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DNA intercalation

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https://www.readbyqxmd.com/read/27933484/dna-as-a-target-for-anticancer-phen-imidazole-pd-ii-complexes
#1
Maryam Heydari, Mahboube Eslami Moghadam, AliAkbar Tarlani, Hossein Farhangian
Imidazole ring is a known structure in many natural or synthetic drug molecules and its metal complexes can interact with DNA and do the cleavage. Hence, to study the influence of the structure and size of the ligand on biological behavior of metal complexes, two water-soluble Pd(II) complexes of phen and FIP ligands (where phen is 1,10-phenanthroline and FIP is 2-(Furan-2-yl)-1H-Imidazo[4,5-f][1, 10]phenanthroline) with the formula of [Pd(phen)(FIP)](NO3)2 and [Pd(FIP)2]Cl2, that were activated against chronic myelogenous leukemia cell line, K562, were selected...
December 8, 2016: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/27924438/correlation-between-molecular-modelling-and-spectroscopic-techniques-in-investigation-with-dna-binding-interaction-of-ruthenium-ii-complexes
#2
REVIEW
B Thulasiram, C Shobha Devi, Yata Praveen Kumar, Rajeshwar Rao Aerva, S Satyanarayana, Penumaka Nagababu
The DNA binding studies of rutheniumu(II) polypyridyl complexes {[Ru(phen)2Mipc](2+), [Ru(bpy)2Mipc](2+), [Ru(dmb)2Mipc](2+), [Ru(phen)2BrIPC](2+), [Ru(bpy)2BrIPC](2+), [Ru(dmb)2BrIPC](2+), [Ru(phen)2PIP-Cl](2+), [Ru(bpy)2PIP-Cl](2+), [Ru(dmb)2PIP-Cl](2+), [Ru(phen)2IPPBA](2+), [Ru(bpy)2IPPBA](2+), [Ru(dmb)2IPPBA](2+)} with DNA investigated by electronic absorption titration, emission and molecular modelling studies to identify the binding interactions. All these complexes are showing good binding constant values ~10(4) to 10(5)...
December 6, 2016: Journal of Fluorescence
https://www.readbyqxmd.com/read/27923993/specific-targeting-of-telomeric-multimeric-g-quadruplexes-by-a-new-triaryl-substituted-imidazole
#3
Ming-Hao Hu, Shuo-Bin Chen, Bo Wang, Tian-Miao Ou, Lian-Quan Gu, Jia-Heng Tan, Zhi-Shu Huang
Multiple G-quadruplex units in the 3'-terminal overhang of human telomeric DNA can associate and form multimeric structures. The specific targeting of such distinctive higher-order G-quadruplexes might be a promising strategy for developing selective anticancer agents with fewer side effects. However, thus far, only a few molecules were found to selectively bind to telomeric multimeric G-quadruplexes, and their effects on cancer cells were unknown. In this study, a new triaryl-substituted imidazole derivative called IZNP-1: was synthesized and found to specifically bind to and strongly stabilize telomeric multimeric G-quadruplexes through intercalating into the pocket between the two quadruplex units...
December 6, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27920757/advances-and-challenges-in-viability-detection-of-foodborne-pathogens
#4
REVIEW
Dexin Zeng, Zi Chen, Yuan Jiang, Feng Xue, Baoguang Li
Foodborne outbreaks are a serious public health and food safety concern worldwide. There is a great demand for rapid, sensitive, specific, and accurate methods to detect microbial pathogens in foods. Conventional methods based on cultivation of pathogens have been the gold standard protocols; however, they take up to a week to complete. Molecular assays such as polymerase chain reaction (PCR), sequencing, microarray technologies have been widely used in detection of foodborne pathogens. Among molecular assays, PCR technology [conventional and real-time PCR (qPCR)] is most commonly used in the foodborne pathogen detection because of its high sensitivity and specificity...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27918296/crystal-structures-of-deprotonated-nucleobases-from-an-expanded-dna-alphabet
#5
Mariko F Matsuura, Hyo Joong Kim, Daisuke Takahashi, Khalil A Abboud, Steven A Benner
Reported here is the crystal structure of a heterocycle that implements a donor-donor-acceptor hydrogen-bonding pattern, as found in the Z component [6-amino-5-nitropyridin-2(1H)-one] of an artificially expanded genetic information system (AEGIS). AEGIS is a new form of DNA from synthetic biology that has six replicable nucleotides, rather than the four found in natural DNA. Remarkably, Z crystallizes from water as a 1:1 complex of its neutral and deprotonated forms, and forms a `skinny' pyrimidine-pyrimidine pair in this structure...
December 1, 2016: Acta Crystallographica. Section C, Structural Chemistry
https://www.readbyqxmd.com/read/27917901/fish-dna-modified-clays-towards-highly-flame-retardant-polymer-nanocomposite-with-improved-interfacial-and-mechanical-performance
#6
Omid Zabihi, Mojtaba Ahmadi, Hamid Khayyam, Minoo Naebe
Deoxyribonucleic Acid (DNA) has been recently found to be an efficient renewable and environmentally-friendly flame retardant. In this work, for the first time, we have used waste DNA from fishing industry to modify clay structure in order to increase the clay interactions with epoxy resin and take benefit of its additional thermal property effect on thermo-physical properties of epoxy-clay nanocomposites. Intercalation of DNA within the clay layers was accomplished in a one-step approach confirmed by FT-IR, XPS, TGA, and XRD analyses, indicating that d-space of clay layers was expanded from ~1...
December 5, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27917863/dna-intercalation-optimized-by-two-step-molecular-lock-mechanism
#7
Ali A Almaqwashi, Johanna Andersson, Per Lincoln, Ioulia Rouzina, Fredrik Westerlund, Mark C Williams
The diverse properties of DNA intercalators, varying in affinity and kinetics over several orders of magnitude, provide a wide range of applications for DNA-ligand assemblies. Unconventional intercalation mechanisms may exhibit high affinity and slow kinetics, properties desired for potential therapeutics. We used single-molecule force spectroscopy to probe the free energy landscape for an unconventional intercalator that binds DNA through a novel two-step mechanism in which the intermediate and final states bind DNA through the same mono-intercalating moiety...
December 5, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27917540/interaction-of-procarbazine-with-calf-thymus-dna-a-biophysical-and-molecular-docking-study
#8
Razique Anwer, Nazia Ahmad, Khalid I Al Qumaizi, Osama A Al Khamees, Waleed Mohammed Al Shaqha, Tasneem Fatma
Interaction of procarbazine (PCZ) with calf thymus DNA was studied using biophysical and molecular docking studies. Procarbazine was to interact with DNA with a binding constant of 6.52 × 10(3)  M(-1) as calculated using ultraviolet-visible spectroscopy. To find out the binding mode, molecular docking was performed that predicted PCZ to interact with DNA through groove binding mode with binding affinity of -6.7 kcal/mole. To confirm the groove binding nature, different experiments were performed. Dye displacement assays confirmed the non-intercalative binding mode...
December 5, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27912879/how-do-the-alkaloids-emetine-and-homoharringtonine-kill-trypanosomes-an-insight-into-their-molecular-modes-of-action
#9
Sonja Krstin, Tamer Mohamed, Xiaojuan Wang, Michael Wink
BACKGROUND: Although Trypanosoma brucei causes deadly sleeping sickness, the number of the registered medications is rather limited. Some plant alkaloids are potent trypanocidal agents. PURPOSE: In this study, we wanted to elucidate the molecular modes of trypanocidal activity of the alkaloids emetine and homoharringtonine against Trypanosoma brucei brucei. METHODS: We investigated the activity of both alkaloids regarding growth recovery from alkaloid-induced stress...
December 15, 2016: Phytomedicine: International Journal of Phytotherapy and Phytopharmacology
https://www.readbyqxmd.com/read/27890659/rna-nanoparticles-harboring-annexin-a2-aptamer-can-target-ovarian-cancer-for-tumor-specific-doxorubicin-delivery
#10
Fengmei Pi, Hui Zhang, Hui Li, Varatharasa Thiviyanathan, David G Gorenstein, Anil K Sood, Peixuan Guo
A novel modified nucleic acid nanoparticle harboring an annexin A2 aptamer for ovarian cancer cell targeting and a GC rich sequence for doxorubicin loading is designed and constructed. The system utilizes a highly stable three-way junction (3WJ) motif from phi29 packaging RNA as a core structure. A phosphorothioate-modified DNA aptamer targeting annexin A2, Endo28, was conjugated to one arm of the 3WJ. The pRNA-3WJ motif retains correct folding of attached aptamer, keeping its functions intact. It is of significant utility for aptamer-mediated targeted delivery...
November 25, 2016: Nanomedicine: Nanotechnology, Biology, and Medicine
https://www.readbyqxmd.com/read/27888684/ultrasensitive-non-enzymatic-multiple-immunosensor-for-tumor-markers-detection-by-coupling-dna-hybridization-chain-reaction-with-intercalated-molecules
#11
Jinjin Guo, Junchun Wang, Junjun Zhang, Wenjuan Zhang, Yuzhong Zhang
In this study, we tried coupling the small signal molecules that could intercalate into DNA double helix with hybridization chain reaction (HCR) technique to fabricate a multiple immunosensor. Doxorubicin hydrochloride (DXH) and methylene blue (MB) were used as signal molecules and alpha-fetoprotein (AFP) and carcinoembryonic antigen (CEA) were selected as model biomarkers. The immunosensor mainly consists of three parts as follows: First, two different primary antibodies (Ab1) immobilized on the surface of gold nanoparticles (Au NPs); Second, secondary antibodies (Ab2) conjugated with DNA primer; Third, long DNA concatemers from HCR were used as a carrier to intercalate amounts of signal molecules (DXH or MB)...
November 21, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27886600/a-lifetime-sensitive-fluorescence-anisotropy-probe-for-dna-based-bioassays-the-case-of-sybr-green
#12
Benoit Chovelon, Emmanuelle Fiore, Patrice Faure, Eric Peyrin, Corinne Ravelet
In standard steady-state fluorescence anisotropy (FA) DNA-based assays, the ligand binding to a given receptor is typically signalled by the rotational correlation time changes of the tracer. Herein, we report a radically different strategy that relies on the peculiar excited state lifetime features of the SYBR Green (SG) dye. This DNA-binding probe exhibits a drastically short lifetime in solution, leading to a high FA signal. Its complexation to oligonucleotides determines a singular and very large depolarization depending on the concerted effects of extreme lifetime enhancement and resonance energy homotransfer...
November 21, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27886594/proposed-binding-mechanism-of-galbanic-acid-extracted-from-ferula-assa-foetida-to-dna
#13
F Ahmadi, Y Shokoohinia, Sh Javaheri, H Azizian
Recently, galbanic acid (GA), a sesquiterpenoid coumarin, has been introduced as an apoptotic and geno/cytotoxicity agent. In the present study, GA has been extracted from Ferula assa-foetida, a native medicinal plant in Iran, and characterized by (1)H NMR, mass spectroscopy. Additionally, spectroscopic studies have been performed in order to investigate its DNA-interaction mode. The electrochemical behavior of GA has been studied by cyclic voltammetry (CV) in various scan rates. In neutral media (pH=7.3) one irreversible cathodic peak was obtained at -1...
November 16, 2016: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/27884695/linker-dependent-intercalation-of-bisbenzimidazole-aminosugars-in-an-rna-duplex-selectivity-in-rna-vs-dna-binding
#14
Nihar Ranjan, Dev P Arya
Neomycin and Hoechst 33258 are two well-known nucleic acid binders that interact with RNA and DNA duplexes with high affinities respectively. In this manuscript, we report that covalent attachment of bisbenzimidazole unit derived from Hoechst 33258 to neomycin leads to intercalative binding of the bisbenzimidazole unit (oriented at 64-74° with respected to the RNA helical axis) in a linker length dependent manner. The dual binding and intercalation of conjugates were supported by thermal denaturation, CD, LD and UV-Vis absorption experiments...
December 15, 2016: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/27877881/crosslinked-duplex-dna-nanogels-that-target-specified-proteins
#15
Yasuhiko Iwasaki, Jun-Ichi Kondo, Akinori Kuzuya, Rui Moriyama
Specific detection of protein biomarkers plays an important role in diagnostics and therapeutics. We have fabricated polymeric nanogels, which can specifically interact with the cancer biomarker thrombin to serve as a model. Two types of 2-methacryloyloxyethyl phosphorylcholine (MPC) copolymers bearing a thrombin-binding oligonucleotide aptamer and its complementary chain were independently synthesized by redox-initiated radical polymerization. These MPC polymers associate in a complimentary fashion due to double strand formation of the oligonucleotides in aqueous media, leading to the spontaneous formation of spherical nanogels...
2016: Science and Technology of Advanced Materials
https://www.readbyqxmd.com/read/27877846/a-label-free-g-quadruplex-based-mercury-detection-assay-employing-the-exonuclease-iii-mediated-cleavage-of-t-hg-2-t-mismatched-dna
#16
Wanhe Wang, Tian-Shu Kang, Philip Wai Hong Chan, Jin-Jian Lu, Xiu-Ping Chen, Chung-Hang Leung, Dik-Lung Ma
We report herein the use of an exonuclease III and G-quadruplex probe to construct a G-quadruplex-based luminescence detection platform for Hg(2+). Unlike common DNA-based Hg(2+) detection methods, when using the dsDNA probe to monitor the hairpin formation, the intercalation of the dsDNA probe may be influenced by the distortion of dsDNA. This 'mix-and-detect' methodology utilized the G-quadruplex probe as the signal transducer and is simple, rapid, convenient to use and can detect down to 20 nM of Hg(2+).
December 2015: Science and Technology of Advanced Materials
https://www.readbyqxmd.com/read/27868127/digital-dna-detection-based-on-a-compact-optofluidic-laser-with-ultra-low-sample-consumption
#17
Wonsuk Lee, Qiushu Chen, Xudong Fan, Dong Ki Yoon
DNA lasers self-amplify optical signals from a DNA analyte as well as thermodynamic differences between sequences, allowing quasi-digital DNA detection. However, these systems have drawbacks, such as relatively large sample consumption and complicated dye labelling. Moreover, although the lasing signal can detect the target DNA, it is superimposed on an unintended fluorescence background, which persists for non-target DNA samples as well. From an optical point of view, it is thus not truly digital detection and requires spectral analysis to identify the target...
November 29, 2016: Lab on a Chip
https://www.readbyqxmd.com/read/27865131/evaluation-of-cellular-uptake-cytotoxicity-and-cellular-ultrastructural-effects-of-heteroleptic-oxidovanadium-iv-complexes-of-salicylaldimines-and-polypyridyl-ligands
#18
Gonzalo Scalese, Isabel Correia, Julio Benítez, Santiago Rostán, Fernanda Marques, Filipa Mendes, António Pedro Matos, João Costa Pessoa, Dinorah Gambino
Searching for prospective vanadium-based drugs for cancer treatment, a new series of structurally related [V(IV)O(L-2H)(NN)] compounds (1-8) was developed. They include a double deprotonated salicylaldimine Schiff base ligand (L-2H) and different NN-polypyridyl co-ligands having DNA intercalating capacity. Compounds were characterized in solid state and in solution. EPR spectroscopy suggests that the NN ligands act as bidentate and bind through both nitrogen donor atoms in an axial-equatorial mode. The cytotoxicity was evaluated in human tumoral cells (ovarian A2780, breast MCF7, prostate PC3)...
November 9, 2016: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/27858165/nmr-study-of-the-effects-of-some-bleomycin-c-termini-on-the-structure-of-a-dna-hairpin-with-the-5-gc-3-binding-site
#19
Teresa E Lehmann, Sally A Murray, Azure D Ingersoll, Teresa M Reilly, Shelby E Follett, Kevin E Macartney, Mark H Harpster
The antibiotics known as bleomycins constitute a family of natural products clinically employed for the treatment of a wide spectrum of cancers. The drug acts as an antitumor agent by virtue of the ability of a metal complex of the antibiotic to cleave DNA. Bleomycins are differentiated by their C-terminal regions. Previous structural studies involving metal-bleomycin-DNA triads have allowed the identification of the bithiazole-(C-terminus substituent) segment in this molecule as the one that most closely interacts with DNA...
November 17, 2016: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/27835775/synthesis-of-ag-i-camphor-sulphonylimine-complexes-and-assessment-of-their-cytotoxic-properties-against-cisplatin-resistant-a2780cisr-and-a2780-cell-lines
#20
João M S Cardoso, Isabel Correia, Adelino M Galvão, Fernanda Marques, M Fernanda N N Carvalho
Camphorsulphonylimine complexes [Ag(NO3)((I)L)2] ((I)L=C12H19N3SO2, 1) and [(AgNO3)2((II)L)] ((II)L=C22H23N3SO2, 2) were synthesized and characterized by elemental analysis, spectroscopy (IR, NMR) and cyclic voltammetry. [Ag(NO3)((I)L)2] crystalizes in the monoclinic C2 space group with a triangular geometry assuming a chalice-type shape. The anti-proliferative properties of the new complexes 1 and 2 and those of the previously reported [Ag(NO3)((III)L)] ((III)L=C16H18N3SO2, 3) were assessed against the human ovarian cancer cells (cisplatin-sensitive A2780, cisplatin-resistant A2780cisR) and the non-tumoral human HEK 293 cell line, using the MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] assay...
November 4, 2016: Journal of Inorganic Biochemistry
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