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Li X, Wang Z, Hao X, Zhang J, Zhao X, Yao Y, Wei W, Cai R, He C, Duan C, Guo Z, Zhao J, Wang X. Optically Pure Double-Stranded Dinuclear Ir(III) Metallohelices Enabled Chirality-Induced Photodynamic Responses. J Am Chem Soc 2023. [PMID: 37366343 DOI: 10.1021/jacs.3c03310] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Investigation on the interactions between enantiomers of chiral drugs and biomolecules can help precisely understand their biological behaviors in vivo and provide insights into the design of new drugs. Herein, we designed and synthesized a pair of optically pure, cationic, double-stranded dinuclear Ir(III)-metallohelices (Λ2R4-H and Δ2S4-H), and their dramatic enantiomer-dependent photodynamic therapy (PDT) responses were thoroughly studied in vitro and in vivo. Compared to the mononuclear enantiomeric or racemic [Ir(ppy)2(dppz)][PF6] (Λ-/Δ-Ir, rac-Ir) that with high dark toxicity and low photocytotoxicity index (PI) values, both of the optically pure metallohelices displayed negligible toxicity in the dark while exhibiting very distinctive light toxicity upon light irradiation. The PI value of Λ2R4-H was approximately 428, however, Δ2S4-H significantly reached 63,966. Interestingly, only Δ2S4-H was found to migrate from mitochondria to nucleus after light irradiation. Further proteomic analysis verified that Δ2S4-H activated the ATP-dependent migration process after light irradiation, and subsequently inhibited the activities of the nuclear proteins such as superoxide dismutase 1 (SOD1) and eukaryotic translation initiation factor 5A (EIF5A) to trigger the accumulation of superoxide anions and downregulate mRNA splicing processes. Molecular docking simulations suggested that the interactions between metallohelices and nuclear pore complex NDC1 dominated the migration process. This work presents a new kind of Ir(III) metallohelices-based agent with the highest PDT efficacy, highlights the importance of metallohelices' chirality, and provides inspirations for the future design of chiral helical metallodrugs.
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Affiliation(s)
- Xuezhao Li
- School of Chemistry, State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Zhicheng Wang
- School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xiaorou Hao
- School of Chemistry, State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Jingyi Zhang
- Chemistry and Biomedicine Innovation Center (ChemBIC), State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xing Zhao
- School of Chemistry, State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Yougang Yao
- School of Chemistry, State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Wei Wei
- School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Rui Cai
- Instrumental Analysis Center of Dalian University of Technology, Dalian University of Technology, Dalian 116024, China
| | - Cheng He
- School of Chemistry, State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Chunying Duan
- School of Chemistry, State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China
| | - Zijian Guo
- School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Jing Zhao
- Chemistry and Biomedicine Innovation Center (ChemBIC), State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xiuxiu Wang
- Chemistry and Biomedicine Innovation Center (ChemBIC), State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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2
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Zhu Y, Li Z, Wang P, Qiu QM, Ma H, Li H. The Research of G-Motif Construction and Chirality in Deoxyguanosine Monophosphate Nucleotide Complexes. Front Chem 2021; 9:709777. [PMID: 34277575 PMCID: PMC8278404 DOI: 10.3389/fchem.2021.709777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 06/07/2021] [Indexed: 11/13/2022] Open
Abstract
A detailed understanding of the mismatched base-pairing interactions in DNA will help reveal genetic diseases and provide a theoretical basis for the development of targeted drugs. Here, we utilized mononucleotide fragment to simulate mismatch DNA interactions in a local hydrophobic microenvironment. The bipyridyl-type bridging ligands were employed as a mild stabilizer to stabilize the GG mismatch containing complexes, allowing mismatch to be visualized based on X-ray crystallography. Five single crystals of 2′-deoxyguanosine–5′–monophosphate (dGMP) metal complexes were designed and obtained via the process of self-assembly. Crystallographic studies clearly reveal the details of the supramolecular interaction between mononucleotides and guest intercalators. A novel guanine–guanine base mismatch pattern with unusual (high anti)–(high anti) type of arrangement around the glycosidic angle conformations was successfully constructed. The solution state 1H–NMR, ESI–MS spectrum studies, and UV titration experiments emphasize the robustness of this g–motif in solution. Additionally, we combined the methods of single-crystal and solution-, solid-state CD spectrum together to discuss the chirality of the complexes. The complexes containing the g–motif structure, which reduces the energy of the system, following the solid-state CD signals, generally move in the long-wave direction. These results provided a new mismatched base pairing, that is g–motif. The interaction mode and full characterizations of g–motif will contribute to the study of the mismatched DNA interaction.
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Affiliation(s)
- Yanhong Zhu
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Zhongkui Li
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Pengfei Wang
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Qi-Ming Qiu
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Hongwei Ma
- Analytical and Testing Centre, Beijing Institute of Technology, Beijing, China
| | - Hui Li
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
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3
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Satange R, Chuang CY, Neidle S, Hou MH. Polymorphic G:G mismatches act as hotspots for inducing right-handed Z DNA by DNA intercalation. Nucleic Acids Res 2019; 47:8899-8912. [PMID: 31361900 PMCID: PMC6895262 DOI: 10.1093/nar/gkz653] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/06/2019] [Accepted: 07/17/2019] [Indexed: 12/13/2022] Open
Abstract
DNA mismatches are highly polymorphic and dynamic in nature, albeit poorly characterized structurally. We utilized the antitumour antibiotic CoII(Chro)2 (Chro = chromomycin A3) to stabilize the palindromic duplex d(TTGGCGAA) DNA with two G:G mismatches, allowing X-ray crystallography-based monitoring of mismatch polymorphism. For the first time, the unusual geometry of several G:G mismatches including syn–syn, water mediated anti–syn and syn–syn-like conformations can be simultaneously observed in the crystal structure. The G:G mismatch sites of the d(TTGGCGAA) duplex can also act as a hotspot for the formation of alternative DNA structures with a GC/GA-5′ intercalation site for binding by the GC-selective intercalator actinomycin D (ActiD). Direct intercalation of two ActiD molecules to G:G mismatch sites causes DNA rearrangements, resulting in backbone distortion to form right-handed Z-DNA structures with a single-step sharp kink. Our study provides insights on intercalators-mismatch DNA interactions and a rationale for mismatch interrogation and detection via DNA intercalation.
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Affiliation(s)
- Roshan Satange
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, 402, Taiwan.,Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung, 402, Taiwan
| | - Chien-Ying Chuang
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, 402, Taiwan
| | - Stephen Neidle
- The School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, 402, Taiwan.,Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung, 402, Taiwan.,Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan
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4
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5
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Satange R, Chang CK, Hou MH. A survey of recent unusual high-resolution DNA structures provoked by mismatches, repeats and ligand binding. Nucleic Acids Res 2019; 46:6416-6434. [PMID: 29945186 PMCID: PMC6061790 DOI: 10.1093/nar/gky561] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 06/08/2018] [Indexed: 12/20/2022] Open
Abstract
The structure of the DNA duplex is arguably one of the most important biological structures elucidated in modern history. DNA duplex structure is closely associated with essential biological functions such as DNA replication and RNA transcription. In addition to the classical A-, B- and Z-DNA conformations, DNA duplexes are capable of assuming a variety of alternative conformations depending on the sequence and environmental context. A considerable number of these unusual DNA duplex structures have been identified in the past decade, and some of them have been found to be closely associated with different biological functions and pathological conditions. In this manuscript, we review a selection of unusual DNA duplex structures, particularly those originating from base pair mismatch, repetitive sequence motifs and ligand-induced structures. Although the biological significance of these novel structures has not yet been established in most cases, the illustrated conformational versatility of DNA could have relevance for pharmaceutical or nanotechnology development. A perspective on the future directions of this field is also presented.
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Affiliation(s)
- Roshan Satange
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan.,Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Chung-Ke Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan.,Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung, Taiwan
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6
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Jia F, Wang S, Man Y, Kumar P, Liu B. Recent Developments in the Interactions of Classic Intercalated Ruthenium Compounds: [Ru(bpy)₂dppz] 2+ and [Ru(phen)₂dppz] 2+ with a DNA Molecule. Molecules 2019; 24:molecules24040769. [PMID: 30791625 PMCID: PMC6412511 DOI: 10.3390/molecules24040769] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/12/2019] [Accepted: 02/12/2019] [Indexed: 12/19/2022] Open
Abstract
[Ru(bpy)2dppz]2+ and [Ru(phen)2dppz]2+ as the light switches of the deoxyribose nucleic acid (DNA) molecule have attracted much attention and have become a powerful tool for exploring the structure of the DNA helix. Their interactions have been intensively studied because of the excellent photophysical and photochemical properties of ruthenium compounds. In this perspective, this review describes the recent developments in the interactions of these two classic intercalated compounds with a DNA helix. The mechanism of the molecular light switch effect and the selectivity of these two compounds to different forms of a DNA helix has been discussed. In addition, the specific binding modes between them have been discussed in detail, for a better understanding the mechanism of the light switch and the luminescence difference. Finally, recent studies of single molecule force spectroscopy have also been included so as to precisely interpret the kinetics, equilibrium constants, and the energy landscape during the process of the dynamic assembly of ligands into a single DNA helix.
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Affiliation(s)
- Fuchao Jia
- Laboratory of Functional Molecules and Materials, School of Physics and Optoelectronic Engineering, Shandong University of Technology, Zibo 255000, China.
| | - Shuo Wang
- Laboratory of Functional Molecules and Materials, School of Physics and Optoelectronic Engineering, Shandong University of Technology, Zibo 255000, China.
| | - Yan Man
- Beijing Research Center for Agricultural Standards and Testing, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
| | - Parveen Kumar
- Laboratory of Functional Molecules and Materials, School of Physics and Optoelectronic Engineering, Shandong University of Technology, Zibo 255000, China.
| | - Bo Liu
- Laboratory of Functional Molecules and Materials, School of Physics and Optoelectronic Engineering, Shandong University of Technology, Zibo 255000, China.
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7
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Keane PM, Tory J, Towrie M, Sazanovich IV, Cardin CJ, Quinn SJ, Hartl F, Kelly JM, Long C. Spectro-electrochemical Studies on [Ru(TAP) 2(dppz)] 2+-Insights into the Mechanism of its Photosensitized Oxidation of Oligonucleotides. Inorg Chem 2018; 58:663-671. [PMID: 30540448 DOI: 10.1021/acs.inorgchem.8b02859] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[Ru(TAP)2(dppz)]2+ (TAP = 1,4,5,8-tetraazaphenanthrene; dppz = dipyrido[3,2- a:2',3'- c]phenazine) is known to photo-oxidize guanine in DNA. Whether this oxidation proceeds by direct photoelectron transfer or by proton-coupled electron transfer is still unknown. To help distinguish between these mechanisms, spectro-electrochemical experiments have been carried out with [Ru(TAP)2(dppz)]2+ in acetonitrile. The UV-vis and mid-IR spectra obtained for the one-electron reduced product were compared to those obtained by picosecond transient absorption and time-resolved infrared experiments of [Ru(TAP)2(dppz)]2+ bound to guanine-containing DNA. An interesting feature of the singly reduced species is an electronic transition in the near-IR region (with λmax at 1970 and 2820 nm). Density functional and time-dependent density functional theory simulations of the vibrational and electronic spectra of [Ru(TAP)2(dppz)]2+, the reduced complex [Ru(TAP)2(dppz)]+, and four isomers of [Ru(TAP)(TAPH)(dppz)]2+ (a possible product of proton-coupled electron transfer) were performed. Significantly, these predict absorption bands at λ > 1900 nm (attributed to a ligand-to-metal charge-transfer transition) for [Ru(TAP)2(dppz)]+ but not for [Ru(TAP)(TAPH)(dppz)]2+. Both the UV-vis and mid-IR difference absorption spectra of the electrochemically generated singly reduced species [Ru(TAP)2(dppz)]+ agree well with the transient absorption and time-resolved infrared spectra previously determined for the transient species formed by photoexcitation of [Ru(TAP)2(dppz)]2+ intercalated in guanine-containing DNA. This suggests that the photochemical process in DNA proceeds by photoelectron transfer and not by a proton-coupled electron transfer process involving formation of [Ru(TAP)(TAPH)(dppz)]2+, as is proposed for the reaction with 5'-guanosine monophosphate. Additional infrared spectro-electrochemical measurements and density functional calculations have also been carried out on the free TAP ligand. These show that the TAP radical anion in acetonitrile also exhibits strong broad near-IR electronic absorption (λmax at 1750 and 2360 nm).
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Affiliation(s)
- Páraic M Keane
- School of Chemistry , University of Dublin, Trinity College , Dublin 2 , Ireland.,Department of Chemistry , University of Reading , Whiteknights, Reading RG6 6AD , United Kingdom
| | - Joanne Tory
- Department of Chemistry , University of Reading , Whiteknights, Reading RG6 6AD , United Kingdom
| | - Michael Towrie
- Science and Technology Facilities Council , Rutherford Appleton Laboratory, Research Complex at Harwell , Didcot, Oxfordshire OX11 0QX , United Kingdom
| | - Igor V Sazanovich
- Science and Technology Facilities Council , Rutherford Appleton Laboratory, Research Complex at Harwell , Didcot, Oxfordshire OX11 0QX , United Kingdom
| | - Christine J Cardin
- Department of Chemistry , University of Reading , Whiteknights, Reading RG6 6AD , United Kingdom
| | - Susan J Quinn
- School of Chemistry , University College Dublin , Belfield, Dublin 4 , Ireland
| | - František Hartl
- Department of Chemistry , University of Reading , Whiteknights, Reading RG6 6AD , United Kingdom
| | - John M Kelly
- School of Chemistry , University of Dublin, Trinity College , Dublin 2 , Ireland
| | - Conor Long
- School of Chemical Sciences , Dublin City University , Dublin 9 , Ireland
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8
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McQuaid K, Hall JP, Brazier JA, Cardin DJ, Cardin CJ. X-ray Crystal Structures Show DNA Stacking Advantage of Terminal Nitrile Substitution in Ru-dppz Complexes. Chemistry 2018; 24:15859-15867. [DOI: 10.1002/chem.201803021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 07/26/2018] [Indexed: 12/24/2022]
Affiliation(s)
- Kane McQuaid
- Department of Chemistry; University of Reading; Whiteknights Reading RG6 6AD UK
- Diamond Light Source; Harwell Science and Innovation Campus; Didcot Oxfordshire OX11 0DE UK
| | - James P. Hall
- Department of Chemistry; University of Reading; Whiteknights Reading RG6 6AD UK
- Department of Pharmacy; University of Reading; Whiteknights Reading RG6 6AD UK
- Diamond Light Source; Harwell Science and Innovation Campus; Didcot Oxfordshire OX11 0DE UK
| | - John A. Brazier
- Department of Pharmacy; University of Reading; Whiteknights Reading RG6 6AD UK
| | - David J. Cardin
- Department of Chemistry; University of Reading; Whiteknights Reading RG6 6AD UK
| | - Christine J. Cardin
- Department of Chemistry; University of Reading; Whiteknights Reading RG6 6AD UK
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9
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Keane PM, Kelly JM. Transient absorption and time-resolved vibrational studies of photophysical and photochemical processes in DNA-intercalating polypyridyl metal complexes or cationic porphyrins. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2018.02.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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10
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Keane PM, Hall JP, Poynton FE, Poulsen BC, Gurung SP, Clark IP, Sazanovich IV, Towrie M, Gunnlaugsson T, Quinn SJ, Cardin CJ, Kelly JM. Inosine Can Increase DNA′s Susceptibility to Photo‐oxidation by a RuIIComplex due to Structural Change in the Minor Groove. Chemistry 2017; 23:10344-10351. [DOI: 10.1002/chem.201701447] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Páraic M. Keane
- Department of ChemistryUniversity of Reading, Whiteknights Reading RG6 6AD UK
- School of ChemistryTrinity College Dublin Dublin 2 Ireland
| | - James P. Hall
- Department of ChemistryUniversity of Reading, Whiteknights Reading RG6 6AD UK
- Diamond Light Source, Harwell Science and Innovation CampusDidcot Oxfordshire OX11 0DE UK
| | - Fergus E. Poynton
- School of ChemistryTrinity College Dublin Dublin 2 Ireland
- Trinity Biomedical Sciences Institute Pearse St. Dublin 2 Ireland
| | - Bjørn C. Poulsen
- School of ChemistryTrinity College Dublin Dublin 2 Ireland
- Trinity Biomedical Sciences Institute Pearse St. Dublin 2 Ireland
| | - Sarah P. Gurung
- Department of ChemistryUniversity of Reading, Whiteknights Reading RG6 6AD UK
- Diamond Light Source, Harwell Science and Innovation CampusDidcot Oxfordshire OX11 0DE UK
| | - Ian P. Clark
- Central Laser FacilityResearch Complex at Harwell, STFC Rutherford Appleton LaboratoriesDidcot Oxfordshire OX11 0QX UK
| | - Igor V. Sazanovich
- Central Laser FacilityResearch Complex at Harwell, STFC Rutherford Appleton LaboratoriesDidcot Oxfordshire OX11 0QX UK
| | - Michael Towrie
- Central Laser FacilityResearch Complex at Harwell, STFC Rutherford Appleton LaboratoriesDidcot Oxfordshire OX11 0QX UK
| | - Thorfinnur Gunnlaugsson
- School of ChemistryTrinity College Dublin Dublin 2 Ireland
- Trinity Biomedical Sciences Institute Pearse St. Dublin 2 Ireland
| | - Susan J. Quinn
- School of ChemistryUniversity College Dublin, Belfield Dublin 4 Ireland
| | - Christine J. Cardin
- Department of ChemistryUniversity of Reading, Whiteknights Reading RG6 6AD UK
| | - John M. Kelly
- School of ChemistryTrinity College Dublin Dublin 2 Ireland
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11
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Cardin CJ, Kelly JM, Quinn SJ. Photochemically active DNA-intercalating ruthenium and related complexes - insights by combining crystallography and transient spectroscopy. Chem Sci 2017; 8:4705-4723. [PMID: 28936338 PMCID: PMC5596416 DOI: 10.1039/c7sc01070b] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 04/05/2017] [Indexed: 11/21/2022] Open
Abstract
Recent research on the study of the interaction of ruthenium polypyridyl compounds and defined sequence nucleic acids is reviewed. Particular emphasis is paid to complexes [Ru(LL)2(Int)]2+ containing potentially intercalating ligands (Int) such as dipyridophenazine (dppz), which are known to display light-switching or photo-oxidising behaviour, depending on the nature of the ancillary ligands. X-ray crystallography has made a key contribution to our understanding, and the first complete survey of structural results is presented. These include sequence, enantiomeric, substituent and structural specificities. The use of ultrafast transient spectroscopic methods to probe the ultrafast processes for complexes such as [Ru(TAP)2(dppz)]2+ and [Ru(phen)2(dppz)]2+ when bound to mixed sequence oligonucleotides are reviewed with particular attention being paid to the complementary advantages of transient (visible) absorption and time-resolved (mid) infra-red techniques to probe spectral changes in the metal complex and in the nucleic acid. The observed photophysical properties are considered in light of the structural information obtained from X-ray crystallography. In solution, metal complexes can be expected to bind at more than one DNA step, so that a perfect correlation of the photophysical properties and factors such as the orientation or penetration of the ligand into the intercalation pocket should not be expected. This difficulty can be obviated by carrying out TRIR studies in the crystals. Dppz complexes also undergo insertion, especially with mismatched sequences. Future areas for study such as those involving non-canonical forms of DNA, such as G-quadruplexes or i-motifs are also briefly considered.
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Affiliation(s)
- Christine J Cardin
- School of Chemistry , University of Reading , Whiteknights , RG6 6AD , UK .
| | - John M Kelly
- School of Chemistry , Trinity College Dublin , Dublin 2 , Ireland .
| | - Susan J Quinn
- School of Chemistry , University College Dublin , Belfield , Dublin 4 , Ireland .
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12
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Mikek CG, DuPont JI, Machha VR, White JC, Martin LR, Alatrash N, MacDonnell FM, Lewis EA. The Thermodynamic Effects of Ligand Structure on the Molecular Recognition of Mononuclear Ruthenium Polypyridyl Complexes with B‐DNA. Eur J Inorg Chem 2017. [DOI: 10.1002/ejic.201700462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Clinton G. Mikek
- Department of Chemistry Mississippi State University 39762 Mississippi State Mississippi USA
| | - Jesse I. DuPont
- Department of Chemistry Mississippi State University 39762 Mississippi State Mississippi USA
- USDA‐ARS Grazinglands Laboratory Forage and Livestock Production Research Unit 73036 El Reno Oklahoma USA
| | - Venkata R. Machha
- Division of Hematology Departments of Internal Medicine and Biochemistry and Molecular Biology Mayo Clinic 55905 Rochester Minnesota USA
| | - Jake C. White
- Department of Chemistry Mississippi State University 39762 Mississippi State Mississippi USA
| | - Logan R. Martin
- Department of Chemistry Mississippi State University 39762 Mississippi State Mississippi USA
| | - Nagham Alatrash
- Department of Chemistry and Biochemistry University of Texas at Arlington 76019 Arlington Texas USA
| | - Frederick M. MacDonnell
- Department of Chemistry and Biochemistry University of Texas at Arlington 76019 Arlington Texas USA
| | - Edwin A. Lewis
- Department of Chemistry Mississippi State University 39762 Mississippi State Mississippi USA
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13
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Galliot A, Gil A, Calhorda MJ. Effects of oxygenation on the intercalation of 1,10-phenanthroline-5,6/4,7-dione between DNA base pairs: a computational study. Phys Chem Chem Phys 2017. [PMID: 28621352 DOI: 10.1039/c7cp00532f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The effects of oxygen in positions 4,7 and 5,6 of phenanthroline have been studied computationally when this ligand intercalates between DNA base pairs. Our results indicate that solvation energy could be the driving force of the process and thus, it can be also related with the cytotoxicity of the drug.
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Affiliation(s)
- Aurellia Galliot
- Centro de Química e Bioquímica
- DQB
- Faculdade de Ciências
- Universidade de Lisboa
- Campo Grande 1749-016 Lisboa
| | - Adrià Gil
- Centro de Química e Bioquímica
- DQB
- Faculdade de Ciências
- Universidade de Lisboa
- Campo Grande 1749-016 Lisboa
| | - Maria José Calhorda
- Centro de Química e Bioquímica
- DQB
- Faculdade de Ciências
- Universidade de Lisboa
- Campo Grande 1749-016 Lisboa
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14
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Chen L, Chao H, Zhao Q, Zheng X, Li H. Photoluminescence quenching of [Ru(bpy)2(atatp)]2+ bound to a condensed DNA matrix. J Inorg Biochem 2016; 154:1-6. [DOI: 10.1016/j.jinorgbio.2015.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Revised: 09/24/2015] [Accepted: 10/05/2015] [Indexed: 12/25/2022]
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15
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Li G, Sun L, Ji L, Chao H. Ruthenium(ii) complexes with dppz: from molecular photoswitch to biological applications. Dalton Trans 2016; 45:13261-76. [DOI: 10.1039/c6dt01624c] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The present article describes the recent advances in biological applications of the Ru-dppz systems in DNA binding, cellular imaging, anticancer drugs, phototherapy, protein aggregation detecting and chemosensors.
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Affiliation(s)
- Guanying Li
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-sen University
- Guangzhou
- P. R. China
| | - Lingli Sun
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-sen University
- Guangzhou
- P. R. China
| | - Liangnian Ji
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-sen University
- Guangzhou
- P. R. China
| | - Hui Chao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-sen University
- Guangzhou
- P. R. China
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16
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Monitoring one-electron photo-oxidation of guanine in DNA crystals using ultrafast infrared spectroscopy. Nat Chem 2015; 7:961-7. [PMID: 26587711 DOI: 10.1038/nchem.2369] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 09/04/2015] [Indexed: 12/19/2022]
Abstract
To understand the molecular origins of diseases caused by ultraviolet and visible light, and also to develop photodynamic therapy, it is important to resolve the mechanism of photoinduced DNA damage. Damage to DNA bound to a photosensitizer molecule frequently proceeds by one-electron photo-oxidation of guanine, but the precise dynamics of this process are sensitive to the location and the orientation of the photosensitizer, which are very difficult to define in solution. To overcome this, ultrafast time-resolved infrared (TRIR) spectroscopy was performed on photoexcited ruthenium polypyridyl-DNA crystals, the atomic structure of which was determined by X-ray crystallography. By combining the X-ray and TRIR data we are able to define both the geometry of the reaction site and the rates of individual steps in a reversible photoinduced electron-transfer process. This allows us to propose an individual guanine as the reaction site and, intriguingly, reveals that the dynamics in the crystal state are quite similar to those observed in the solvent medium.
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Klingl S, Scherer M, Stamminger T, Muller YA. Controlled crystal dehydration triggers a space-group switch and shapes the tertiary structure of cytomegalovirus immediate-early 1 (IE1) protein. ACTA ACUST UNITED AC 2015; 71:1493-504. [PMID: 26143921 DOI: 10.1107/s1399004715008792] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 05/06/2015] [Indexed: 11/10/2022]
Abstract
Cytomegalovirus immediate-early 1 (IE1) protein is a key viral effector protein that reprograms host cells. Controlled dehydration experiments with IE1 crystals not only extended their diffraction limit from 2.85 to 2.3 Å resolution but also triggered a monoclinic to tetragonal space-group transition with only minor alterations in the unit-cell parameters. An analysis of the pre-dehydration and post-dehydration crystal structures shows how dehydration rearranges the packing of IE1 molecules to meet the unit-cell constraints of the higher lattice symmetry. The transition from P21 to P43 reduces the number of copies in the asymmetric unit from four to two, and molecules previously related by noncrystallographic symmetry merge into identical crystallographic copies in the tetragonal space group. At the same time, dehydration considerably alters the tertiary structure of one of the two remaining IE1 chains in the asymmetric unit. It appears that this conformational switch is required to compensate for a transition that is assumed to be unfavourable, namely from a highly preferred to a rarely observed space group. At the same time, the dehydration-triggered molecular reshaping could reveal an inherent molecular flexibility that possibly informs on the biological function of IE1, namely on its binding to target proteins from the host cell.
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Affiliation(s)
- Stefan Klingl
- Division of Biotechnology, Department of Biology, Friedrich-Alexander University Erlangen-Nuremberg, Henkestrasse 91, 91052 Erlangen, Germany
| | - Myriam Scherer
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University Erlangen-Nuremberg, Schlossgarten 4, 91054 Erlangen, Germany
| | - Thomas Stamminger
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University Erlangen-Nuremberg, Schlossgarten 4, 91054 Erlangen, Germany
| | - Yves A Muller
- Division of Biotechnology, Department of Biology, Friedrich-Alexander University Erlangen-Nuremberg, Henkestrasse 91, 91052 Erlangen, Germany
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Hall JP, Beer H, Buchner K, Cardin DJ, Cardin CJ. The Structural Effect of Methyl Substitution on the Binding of Polypyridyl Ru–dppz Complexes to DNA. Organometallics 2015. [DOI: 10.1021/om501208x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- James P. Hall
- Department
of Chemistry, University of Reading, Whiteknights, Reading, Berkshire RG6 6AD, U.K
- Diamond Light Source, Harwell Science and Innovation
Campus, Fermi Avenue, Didcot, Oxfordshire OX11 0QX, U.K
| | - Hanna Beer
- Department
of Chemistry, University of Reading, Whiteknights, Reading, Berkshire RG6 6AD, U.K
| | - Katrin Buchner
- Department
of Chemistry, University of Reading, Whiteknights, Reading, Berkshire RG6 6AD, U.K
| | - David J. Cardin
- Department
of Chemistry, University of Reading, Whiteknights, Reading, Berkshire RG6 6AD, U.K
| | - Christine J. Cardin
- Department
of Chemistry, University of Reading, Whiteknights, Reading, Berkshire RG6 6AD, U.K
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