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Zhao X, Liu Y, Chen X, Mi Z, Li W, Wang P, Shan X, Lu X. Detection and Characterization of Single Cisplatin Adducts on DNA by Nanopore Sequencing. ACS OMEGA 2021; 6:17027-17034. [PMID: 34250360 PMCID: PMC8264939 DOI: 10.1021/acsomega.1c02106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/07/2021] [Indexed: 05/13/2023]
Abstract
Detection and characterization of an individual cisplatin adduct on a single DNA molecule is a demanding task. We explore the characteristic features of cisplatin adducts in the nanopore sequencing signal in aspects of dwell time, genome anchored current trace, and basecalling accuracy. The offset between the motor protein and the nanopore constriction region is revealed by dwell time analysis to be about 14 bases in the nanopore device as we examined. Characteristic distortions due to cisplatin adducts are illustrated in genome anchored current trace analysis, constituting the fingerprint for identification of cisplatin adduct. The sharp increase in odds ratio at the location of adducting sites provides additional feature in the detection of the adduct. By these combined methods, single cisplatin adducts can be detected with high fidelity on a single read of the DNA sequence. The study demonstrates an effective method in the detection and characterization of single cisplatin adducts on DNA at the single-molecule level and with single nucleotide spatial resolution.
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Affiliation(s)
- Xinjia Zhao
- Beijing
National Laboratory for Condensed-Matter Physics and Institute of
Physics, Chinese Academy of Sciences, Beijing 100190, China
- School
of Physical Sciences, University of Chinese
Academy of Sciences, Beijing 100190, China
| | - Yuru Liu
- Beijing
National Laboratory for Condensed-Matter Physics and Institute of
Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Xiaoyu Chen
- Beijing
National Laboratory for Condensed-Matter Physics and Institute of
Physics, Chinese Academy of Sciences, Beijing 100190, China
- School
of Physical Sciences, University of Chinese
Academy of Sciences, Beijing 100190, China
| | - Zhuang Mi
- Beijing
National Laboratory for Condensed-Matter Physics and Institute of
Physics, Chinese Academy of Sciences, Beijing 100190, China
- School
of Physical Sciences, University of Chinese
Academy of Sciences, Beijing 100190, China
| | - Wei Li
- Beijing
National Laboratory for Condensed-Matter Physics and Institute of
Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Pengye Wang
- Beijing
National Laboratory for Condensed-Matter Physics and Institute of
Physics, Chinese Academy of Sciences, Beijing 100190, China
- School
of Physical Sciences, University of Chinese
Academy of Sciences, Beijing 100190, China
- Songshan
Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Xinyan Shan
- Beijing
National Laboratory for Condensed-Matter Physics and Institute of
Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Xinghua Lu
- Beijing
National Laboratory for Condensed-Matter Physics and Institute of
Physics, Chinese Academy of Sciences, Beijing 100190, China
- School
of Physical Sciences, University of Chinese
Academy of Sciences, Beijing 100190, China
- Center
for Excellence in Topological Quantum Computation, Chinese Academy of Sciences, Beijing 100190, China
- Songshan
Lake Materials Laboratory, Dongguan, Guangdong 523808, China
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Sofińska K, Wilkosz N, Szymoński M, Lipiec E. Molecular Spectroscopic Markers of DNA Damage. Molecules 2020; 25:E561. [PMID: 32012927 PMCID: PMC7037412 DOI: 10.3390/molecules25030561] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 01/20/2020] [Accepted: 01/20/2020] [Indexed: 12/12/2022] Open
Abstract
Every cell in a living organism is constantly exposed to physical and chemical factors which damage the molecular structure of proteins, lipids, and nucleic acids. Cellular DNA lesions are the most dangerous because the genetic information, critical for the identity and function of each eukaryotic cell, is stored in the DNA. In this review, we describe spectroscopic markers of DNA damage, which can be detected by infrared, Raman, surface-enhanced Raman, and tip-enhanced Raman spectroscopies, using data acquired from DNA solutions and mammalian cells. Various physical and chemical DNA damaging factors are taken into consideration, including ionizing and non-ionizing radiation, chemicals, and chemotherapeutic compounds. All major spectral markers of DNA damage are presented in several tables, to give the reader a possibility of fast identification of the spectral signature related to a particular type of DNA damage.
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Affiliation(s)
| | | | | | - Ewelina Lipiec
- M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland; (K.S.); (N.W.); or (M.S.)
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3
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Komeda S, In Y, Tomoo K, Minoura K, Sato T, Reedijk J, Ishida T, Chikuma M. Associative intraligand substitution of anticancer azolato-bridged compounds without a square-pyramidal intermediate: Formation of a unique tetranuclear, µ3-1,2,3-triazolato-N1,N2,N3-bridged Pt(II) compound. Inorganica Chim Acta 2019. [DOI: 10.1016/j.ica.2019.118999] [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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4
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Ranasinghe K, Pakhomova S, Marzilli PA, Marzilli LG. A Very Rare Example of a Structurally Characterized 3'-GMP Metal Complex. NMR and Synthetic Assessment of Adducts Formed by Guanine Derivatives with [Pt(L tri)Cl]Cl Complexes with an N,N',N″ Tridentate Ligand (L tri) Terminated by Imidazole Rings. Inorg Chem 2017; 56:8462-8477. [PMID: 28682064 DOI: 10.1021/acs.inorgchem.7b01176] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[Pt(N(R)-1,1'-Me2dma)Cl]Cl complexes with tridentate ligands (bis(1-methyl-2-methylimidazolyl)amine, R = H; N-(methyl)bis(1-methyl-2-methylimidazolyl)amine, R = Me) were prepared in order to investigate Pt(N(R)-1,1'-Me2dma)G adducts (G = monodentate N9-substituted guanine or hypoxanthine derivative). Solution NMR spectroscopy is the primary tool for studying metal complexes of nucleosides and nucleotides because such adducts rarely crystallize. However, [Pt(N(H)-1,1'-Me2dma)(3'-GMPH)]NO3·5H2O (5) was crystallized, allowing, to our knowledge, the first crystallographic molecular structure determination for a 3'-GMP platinum complex. The structure is one of only a very few structures of a 3'-GMP complex with any metal. Complex 5 has the syn rotamer conformation, with 3'-GMP bound by N7. All Pt(N(R)-1,1'-Me2dma)G adducts exhibit two new downfield-shifted G H8 signals, consistent with G bound to platinum by N7 and a syn/anti rotamer mixture. Anticancer-active monofunctional platinum(II) complexes have bulky carrier ligands that cause DNA adducts to be distorted. Hence, understanding carrier-ligand steric effects is key in designing new platinum drugs. Ligand bulk can be correlated with the degree of impeded rotation of the G nucleobase about the Pt-N7 bond, as assessed by the observation of rotamers. The signals of syn and anti rotamers are connected by EXSY cross-peaks in 2D ROESY spectra of Pt(N(H)-1,1'-Me2dma)G adducts but not in spectra of Pt(N(H)dpa)G adducts (N(H)dpa = bis(2-picolyl)amine), indicating that rotamer interchange is more facile and carrier-ligand bulk is lower in Pt(N(H)-1,1'-Me2dma)G than in Pt(N(H)dpa)G adducts. The lower steric hindrance is a direct consequence of the greater distance of the G nucleobase from the H4/4' protons in the N(R)-1,1'-Me2dma carrier ligand in comparison to that from the H6/6' protons in the N(H)dpa carrier ligand. Although in 5 the nucleotide is 3'-GMP (not the usual 5'-GMP) and the N(H)-1,1'-Me2dma carrier ligand is very different from those typically present in structurally characterized Pt(II) G complexes, the rocking and canting angles in 5 adhere to long-recognized trends.
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Affiliation(s)
- Kokila Ranasinghe
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Svetlana Pakhomova
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Patricia A Marzilli
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Luigi G Marzilli
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
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5
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Li LJ, Yan QQ, Liu GJ, Yuan Z, Lv ZH, Fu B, Han YJ, Du JL. Synthesis characterization and cytotoxicity studies of platinum(II) complexes with reduced amino pyridine schiff base and its derivatives as ligands. Biosci Biotechnol Biochem 2017; 81:1081-1089. [PMID: 28290776 DOI: 10.1080/09168451.2016.1259550] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A series of reduced amino pyridine Schiff base platinum(II) complexes were prepared as potential anticancer drugs, and characterized by NMR, IR spectroscopy, elemental analysis, and molar conductivity. UV and CD results showed the binding mode between these compounds and salmon sperm DNA may be intercalation. The cytotoxicity of these complexes was validated against A549, Hela, and MCF-7 cell lines by MTT assay. Some complexes exhibited better cytotoxic activity than cisplatin against Hela and MCF-7 cell lines.
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Affiliation(s)
- Li-Jun Li
- a Chemical Biology Key Laboratory of Hebei Province , Hebei University , Baoding , P.R. China
| | - Qin-Qin Yan
- a Chemical Biology Key Laboratory of Hebei Province , Hebei University , Baoding , P.R. China
| | - Guo-Jun Liu
- a Chemical Biology Key Laboratory of Hebei Province , Hebei University , Baoding , P.R. China
| | - Zhen Yuan
- a Chemical Biology Key Laboratory of Hebei Province , Hebei University , Baoding , P.R. China
| | - Zhen-Hua Lv
- a Chemical Biology Key Laboratory of Hebei Province , Hebei University , Baoding , P.R. China
| | - Bin Fu
- a Chemical Biology Key Laboratory of Hebei Province , Hebei University , Baoding , P.R. China
| | - Yan-Jun Han
- a Chemical Biology Key Laboratory of Hebei Province , Hebei University , Baoding , P.R. China
| | - Jian-Long Du
- a Chemical Biology Key Laboratory of Hebei Province , Hebei University , Baoding , P.R. China
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He Y, Yuan J, Qiao Y, Wang D, Chen W, Liu X, Chen H, Guo Z. The role of carrier ligands of platinum(II) anticancer complexes in the protein recognition of Pt-DNA adducts. Chem Commun (Camb) 2016; 51:14064-7. [PMID: 26248639 DOI: 10.1039/c5cc05257b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In order to systematically investigate the influence of carrier ligands on the interaction of Pt-DNA adducts with damage recognition proteins, a series of DNA probes containing 1,2-GG platinum compound crosslinks using cisplatin, oxaliplatin, (S,S-DACH)PtCl2 and (cis-1,4-DACH)PtCl2 (kiteplatin) has been constructed. These complexes share similar DNA binding properties although they exhibit quite different cytotoxicity. It is revealed that HMGB1 (high-mobility group protein B1) was the most commonly found protein that recognizes all Pt(II)-DNA probes and prefers cisplatin-DNA probes more than the others. Interestingly, an important component of the replication protein A complex, RPA2, was found to bind to kiteplatin much more tightly than other proteins. These results may be important for the interpretation of the roles of carrier ligands in platinum(II)-based anticancer complexes.
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Affiliation(s)
- Yafeng He
- State Key Laboratory of Coordination Chemistry, Coordination Chemistry Institute, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Collaborative Innovation Centre of Chemistry for Life Sciences, Nanjing University, 22 Hankou Road, Nanjing, 210093, P. R. China.
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7
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Andrepont C, Marzilli PA, Pakhomova S, Marzilli LG. Guanine nucleobase adducts formed by a monofunctional complex: [Pt(N-(6-methyl-2-picolyl)-N-(2-picolyl)amine)Cl]Cl. J Inorg Biochem 2015; 153:219-230. [DOI: 10.1016/j.jinorgbio.2015.06.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 06/12/2015] [Accepted: 06/30/2015] [Indexed: 01/18/2023]
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8
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Andrepont C, Pakhomova S, Marzilli PA, Marzilli LG. Unusual Example of Chelate Ring Opening upon Coordination of the 9-Ethylguanine Nucleobase to [Pt(di-(6-methyl-2-picolyl)amine)Cl]Cl. Inorg Chem 2015; 54:4895-908. [DOI: 10.1021/acs.inorgchem.5b00496] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Chase Andrepont
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Svetlana Pakhomova
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Patricia A. Marzilli
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Luigi G. Marzilli
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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9
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10
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Structural changes of linear DNA molecules induced by cisplatin. Biochem Biophys Res Commun 2015; 457:688-92. [DOI: 10.1016/j.bbrc.2015.01.050] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Accepted: 01/13/2015] [Indexed: 11/20/2022]
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11
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Margiotta N, Petruzzella E, Platts JA, Mutter ST, Deeth RJ, Ranaldo R, Papadia P, Marzilli PA, Marzilli LG, Hoeschele JD, Natile G. DNA fragment conformations in adducts with Kiteplatin. Dalton Trans 2015; 44:3544-56. [DOI: 10.1039/c4dt01796j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The anticancer-active platinum complex with cis-1,4-diaminocyclohexane has proved to be very valuable in detecting multiple conformers in adducts with oligonucleotides.
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Affiliation(s)
- Nicola Margiotta
- Dipartimento di Chimica
- Università degli Studi di Bari A. Moro
- 70125 Bari
- Italy
| | | | | | | | | | - Rosa Ranaldo
- Dipartimento di Chimica
- Università degli Studi di Bari A. Moro
- 70125 Bari
- Italy
- Department of Chemistry
| | - Paride Papadia
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali
- Università del Salento
- 73100 Lecce
- Italy
| | | | | | | | - Giovanni Natile
- Dipartimento di Chimica
- Università degli Studi di Bari A. Moro
- 70125 Bari
- Italy
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12
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Vaverkova V, Vrana O, Adam V, Pekarek T, Jampilek J, Babula P. The study of naphthoquinones and their complexes with DNA by using Raman spectroscopy and surface enhanced Raman spectroscopy: new insight into interactions of DNA with plant secondary metabolites. BIOMED RESEARCH INTERNATIONAL 2014; 2014:461393. [PMID: 25045679 PMCID: PMC4090563 DOI: 10.1155/2014/461393] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Accepted: 05/21/2014] [Indexed: 11/17/2022]
Abstract
Naphthoquinones represent the group of plant secondary metabolites with cytotoxic properties based on their ability to generate reactive oxygen species and interfere with the processes of cell respiration. Due to this fact, the possible cytotoxic mechanisms on cellular and subcellular levels are investigated intensively. There are many targets of cytotoxic action on the cellular level; however, DNA is a critical target of many cytotoxic compounds. Due to the cytotoxic properties of naphthoquinones, it is necessary to study the processes of naphthoquinones, DNA interactions (1,4-naphthoquinone, binapthoquinone, juglone, lawsone, plumbagin), especially by using modern analytical techniques. In our work, the Raman spectroscopy was used to determine the possible binding sites of the naphthoquinones on the DNA and to characterize the bond of naphthoquinone to DNA. Experimental data reveals the relationships between the perturbations of structure-sensitive Raman bands and the types of the naphthoquinones involved. The modification of DNA by the studied naphthoquinones leads to the nonspecific interaction, which causes the transition of B-DNA into A-DNA conformation. The change of the B-conformation of DNA for all measured DNA modified by naphthoquinones except plumbagin is obvious.
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Affiliation(s)
- Veronika Vaverkova
- Department of Natural Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Palackeho 1-3, 612 42 Brno, Czech Republic
| | - Oldrich Vrana
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, C612 65 Brno, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Faculty of Agronomy, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic
| | - Tomas Pekarek
- Zentiva, k.s., Development Department, U Kabelovny 130, 102 37 Praha 10, Czech Republic
| | - Josef Jampilek
- Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Palackeho 1-3, 612 42 Brno, Czech Republic
| | - Petr Babula
- Department of Natural Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Palackeho 1-3, 612 42 Brno, Czech Republic
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13
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Yue H, Yang B, Wang Y, Chen G. Investigations of the binding of [Pt2(DTBPA)Cl2](II) and [Pt2(TPXA)Cl2](II) to DNA via various cross-linking modes. Int J Mol Sci 2013; 14:19556-86. [PMID: 24077126 PMCID: PMC3821573 DOI: 10.3390/ijms141019556] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 08/14/2013] [Accepted: 09/10/2013] [Indexed: 12/14/2022] Open
Abstract
We have constructed models for a series of platinum-DNA adducts that represent the binding of two agents, [Pt2(DTBPA)Cl2](II) and [Pt2(TPXA)Cl2](II), to DNA via inter- and intra-strand cross-linking, and carried out molecular dynamics simulations and DNA conformational dynamics calculations. The effects of trans- and cis-configurations of the centers of these di-nuclear platinum agents, and of different bridging linkers, have been investigated on the conformational distortions of platinum-DNA adducts formed via inter- and intra-strand cross-links. The results demonstrate that the DNA conformational distortions for the various platinum-DNA adducts with differing cross-linking modes are greatly influenced by the difference between the platinum-platinum distance for the platinum agent and the platinum-bound N7–N7 distance for the DNA molecule, and by the flexibility of the bridging linkers in the platinum agent. However, the effects of trans/cis-configurations of the platinum-centers on the DNA conformational distortions in the platinum-DNA adducts depend on the inter- and intra-strand cross-linking modes. In addition, we discuss the relevance of DNA base motions, including opening, shift and roll, to the changes in the parameters of the DNA major and minor grooves caused by binding of the platinum agent.
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Affiliation(s)
| | | | - Yan Wang
- Authors to whom correspondence should be addressed; E-Mails: (Y.W.); (G.C.); Tel.: +86-10-5880-5247 (Y.W.); +86-10-5880-5424 (G.C.); Fax: +86-10-5880-2075 (Y.W. & G.C.)
| | - Guangju Chen
- Authors to whom correspondence should be addressed; E-Mails: (Y.W.); (G.C.); Tel.: +86-10-5880-5247 (Y.W.); +86-10-5880-5424 (G.C.); Fax: +86-10-5880-2075 (Y.W. & G.C.)
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14
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Panikkanvalappil SR, Mahmoud MA, Mackey MA, El-Sayed MA. Surface-enhanced Raman spectroscopy for real-time monitoring of reactive oxygen species-induced DNA damage and its prevention by platinum nanoparticles. ACS NANO 2013; 7:7524-33. [PMID: 23952174 DOI: 10.1021/nn403722x] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
We have successfully demonstrated the potential of surface-enhanced Raman spectroscopy (SERS) in monitoring the real time damage to genomic DNA. To reveal the capabilities of this technique, we exposed DNA to reactive oxygen species (ROS), an agent that has been implicated in causing DNA double-strand breaks, and the various stages of free radical-induced DNA damage have been monitored by using SERS. Besides this, we showed that prompt DNA aggregation followed by DNA double-strand scission and residual damage to the DNA bases caused by the ROS could be substantially reduced by the protective effect of Pt nanocages and nearly cubical Pt nanopartcles. The antioxidant activity of Pt nanoparticles was further confirmed by the cell viability studies. On the basis of SERS results, we identified various stages involved in the mechanism of action of ROS toward DNA damage, which involves the DNA double-strand scission and its aggregation followed by the oxidation of DNA bases. We found that Pt nanoparticles inhibit the DNA double-strand scission to a significant extent by the degradation of ROS. Our method illustrates the capability of SERS technique in giving vital information about the DNA degradation reactions at molecular level, which may provide insight into the effectiveness and mechanism of action of many drugs in cancer therapy.
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Affiliation(s)
- Sajanlal R Panikkanvalappil
- Laser Dynamics Laboratory, School of Chemistry and Biochemistry, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
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15
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Negureanu L, Salsbury FR. Non-specificity and synergy at the binding site of the carboplatin-induced DNA adduct via molecular dynamics simulations of the MutSα-DNA recognition complex. J Biomol Struct Dyn 2013; 32:969-92. [PMID: 23799640 DOI: 10.1080/07391102.2013.799437] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
MutSα is the most abundant mismatch-binding factor of human DNA mismatch repair (MMR) proteins. MMR maintains genetic stability by recognizing and repairing DNA defects. Failure to accomplish their function may lead to cancer. In addition, MutSα recognizes at least some types of DNA damage making it a target for anticancer agents. Here, complementing scarce experimental data, we report unique hydrogen-bonding motifs associated with the recognition of the carboplatin induced DNA damage by MutSα. These data predict that carboplatin and cisplatin induced damaging DNA adducts are recognized by MutSα in a similar manner. Our simulations also indicate that loss of base pairing at the damage site results in (1) non-specific binding and (2) changes in the atomic flexibility at the lesion site and beyond. To further quantify alterations at MutSα-DNA interface in response to damage recognition, non-bonding interactions and salt bridges were investigated. These data indicate (1) possible different packing and (2) disruption of the salt bridges at the MutSα-DNA interface in the damaged complex. These findings (1) underscore the general observation of disruptions at the MutSα-DNA interface and (2) highlight the nature of the anticancer effect of the carboplatin agent. The analysis was carried out from atomistic simulations.
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16
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Barry NPE, Sadler PJ. Exploration of the medical periodic table: towards new targets. Chem Commun (Camb) 2013; 49:5106-31. [DOI: 10.1039/c3cc41143e] [Citation(s) in RCA: 570] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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17
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Andrepont C, Marzilli PA, Marzilli LG. Guanine nucleobase adducts formed by [Pt(di-(2-picolyl)amine)Cl]Cl: evidence that a tridentate ligand with only in-plane bulk can slow guanine base rotation. Inorg Chem 2012; 51:11961-70. [PMID: 23094695 DOI: 10.1021/ic3018634] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pt(II) complexes bind preferentially at N7 of G residues of DNA, causing DNA structural distortions associated with anticancer activity. Some distortions induced by difunctional cisplatin are also found for monofunctional Pt(II) complexes with carrier ligands having bulk projecting toward the guanine base. This ligand bulk can be correlated with impeded rotation about the Pt-N7(guanine) bond. Pt(N(H)dpa)(G) adducts (N(H)dpa = di-(2-picolyl)amine, G = 5'-GMP, 5'-GDP, 5'-GTP, guanosine, 9-EtG, and 5'-IMP) were used to assess whether a tridentate carrier ligand having bulk concentrated in the coordination plane can impede guanine nucleobase rotation. Because the Pt(N(H)dpa) moiety contains a mirror plane but is unsymmetrical with respect to the coordination plane, Pt(N(H)dpa)(G) adducts can form anti or syn rotamers with the guanine O6 and the central N-H of N(H)dpa on the opposite or the same side of the coordination plane, respectively. The observation of two sharp, comparably intense guanine H8 NMR signals provided evidence that these Pt(N(H)dpa)(G) adducts exist as mixtures of syn and anti rotamers, that rotational interchange is impeded by N(H)dpa, and that the key interactions involves steric repulsions between the pyridyl and guanine rings. The relative proximity of the guanine H8 to the anisotropic pyridyl rings allowed us to conclude that the syn rotamer was usually more abundant. However, the anti rotamer was more abundant for the Pt(N(H)dpa)(5'-GTP) adduct, in which a hydrogen bond between the 5'-GTP γ-phosphate group and the N(H)dpa central N-H is geometrically possible. In all previous examples of the influence of hydrogen bond formation on rotamer abundance in Pt(II) guanine adducts, these hydrogen bonding interactions occurred between ligand groups in cis positions. Thus, the role of a trans ligand group in influencing rotamer abundance, as found here, is unusual.
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Affiliation(s)
- Chase Andrepont
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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18
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Abstract
The review will discuss the influence of metal ions on conformational changes of oligonucleotides. First, a short definition of the torsion angles is given, followed by a concise yet critical overview of the commonly applied experimental techniques. Finally, the possible role of metals upon the following conformational changes of oligonucleotides is discussed: (i) the denaturation of double-strands, (ii) the transition from B- to A-DNA, (iii) the transition from right- to left-handed DNA and RNA, (iv) the condensation, (v) and other conformational changes. We conclude with a summary and outlook.
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Affiliation(s)
- Bernhard Spingler
- Institute of Inorganic Chemistry, University of Zürich, Zürich, Switzerland.
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19
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Cerón-Carrasco JP, Jacquemin D, Cauët E. Cisplatin cytotoxicity: a theoretical study of induced mutations. Phys Chem Chem Phys 2012; 14:12457-64. [DOI: 10.1039/c2cp40515f] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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20
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Zabost E, Nowicka AM, Mazerska Z, Stojek Z. Influence of temperature and interactions with ligands on dissociation of dsDNA and ligand–dsDNA complexes of various types of binding. An electrochemical study. Phys Chem Chem Phys 2012; 14:3408-13. [DOI: 10.1039/c2cp23824a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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21
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Shoukry MM, Al-Najjar AA, Hosny WM, Mahgoub AE, Abdelhadi AK, Khalf-Alaa PA. Thermodynamics of the reactions of [Pd(Et4en)(H2O)2]2+ with ligands of biological significance: deactivation of based-drug by the sulfur-containing biomolecules. J Sulphur Chem 2011. [DOI: 10.1080/17415993.2011.622393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Mohamed M. Shoukry
- a Department of Chemistry, Faculty of Science , University of Cairo , Egypt
| | | | - Wafaa M. Hosny
- a Department of Chemistry, Faculty of Science , University of Cairo , Egypt
| | - Afaf E. Mahgoub
- a Department of Chemistry, Faculty of Science , University of Cairo , Egypt
| | - Afkar K. Abdelhadi
- a Department of Chemistry, Faculty of Science , University of Cairo , Egypt
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22
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Stefanopoulou M, Kokoschka M, Sheldrick WS, Wolters DA. Cell response of Escherichia coli
to cisplatin-induced stress. Proteomics 2011; 11:4174-88. [DOI: 10.1002/pmic.201100203] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 07/19/2011] [Accepted: 08/04/2011] [Indexed: 11/08/2022]
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23
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Bhattacharyya D, Ramachandran S, Sharma S, Pathmasiri W, King CL, Baskerville-Abraham I, Boysen G, Swenberg JA, Campbell SL, Dokholyan NV, Chaney SG. Flanking bases influence the nature of DNA distortion by platinum 1,2-intrastrand (GG) cross-links. PLoS One 2011; 6:e23582. [PMID: 21853154 PMCID: PMC3154474 DOI: 10.1371/journal.pone.0023582] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2010] [Accepted: 07/21/2011] [Indexed: 11/28/2022] Open
Abstract
The differences in efficacy and molecular mechanisms of platinum anti-cancer drugs cisplatin (CP) and oxaliplatin (OX) are thought to be partially due to the differences in the DNA conformations of the CP and OX adducts that form on adjacent guanines on DNA, which in turn influence the binding of damage-recognition proteins that control downstream effects of the adducts. Here we report a comprehensive comparison of the structural distortion of DNA caused by CP and OX adducts in the TGGT sequence context using nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations. When compared to our previous studies in other sequence contexts, these structural studies help us understand the effect of the sequence context on the conformation of Pt-GG DNA adducts. We find that both the sequence context and the type of Pt-GG DNA adduct (CP vs. OX) play an important role in the conformation and the conformational dynamics of Pt-DNA adducts, possibly explaining their influence on the ability of many damage-recognition proteins to bind to Pt-DNA adducts.
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Affiliation(s)
- Debadeep Bhattacharyya
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Srinivas Ramachandran
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Program in Cellular and Molecular Biophysics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Shantanu Sharma
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Wimal Pathmasiri
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Candice L. King
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Irene Baskerville-Abraham
- Department of Environmental Sciences and Engineering, School of Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Gunnar Boysen
- Department of Environmental Sciences and Engineering, School of Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - James A. Swenberg
- Department of Environmental Sciences and Engineering, School of Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Sharon L. Campbell
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
- * E-mail: (SLC); (NVD); (SGC)
| | - Nikolay V. Dokholyan
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
- * E-mail: (SLC); (NVD); (SGC)
| | - Stephen G. Chaney
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
- * E-mail: (SLC); (NVD); (SGC)
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Saad JS, Marzilli PA, Intini FP, Natile G, Marzilli LG. Single-stranded oligonucleotide adducts formed by Pt complexes favoring left-handed base canting: steric effect of flanking residues and relevance to DNA adducts formed by Pt anticancer drugs. Inorg Chem 2011; 50:8608-20. [PMID: 21819051 DOI: 10.1021/ic2011716] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Platinum anticancer drug binding to DNA creates large distortions in the cross-link (G*G*) and the adjacent XG* base pair (bp) steps (G* = N7-platinated G). These distortions, which are responsible for anticancer activity, depend on features of the duplex (e.g., base pairing) and of the cross-link moiety (e.g., the position and canting of the G* bases). The duplex structure stabilizes the head-to-head (HH) over the head-to-tail (HT) orientation and right-handed (R) over left-handed (L) canting of the G* bases. To provide fundamental chemical information relevant to the assessment of such duplex effects, we examine (S,R,R,S)-BipPt(oligo) adducts (Bip = 2,2'-bipiperidine with S,R,R,S chiral centers at the N, C, C, and N chelate ring atoms, respectively; oligo = d(G*pG*) with 3'- and/or 5'-substituents). The moderately bulky (S,R,R,S)-Bip ligand favors L canting and slows rotation about the Pt-G* bonds, and the (S,R,R,S)-BipPt(oligo) models provide more useful data than do dynamic models derived from active Pt drugs. All 5'-substituents in (S,R,R,S)-BipPt(oligo) adducts favor the normal HH conformer (∼97%) by destabilizing the HT conformer through clashes with the 3'-G* residue rather than through favorable H-bonding interactions with the carrier ligand in the HH conformer. For all (S,R,R,S)-BipPt(oligo) adducts, the S pucker of the 5'-X residue is retained. For these adducts, a 5'-substituent had only modest effects on the degree of L canting for the (S,R,R,S)-BipPt(oligo) HH conformer. This small flanking 5'-substituent effect on an L-canted HH conformer contrasts with the significant decrease in the degree of R canting previously observed for flanking 5'-substituents in the R-canted (R,S,S,R)-BipPt(oligo) analogues. The present data support our earlier hypothesis that the distortion distinctive to the XG* bp step (S to N pucker change and movement of the X residue) is required for normal stacking and X·X' WC H bonding and to prevent XG* residue clashes.
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Affiliation(s)
- Jamil S Saad
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA.
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25
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Maheshwari V, Marzilli PA, Marzilli LG. Investigation Relevant to the Conformation of the 17-Membered Pt(d(GpG)) Macrocyclic Ring Formed by Pt Anticancer Drugs with DNA: Pt Complexes with a Goldilocks Carrier Ligand. Inorg Chem 2011; 50:6626-36. [DOI: 10.1021/ic200512m] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vidhi Maheshwari
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Patricia A. Marzilli
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Luigi G. Marzilli
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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26
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Saad JS, Benedetti M, Natile G, Marzilli LG. NMR studies of models having the Pt(d(GpG)) 17-membered macrocyclic ring formed in DNA by platinum anticancer drugs: Pt complexes with bulky chiral diamine ligands. Inorg Chem 2011; 50:4559-71. [PMID: 21510625 DOI: 10.1021/ic200259s] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The highly distorted Pt(d(G*pG*)) (G* = N7-platinated G) 17-membered macrocyclic ring formed by cisplatin anticancer drug binding to DNA alters the structure of the G*G* base pair steps, canting one base, and increases dynamic motion, complicating solution structural studies. However, the ring appears to favor the HH1 conformation (HH1 denotes head-to-head guanine bases, 1 denotes the normal direction of backbone propagation). Compared to cisplatin, analogues with NH groups in the carrier ligand replaced by bulky N-alkyl groups are more toxic and less active and form less dynamic adducts. To examine the molecular origins for the biological effects of steric bulk, we evaluate Me(4)DABPt(d(G*pG*)) models; the bulk and chirality of Me(4)DAB (N,N,N',N'-tetramethyl-2,3-diaminobutane with S,S or R,R configurations at the chelate ring carbons) impede dynamic motion and enhance the utility of NMR methods for identifying and characterizing conformers. Unlike past studies of adducts with such bulky carrier ligands, in which no HH conformer was found, the Me(4)DABPt(d(G*pG*)) adducts did form the HH1 conformer, providing compelling evidence that the sugar-phosphate backbone can impose constraints sufficient to overcome the alkyl-group steric effects. The HH1 conformer exhibits no significant canting. The (S,S)-Me(4)DABPt(d(G*pG*)) adduct has the least amount of the "normal" HH1 conformer and the greatest amount of the ΔHT1 conformer (ΔHT1 = head-to-tail G* bases with Δ chirality) ever observed (88% under some conditions). Thus, our results lead us to hypothesize that the low activity and high toxicity of analogues of cisplatin having carrier ligands with N-alkyl groups arise from the low abundance and minimal canting of the HH1 conformer and possibly from the adverse effects of an abundant ΔHT1 conformer. The new findings advance our understanding of the chemistry of the Pt(d(G*pG*)) macrocyclic ring and of the effects of carrier-ligand steric bulk on the properties of the ring.
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Affiliation(s)
- Jamil S Saad
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA.
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Truflandier LA, Sutter K, Autschbach J. Solvent Effects and Dynamic Averaging of 195Pt NMR Shielding in Cisplatin Derivatives. Inorg Chem 2011; 50:1723-32. [DOI: 10.1021/ic102174b] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Lionel A. Truflandier
- Department of Chemistry, University at Buffalo State University of New York, Buffalo, New York 14260-3000, United States
| | - Kiplangat Sutter
- Department of Chemistry, University at Buffalo State University of New York, Buffalo, New York 14260-3000, United States
| | - Jochen Autschbach
- Department of Chemistry, University at Buffalo State University of New York, Buffalo, New York 14260-3000, United States
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Intini FP, Cini R, Tamasi G, Hursthouse MB, Marzilli LG, Natile G. X-Ray Structural Characterization of the Bis-Guanine Derivative of a Cisplatin Analogue Having Just One Proton on Each Coordinated Nitrogen and a Head-to-Head Conformation: [Pt{(±)-N,N′-Dimethyl-2,3-diaminobutane}(9-ethyl-guanine)2]dinitrate. Inorg Chem 2010; 49:7853-60. [DOI: 10.1021/ic100972s] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Francesco P. Intini
- Dipartimento Farmaco-Chimico, Università di Bari, Via E. Orabona 4, 70125 Bari, Italy
| | - Renzo Cini
- Dipartimento di Chimica, Università di Siena, Via A. Moro 2, I-53100 Siena, Italy
| | - Gabriella Tamasi
- Dipartimento di Chimica, Università di Siena, Via A. Moro 2, I-53100 Siena, Italy
| | - Michael B. Hursthouse
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - Luigi G. Marzilli
- Departments of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803
- Emory University, Atlanta, Georgia 30322
| | - Giovanni Natile
- Dipartimento Farmaco-Chimico, Università di Bari, Via E. Orabona 4, 70125 Bari, Italy
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29
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Saad JS, Benedetti M, Natile G, Marzilli LG. Basic Coordination Chemistry Relevant to DNA Adducts Formed by the Cisplatin Anticancer Drug. NMR Studies on Compounds with Sterically Crowded Chiral Ligands. Inorg Chem 2010; 49:5573-83. [DOI: 10.1021/ic100494f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Jamil S. Saad
- Departments of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803 and Emory University, Atlanta, Georgia 30322
| | - Michele Benedetti
- Dipartimento Farmaco-Chimico, Università di Bari, Via E. Orabona, 4, 70125 bari, Italy
| | - Giovanni Natile
- Dipartimento Farmaco-Chimico, Università di Bari, Via E. Orabona, 4, 70125 bari, Italy
| | - Luigi G. Marzilli
- Departments of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803 and Emory University, Atlanta, Georgia 30322
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Todd RC, Lippard SJ. Structure of duplex DNA containing the cisplatin 1,2-{Pt(NH3)2}2+-d(GpG) cross-link at 1.77 A resolution. J Inorg Biochem 2010; 104:902-8. [PMID: 20541266 DOI: 10.1016/j.jinorgbio.2010.04.005] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Revised: 04/11/2010] [Accepted: 04/13/2010] [Indexed: 01/07/2023]
Abstract
We report the 1.77-A resolution X-ray crystal structure of a dodecamer DNA duplex with the sequence 5'-CCTCTGGTCTCC-3' that has been modified to contain a single engineered 1,2-cis-{Pt(NH(3))(2)}(2+)-d(GpG) cross-link, the major DNA adduct of cisplatin. These data represent a significant improvement in resolution over the previously published 2.6-A structure. The ammine ligands in this structure are clearly resolved, leading to improved visualization of the cross-link geometry with respect to both the platinum center and to the nucleobases, which adopt a higher energy conformation. Also better resolved are the deoxyribose sugar puckers, which allow us to re-examine the global structure of platinum-modified DNA. Another new feature of this model is the location of four octahedral [Mg(H(2)O)(6)](2+) ions associated with bases in the DNA major groove and the identification of 124 ordered water molecules that participate in hydrogen-bonding interactions with either the nucleic acid or the diammineplatinum(II) moiety.
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Affiliation(s)
- Ryan C Todd
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
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31
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Téletchéa S, Skauge T, Sletten E, Kozelka J. Cisplatin Adducts on a GGG Sequence within a DNA Duplex Studied by NMR Spectroscopy and Molecular Dynamics Simulations. Chemistry 2009; 15:12320-37. [DOI: 10.1002/chem.200901158] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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32
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Saad JS, Natile G, Marzilli LG. Origins of the Distortions in the Base Pair Step Adjacent to Platinum Anticancer Drug−DNA Adducts. Fundamental NMR Solution Studies Utilizing Right-Handed Cross-Link Models Having 5′- and 3′-Flanking Residues. J Am Chem Soc 2009; 131:12314-24. [DOI: 10.1021/ja903787m] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Jamil S. Saad
- Departments of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, and Emory University, Atlanta, Georgia 30322, and Dipartimento Farmaco-Chimico, Università di Bari, Via E. Orabona 4, 70125 Bari, Italy
| | - Giovanni Natile
- Departments of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, and Emory University, Atlanta, Georgia 30322, and Dipartimento Farmaco-Chimico, Università di Bari, Via E. Orabona 4, 70125 Bari, Italy
| | - Luigi G. Marzilli
- Departments of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, and Emory University, Atlanta, Georgia 30322, and Dipartimento Farmaco-Chimico, Università di Bari, Via E. Orabona 4, 70125 Bari, Italy
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Zhu Y, Wang Y, Chen G. Differences in conformational dynamics of [Pt3(HPTAB)]6+-DNA adducts with various cross-linking modes. Nucleic Acids Res 2009; 37:5930-42. [PMID: 19654239 PMCID: PMC2761282 DOI: 10.1093/nar/gkp618] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
We present here molecular dynamics simulations and DNA conformational dynamics for a series of trinuclear platinum [Pt3(HPTAB)]6+-DNA adducts [HPTAB = N,N,N′,N′,N′′,N′′-hexakis (2-pyridyl-methyl)-1,3,5-tris(aminomethyl) benzene], including three types of bifunctional crosslinks and four types of trifunctional crosslinks. Our simulation results reveal that binding of the trinuclear platinum compound to a DNA duplex induces the duplex unwinding in the vicinity of the platination sites, and causes the DNA to bend toward the major groove. As a consequence, this produces a DNA molecule whose minor groove is more widened and shallow compared to that of an undamaged bare-DNA molecule. Notably, for trifunctional crosslinks, we have observed extensive DNA conformational distortions, which is rarely seen for normal platinum–DNA adducts. Our findings, in this study, thus provide further support for the idea that platinum compounds with trifunctional intra-strand or long-range-inter-strand cross-linking modes can generate larger DNA conformational distortions than other types of cross-linking modes.
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Affiliation(s)
- Yanyan Zhu
- College of Chemistry, Beijing Normal University, Beijing 100875, P R China
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Diakos CI, Messerle BA, Murdoch PDS, Parkinson JA, Sadler PJ, Fenton RR, Hambley TW. Identification by NMR spectroscopy of the two stereoisomers of the platinum complex [PtCl2(S-ahaz)] (S-ahaz = 3(S)-aminohexahydroazepine) bound to a DNA 14-mer oligonucleotide. NMR evidence of structural alteration of a platinated A x T-rich 14-mer DNA duplex. Inorg Chem 2009; 48:3047-56. [PMID: 19265406 DOI: 10.1021/ic802207m] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The enantiomers of the asymmetric, chiral platinum(II) complex [PtCl(2)(S-ahaz)] (S-ahaz = 3(S)-aminohexahydroazepine) each form two stereoisomers on binding to GpG sequences of DNA: one in which the primary amine is directed toward the 5' end of the DNA and one in which it is directed toward the 3' end. Previous binding studies have revealed that the S-enantiomer forms the two stereoisomers in a 7:1 ratio while the R-enantiomer forms them in close to a 1:1 ratio. In an attempt to elucidate the reasons behind the stereoselectivity displayed by the S-enantiomer and to establish which isomer is formed in the greater amount, we report here its reaction with a 14-mer oligodeoxyribonucleotide having a single GpG site. The two stereoisomers that formed were separated using HPLC methods, and their integrities were confirmed by electrospray ionization mass spectrometry. The DNA duplex was formed by combination of each of the purified reaction products with the complementary strand of DNA. Identification of both of the stereoisomers was achieved using 2D NMR spectroscopy, which is the first time this has been achieved for an unsymmetric platinum complex bound to DNA. The minor stereoisomer, with the bulk of the ahaz ring directed toward the 3' end of the platinated strand, induced considerable disruption to the 14-mer DNA duplex structure. The primary amine of the ahaz ligand was oriented toward the 3' side of the duplex in the major isomer, giving a DNA structure that was less disrupted and was more akin to the structure of the DNA on binding of cisplatin to the same sequence.
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Affiliation(s)
- Connie I Diakos
- School of Chemistry, University of Sydney, NSW 2006, Australia
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35
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Molecular structure and antitumor activity of platinum(II) complexes containing purine analogs. Inorganica Chim Acta 2009. [DOI: 10.1016/j.ica.2008.02.030] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Abstract
Cisplatin, carboplatin, and oxaliplatin are three FDA-approved members of the platinum anticancer drug family. These compounds induce apoptosis in tumor cells by binding to nuclear DNA, forming a variety of structural adducts and triggering cellular responses, one of which is the inhibition of transcription. In this report we present (i) a detailed review of the structural investigations of various Pt-DNA adducts and the effects of these lesions on global DNA geometry; (ii) research detailing inhibition of cellular transcription by Pt-DNA adducts; and (iii) a mechanistic analysis of how DNA structural distortions induced by platinum damage may inhibit RNA synthesis in vivo. A thorough understanding of the molecular mechanism of action of platinum antitumor agents will aid in the development of new compounds in the family.
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Affiliation(s)
- Ryan C. Todd
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Stephen J. Lippard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
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37
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Lippert B. Coordinative Bond Formation Between Metal Ions and Nucleic Acid Bases. NUCLEIC ACID–METAL ION INTERACTIONS 2008. [DOI: 10.1039/9781847558763-00039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Bernhard Lippert
- Fakultät für Chemie, Technische Universität Dortmund Otto-Hahn-Strasse 6 D-44227 Dortmund Germany
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38
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Maheshwari V, Marzilli PA, Marzilli LG. Neglected Bidentate sp2 N-Donor Carrier Ligands with Triazine Nitrogen Lone Pairs: Platinum Complexes Retromodeling Cisplatin Guanine Nucleobase Adducts. Inorg Chem 2008; 47:9303-13. [DOI: 10.1021/ic800836t] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vidhi Maheshwari
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Patricia A. Marzilli
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Luigi G. Marzilli
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803
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39
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Reedijk J. Medicinal Applications of Metal Complexes Binding to Biological Macromolecules. ACTA ACUST UNITED AC 2008. [DOI: 10.1002/masy.200851023] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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cis-Diammine(pyridine)chloroplatinum(II), a monofunctional platinum(II) antitumor agent: Uptake, structure, function, and prospects. Proc Natl Acad Sci U S A 2008; 105:8902-7. [PMID: 18579768 DOI: 10.1073/pnas.0803441105] [Citation(s) in RCA: 200] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We have identified unique chemical and biological properties of a cationic monofunctional platinum(II) complex, cis-diammine(pyridine)chloroplatinum(II), cis-[Pt(NH(3))(2)(py)Cl](+) or cDPCP, a coordination compound previously identified to have significant anticancer activity in a mouse tumor model. This compound is an excellent substrate for organic cation transporters 1 and 2, also designated SLC22A1 and SLC22A2, respectively. These transporters are abundantly expressed in human colorectal cancers, where they mediate uptake of oxaliplatin, cis-[Pt(DACH)(oxalate)] (DACH = trans-R,R-1,2-diaminocyclohexane), an FDA-approved first-line therapy for colorectal cancer. Unlike oxaliplatin, however, cDPCP binds DNA monofunctionally, as revealed by an x-ray crystal structure of cis-{Pt(NH(3))(2)(py)}(2+) bound to the N7 atom of a single guanosine residue in a DNA dodecamer duplex. Although the quaternary structure resembles that of B-form DNA, there is a base-pair step to the 5' side of the Pt adduct with abnormally large shift and slide values, features characteristic of cisplatin intrastrand cross-links. cDPCP effectively blocks transcription from DNA templates carrying adducts of the complex, unlike DNA lesions of other monofunctional platinum(II) compounds like {Pt(dien)}(2+). cDPCP-DNA adducts are removed by the nucleotide excision repair apparatus, albeit much less efficiently than bifunctional platinum-DNA intrastrand cross-links. These exceptional characteristics indicate that cDPCP and related complexes merit consideration as therapeutic options for treating colorectal and other cancers bearing appropriate cation transporters.
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Intini FP, Cini R, Tamasi G, Hursthouse MB, Natile G. NMR and X-ray Structural Characterization of a Cisplatin Analogue Able To Slow Down the Pt−N7 Rotation of a Coordinated Guanine Base by a Billion-Fold Times: 2,2′-Bipiperidine(dimethylmalonato)platinum(II) Complex. Inorg Chem 2008; 47:4909-17. [DOI: 10.1021/ic800230p] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Francesco P. Intini
- Dipartimento Farmaco-Chimico, Università di Bari, Via E. Orabona 4, I-70125 Bari, Italy, Dipartimento di Scienze e Tecnologie Chimiche e dei Biosistemi, Università di Siena, Via A. Moro 2, I-53100 Siena, Italy, and School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Renzo Cini
- Dipartimento Farmaco-Chimico, Università di Bari, Via E. Orabona 4, I-70125 Bari, Italy, Dipartimento di Scienze e Tecnologie Chimiche e dei Biosistemi, Università di Siena, Via A. Moro 2, I-53100 Siena, Italy, and School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Gabriella Tamasi
- Dipartimento Farmaco-Chimico, Università di Bari, Via E. Orabona 4, I-70125 Bari, Italy, Dipartimento di Scienze e Tecnologie Chimiche e dei Biosistemi, Università di Siena, Via A. Moro 2, I-53100 Siena, Italy, and School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Michael B. Hursthouse
- Dipartimento Farmaco-Chimico, Università di Bari, Via E. Orabona 4, I-70125 Bari, Italy, Dipartimento di Scienze e Tecnologie Chimiche e dei Biosistemi, Università di Siena, Via A. Moro 2, I-53100 Siena, Italy, and School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Giovanni Natile
- Dipartimento Farmaco-Chimico, Università di Bari, Via E. Orabona 4, I-70125 Bari, Italy, Dipartimento di Scienze e Tecnologie Chimiche e dei Biosistemi, Università di Siena, Via A. Moro 2, I-53100 Siena, Italy, and School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
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42
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Ranaldo R, Margiotta N, Intini FP, Pacifico C, Natile G. Conformer distribution in (cis-1,4-DACH)bis(guanosine-5'-phosphate)platinum(II) adducts: a reliable model for DNA adducts of antitumoral cisplatin. Inorg Chem 2008; 47:2820-30. [PMID: 18284193 DOI: 10.1021/ic702202x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In [PtCl2(cis-1,4-DACH)] (DACH = diaminocyclohexane), the N-Pt-N bite angle (> or =97 degrees , as determined by X-ray diffraction analysis) is much larger than those found in other Pt complexes with bidentate diamines or in cisplatin (approximately 91 degrees ). Hence, the possibility exists that in (cis-1,4-DACH)PtG 2 adducts, rotation of the G's around the Pt-N7 bonds is slowed enough to allow observation of different conformers. In accord with this prevision, decreasing the temperature to 238 K enabled us to observe different conformers of (cis-1,4-DACH)Pt(5'-GMP) 2 (GMP = guanosine monophosphate). This observation is the first case in which such conformers for a platinum derivative with primary diamines and untethered guanines have been resolved and represents the closest model to clinically effective cisplatin obtained to date. We also found that the presence of the 1,4-DACH ligand increased the intensity of the circular dichroism signal stemming from the dominance of an HT conformer (DeltaHT in the adduct with 3'-GMPs and LambdaHT in the adduct with 5'-GMPs).
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Affiliation(s)
- Rosa Ranaldo
- Dipartimento Farmaco-Chimico, Università degli Studi di Bari, Via E. Orabona 4, 70125 Bari, Italy
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43
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Kang M, Chifotides HT, Dunbar KR. 2D NMR study of the DNA duplex d(CTCTC*A*ACTTCC).d(GGAAGTTGAGAG) cross-linked by the antitumor-active dirhodium(II,II) unit at the cytosine-adenine step. Biochemistry 2008; 47:2265-76. [PMID: 18232716 DOI: 10.1021/bi701901c] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The 2D NMR analysis in solution of the DNA duplex d(CTCTC*A*ACTTCC).d(GGAAGTTGAGAG) binding to the dirhodium unit cis-[Rh2(mu-O2CCH3)2(eta1-O2CCH3)]+ showed that an unprecedented intrastrand adduct, dsII, is formed with the dirhodium unit cross-linking in the major groove residues C5 and A6 (indicated with asterisks), also corroborated by enzyme digestion studies. Formation of the dirhodium complex dsII destabilizes significantly the duplex as indicated by the substantial decrease in its melting temperature (DeltaTm = -22.9 degrees C). The reduced thermal stability of dsII is attributed to the decreased stacking of the bases and the complete disruption and/or weakening of the hydrogen bonds within the base pairs in the immediate vicinity of the metalation site (C5.G20 and A6.T19), but the effects due to the metal binding are more severe for the base pairs in the 5' direction to the lesion site. The NMR spectroscopic data indicate that Watson-Crick hydrogen bonding is completely disrupted for the C5.G20 site and considerably weakened for A6.T19. In dsII, the bases C5 and A6 bind to eq positions of the dirhodium unit cis-[Rh2(mu-O2CCH3)2(eta1-O2CCH3)]+, which retains one monodentate and two bridging acetate groups, presumably due to steric reasons. Binding of A6 takes place via N7, whereas binding of the C5 base takes place via the exocyclic N4 site, resulting in the anti-cytosine rotamer with respect to site N3 in its metal-stabilized rare iminooxo form.
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Affiliation(s)
- Mijeong Kang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, USA
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44
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Sharma S, Gong P, Temple B, Bhattacharyya D, Dokholyan NV, Chaney SG. Molecular dynamic simulations of cisplatin- and oxaliplatin-d(GG) intrastand cross-links reveal differences in their conformational dynamics. J Mol Biol 2007; 373:1123-40. [PMID: 17900616 PMCID: PMC2129172 DOI: 10.1016/j.jmb.2007.07.079] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2007] [Revised: 07/26/2007] [Accepted: 07/28/2007] [Indexed: 11/18/2022]
Abstract
Mismatch repair proteins, DNA damage-recognition proteins and translesion DNA polymerases discriminate between Pt-GG adducts containing cis-diammine ligands (formed by cisplatin (CP) and carboplatin) and trans-RR-diaminocyclohexane ligands (formed by oxaliplatin (OX)) and this discrimination is thought to be important in determining differences in the efficacy, toxicity and mutagenicity of these platinum anticancer agents. We have postulated that these proteins recognize differences in conformation and/or conformational dynamics of the DNA containing the adducts. We have previously determined the NMR solution structure of OX-DNA, CP-DNA and undamaged duplex DNA in the 5'-d(CCTCAGGCCTCC)-3' sequence context and have shown the existence of several conformational differences in the vicinity of the Pt-GG adduct. Here we have used molecular dynamics simulations to explore differences in the conformational dynamics between OX-DNA, CP-DNA and undamaged DNA in the same sequence context. Twenty-five 10 ns unrestrained fully solvated molecular dynamics simulations were performed starting from two different DNA conformations using AMBER v8.0. All 25 simulations reached equilibrium within 4 ns, were independent of the starting structure and were in close agreement with previous crystal and NMR structures. Our data show that the cis-diammine (CP) ligand preferentially forms hydrogen bonds on the 5' side of the Pt-GG adduct, while the trans-RR-diaminocyclohexane (OX) ligand preferentially forms hydrogen bonds on the 3' side of the adduct. In addition, our data show that these differences in hydrogen bond formation are strongly correlated with differences in conformational dynamics, specifically the fraction of time spent in different DNA conformations in the vicinity of the adduct, for CP- and OX-DNA adducts. We postulate that differential recognition of CP- and OX-GG adducts by mismatch repair proteins, DNA damage-recognition proteins and DNA polymerases may be due, in part, to differences in the fraction of time that the adducts spend in a conformation favorable for protein binding.
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Affiliation(s)
- Shantanu Sharma
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599-7260, USA
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45
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Teletchéa S, Komeda S, Teuben JM, Elizondo-Riojas MA, Reedijk J, Kozelka J. A pyrazolato-bridged dinuclear platinum(II) complex induces only minor distortions upon DNA-binding. Chemistry 2007; 12:3741-53. [PMID: 16514681 DOI: 10.1002/chem.200500923] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The cytotoxic, pyrazolato-bridged dinuclear platinum(II) complex [(cis-{Pt(NH3)2})2(mu-OH)(mu-pz)]2+ (pz=pyrazolate) has been found to cross-link two adjacent guanines of a double-stranded DNA decamer without destabilizing the duplex and without changing the directionality of the helix axis. A 1H NMR study of the oligonucleotide d(CTCTG*G*TCTC)-d(GAGACCAGAG), cross-linked at the two G* guanines by [(cis-{Pt(NH3)2})2(mu-pz)]3+, and molecular dynamics simulations of the explicitly solvated duplex were performed to characterize the structural details of the adduct. The dinuclear platinum cross-link unwinds the helix by approximately 15 degrees , that is, to a similar extent as the widely used antitumor drug cisplatin, but, in contrast to the latter, induces no significant bend in the helix axis. The Watson-Crick base-pairing remains intact, and the melting temperature of the duplex is unaffected by the cross-link. The helical twist is considerably reduced between the two platinated bases, as becomes manifest in an unusually short sequential H1'-H1' distance. This unwinding also affects the sugar ring of the guanosine in the 3'-position to the cross-link, which presents an N<-->S equilibrium. This is the first cytotoxic platinum complex that has been successfully designed by envisioning the structural consequences of its binding to DNA.
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Affiliation(s)
- Stéphane Teletchéa
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université René Descartes, UMR 8601 CNRS, 45, rue des Saints-Pères, 75270 Paris Cedex 06, France
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46
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Vinje J, Sletten E. Internal versus terminal metalation of double-helical oligodeoxyribonucleotides. Chemistry 2007; 12:676-88. [PMID: 16208725 DOI: 10.1002/chem.200500731] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The formation of adducts between cis-[Pt(NH(3))(2)Cl(2)], Zn(II), and Mn(II) and double-stranded oligodeoxynucleotides was studied by 1D and 2D (1)H, (31)P, and (15)N NMR spectroscopy. For labile adducts involving Zn(II) and Mn(II), both (1)H chemical shifts (Zn(II)) and (1)H line-broadening effects (Mn(II)) showed that in the hexamer [d(GGCGCC)](2) I, the terminal G(1)-N7 is the exclusive binding site, while for the dodecamer [d(GGTACCGGTACC)](2) II, which contains both a terminal and internal GG pair, the preference for metal binding is the internal guanine G(7). Zn(II) binding to II was confirmed by natural-abundance 2D [(1)H,(15)N] HMBC NMR spectroscopy, which unambiguously showed that G(7)-N7 is the preferred binding site. The long duplex [d(GGTATATATACCGGTATATATACC)](2) III was expected to have a more pronounced accumulation of electrostatic potential towards the central part of the sequence (vs the terminal part) than does II. However, the Zn(II) titration of III showed no increase in coordination with the internal Gs (vs the terminal Gs), compared with what was observed for II. The reaction between the nonlabile metal complex cis-[PtCl(2)((15)NH(3))(2)] (cisplatin) and II showed a slight preference for the internal GG pair over the terminal GG pair. However, when the diaqua form of cisplatin cis-[Pt((15)NH(3))(2)(H(2)O)(2)] was reacted with II a more pronounced binding preference for the internal GG pair was observed.
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Affiliation(s)
- Jo Vinje
- Centre of Pharmacy, Department of Chemistry, University of Bergen, Norway.
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47
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Chifotides HT, Dunbar KR. Head-to-head cross-linked adduct between the antitumor unit bis(mu-N,N'-di-p-tolylformamidinato)dirhodium(II,II) and the DNA fragment d(GpG). Chemistry 2007; 12:6458-68. [PMID: 16900545 DOI: 10.1002/chem.200600401] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Reactions of the compound cis-[Rh2(DTolF)2(CH3CN)6](BF4)2, a formamidinate derivative of the class of antitumor compounds [Rh2(O2CR)4] (R=Me, Et, Pr), with 9-ethylguanine (9-EtGuaH) or the dinucleotide d(GpG) proceed by substitution of the acetonitrile groups, with the guanine bases spanning the Rh--Rh bond, in a bridging fashion, through sites N7/O6. In the case of 9-EtGuaH, both head-to-head (HH) and head-to-tail (HT) isomers are formed, whereas with the tethered bases in d(GpG), only one right-handed conformer HH1R [Rh2(DTolF)2{d(GpG)}] is present in solution. For both cis-[Rh2(DTolF)2(9-EtGuaH)2](BF4)2 and [Rh2(DTolF)2{d(GpG)}], the absence of N7 protonation at low pH and the substantial decrease of the pKa values for N1-H deprotonation, support N7/O6 binding of the bases to the dirhodium core. The N7/O6 binding of the bases is further corroborated by the downfield shift by Deltadelta approximately 4.0 ppm of the 13C NMR resonances for the C6 nuclei as compared to the corresponding resonances of the free ligands. The HH arrangement of the guanine bases in [Rh2(DTolF)2{d(GpG)}] is indicated by the intense H8/H8 ROE cross-peaks in the 2D ROESY NMR spectrum. Complete characterization of the [Rh2(DTolF)2{d(GpG)}] conformer by 2D NMR spectroscopy supports anti-orientation and N (C3'-endo) conformation for both deoxyribose residues. The N-pucker for the 5'-G base is universal in such cross-links, but it is very unusual for platinum and unprecedented for dirhodium HH cross-linked adducts to have both deoxyribose residues in the N-type conformation. The bulk, the nonlabile character, and the electron-donating ability of the formamidinate bridging groups spanning the dirhodium core affect the nature of the preferred dirhodium DNA adducts. Molecular modeling studies performed on [Rh2(DTolF)2{d(GpG)}] corroborate the structural features obtained by NMR spectroscopy.
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Affiliation(s)
- Helen T Chifotides
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA.
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48
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Benedetti M, Tamasi G, Cini R, Marzilli LG, Natile G. The first pure LambdaHT rotamer of a complex with a cis-[metal(nucleotide)2] unit: a cis-[Pt(amine)2(nucleotide)2] LambdaHT rotamer with unique molecular structural features. Chemistry 2007; 13:3131-42. [PMID: 17225220 DOI: 10.1002/chem.200601211] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
cis-[PtA2(nucleotide)2] complexes (A2 stands for two amines or a diamine) have been extensively investigated as model compounds for key cisplatin-DNA adducts. All cis-[metal(nucleotide/nucleoside)2] complexes with guanine and related purines characterized in the solid state thus far have the DeltaHT conformation (head-to-tail orientation of the two bases and right-handed chirality). In sharp contrast, the LambdaHT conformation (left-handed chirality) dominates in acidic and neutral aqueous solutions of cis-[PtA2(5'-GMP)2] complexes. Molecular models and solution experiments indicate that the LambdaHT conformer is stabilized by 5'-phosphate/N1H hydrogen-bond interactions between cis nucleotides with the normal anti conformation. However, this evidence, while compelling, is indirect. At last, conditions have been defined to allow crystallization of this elusive conformer. The structure obtained reveals three unique features not present in all other cis-[PtA2(nucleotide)2] solid-state structures: a LambdaHT conformation, very strong hydrogen-bond interactions between the phosphate and N1H of cis nucleotides, and a very small dihedral angle between the planes of the two guanines lying nearly perpendicular to the coordination plane. These new results indicate that, because there are no local base-base repulsions precluding the LambdaHT conformer, global forces rather than local interactions account for the predominance of the DeltaHT conformer over the LambdaHT conformer in the solid state and in both inter- and intrastrand HT crosslinks of oligonucleotides and DNA.
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Affiliation(s)
- Michele Benedetti
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università degli Studi di Lecce, Via Monteroni, 73100 Lecce, Italy
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49
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Adams KM, Marzilli LG. fac-[Re(CO)3(H2O)3]+ nucleoside monophosphate adducts investigated in aqueous solution by multinuclear NMR spectroscopy. Inorg Chem 2007; 46:4926-36. [PMID: 17506550 DOI: 10.1021/ic062410f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The fac-[Re(CO)3(H2O)3]+ cation, the putative DNA-binding species accounting for the biological activity of related Re(I) complexes, binds reversibly to N7 of 6-oxopurine nucleotide monophosphates (NMPs), in contrast to Pt(II) anticancer drugs. A relatively high amount of NMP is needed to convert all of the fac-[Re(CO)3(H2O)3]+ to adducts. The Re/nucleotide 1:1 adduct forms more rapidly and builds up to a higher concentration for guanosine 5'-monophosphate (5'-GMP) and inosine 5'-monophosphate (5'-IMP) than for the respective 3'-monophosphates (3'-GMP and 3'-IMP). These results are attributable to the 5'-positioning of the 5'-NMP phosphate group that allows it to approach the metal inner sphere for more favorable cation electrostatic and aqua ligand H-bonding interactions, both in the initial productive ion pair encounter complexes and in the N7-bound 1:1 adducts. A higher reactivity of 5'-GMP over 3'-GMP is known for cisplatin. In contrast, more Re/nucleotide 1:2 adduct was formed by 3'-GMP (and 3'-IMP) than by 5'-GMP (and 5'-IMP). Because the 3'-phosphate group cannot closely approach the metal inner coordination sphere, the greater stability for the 3'-GMP 1:2 adduct reflects the more favorable G N1H-phosphate interligand GMP-GMP interactions for 3'-GMP vs 5'-GMP (G=guanine base derivative). This type of interaction is known for platinum adducts. In 1:2 adducts the bound nucleotides are inequivalent, prompting us to perform mixed 5'-GMP/3'-GMP experiments, leading to the observation of major (M) and minor (m) mixed Re/5'-GMP/3'-GMP 1:1:1 adducts. The order of abundance at equilibrium in a typical experiment was M>bis 3'-GMP>m>or=bis 5'-GMP. This stability order was rationalized by invoking the phosphate interactions described above. When methionine and 5'-GMP were allowed to compete for fac-[Re(CO)3(H2O)3]+, the Re/5'-GMP 1:1 adduct was the kinetic product and the S-bound Re/methionine adduct was the thermodynamic product, a result opposite to that typically found for cisplatin.
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Affiliation(s)
- Kristie M Adams
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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50
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Wu Y, Bhattacharyya D, King CL, Baskerville-Abraham I, Huh SH, Boysen G, Swenberg JA, Temple B, Campbell SL, Chaney SG. Solution structures of a DNA dodecamer duplex with and without a cisplatin 1,2-d(GG) intrastrand cross-link: comparison with the same DNA duplex containing an oxaliplatin 1,2-d(GG) intrastrand cross-link. Biochemistry 2007; 46:6477-87. [PMID: 17497831 PMCID: PMC2129171 DOI: 10.1021/bi062291f] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Proteins that discriminate between cisplatin-DNA adducts and oxaliplatin-DNA adducts are thought to be responsible for the differences in tumor range, toxicity, and mutagenicity of these two important chemotherapeutic agents. However, the structural basis for differential protein recognition of these adducts has not been determined and could be important for the design of more effective platinum anticancer agents. We have determined high-resolution NMR structures for cisplatin-GG and undamaged DNA dodecamers in the AGGC sequence context and have compared these structures with the oxaliplatin-GG structure in the same sequence context determined previously in our laboratory. This structural study allows the first direct comparison of cisplatin-GG DNA and oxaliplatin-GG DNA solution structures referenced to undamaged DNA in the same sequence context. Non-hydrogen atom rmsds of 0.81 and 1.21 were determined for the 15 lowest-energy structures for cisplatin-GG DNA and undamaged DNA, respectively, indicating good structural convergence. The theoretical NOESY spectra obtained by back-calculation from the final average structures showed excellent agreement with the experimental data, indicating that the final structures are consistent with the NMR data. Several significant conformational differences were observed between the cisplatin-GG adduct and the oxaliplatin-GG adduct, including buckle at the 5' G6.C19 base pair, opening at the 3' G7.C18 base pair, twist at the A5G6.T20C19 base pair step, slide, twist, and roll at the G6G7.C19C18 base pair step, slide at the G7C8.C18G17 base pair step, G6G7 dihedral angle, and overall bend angle. We hypothesize that these conformational differences may be related to the ability of various DNA repair proteins, DNA binding proteins, and DNA polymerases to discriminate between cisplatin-GG and oxaliplatin-GG adducts.
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Affiliation(s)
- Yibing Wu
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599-7260
| | - Debadeep Bhattacharyya
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599-7260
| | - Candice L. King
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599-7260
| | - Irene Baskerville-Abraham
- Department of Environmental Sciences and Engineering, School of Public Health, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Sung-Ho Huh
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Gunnar Boysen
- Department of Environmental Sciences and Engineering, School of Public Health, University of North Carolina, Chapel Hill, North Carolina 27599
| | - James A. Swenberg
- Department of Environmental Sciences and Engineering, School of Public Health, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Brenda Temple
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Sharon L. Campbell
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599-7260
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
- * To whom correspondence should be addressed: Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599-7260. Telephone: (919) 966-3286. E-mail: or
| | - Stephen G. Chaney
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599-7260
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
- * To whom correspondence should be addressed: Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599-7260. Telephone: (919) 966-3286. E-mail: or
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