TPT molecules form dimers with a dimerization constant of (4.0 +/- 0.7) x 10(3) M(-1) and the presence of DNA provokes more than a 400-fold increase of the effective dimerization constant. Flow linear dichroism spectroscopy accompanied by circular dichroism, fluorescence, and surface-enhanced Raman scattering experiments provide evidence that TPT dimers are able to bind DNA by bridging different DNA molecules or distant DNA structural domains. This effect may provoke modification of the intrinsic geometry of the cruciform DNA structures, leading to the appearance of new crossover points that serve as the sites of the top1 loading position. The data presume the hypothesis of TPT-mediated modulation of top1-DNA recognition before ternary complex formation.
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Affiliation(s)
- Sergei Streltsov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Ul. Vavilova 32, 119991 Moscow, Russia
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13
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Brezova V, Valko M, Breza M, Morris H, Telser J, Dvoranova D, Kaiserova K, Varecka L, Mazur M, Leibfritz D. Role of Radicals and Singlet Oxygen in Photoactivated DNA Cleavage by the Anticancer Drug Camptothecin: An Electron Paramagnetic Resonance Study. J Phys Chem B 2003. [DOI: 10.1021/jp027743m] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- V. Brezova
- School of Pharmacy and Chemistry, Liverpool John Moores University, Liverpool L3 3AF, United Kingdom, Faculty of Chemical and Food Technology, Slovak Technical University, SK-812 37 Bratislava, Slovakia, Department of Organic Chemistry 2/NW2, Bremen University, D-283 59 Bremen, Germany, and Chemistry Program, Roosevelt University, 430 South Michigan Avenue, Chicago, Illinois 60605
| | - M. Valko
- School of Pharmacy and Chemistry, Liverpool John Moores University, Liverpool L3 3AF, United Kingdom, Faculty of Chemical and Food Technology, Slovak Technical University, SK-812 37 Bratislava, Slovakia, Department of Organic Chemistry 2/NW2, Bremen University, D-283 59 Bremen, Germany, and Chemistry Program, Roosevelt University, 430 South Michigan Avenue, Chicago, Illinois 60605
| | - M. Breza
- School of Pharmacy and Chemistry, Liverpool John Moores University, Liverpool L3 3AF, United Kingdom, Faculty of Chemical and Food Technology, Slovak Technical University, SK-812 37 Bratislava, Slovakia, Department of Organic Chemistry 2/NW2, Bremen University, D-283 59 Bremen, Germany, and Chemistry Program, Roosevelt University, 430 South Michigan Avenue, Chicago, Illinois 60605
| | - H. Morris
- School of Pharmacy and Chemistry, Liverpool John Moores University, Liverpool L3 3AF, United Kingdom, Faculty of Chemical and Food Technology, Slovak Technical University, SK-812 37 Bratislava, Slovakia, Department of Organic Chemistry 2/NW2, Bremen University, D-283 59 Bremen, Germany, and Chemistry Program, Roosevelt University, 430 South Michigan Avenue, Chicago, Illinois 60605
| | - J. Telser
- School of Pharmacy and Chemistry, Liverpool John Moores University, Liverpool L3 3AF, United Kingdom, Faculty of Chemical and Food Technology, Slovak Technical University, SK-812 37 Bratislava, Slovakia, Department of Organic Chemistry 2/NW2, Bremen University, D-283 59 Bremen, Germany, and Chemistry Program, Roosevelt University, 430 South Michigan Avenue, Chicago, Illinois 60605
| | - D. Dvoranova
- School of Pharmacy and Chemistry, Liverpool John Moores University, Liverpool L3 3AF, United Kingdom, Faculty of Chemical and Food Technology, Slovak Technical University, SK-812 37 Bratislava, Slovakia, Department of Organic Chemistry 2/NW2, Bremen University, D-283 59 Bremen, Germany, and Chemistry Program, Roosevelt University, 430 South Michigan Avenue, Chicago, Illinois 60605
| | - K. Kaiserova
- School of Pharmacy and Chemistry, Liverpool John Moores University, Liverpool L3 3AF, United Kingdom, Faculty of Chemical and Food Technology, Slovak Technical University, SK-812 37 Bratislava, Slovakia, Department of Organic Chemistry 2/NW2, Bremen University, D-283 59 Bremen, Germany, and Chemistry Program, Roosevelt University, 430 South Michigan Avenue, Chicago, Illinois 60605
| | - L. Varecka
- School of Pharmacy and Chemistry, Liverpool John Moores University, Liverpool L3 3AF, United Kingdom, Faculty of Chemical and Food Technology, Slovak Technical University, SK-812 37 Bratislava, Slovakia, Department of Organic Chemistry 2/NW2, Bremen University, D-283 59 Bremen, Germany, and Chemistry Program, Roosevelt University, 430 South Michigan Avenue, Chicago, Illinois 60605
| | - M. Mazur
- School of Pharmacy and Chemistry, Liverpool John Moores University, Liverpool L3 3AF, United Kingdom, Faculty of Chemical and Food Technology, Slovak Technical University, SK-812 37 Bratislava, Slovakia, Department of Organic Chemistry 2/NW2, Bremen University, D-283 59 Bremen, Germany, and Chemistry Program, Roosevelt University, 430 South Michigan Avenue, Chicago, Illinois 60605
| | - D. Leibfritz
- School of Pharmacy and Chemistry, Liverpool John Moores University, Liverpool L3 3AF, United Kingdom, Faculty of Chemical and Food Technology, Slovak Technical University, SK-812 37 Bratislava, Slovakia, Department of Organic Chemistry 2/NW2, Bremen University, D-283 59 Bremen, Germany, and Chemistry Program, Roosevelt University, 430 South Michigan Avenue, Chicago, Illinois 60605
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