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DNA intercalation

Burak Barut, Ümit Demirbaş, Arzu Özel, Halit Kantekin
In this study, novel peripherally tetra 3-morpholinophenol substituted zinc(II) phthalocyanine (4) and its water soluble form quaternized zinc(II) phthalocyanine (ZnQ) were synthesized for the first time. These novel compounds were characterized by a combination of different spectroscopic techniques such as FT-IR, (1)H NMR, (13)C NMR, UV-Vis and mass. The DNA binding of ZnQ was investigated using UV-vis absorption titration, competitive ethidium bromide, thermal denaturation and viscosity experiments that the ZnQ bound to CT-DNA via intercalation mode...
July 15, 2017: International Journal of Biological Macromolecules
Alexander Schmidt, Rweetuparna Guha, Alexander Hepp, Jens Müller
Several tridentate hydrazone-based ligands, synthesized by a condensation reaction of either 2-(1-methylhydrazinyl)pyridine or 2-(1-methylhydrazinyl)quinoline with an aldehyde (picolinaldehyde, 1H-pyrrole-2-carbaldehyde, 2-mercaptobenzaldehyde, 2-aminobenzaldehyde) have been reacted with palladium(II) and platinum(II) salts and precursor complexes to yield nine new metal complexes. These planar complexes were investigated with respect to their capability to interact with guanine quadruplex DNA. Two sequences (H-telo, derived from the human telomeric sequence, and c-myc, representing an excerpt of the promoter region of the c-Myc oncogene) were investigated...
July 5, 2017: Journal of Inorganic Biochemistry
Maximiliam F S J Menger, Stefano Caprasecca, Benedetta Mennucci
Charge and structural relaxation of electronically excited states in embedded systems are strongly affected by the environment. It is known that the largest part of environment effects comes from electrostatics. However, polarization can also play a role by tuning the electronic and geometrical properties of the states, finally modifying the fluorescence. Here we present the formulation of analytical excited state gradients within a polarizable QM/MM approach, and their implementation within the ONIOM framework...
July 12, 2017: Journal of Chemical Theory and Computation
Ibrahim H Eissa, Abeer M El-Naggar, Nour E A Abd El-Sattar, Ahmed S A Youssef
In attempt to develop new potent anti-tumor agents, a series of quinoxaline derivatives was designed and synthesized. The novel compounds were tested in vitro for their anti-proliferative activities against HePG-2, MCF-7 and HCT-116 cell lines. Additionally, DNA binding affinities as well as DNA-top II inhibitory activities of the synthesized compounds were investigated as potential mechanism for the anticancer activity. Compounds 13, 15, 16 and 19 exhibited good cytotoxicity activities against the three cell lines (IC50 ranging from 7...
July 10, 2017: Anti-cancer Agents in Medicinal Chemistry
Nirmalya Bandyopadhyay, Pritha Basu, Gopinatha Suresh Kumar, Bhargab Guhathakurta, Pijush Singh, Jnan Prakash Naskar
A novel oxime based palladium(II) complex (1) has been synthesized out of the reaction of a Schiff base ligand, 1-phenyl-1-(pyridin-2-yl-hydrazono)-propan-2-one oxime (LH2) with Na2[PdCl4] in THF. Red and diamagnetic 1 has thoroughly been characterized by several analytical and spectroscopic means like CHN, ESI-MS, FAB-MS, FT-IR, (1)H NMR, (13)C NMR, UV-Vis and molar electrical conductivity measurements. Geometry optimizations at the level of DFT reveals that the Pd(II) centre in 1 is nested in a square-planar 'N3Cl' coordination environment...
July 1, 2017: Journal of Photochemistry and Photobiology. B, Biology
Kelly Mulholland, Farzana Siddiquei, Chun Wu
RHPS4, a potent binder to human telomeric DNA G-quadruplex, shows high efficacy in tumor cell growth inhibition. However, it's preferential binding to DNA G-quadruplex over DNA duplex (about 10 fold) remains to be improved toward its clinical application. A high resolution structure of the single-stranded telomeric DNA G-quadruplexes, or B-DNA duplex, in complex with RHPS4 is not available yet, and the binding nature of this ligand to these DNA forms remains to be elusive. In this study, we carried out 40 μs molecular dynamics binding simulations with a free ligand to decipher the binding pathway of RHPS4 to a DNA duplex and three G-quadruplex folders (parallel, antiparallel and hybrid) of the human telomeric DNA sequence...
July 11, 2017: Physical Chemistry Chemical Physics: PCCP
A Blachowicz, T Mayer, M Bashir, T R Pieber, P De León, K Venkateswaran
BACKGROUND: An inflatable lunar/Mars analog habitat (ILMAH), simulated closed system isolated by HEPA filtration, mimics International Space Station (ISS) conditions and future human habitation on other planets except for the exchange of air between outdoor and indoor environments. The ILMAH was primarily commissioned to measure physiological, psychological, and immunological characteristics of human inhabiting in isolation, but it was also available for other studies such as examining its microbiological aspects...
July 11, 2017: Microbiome
Nazir M Khan, Imran Ahmad, Mohammad Y Ansari, Tariq M Haqqi
Wogonin has recently been shown to possess anti-inflammatory and chondroprotective properties and is of considerable interest due to its broad pharmacological activities. The present study highlights that Wogonin binds DNA and exerts chondroprotective effects in vitro. Wogonin showed strong binding with chondrocytes genomic DNA in vitro. The mode of binding of Wogonin to genomic-DNA was assessed by competing Wogonin with EtBr or DAPI, known DNA intercalator and a minor groove binder, respectively. EtBr fluorescence reduced significantly with increase in Wogonin concentration suggesting possible DNA intercalation of Wogonin...
July 5, 2017: Chemico-biological Interactions
T Daniel Prakash, V Violet Dhayabaran
Three novel mixed ligand M(II) complexes, namely [CoL(1)L(2)Cl2] (1), [CuL(1)L(2)Cl2] (2), and [ZnL(1)L(2)Cl2] (3), were synthesized using 1,4-naphthoquinone, L-histidine, and 1,10-phenanthroline as ligands. The ligand framework and the corresponding structural changes on complexation were ascertained based on the results of elemental analysis, conductivity measurements, magnetic behavior, FT-IR, UV-visible, (1)H NMR, (13)C NMR, ESR spectral studies, and ESI mass spectrometry. The biological action of the ligand (L) and complexes 1-3 such as DNA binding and cleaving ability were studied...
July 2017: Journal of Chemical Biology
Christian Reichardt, Kilian R A Schneider, Tariq Sainuddin, Maria Wächtler, Sherri A McFarland, Benjamin Dietzek
In this study femtosecond and nanosecond time-resolved transient absorption spectroscopy was used to investigate the influence of ionic strength and complexity on the excited state dynamics of a Ru(II)-based metal-organic dyad. The bis-heteroleptic complex [Ru(bpy)2(ippy)]2+ (1), where bpy=2,2'-bipyridine and ippy=2-(1-pyrenyl-1H-imidazo[4,5-f][1,10]phenanthroline, is a potent photosensitizer for in vitro photodynamic therapy (PDT) and photodynamic inactivation (PDI) of microorganisms owing to a long-lived triplet excited state derived from a metal-to-ligand charge transfer (3MLCT) state that is equilibrium with an intraligand (3IL) state...
July 5, 2017: Journal of Physical Chemistry. A
Cuifen Gan, Bingfeng Wang, Junying Huang, Aori Qileng, Zuyu He, Hongtao Lei, Weipeng Liu, Yingju Liu
A novel multiple amplified enzyme-free immunosensor was developed for competitive immunoassay of microcystin-LR (MC-LR). Classical electrochemical immunosensors usually employ enzymes as biocatalysts to afford amplified signals, but the proteolytic degradation and poor stability are still crucial problem. Herein, monodisperse core-shell mesoporous silica (SiO2@MSN)-functionalized DNAzyme concatamers were synthesized to load hemin and methylene blue (MB) as the mimic enzyme. Firstly, the surface of SiO2@MSN was conjugated with secondary antibody as the recognition of MC-LR antibody and with a DNA strand as the initiator...
June 23, 2017: Biosensors & Bioelectronics
Reinhard Schwartz-Albiez, Othmar Dill
A small percentage of the Western population carries antibodies in the peripheral blood, which are able to kill human tumors such as neuroblastoma or melanoma. Several observations indicate that these antibodies, preferentially of IgM isotype, belong to the class of naturally occurring antibodies. Here, we describe two screening methods for the detection and quantification of such antibodies in human blood samples: a cellular ELISA technique and a flow cytometric assay, based on intercalation of fluorescent propidium iodide into the DNA of dying or dead cells...
2017: Methods in Molecular Biology
Kyrylo Klimenko, Sergey Lyakhov, Marina Shibinskaya, Alexander Karpenko, Gilles Marcou, Dragos Horvath, Marina Zenkova, Elena Goncharova, Rinat Amirkhanov, Andrei Krysko, Sergei Andronati, Igor Levandovskiy, Pavel Polishchuk, Victor Kuz'min, Alexandre Varnek
This paper describes computer-aided design of new anti-viral agents against Vaccinia virus (VACV) potentially acting as nucleic acid intercalators. Earlier obtained experimental data for DNA intercalation affinities and activities against Vesicular stomatitis virus (VSV) have been used to build, respectively, pharmacophore and QSAR models. These models were used for virtual screening of a database of 245 molecules generated around typical scaffolds of known DNA intercalators. This resulted in 12 hits which then were synthesized and tested for antiviral activity against VaV together with 43 compounds earlier studied against VSV...
June 13, 2017: Bioorganic & Medicinal Chemistry Letters
Sizhe Zhu, Si Yao, Fengshou Wu, Lijun Jiang, Ka-Leung Wong, Ji Zhou, Kai Wang
Organelle and nucleus dual-targeted anticancer drugs are being increasingly used for efficient cancer therapy as they can attack the double vital sites of tumor cells. In this work, we synthesized and characterized two new porphyrin compounds Pt-Por-RB and Me-Por-RB. The spectral titration results suggest that both Pt-Por-RB and Me-Por-RB bind to DNA efficiently in an intercalation binding mode. Upon irradiation, Pt-Por-RB with low dark-cytotoxicity can rapidly generate singlet oxygen to damage the tumor cells through the process of photodynamic therapy...
June 29, 2017: Organic & Biomolecular Chemistry
Pauline Basso, Pierre Wallet, Sylvie Elsen, Emmanuelle Soleilhac, Thomas Henry, Eric Faudry, Ina Attrée
Pathogenic bacteria secrete protein toxins that provoke apoptosis or necrosis of eukaryotic cells. Here, we developed a live-imaging method, based on incorporation of a DNA-intercalating dye into membrane-damaged host cells, to study the kinetics of primary bone marrow-derived macrophages (BMDMs) mortality induced by opportunistic pathogen Pseudomonas aeruginosa expressing either Type III Secretion System (T3SS) toxins or the pore-forming toxin, Exolysin (ExlA). We found that ExlA promotes the activation of Caspase-1 and maturation of interleukin-1β...
June 27, 2017: Environmental Microbiology
Young Cheun, Myong-Chul Koag, Youssef W Naguib, Hala Ouzon-Shubeita, Zhengrong Cui, Danaya Pakotiprapha, Seongmin Lee
Cisplatin resistance is caused, in part, by the efficient removal of the helix-distorting cisplatin 1,2-intrastrand crosslinks by nucleotide excision repair (NER) machinery. To make a platinum-DNA adduct that causes less helical distortion than the cisplatin 1,2-intrastrand adduct, we designed and synthesized a monofunctional platinum-carbazole conjugate (carbazoleplatin). The 2.5Å crystal structure of carbazoleplatin-DNA adduct revealed both the monoplatination of the N7 of a guanine (G) base and the intercalation into two G:C base pairs while causing a minor distortion of the DNA helix...
June 26, 2017: Chemical Biology & Drug Design
Francis Prija, Ranjan Prasad
DrrC is a DNA-binding protein of Streptomyces peucetius that provides self-resistance against daunorubicin, the antibiotic produced by the organism. DrrC was expressed in E.coli and purified by using N-terminal MBP-tag which retained DNA-binding property in spite of the tag. Mobility shift assay confirmed the interaction of 313bp DNA that has the dnrI promoter, daunorubicin and MBP-DrrC in the presence of ATP. Biotinylated and immobilized 313bp DNA was intercalated with daunorubicin to observe the release of the drug when MBP-DrrC is allowed to act on the DNA...
September 2017: Microbiological Research
Pavel A Puchkov, Irina A Kartashova, Elena V Shmendel, Anastasya S Luneva, Nina G Morozova, Marina A Zenkova, Mikhail A Maslov
Three novel polycationic gemini amphiphiles with different spacers were developed and evaluated in terms of their physiochemical properties and transfection efficiencies. Cationic liposomes formed by these amphiphiles and the helper lipid DOPE were able to successfully condense DNA, as shown by gel mobility shift and ethidium bromide intercalation assays. Transfection activity of the liposomes was superior to Lipofectamine(®) 2000 and was dependent on spacer structure, hydrophobicity, and nucleic acid type (pDNA or siRNA)...
August 1, 2017: Bioorganic & Medicinal Chemistry Letters
Raju Nomula, Xueyan Wu, Jianzhang Zhao, Nagegownivari R Munirathnam
Two coumarin based Ru(II)-polyimine complexes (Ru-1 and Ru-2) showing intense absorption of visible light and long-lived triplet excited states (~12-15μs) were used for study of the interaction with DNA. The binding of the complexes with CT-DNA were studied by UV-vis, fluorescence and time-resolved nanosecond transient absorption (ns-TA) spectroscopy. The results suggesting that the complexes interact with CT-DNA by intercalation mode of binding, showing the binding constants (Kb) 6.47×10(4) for Ru-1 and 5...
October 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
Filipe Vultos, Célia Fernandes, Filipa Mendes, Fernanda Marques, João D G Correia, Isabel Santos, Lurdes Gano
A straightforward synthetic route for a new multifunctional 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) derivative is described. To demonstrate the versatility of this pro-chelator for the preparation of radiolabeled hybrid compounds containing two different biological targeting moieties, an antitumor agent (e.g., a DNA-intercalating agent) and an estrogen receptor (ER) ligand (e.g., LXXLL-based peptide) were regiospecifically conjugated to the DOTA derivative. The bifunctional probe was radiolabeled with the auger electron emitter indium-111, and the resulting radioconjugate was demonstrated to induce DNA damage in vitro, which, along with the nuclear internalization exhibited in breast cancer cells, might enhance its therapeutic activity...
June 19, 2017: ChemMedChem
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