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Abstract
Threading intercalators bind DNA with high affinities. Here, we describe single-molecule studies on a cell-permeant luminescent dinuclear ruthenium(II) complex that has been previously shown to thread only into short, unstable duplex structures. Using optical tweezers and confocal microscopy, we show that this complex threads and locks into force-extended duplex DNA in a two-step mechanism. Detailed kinetic studies reveal that an individual stereoisomer of the complex exhibits the highest binding affinity reported for such a mono-intercalator. This stereoisomer better preserves the biophysical properties of DNA than the widely used SYTOX Orange. Interestingly, threading into torsionally constrained DNA decreases dramatically, but is rescued on negatively supercoiled DNA. Given the "light-switch" properties of this complex on binding DNA, it can be readily used as a long-lived luminescent label for duplex or negatively supercoiled DNA through a unique "load-and-lock" protocol.
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Anticancer effect evaluation in vitro and in vivo of iridium(III) polypyridyl complexes targeting DNA and mitochondria. Bioorg Chem 2021; 115:105290. [PMID: 34426145 DOI: 10.1016/j.bioorg.2021.105290] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/30/2021] [Accepted: 08/16/2021] [Indexed: 12/26/2022]
Abstract
To investigate the antitumor effect of iridium complexes, three iridium (III) complexes [Ir(ppy)2(dcdppz)]PF6 (ppy = 2-phenylpyridine, dcdppz = 11,12-dichlorodipyrido[3,2-a:2',3'-c]phenazine) (Ir1), [Ir(bzq)2(dcdppz)]PF6 (bzq = benzo[h]quinoline) (Ir2) and [Ir(piq)2(dcdppz)]PF6 (piq = 1-phenylisoquinoline) (Ir3) were synthesized and characterized. Geometry optimization, molecular dynamics simulation and docking studies have been performed to further explore the antitumor mechanism. The cytotoxicity of Ir1-3 toward cancer cells was studied by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) method. The localization of complexes Ir1-3 in the mitochondria, intracellular accumulation of reactive oxygen species (ROS) levels, the changes of mitochondrial membrane potential and morphological changes in apoptosis were investigated. Flow cytometry was applied to quantify fluorescence intensity and determine cell cycle distribution. Western blotting was used to detect the expression of apoptosis-related proteins. The anti-tumor effect of Ir1 in vivo was evaluated. The results showed that Ir1-3 had high cytotoxicity to most tumor cells, especially to SGC-7901 cells with a low IC50 value. Ir1-3 can increase the intracellular ROS levels, reduce the mitochondrial membrane potential. Additionally, the complexes induce an increase of apoptosis-related protein expression, enhance the percentage of apoptosis. The complexes inhibit the cell proliferation at G0/G1 phase. The results obtained from antitumor in vivo indicate that Ir1 can significantly inhibit the growth of tumors with an inhibitory rate of 54.08%. The docking studies show that complexes Ir1-3 interact with DNA through minor-groove intercalation, which increases the distance of DNA base pairs, leading to a change of DNA helix structure. These experimental and theoretical findings indicate that complexes Ir1-3 can induce apoptosis in SGC-7901 cells through the mitochondrial dysfunction and DNA damage pathways, and then exerting anti-tumor activity in vitro and vivo.
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DNA Minor Groove-Induced cis- trans Isomerization of a Near-Infrared Fluorescent Probe. Biochemistry 2021; 60:2084-2097. [PMID: 34142803 DOI: 10.1021/acs.biochem.1c00281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The discovery of small molecules that exhibit turn-on far-red or near-infrared (NIR) fluorescence upon DNA binding and understanding how they bind DNA are important for imaging and bioanalytical applications. Here we report the DNA-bound structure and the DNA binding mechanism of quinone cyanine dithiazole (QCy-DT), a recently reported AT-specific turn-on NIR fluorescent probe for double-stranded DNA. The nuclear magnetic resonance (NMR)-derived structure showed minor groove binding but no specific ligand-DNA interactions, consistent with an endothermic and entropy-driven binding mechanism deduced from isothermal titration calorimetry. Minor groove binding is typically fast because it minimally perturbs the DNA structure. However, QCy-DT exhibited unusually slow DNA binding. The cyanine-based probe is capable of cis-trans isomerization due to overlapping methine bridges, with 16 possible slowly interconverting cis/trans isomers. Using NMR, density functional theory, and free energy calculations, we show that the DNA-free and DNA-bound environments of QCy-DT prefer distinctly different isomers, indicating that the origin of the slow kinetics is a cis-trans isomerization and that the minor groove preferentially selects an otherwise unstable cis/trans isomer of QCy-DT. Flux analysis showed the conformational selection pathway to be the dominating DNA binding mechanism at low DNA concentrations, which switches to the induced fit pathway at high DNA concentrations. This report of cis/trans isomerization of a ligand, upon binding the DNA minor groove, expands the prevailing understanding of unique discriminatory powers of the minor groove and has an important bearing on using polymethine cyanine dyes to probe the kinetics of molecular interactions.
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DNA-Targeted Metallodrugs: An Untapped Source of Artificial Gene Editing Technology. Chembiochem 2021; 22:2184-2205. [PMID: 33570813 DOI: 10.1002/cbic.202000838] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 02/09/2021] [Indexed: 12/20/2022]
Abstract
DNA binding metal complexes are synonymous with anticancer drug discovery. Given the array of structural and chemical reactivity properties available through careful design, metal complexes have been directed to bind nucleic acid structures through covalent or noncovalent binding modes. Several recognition modes - including crosslinking, intercalation, and oxidation - are central to the clinical success of broad-spectrum anticancer metallodrugs. However, recent progress in nucleic acid click chemistry coupled with advancement in our understanding of metal complex-nucleic acid interactions has opened up new avenues in genetic engineering and targeted therapies. Several of these applications are enabled by the hybridisation of oligonucleotide or polyamine probes to discrete metal complexes, which facilitate site-specific reactivity at the nucleic acid interface under the guidance of the probe. This Review focuses on recent advancements in hybrid design and, by way of an introduction to this topic, we provide a detailed overview of nucleic acid structures and metal complex-nucleic acid interactions. Our aim is to provide readers with an insight on the rational design of metal complexes with DNA recognition properties and an understanding of how the sequence-specific targeting of these interactions can be achieved for gene engineering applications.
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DNA threading intercalation of enantiopure [Ru(phen) 2bidppz] 2+ induced by hydrophobic catalysis. Phys Chem Chem Phys 2021; 23:2238-2244. [PMID: 33439155 DOI: 10.1039/d0cp00845a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The enantiomers of a novel mononuclear ruthenium(ii) complex [Ru(phen)2bidppz]2+ with an elongated dppz moiety were synthesized. Surprisingly, the complex showed no DNA intercalating capability in an aqueous environment. However, by the addition of water-miscible polyethylene glycol ether PEG-400, self-aggregation of the hydrophobic ruthenium(ii) complexes was counter-acted, thus strongly promoting the DNA intercalation binding mode. This mild alteration of the environment surrounding the DNA polymer does not damage or alter the DNA structure but instead enables more efficient binding characterization studies of potential DNA binding drugs.
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Structural Investigation into the Threading Intercalation of a Chiral Dinuclear Ruthenium(II) Polypyridyl Complex through a B-DNA Oligonucleotide. J Am Chem Soc 2019; 141:4644-4652. [PMID: 30799603 DOI: 10.1021/jacs.8b12280] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Herein we report the separation of the three stereoisomers of the DNA light-switch compound [{Ru(bpy)2}2(tpphz)]4+ (tpphz = tetrapyrido[3,2-a:2',3'-c:3″,2″-h:2‴,3‴-j]phenazine) by column chromatography and the characterization of each stereoisomer by X-ray crystallography. The interaction of these compounds with a DNA octanucleotide d(GCATATCG).d(CGATATGC) has been studied using NMR techniques. Selective deuteration of the bipyridyl rings was needed to provide sufficient spectral resolution to characterize structures. NMR-derived structures for these complexes show a threading intercalation binding mode with slow and chirality-dependent rates. This represents the first solution structure of an intercalated bis-ruthenium ligand. Intriguingly, we find that the binding site selectivity is dependent on the nature of the stereoisomer employed, with Λ RuII centers showing a better intercalation fit.
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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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Stepwise synthesis, characterization, DNA binding properties and cytotoxicity of diruthenium oligopyridine compounds conjugated with peptides. Dalton Trans 2018; 47:3549-3567. [PMID: 29436543 DOI: 10.1039/c7dt04639a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Although the interactions of oligopyridine ruthenium complexes with DNA have been widely studied, the biological activity of similar diruthenium oligopyridine complexes conjugated with peptides has not been investigated. Herein, we report the stepwise synthesis and characterization of diruthenium complexes with the general formula [(La)Ru(tppz)Ru(Lb)]n+ (tppz = 2,3,5,6-tetra(2-pyridyl)pyrazine, La = 2,2':6',2''-terpyridine or 4-phenyl-2,2':6',2''-terpyridine and Lb = 2,2':6',2''-terpyridine-4'-CO(Gly1-Gly2-Gly3-LysCONH2) (5), (6), n = 5; 2,2':6',2''-terpyridine-4'-CO(Gly1-Gly2-Lys1-Lys2CONH2) (7), (8), n = 6; 2,2':6',2''-terpyridine-4'-CO(Ahx-Lys1Lys2CONH2) (9), (10), n = 5, Ahx = 6-aminohexanoic acid). The compounds [(trpy)Ru(tppz)Ru(trpy-CO2H)](PF6)4, (2)(PF6)4, [(ptrpy)Ru(tppz)Ru(trpy-CO2H)](PF6)4, (3)(PF6)4 and [(ptrpy)Ru(tppz)Ru(trpy)](PF6)4, (4)(PF6)4 were also characterized by single crystal X-ray methods. Moreover, the interactions of the chloride salts (5), (6) and (4) with the self-complementary dodecanucleotide duplex d(5'-CGCGAATTCGCG-3')2 were studied by NMR spectroscopic techniques. The results show that complex (4) binds in the central part of the oligonucleotide, from the minor groove through the ligand ptrpy, while the ligand trpy, which was located on the other side of the diruthenium core, does not contribute to the binding. Complex (5) binds similarly, through the ligand ptrpy. However, the induced upfield shifts of the ptrpy proton signals are significantly lower than the corresponding ones in the case of (4), indicating much lower binding affinity. This is clear evidence that the tethered peptide Gly1-Gly2-Gly3-Lys1CONH2 hinders the complex binding, even though it contains groups that are able to assist it (e.g., the positively charged amino group of lysine, the peptidic backbone, the terminal amide). Complex (6) shows a non-specific binding, interacting through electrostatic forces. The chloride salts of (4), (5) and (6) had insignificant effects on the cell cycle distribution and marginal cytotoxicity (IC50 > 750 μM) against human lung cancer cell lines H1299 and H1437, indicating that their binding to the oligonucleotide is not a sufficient condition for their cytotoxicity.
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Bimetallic Ru(ii) and Os(ii) complexes based on a pyrene-bisimidazole spacer: synthesis, photophysics, electrochemistry and multisignalling DNA binding studies in the near infrared region. Dalton Trans 2018; 46:17010-17024. [PMID: 29184930 DOI: 10.1039/c7dt03355a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We report in this paper the synthesis, characterization, photophysical and electrochemical properties, and detailed DNA binding affinities of two homobimetallic Ru(ii) and Os(ii) complexes derived from a new bridging ligand consisting of two pyridyl-imidazole coordinating units rigidly coupled with a central pyrene moiety. The structure of the diruthenium complex was confirmed by X-ray crystallography. Both complexes exhibit luminescence at room temperature from their 3MLCT states, with lifetimes of τ1 = 12.6 ns and τ2 = 48.8 ns for the Ru(ii) complex (1) and τ1 = 23.7 ns for the Os(ii) complex (2). For 2, the luminescence maximum stretches to the NIR region, which is suitable for potential biological applications. Both complexes exhibit two successive one-electron reversible metal-centered oxidations in the positive potential window. Computational studies employing DFT and TD-DFT methods were also performed to assign the experimentally observed optical spectral bands in the complexes. The binding affinities of the complexes towards DNA were thoroughly investigated through a variety of techniques, viz. absorption, luminescence, excited state lifetime, circular dichroism, thermal denaturation, viscosity measurement, and relative DNA binding studies using ethidium bromide. Finally, molecular docking studies were also carried out to visualize the modes of interaction between the complexes and DNA.
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Isolation and structural analysis of the covalent adduct formed between a bis-amino mitoxantrone analogue and DNA: a pathway to major-minor groove cross-linked adducts. Org Biomol Chem 2018; 14:10217-10221. [PMID: 27735959 DOI: 10.1039/c6ob02100j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The major covalent adduct formed between a 13C-labelled formaldehyde activated bis-amino mitoxantrone analogue (WEHI-150) and the hexanucleotide d(CG5MeCGCG)2 has been isolated by HPLC chromatography and the structure determined by NMR spectroscopy. The results indicate that WEHI-150 forms one covalent bond through a primary amine to the N-2 of the G2 residue, with the polycyclic ring structure intercalated at the 5MeC3pG4/G10p5MeC9 site. Furthermore, the WEHI-150 aromatic ring system is oriented approximately parallel to the long axis of the base pairs, with one aliphatic side-chain in the major groove and the other side-chain in the minor groove. This study indicates that mitoxantrone derivatives like WEHI-150 should be capable of forming major-minor groove cross-linked adducts that will likely produce considerably different intracellular biological properties compared to known anthracycline and anthracenedione anticancer drugs.
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Turning intercalators into groove binders: synthesis, photophysics and DNA binding properties of tetracationic mononuclear ruthenium(ii)-based chromophore–quencher complexes. Dalton Trans 2018; 47:12300-12307. [DOI: 10.1039/c8dt02633e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Despite incorporating an extended planar polyaromatic ligand two newly synthesized RuII complexes are not DNA intercalators but groove binders.
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The Structure of Linkers Affects the DNA Binding Properties of Tethered Dinuclear Ruthenium(II) Metallo-Intercalators. Chemistry 2017; 23:5467-5477. [PMID: 28072487 DOI: 10.1002/chem.201605750] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Indexed: 12/12/2022]
Abstract
With the long-term aim of enhancing the binding properties of dinuclear RuII -based DNA light-switch complexes, a series of eight structurally related mono- and dinuclear systems are reported in which the linker of the bridging ligand has been modulated. These tethered systems have been designed to explore issues of steric demand at the binding site and the thermodynamic cost of entropy loss upon binding. Detailed spectroscopic and isothermal titration calorimetry (ITC) studies on the new complexes reveal that one of the linkers produces a dinuclear system that binds to duplex DNA with an affinity (Kb >107 m-1 ) that is higher than its corresponding monometallic complex and is the highest affinity for a non-threading bis-intercalating metal complex. These studies confirm that the tether has a major effect on the binding properties of dinuclear complexes containing intercalating units and establishes key design rules for the construction of dinuclear complexes with enhanced DNA binding characteristics.
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Imidazolyl-Naphthalenediimide-Based Threading Intercalators of DNA. Chembiochem 2016; 17:2162-2171. [DOI: 10.1002/cbic.201600478] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Indexed: 12/22/2022]
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Counterintuitive Solid-State Syntheses of Indium-Thiolate-Phen Cations as Efficient and Selective Fluorescent Biosensors for HIV-1 ds-DNA and Sudan Ebolavirus RNA Sequences. ChemistrySelect 2016. [DOI: 10.1002/slct.201600554] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Mechanisms of small molecule-DNA interactions probed by single-molecule force spectroscopy. Nucleic Acids Res 2016; 44:3971-88. [PMID: 27085806 PMCID: PMC4872107 DOI: 10.1093/nar/gkw237] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 03/24/2016] [Indexed: 12/31/2022] Open
Abstract
There is a wide range of applications for non-covalent DNA binding ligands, and optimization of such interactions requires detailed understanding of the binding mechanisms. One important class of these ligands is that of intercalators, which bind DNA by inserting aromatic moieties between adjacent DNA base pairs. Characterizing the dynamic and equilibrium aspects of DNA-intercalator complex assembly may allow optimization of DNA binding for specific functions. Single-molecule force spectroscopy studies have recently revealed new details about the molecular mechanisms governing DNA intercalation. These studies can provide the binding kinetics and affinity as well as determining the magnitude of the double helix structural deformations during the dynamic assembly of DNA–ligand complexes. These results may in turn guide the rational design of intercalators synthesized for DNA-targeted drugs, optical probes, or integrated biological self-assembly processes. Herein, we survey the progress in experimental methods as well as the corresponding analysis framework for understanding single molecule DNA binding mechanisms. We discuss briefly minor and major groove binding ligands, and then focus on intercalators, which have been probed extensively with these methods. Conventional mono-intercalators and bis-intercalators are discussed, followed by unconventional DNA intercalation. We then consider the prospects for using these methods in optimizing conventional and unconventional DNA-intercalating small molecules.
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Preparation of ds-DNA functionalized magnetic nanobaits for screening of bioactive compounds from medicinal plant. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2015; 56:401-8. [DOI: 10.1016/j.msec.2015.06.050] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 05/23/2015] [Accepted: 06/25/2015] [Indexed: 11/22/2022]
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Reversal of a Single Base-Pair Step Controls Guanine Photo-Oxidation by an Intercalating Ruthenium(II) Dipyridophenazine Complex. Angew Chem Int Ed Engl 2015; 54:8364-8. [PMID: 26096623 PMCID: PMC4985698 DOI: 10.1002/anie.201502608] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 04/20/2015] [Indexed: 01/05/2023]
Abstract
Small changes in DNA sequence can often have major biological effects. Here the rates and yields of guanine photo‐oxidation by Λ‐[Ru(TAP)2(dppz)]2+ have been compared in 5′‐{CCGGATCCGG}2 and 5′‐{CCGGTACCGG}2 using pico/nanosecond transient visible and time‐resolved IR (TRIR) spectroscopy. The inefficiency of electron transfer in the TA sequence is consistent with the 5′‐TA‐3′ versus 5′‐AT‐3′ binding preference predicted by X‐ray crystallography. The TRIR spectra also reveal the differences in binding sites in the two oligonucleotides.
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Reversal of a Single Base-Pair Step Controls Guanine Photo-Oxidation by an Intercalating Ruthenium(II) Dipyridophenazine Complex. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502608] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Synthesis, characterization, biological evaluation and molecular docking of steroidal spirothiazolidinones. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2014.12.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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A unique perylene-based DNA intercalator: localization in cell nuclei and inhibition of cancer cells and tumors. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:4087-4092. [PMID: 24976526 DOI: 10.1002/smll.201401262] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 05/22/2014] [Indexed: 06/03/2023]
Abstract
To date, perylene derivatives have not been explored as DNA intercalator to inhibit cancer cells by intercalating into the base pairs of DNA. Herein, a water-soluble perylene bisimide (PBDI) that efficiently intercalates into the base pairs of DNA is synthesized. Excitingly, PBDI is superior to the commercial DNA intercalator, amonafide, for specific nuclear accumulation and effective suppression of cancer cells and tumors.
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Abstract
Copper complexes from Schiff-base ligands show high cytotoxicity against diverse cancer cell lines, with IC50 values down to 0.23 μM.
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Structural studies on dinuclear ruthenium(II) complexes that bind diastereoselectively to an antiparallel folded human telomere sequence. J Med Chem 2013; 56:8674-83. [PMID: 24088028 PMCID: PMC3835060 DOI: 10.1021/jm401119b] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
We report DNA binding studies of
the dinuclear ruthenium ligand
[{Ru(phen)2}2tpphz]4+ in enantiomerically
pure forms. As expected from previous studies of related complexes,
both isomers bind with similar affinity to B-DNA and have enhanced
luminescence. However, when tested against the G-quadruplex from human
telomeres (which we show to form an antiparallel basket structure
with a diagonal loop across one end), the ΛΛ isomer binds
approximately 40 times more tightly than the ΔΔ, with
a stronger luminescence. NMR studies show that the complex binds at
both ends of the quadruplex. Modeling studies, based on experimentally
derived restraints obtained for the closely related [{Ru(bipy)2}2tpphz]4+, show that the ΛΛ
isomer fits neatly under the diagonal loop, whereas the ΔΔ
isomer is unable to bind here and binds at the lateral loop end. Molecular
dynamics simulations show that the ΔΔ isomer is prevented
from binding under the diagonal loop by the rigidity of the loop.
We thus present a novel enantioselective binding substrate for antiparallel
basket G-quadruplexes, with features that make it a useful tool for
quadruplex studies.
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