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Estalayo-Adrián S, Blasco S, Bright SA, McManus GJ, Orellana G, Williams DC, Kelly JM, Gunnlaugsson T. Effect of Alkyl Chain Length on the Photophysical, Photochemical, and Photobiological Properties of Ruthenium(II) Polypyridyl Complexes for Their Application as DNA-Targeting, Cellular-Imaging, and Light-Activated Therapeutic Agents. ACS APPLIED BIO MATERIALS 2021; 4:6664-6681. [PMID: 35006970 DOI: 10.1021/acsabm.1c00284] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A family of six Ru(II) polypyridyl complexes (1-6) which contain phenanthroline-based ligands functionalized with alkyl chains of different lengths (one methyl group, 10 and 21 carbon alkyl chains) and either 1,10-phenanthroline (phen) or 1,4,5,8-tetraazaphenanthrene (TAP) as ancillary ligands have been synthesized and characterized. The influence of the alkyl chain length on their photophysical and photochemical properties as well as in their photobiological applications has been elucidated by monitoring the changes in their MLCT-centered absorption and emission bands. The presence of one methyl group or 10 carbon alkyl chains does not seem to significantly affect the photophysical and photochemical properties of the resulting Ru(II) complexes when compared to the well-known [Ru(phen)3]2+ and [Ru(TAP)2phen]2+. However, an effect on their emission properties and in their ability to photosensitize singlet oxygen is observed for the Ru(II) complexes containing 21 carbon alkyl chains. The binding of these complexes to salmon testes DNA (stDNA) was investigated by observing the changes in the photophysical properties. Complexes 1, 2, 4, and 5 all showed changes in their MLCT bands that could be analyzed using conventional fitting methods, such as the Bard equation. In contrast, complexes 3 and 6, possessing long aliphatic chains, gave rise to nonclassic behavior. In addition to these analyses, both thermal denaturation and circular dichroism studies of 1-6 were carried out in the presence of stDNA which confirmed that these complexes bind to DNA. Confocal microscopy and viability studies in HeLa cervical cancer cells reveal an alkyl chain-length dependence on the cellular uptake and cytotoxicity of the resulting Ru(II) complexes due to an enhancement of their lipophilicity with increasing alkyl chain length. Thus, complexes containing 10 and 21 carbon alkyl chains are rapidly taken up into HeLa cells and, in particular, those with 21 carbon alkyl chains show a significant phototoxicity against the same cell line. Therefore, this study provides further insight into the possible modulation of the photophysical, photochemical, and photobiological properties of Ru(II) polypyridyl complexes by varying the length of the alkyl chains attached to the polypyridyl ligands coordinated to the Ru(II) center and the nature of the auxiliary groups, which we show has a significant effect on photophysical and biological properties.
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Affiliation(s)
- Sandra Estalayo-Adrián
- School of Chemistry and Trinity Biomedical Sciences Institute (TBSI), Trinity College Dublin, The University of Dublin, Dublin 2, Ireland.,Advanced Materials and BioEngineering Research (AMBER) Centre, Trinity College Dublin, The University of Dublin, Dublin 2, Ireland
| | - Salvador Blasco
- School of Chemistry and Trinity Biomedical Sciences Institute (TBSI), Trinity College Dublin, The University of Dublin, Dublin 2, Ireland
| | - Sandra A Bright
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute (TBSI), Trinity College Dublin, The University of Dublin, Dublin 2, Ireland
| | - Gavin J McManus
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute (TBSI), Trinity College Dublin, The University of Dublin, Dublin 2, Ireland
| | - Guillermo Orellana
- Department of Organic Chemistry, Faculty of Chemistry, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - D Clive Williams
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute (TBSI), Trinity College Dublin, The University of Dublin, Dublin 2, Ireland
| | - John M Kelly
- School of Chemistry and Trinity Biomedical Sciences Institute (TBSI), Trinity College Dublin, The University of Dublin, Dublin 2, Ireland
| | - Thorfinnur Gunnlaugsson
- School of Chemistry and Trinity Biomedical Sciences Institute (TBSI), Trinity College Dublin, The University of Dublin, Dublin 2, Ireland.,Advanced Materials and BioEngineering Research (AMBER) Centre, Trinity College Dublin, The University of Dublin, Dublin 2, Ireland
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Khalid S, Rodger P. Molecular Dynamics Simulations of Dna and Its Complexes. PROGRESS IN REACTION KINETICS AND MECHANISM 2019. [DOI: 10.3184/007967404777726232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
This article describes how classical molecular simulation methods are being used to gain a molecular-level understanding of the interaction mechanisms responsible for DNA–ligand recognition, and that govern the response of DNA to ligand binding. Case studies using a variety of different ligands—including small pharmaceutical drugs, proteins and lipids—are used to illustrate the power of modern molecular dynamics simulation methods for understanding how we may control the function and structure of DNA.
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Affiliation(s)
- Syma Khalid
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
- Current address: Laboratory of Molecular Biophysics, University of Oxford, South Parks Rd, Oxford, OX1 3QU, UK
| | - P.Mark Rodger
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
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Kore PP, Mutha MM, Antre RV, Oswal RJ, Kshirsagar SS. Computer-Aided Drug Design: An Innovative Tool for Modeling. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/ojmc.2012.24017] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Liu YI, Liu YJ, Yao JH, Mei WJ, Wu FH. Effect of substituents on DNA-binding behaviors of ruthenium(II) complexes: [Ru(dmb)2(dtmi)]2+ and [Ru(dmb)2(dtni)]2+. J COORD CHEM 2009. [DOI: 10.1080/00958970802649984] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- YI Liu
- a School of Pharmacy, Guangdong Pharmaceutical University , Guangzhou, P.R. China
| | - Yun-Jun Liu
- a School of Pharmacy, Guangdong Pharmaceutical University , Guangzhou, P.R. China
| | - Jun-Hua Yao
- b Instrumentation Analysis and Research Center, Sun Yat-Sen University , Guangzhou, P.R. China
| | - Wen-Jie Mei
- a School of Pharmacy, Guangdong Pharmaceutical University , Guangzhou, P.R. China
| | - Fu-Hai Wu
- c School of Public Health, Guangdong Pharmaceutical University , Guangzhou, P.R. China
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Urathamakul T, Waller DJ, Beck JL, Aldrich-Wright JR, Ralph SF. Comparison of Mass Spectrometry and Other Techniques for Probing Interactions Between Metal Complexes and DNA. Inorg Chem 2008; 47:6621-32. [DOI: 10.1021/ic702179a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thitima Urathamakul
- Department of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, 2522, Australia, and University of Western Sydney, School of Biomedical and Health Sciences, Locked Bag 1797, Penrith, NSW 1797 Australia
| | - Daniel J. Waller
- Department of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, 2522, Australia, and University of Western Sydney, School of Biomedical and Health Sciences, Locked Bag 1797, Penrith, NSW 1797 Australia
| | - Jennifer L. Beck
- Department of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, 2522, Australia, and University of Western Sydney, School of Biomedical and Health Sciences, Locked Bag 1797, Penrith, NSW 1797 Australia
| | - Janice R. Aldrich-Wright
- Department of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, 2522, Australia, and University of Western Sydney, School of Biomedical and Health Sciences, Locked Bag 1797, Penrith, NSW 1797 Australia
| | - Stephen F. Ralph
- Department of Chemistry, University of Wollongong, Northfields Avenue, Wollongong, 2522, Australia, and University of Western Sydney, School of Biomedical and Health Sciences, Locked Bag 1797, Penrith, NSW 1797 Australia
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Khalid S, Hannon MJ, Rodger A, Rodger PM. Simulations of DNA Coiling around a Synthetic Supramolecular Cylinder That Binds in the DNA Major Groove. Chemistry 2006; 12:3493-506. [PMID: 16496427 DOI: 10.1002/chem.200501168] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In this work we present the results of a molecular simulation study of the interaction between a tetracationic bis iron(II) supramolecular cylinder, [Fe2(C25H20N4)3]4+, and DNA. This supramolecular cylinder has been shown to bind in the major groove of DNA and to induce dramatic coiling of the DNA. The simulations have been designed to elucidate the interactions that lead the cylinder to target the major groove and that drive the subsequent DNA conformational changes. Three sets of multi-nanosecond simulations have been performed: one of the uncomplexed d(CCCCCTTTTTCC) d(GGAAAAAGGGGG) dodecamer; one of this DNA complexed with the cylinder molecule; and one of this DNA complexed with a neutralised version of the cylinder. Coiling of the DNA was observed in the DNA-cylinder simulations, giving insight into the molecular level nature of the supramolecular coiling observed experimentally. The cylinder charge was found not to be essential for the DNA coiling, which implies that the DNA response is moderated by the short range interactions that define the molecular shape. Cylinder charge did, however, affect the integrity of the DNA duplex, to the extent that, under some circumstances, the tetracationic cylinder induced defects in the DNA base pairing at locations adjacent to the cylinder binding site.
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Affiliation(s)
- Syma Khalid
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
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Liu F, Wang K, Bai G, Zhang Y, Gao L. The pH-Induced Emission Switching and Interesting DNA-Binding Properties of a Novel Dinuclear Ruthenium(II) Complex. Inorg Chem 2004; 43:1799-806. [PMID: 14989674 DOI: 10.1021/ic035109x] [Citation(s) in RCA: 133] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A novel dinuclear Ru(II) complex, [(bpy)(2)Ru(ebipcH(2))Ru(bpy)(2)](ClO(4))(4), where bpy = 2,2'-bipyridine and ebipcH(2) = N-ethyl-4,7-bis([1,10]-phenanthroline[5,6-f]imidazol-2-yl)carbazole, has been newly synthesized. The pH effects on UV-vis absorption and emission spectra of the complex are studied, and ground- and excited-state ionization constants of the complex are derived. The binding of the complex to calf thymus (ct) DNA is investigated with absorption and luminescence titrations, steady-state emission quenching, and viscosity measurements. The complex acts as a pH-induced "on-off" emission switch between pH 8.0 and pH 10.0 with a maximum on-off ratio of approximately 100 which is favorably compared with the other imidazole-containing Ru(II) complex congeners, and a strong ct-DNA intercalator with an intrinsic binding constant of 1.31(+/-0.08) x 10(6) M(-)(1) in buffered 50 mM NaCl.
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Affiliation(s)
- Furong Liu
- Department of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
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HOWARD BRIANJ, GRANT GUYH. (William) Graham Richards. Mol Phys 2003. [DOI: 10.1080/00268970310001605741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Xiong Y, Ji LN. Synthesis, DNA-binding and DNA-mediated luminescence quenching of Ru(II) polypyridine complexes. Coord Chem Rev 1999. [DOI: 10.1016/s0010-8545(99)00019-3] [Citation(s) in RCA: 188] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Mesmaeker AKD, Lecomte JP, Kelly JM. Photoreactions of metal complexes with DNA, especially those involving a primary photo-electron transfer. ELECTRON TRANSFER II 1996. [DOI: 10.1007/3-540-60110-4_2] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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11
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Blaskó A, Browne KA, Bruice TC. NMR structure of d(CGCA3T3GCG)2:tren-microgonotropen-b:Zn(II) complex and solution studies of metal ion complexes of tren-microgonotropen-b interacting with DNA. Bioorg Med Chem 1995; 3:631-46. [PMID: 7582942 DOI: 10.1016/0968-0896(95)00051-h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The solution structure of a 1:1 complex of zinc tren-microgonotropen-b [6b:Zn(II)] with d(CGCAAATTTGCG)2 has been determined by 2D nuclear Overhauser effect 1H NMR spectroscopy and restrained molecular modeling. The exchangeable and nonexchangeable proton resonances of d(CGCA3T3GCG)2:6b:Zn(II) indicate that the Zn(II) is interacting in the A+T-rich region of the dsDNA and the tren region of 6b, while 31P NMR shows interaction of the Zn(II) with the phosphate backbone. Proton chemical shift differences between d(CGCA3T3GCG)2:6b:Zn(II) and d(CGCA3T3GCG)2:6b are in agreement with the polyamino substituent of 6b [-(CH2)4N(CH2CH2)N-(CH2CH2NH2)2] forming a four-coordinated Zn(II) complex similar to that found in the X-ray structure of 'tren-chloride':Zn(II). The P9 and P10 phosphate oxygens that are held by hydrogen bonding to the tren substituent of 6b in the DNA:6b complex become ligands to the tren-complexed Zn(II) in DNA:6b:Zn(II). To do so there is a 2 A decrease in the adjacent phosphate-to-phosphate distance at the Zn(II) binding site. This motion brings about an increased bend of 14.6 degrees in the helical axis of d(CGCA3T3GCG)2:6b:Zn(II) compared to that found in d(CGCA3T3GCG)2:6b. Single stranded cleavage of linear DNA fragments was not observed in the presence of 6b and Fe(II), Co(II), Ni(II), Cu(II), Zn(II), La(III) or Ce(III); this is likely due to the metal ion being sequestered as in the structure of d(CGCA3T3GCG)2:6b:Zn(II) complex. Supercoiled DNA was susceptible to cleavage by 6b:Cu(II) in the presence of O2 and a reducing agent.
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Affiliation(s)
- A Blaskó
- Department of Chemistry, University of California, Santa Barbara 93106, USA
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Sanghani SR, Elcock AH, Haworth IS. SUBCUR: visualization of structural differences between DNA duplexes. JOURNAL OF MOLECULAR GRAPHICS 1993; 11:211-3. [PMID: 8110667 DOI: 10.1016/0263-7855(93)80075-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A computer program, SUBCUR, is described which permits analysis and rapid identification of geometrical differences and patterns of variance between two DNA duplexes. The program is compatible with the CURVES 3.1 package and allows graphical visualization of the structural differences. Examples are provided which illustrate the applicability of the program in analyzing the different backbone conformations of two helices and the different curvatures of two helices.
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Affiliation(s)
- S R Sanghani
- Physical Chemistry Laboratory, Oxford University, UK
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