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DNA intercalation

Muhammad Arba, Ruslin, Sunandar Ihsan, Setyanto Tri Wahyudi, Daryono H Tjahjono
Human DNA Topoisomerase II has been regarded as a promising target in anticancer drug discovery. In the present study, we designed six porphyrin-anthraquinone hybrids bearing pyrazole or pyridine group as meso substituents and evaluated their potentials as DNA Topoisomerase IIβ inhibitor. First, we investigated the binding orientation of porphyrin hybrids into DNA topoisomerase IIβ employing AutoDock 4.2 and then performed 20-ns molecular dynamics simulations to see the dynamic stability of each porphyrin-Topo IIβ complex using Amber 14...
October 5, 2017: Computational Biology and Chemistry
Marco Deiana, Bastien Mettra, Lara Martinez-Fernandez, Leszek Mateusz Mazur, Krzysztof Pawlik, Chantal Andraud, Marek Samoc, Roberto Improta, Cyrille Monnereau, Katarzyna Matczyszyn
The implication of guanine-rich DNA sequences in biologically important roles such as telomerase dysfunction and the regulation of gene expression has prompted the search for structure-specific G-quadruplex agents for targeted diagnostic and therapeutic applications. To date, the number of two-photon absorbing fluorogenic dyes with intrinsically large two-photon absorption (TPA) cross-section (σ2) and quantum yield (φf), capable of specific detection of G-motifs over duplex DNAs is still limited. Herein, we report on a NIR two-photon poly(cationic) anthracene-based macromolecule able to selectively target G-quadruplexes (G4s) over genomic double-stranded DNA...
November 17, 2017: Journal of Physical Chemistry Letters
Ali Nikoomanzar, Matthew R Dunn, John C Chaput
Engineered polymerases that can copy genetic information between DNA and xeno-nucleic acids (XNA) hold tremendous value as reagents in future bio-technology applications. However, current XNA poly-merases function with inferior activity relative to their natural counterparts, indicating that current polymerase engineering efforts would benefit from new benchmark-ing assays. Here, we describe a highly parallel, low cost method for measuring the average rate and substrate specificity of XNA polymerases in a standard qPCR instrument...
November 17, 2017: Analytical Chemistry
Kamilia M Amin, Aly M Taha, Riham F George, Nada M Mohamed, Fardous F Elsenduny
A novel series of coumarin-thiadiazole heterocycle derivatives was synthesized by the nucleophilic substitution reaction. The synthesized compounds were structurally verified by IR, (1) H NMR, (13) C NMR, mass spectra, and elemental analyses. The antitumor activity of the synthesized compounds was evaluated through DNA binding assays and the 60-cell line panel according to the US NCI-DTP protocol or a selection of human tumor cell lines: breast cancer (MCF-7), liver cancer (HepG-2), and colorectal cancer (HCT-116)...
November 17, 2017: Archiv der Pharmazie
Xiao Yu, Ashley M Fuller, Richard Blackmon, Melissa A Troester, Amy L Oldenburg
The ability to assess toxicant exposures of three-dimensional (3D) in vitro mammary models that recapitulate the tissue microenvironment can aid in our understanding of environmental exposure risk over time. Longitudinal studies of 3D model systems, however, are cumbersome and suffer from a lack of high-throughput toxicological assays. In this study, we establish a noninvasive and label-free optical coherence tomography (OCT)-based imaging platform for tracking exposure-response relationships in 3D human mammary epithelial organoid models...
November 10, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
Alexandra M Gade, Margaret K Meadows, Andrew D Ellington, Eric V Anslyn
A series of semi-specific peptides reported in the literature to bind various epitopes on cell surfaces were used in a differential sensing array to pattern cell line identity. The peptides were conjugated to thiazole orange to act as both a fluorescence reporter and a DNA intercalator. Fluorescence data for the peptides exposed to cells, with and without exogenous double stranded DNA (dsDNA), led to chemometric fingerprints for eight cancer cell lines. In contrast to the use of structures meant to act in completely non-specific ways, the use of a limited level of specificity generated linear discriminant score plots with high dimensionality, i...
November 15, 2017: Organic & Biomolecular Chemistry
Duygu İnci, Rahmiye Aydın, Özgür Vatan, Yunus Zorlu, Nilüfer Çinkılıç
New binary copper(II) complexes, - [Cu(4-mphen)2(NO3)]NO3·H2O (1), [Cu(5-mphen)2 (NO3)]NO3·H2O (2), the known complex [Cu(dmphen)2(NO3)]NO3 (3) and [Cu(tmphen)2 (NO3)]NO3·H2O (4) - (4-mphen: 4-methyl-1,10-phenanthroline, 5-mphen: 5-methyl-1,10-phenanthroline, dmphen: 4,7-dimethyl-1,10-phenanthroline, tmphen: 3,4,7,8-tetramethyl-1,10-phenanthroline), have been synthesized and characterized by CHN analysis, ESI-MS, FTIR and single-crystal X-ray diffraction techniques. Interaction of these complexes with calf thymus DNA (CT-DNA) has been investigated by absorption spectral titration, ethidium bromide (EB) and Hoechst 33258 displacement assay and thermal denaturation measurement...
November 13, 2017: Journal of Biomolecular Structure & Dynamics
Hui Chao, Shanshan Zou, Guanying Li, Chengzhi Jin, Juanjuan Huang, Yu Chen, Liangnian Ji, Thomas W Rees
It was noted that DNA can undergo B-Z transformational changes and compaction in the presence of DNA intercalators such as ruthenium(II) polypyridyl complexes. The link between B-Z transition and condensation is weak but can be strengthened under certain circumstances with slight alterations to the structures of ruthenium(II) complexes. Herein, based on our previous work, we report a series ruthenium(II) complexes with imidazophenanthroline ligands which increase in size and planarity. The complexes exhibit distinct effects on DNA structures ranging from little impact, to the transformation of DNA secondary structures to the formation of higher-order DNA structures...
November 7, 2017: Chemistry: a European Journal
Huachao Chen, Yurong Wang, Yongrong Yao, Shenglin Qiao, Hao Wang, Ninghua Tan
A programmed drug delivery system that can achieve sequential release of multiple therapeutics under different stimulus holds great promise to enhance the treatment efficacy and overcome multi-drug resistance (MDR) in tumor. Herein, multi-organelle-targeted and pH/ cytochrome c (Cyt c) dual-responsive nanoparticles were designed for combination therapy on resistant tumor. In this system (designated DGLipo NPs), doxorubicin (Dox) was intercalated into the DNA duplex containing a Cyt c aptamer, which subsequently loaded in the dendrigraftpoly-L-lysines (DGL) cores of DGLipo NPs, while cyclopeptide RA-V was doped into the pH-sensitive liposomal shells...
2017: Theranostics
Fei Liu, Xiaoxin Tan, Xu Han, Xiang Li, Nan Li, Weijun Kang
The cytotoxicities of three aconitum alkaloids- aconitine, hypaconitine and mesaconitine, and their abilities to bind DNA have been explored. Rat myocardial cells H9c2 were treated with aconitum alkaloids and assessed the cytotoxicities by using MTT assay and flow cytometry. Apoptosis was evidenced by the results of the annexin V/propidium iodide (PI) assay. Aconitine was found to be the most toxic in rat myocardial cells H9c2 in three aconitum alkaloids. At the same time, DNA adducts were isolated and then analyzed by UV-Vis spectroscopy after exposure to alkaloids, which indicated that three alkaloids could bind to DNA in rat myocardial cells H9c2...
November 6, 2017: Scientific Reports
Klaudia Jomova, Michael Lawson, Lenka Drostinova, Peter Lauro, Patrik Poprac, Vlasta Brezova, Martin Michalik, Vladimir Lukes, Marian Valko
The radical scavenging and metal chelating properties of flavonoids indicate that they may play a protective role in diseases with perturbed metal homeostasis such as Alzheimer's disease. In this work we investigated the effect of the coordination of quercetin to copper(II) in view of the formation of ROS in Cu-catalyzed Fenton reaction. ABTS and DPPH assays confirmed that the copper(II)-quercetin complex exhibits a stronger radical scavenging activity than does quercetin alone. EPR spin trapping experiments have shown that chelation of quercetin to copper significantly suppressed the formation of hydroxyl radicals in the Cu(II)-Fenton reaction...
October 26, 2017: Food and Chemical Toxicology
Somasundaram Sangeetha, Mariappan Murali
A copper(II) complex [Cu(II)(quamol)Cl]·H2O, where H(quamol) is N-2-(quinolyl-methylidene)aminophenol, has been isolated. The solution structure of the complex has been assessed to be distorted square-planar. The complex displays a ligand field band in the visible region (608nm) and also show axial EPR spectrum in DMF at 77K with g||>g⊥ indicating a dx(2)-y(2) ground state. The g|| and A|| values of 2.265 and 153×10(-4)cm(-1), respectively, conform to a square-based CuN2OCl chromophore. The interaction of the complex with calf thymus (CT) DNA has been explored by using absorption (Kb=2...
November 2, 2017: International Journal of Biological Macromolecules
Hulihalli N KiranKumar, Heggodu G RohitKumar, Gopal M Advirao
Two new derivatives of pyrimido[4',5';4,5]thieno(2,3-b)quinoline (PTQ), 9-hydroxy-4-(3-diethylaminopropylamino)pyrimido[4',5';4,5]thieno(2,3-b)quinoline (Hydroxy-DPTQ) and 8-methoxy-4-(3-diethylaminopropylamino)pyrimido[4',5';4,5]thieno(2,3-b)quinoline (Methoxy-DPTQ) were synthesized and their DNA binding ability was analyzed using spectroscopy (UV-visible, fluorescence and circular dichroism), ethidium bromide dye displacement assay, melting temperature (Tm) analysis and computational docking studies. The hypochromism in UV-visible spectrum and increased fluorescence emission of Hydroxy-DPTQ and Methoxy-DPTQ in the presence of DNA suggested the molecule-DNA interaction...
November 1, 2017: Journal of Photochemistry and Photobiology. B, Biology
Ma Ángeles Martínez, M Pilar Carranza, Anna Massaguer, Lucia Santos, Juan A Organero, Cristina Aliende, Rafael de Llorens, Iteng Ng-Choi, Lidia Feliu, Marta Planas, Ana M Rodríguez, Blanca R Manzano, Gustavo Espino, Félix A Jalón
The synthesis and characterization of Pt(II) (1 and 2) and Ru(II) arene (3 and 4) or polypyridine (5 and 6) complexes is described. With the aim of having a functional group to form bioconjugates, one uncoordinated carboxyl group has been introduced in all complexes. Some of the complexes were selected for their potential in photodynamic therapy (PDT). The molecular structures of complexes 2 and 5, as well as that of the sodium salt of the 4'-(4-carboxyphenyl)-2,2':6',2″-terpyridine ligand (cptpy), were determined by X-ray diffraction...
November 3, 2017: Inorganic Chemistry
Li Li, Changchun Niu, Tian Li, Yafang Wan, Ying Zhou, Haijun Wang, Ruo Yuan, Pu Liao
Herein, a novel electrochemiluminescence (ECL) biosensor was proposed for ultrasensitive detection of laminin (LN), in which DNA dendrimer (D) as a promising nanocarrier for luminophore and DNA nanomachine as tactic for target recycling. The DNA dendrimer was synthesized by hybridization between sense and its antisense Y-shaped DNAs which were formed via reaction between single-stranded DNA (ssDNA) with a thiol group at the 5'-end and a synthesized trimeric cross-linker of tris(2-maleimidoethyl)amine. This dendrimer provided abundant double-stranded DNA (dsDNA) to achieve high loading efficiency for ECL luminophore...
October 11, 2017: Biosensors & Bioelectronics
Kazuhiko Nakatani, Nozomi Natsuhara, Yuki Mori, Sanjukta Mukherjee, Bimolendu Das, Asako Murata
One of the important determinants in the efficiency of a molecular interaction is the necessity for conformational changes in host and/or guest molecules upon binding. In small-molecule interactions with nucleic acids, conformational changes on both molecules are often involved, especially in intercalating binding. Mismatch binding ligands (MBLs) we described here consist of two heterocycles that predominantly exist in one conformation, so it is of interest to determine if such molecules can bind to any DNA and RNA structures...
November 2, 2017: Chemistry, An Asian Journal
Saswata Karmakar, Dale C Guenther, Bradley C Gibbons, Patrick J Hrdlicka
Development of hybridization-based probes that enable recognition of specific mixed-sequence double-stranded DNA (dsDNA) regions is of considerable interest due to their potential applications in molecular biology, biotechnology, and medicine. We have recently demonstrated that nucleic acid duplexes with +1 interstrand zipper arrangements of intercalator-functionalized nucleotides such as 2'-O-(pyren-1-yl)methyl RNA monomers are inherently activated for recognition of mixed-sequence dsDNA targets, including chromosomal DNA...
November 15, 2017: Organic & Biomolecular Chemistry
Zhen-Zhen Li, Lavanya Gopala, Vijai Kumar Reddy Tangadanchu, Wei-Wei Gao, Cheng-He Zhou
A series of nitroimidazole enols as new bacterial DNA-targeting agents were for the first time designed, synthesized and characterized by NMR, IR and HRMS spectra. The antimicrobial screening revealed that 2-methoxyphenyl nitroimidazole enol 3i possessed stronger anti-P. aeruginosa efficacy (MIC = 0.10 μmol/mL) than reference drugs Norfloxacin and Metronidazole. Time-kill kinetic assay manifested that the active molecule 3i could rapidly kill the tested strains. Molecular docking indicated that the interactions between compound 3i and topoisomerase II were driven by hydrogen bonds...
October 25, 2017: Bioorganic & Medicinal Chemistry
Kaviyarasi Renu, Abilash V G, Tirupathi Pichiah P B, Sankarganesh Arunachalam
Doxorubicin is utilized for anti-neoplastic treatment for several decades. The utility of this drug is limited due to its side effects. Generally, doxorubicin toxicity is originated from the myocardium and then other organs are also ruined. The mechanism of doxorubicin is intercalated with the DNA and inhibits topoisomerase 2. There are various signalling mechanisms involved in doxorubicin cardiotoxicity. First and foremost, the doxorubicin-induced cardiotoxicity is due to oxidative stress. Cardiac mitochondrial damage is supposed after few hours following the revelation of doxorubicin...
October 23, 2017: European Journal of Pharmacology
Shengjie Ye, Ruihong Ye, Yuande Shi, Bin Qiu, Longhua Guo, Dihui Huang, Zhenyu Lin, Guonan Chen
Bisphenol A (BPA), a typical endocrine disruptor, is widely used as a key monomer in the packaging industry. Residual monomer can transfer from the package material to the food and thereby pose a risk to the health of the consumer, so determination of BPA migration is highly important for food safety control. In this study, a simple but sensitive electrochemiluminescence (ECL) biosensor, which combines the characteristics of high selectivity of an aptamer and high sensitivity of ECL, has been developed to detect BPA from package materials...
October 24, 2017: Analytical and Bioanalytical Chemistry
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