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DNA intercalation

Christine J Cardin, John M Kelly, Susan J Quinn
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...
July 1, 2017: Chemical Science
S Yousef Ebrahimipour, Maryam Mohamadi, Masoud Torkzadeh Mahani, Jim Simpson, Joel T Mague, Iran Sheikhshoaei
The synthesis and characterization of three dioxo U(VI) complexes, [UO2(L(1))(OH2)], [UO2(L(2))DMF], and [UO2(L(2))DMSO], [L(1)](2-) = 1,1'-(4-methyl-1,2-phenylenebis (nitrilomethylidyne))di-2-naphtholate: [L(2)](2-) = 1,1'-(o-phenylenebis (nitrilomethylidyne)) di-2-naphtholate, are reported. Elemental analysis, FT-IR, (1)HNMR, UV-Vis spectroscopy, molar conductivity and single crystal X-ray diffraction were used to characterize the complexes. It was found that the complexes adopt a distorted pentagonal bipyramidal coordination geometry...
September 4, 2017: European Journal of Medicinal Chemistry
Niggula Praveen Kumar, Pankaj Sharma, S Sujana Kumari, Umarani Brahma, Shalini Nekkanti, Nagula Shankaraiah, Ahmed Kamal
A series of new phenanthrene-9-benzimidazole conjugates has been synthesized by condensing phenanthrene aldehydes with various substituted o-phenylenediamines. The title compounds were evaluated for their in vitro cytotoxic potential against various human cancer cell lines like breast (BT-549), prostate (PC-3 and DU145), triple negative breast cancer (MDA-MB-453), and human colon cancer (HCT-116 and HCT-15) cells. Among the tested compounds, 10o displayed significant in vitro cytotoxic activity against PC-3 prostate cancer cells with an IC50 value of 6...
September 8, 2017: European Journal of Medicinal Chemistry
Zhi Li, Bingchen Li, Yunlei Zhou, Huanshun Yin, Jun Wang, Shiyun Ai
It is extremely important for quantifying trace microRNAs in the biomedical applications. In this study, an ultrasensitive, rapid and efficient label-free fluorescence method was proposed and applied for detecting microRNA-21 in serum of gastric cancer patients based on DNA hybridization chain reaction (HCR). DNA H1 and DNA H2 were designed and used as hairpin probes, the HCR was proceeded in the presence of target microRNAs. Amounts of SYBR Green І dyes were used as signal molecules to intercalate long DNA concatemers from HCR, which guaranteed the model of label-free fluorescence and strong fluorescence density...
September 15, 2017: Analytical Biochemistry
Jiyong Hu, Yan Guo, Jin'an Zhao, Junshuai Zhang
Four benzimidazole-based Cu(II) complexes: Cu2(p-2-bmp)2Br4 (1), Cu2(p-2-bmp)2Cl4 (2), Cu2(p-2-bmb)2(DMF)2Br4·(CHCl3) (3), and Cu(p-2-bmb)(NO3)2·(CHCl3) (4) were isolated and characterized, where p-2-bmp is 1-((2-(pyridine-2-yl)-1H-benzoimidazol-1-yl)methyl)-1H-pyridine and p-2-bmb is 1-((2-(pyridin-2-yl)-1-benzoimidazol-1-yl)methyl)-1H-benzotriazole. Complexes 1 and 2 have binuclear configurations, 3 has a mononuclear structure, and 4has a one-dimensional (1-D) chain skeleton. To evaluate their potential anticancer effects on human carcinoma cells, anti-proliferation, DNA binding and cleavage, and apoptosis elicitation were examined...
September 5, 2017: Bioorganic & Medicinal Chemistry
Huamin Zhong, Yukui Zhong, Qiulian Deng, Zhenwen Zhou, Xiaoshan Guan, Muxia Yan, Tingting Hu, Mingyong Luo
In the Viable but Non-Culturable (VBNC) state, microorganisms may survive under severe external environment. In this study, the specificity and sensitivity of PMA-LAMP assay on the detection of Vibrio Parahemolyticus (V. parahemolyticus) has been developed and evaluated, with further application on a number of food-borne V. parahemolyticus strains. Six primers were designed for recognizing 8 distinct targeting on tlh, tdh and trh gene. Through specific penetration through the damaged cell membrane of dead cells and intercalating into DNA, PMA could prevent DNA amplification of dead bacteria from LAMP, which enabled the differentiation of bacteria between VBNC state and dead state...
September 12, 2017: Microbial Pathogenesis
Xucheng Luo, Zhi Li, Ganglin Wang, Xuewen He, Xiaoqin Shen, Quanhong Sun, Li Wang, Renye Yue, Nan Ma
The use of cancer-relevant microRNA molecules as endogenous drug release stimuli is promising for personalized cancer treatment yet remains a great challenge because of their low abundance. Herein, we report a new type of microRNA-catalyzed drug release system based on DNA-programmed gold nanoparticle (GNP)-quantum dot (QD) complex. We show that a trace amount of miRNA-21 molecules could specifically catalyze the disassembly of doxorubicin (Dox)-loaded GNP-QDs complex through entropy driven process, during which the Dox-intercalating sites are destructed for drug release...
September 15, 2017: ACS Applied Materials & Interfaces
Paul T Wilder, David J Weber, Angela Winstead, Sabreea Parnell, Tiara V Hinton, Monet Stevenson, Dipak Giri, Samira Azemati, Pola Olczak, Brent V Powell, Tijesunimi Odebode, Solomon Tadesse, Yongchao Zhang, Saroj K Pramanik, James M Wachira, Sujan Ghimire, Pumtiwitt McCarthy, Alexis Barfield, Hirendra N Banerjee, Chao Chen, James A Golen, Arnold L Rheingold, Jeanette A Krause, Douglas M Ho, Peter Y Zavalij, Roosevelt Shaw, Santosh K Mandal
Cisplatin and other metal-based drugs often display side effects and tumor resistance after prolonged use. Because rhenium-based anticancer complexes are often less toxic, a novel series of organorhenium complexes were synthesized of the types: XRe(CO)3Z (X = α-diimines and Z = p-toluenesulfonate, 1-naphthalenesulfonate, 2-naphthalenesulfonate, picolinate, nicotinate, aspirinate, naproxenate, flufenamate, ibuprofenate, mefenamate, tolfenamate, N-acetyl-tryptophanate), and their biological properties were examined...
September 14, 2017: Molecular and Cellular Biochemistry
Juan Aranda, Antonio Francés-Monerris, Iñaki Tuñón, Daniel Roca-Sanjuán
Oxidation of nucleic acids are ubiquitous in living beings under metabolic impairments and/or exposed to external agents such as radiation, pollutants, or drugs, playing a central role in the development of many diseases mediated by DNA/RNA degeneration. Great efforts have been devoted to unveil the molecular mechanisms behind the OH radical additions to the double bonds of nucleobases, however, the specific role of the biological environment remains rela-tively unexplored. The present contribution tackles the study of the OH radical addition to uracil from the gas phase to a full RNA macromolecule by means of quantum-chemistry methods combined with molecular dynamics simulations...
September 13, 2017: Journal of Chemical Theory and Computation
Rahul Kalel, Aruna K Mora, Birija S Patro, Dipak K Palit, Sukhendu Nath
Surfactants have often been employed for the sequestration of drugs from DNA. However, for an effective sequestration, the concentration of the surfactant needs to be higher than its critical micellar concentration (CMC). Use of such high concentrations of the surfactant may limit its practical usage as a sequestering agent due to its cytotoxicity. In the present study we have shown that sodium dodecyl sulfate (SDS) itself at a concentration less than its CMC failed to sequester a drug from DNA. However, the sequestration power of SDS at sub-CMC concentration could be enhanced to a significant extent when incorporated into Pluronic polymer micelles in the form of supramolecular assemblies...
September 13, 2017: Physical Chemistry Chemical Physics: PCCP
Jessica Elizabeth Philip, Muhammad Shahid, M R Prathapachandra Kurup, Mohanan Puzhavoorparambil Velayudhan
Two chromone hydrazone ligands HL1 and HL2 were synthesized and characterized by elemental analyses, IR, (1)H NMR &(13)C NMR, electronic absorption and mass spectra. The reactions of the chromone hydrazones with transition metals such as Ni, Cu, and Zn (II) salts of acetate afforded mononuclear metal complexes. Characterization and structure elucidation of the prepared chromone hydrazone metal (II) complexes were done by elemental, IR, electronic, EPR spectra and thermo gravimetric analyses as well as conductivity and magnetic susceptibility measurements...
September 5, 2017: Journal of Photochemistry and Photobiology. B, Biology
Xia Li, Juan Song, Qingwang Xue, Haiyan Zhao, Min Liu, Baoli Chen, Yun Liu, Wei Jiang, Chen-Zhong Li
Developing a sensitive and selective sensing platform for the p53 gene and its mutation analysis is essential and may aid in early cancer screening and assessment of prognosis. Here, we developed a highly sensitive and selective p53 gene assay based on the coupling of a triple-helix magnetic probe (THMP) to a fluorescent liposome hybridization assembly, a process initiated by rolling circle amplification (RCA). In the presence of p53, the THMP unfolds and activates an enzymatic cleavage reaction, thus releasing the RCA primer and initiating the RCA product-assisted fluorescent liposome hybridization assembly...
September 11, 2017: Analyst
Maria M Shchepinova, Andrew G Cairns, Tracy A Prime, Angela Logan, Andrew M James, Andrew R Hall, Sara Vidoni, Sabine Arndt, Stuart T Caldwell, Hiran A Prag, Victoria R Pell, Thomas Krieg, John F Mulvey, Pooja Yadav, James N Cobley, Thomas P Bright, Hans M Senn, Robert F Anderson, Michael P Murphy, Richard C Hartley
Mitochondrial superoxide (O2(⋅-)) underlies much oxidative damage and redox signaling. Fluorescent probes can detect O2(⋅-), but are of limited applicability in vivo, while in cells their usefulness is constrained by side reactions and DNA intercalation. To overcome these limitations, we developed a dual-purpose mitochondrial O2(⋅-) probe, MitoNeoD, which can assess O2(⋅-) changes in vivo by mass spectrometry and in vitro by fluorescence. MitoNeoD comprises a O2(⋅-)-sensitive reduced phenanthridinium moiety modified to prevent DNA intercalation, as well as a carbon-deuterium bond to enhance its selectivity for O2(⋅-) over non-specific oxidation, and a triphenylphosphonium lipophilic cation moiety leading to the rapid accumulation within mitochondria...
August 24, 2017: Cell Chemical Biology
Y Vladimir Pabon-Martinez, You Xu, Alessandra Villa, Karin E Lundin, Sylvain Geny, Chi-Hung Nguyen, Erik B Pedersen, Per T Jørgensen, Jesper Wengel, Lennart Nilsson, C I Edvard Smith, Rula Zain
The anti-gene strategy is based on sequence-specific recognition of double-strand DNA by triplex forming (TFOs) or DNA strand invading oligonucleotides to modulate gene expression. To be efficient, the oligonucleotides (ONs) should target DNA selectively, with high affinity. Here we combined hybridization analysis and electrophoretic mobility shift assay with molecular dynamics (MD) simulations to better understand the underlying structural features of modified ONs in stabilizing duplex- and triplex structures...
September 8, 2017: Scientific Reports
Yingting Liu, Andrea M Berrido, Zi-Chun Hua, Yuk-Ching Tse-Dinh, Fenfei Leng
In this paper we successfully developed a procedure to generate the (+) supercoiled (sc) plasmid DNA template pZXX6 in the milligram range. With the availability of the (+) sc DNA, we are able to characterize and compare certain biochemical and biophysical properties of (+) sc, (-) sc, and relaxed (rx) DNA molecules using different techniques, such as UV melting, circular dichroism, and fluorescence spectrometry. Our results show that (+) sc, (-) sc, and rx DNA templates can only be partially melted due to the fact that these DNA templates are closed circular DNA molecules and the two DNA strands cannot be completely separated upon denaturation at high temperatures...
September 1, 2017: Biophysical Chemistry
Manikanta Murahari, Karanam Vanitha Prakash, Godefridus J Peters, Y C Mayur
Hybrid systems of acridones with substituted pyrimidines were designed with an objective of discovering next generation anticancer agents targeting multiple mechanisms in the cancer cell. Hybrid compounds were synthesized by simple and convenient methods in the lab, characterized by NMR and Mass spectral methods and screened for cytotoxicity against A549 (lung), Hela (cervical), MCF7 (breast) and MDA-MB-231 (breast) cancer cell lines respectively. Evaluation of compounds for cell proliferation identified active compounds 11b, 11d and 11h against MCF7, MDA-MB-231 and A549 cell lines...
August 12, 2017: European Journal of Medicinal Chemistry
Alketa Tarushi, Catherine P Raptopoulou, Vassilis Psycharis, Dimitris P Kessissoglou, Athanasios N Papadopoulos, George Psomas
The reaction of ZnCl2 with the non-steroidal anti-inflammatory drug niflumic acid (Hnif) resulted in the formation of complex [Zn(nif-O)2(MeOH)4], 1. When this reaction was performed in the presence of a N,N'-donor heterocyclic ligand such as 2,2'-bipyridine (bipy), 2,2'-bipyridylamine (bipyam), 1,10-phenanthroline (phen) and 2,2'-dipyridylketone oxime (Hpko), the complexes [Zn(nif-O,O')(bipy)Cl], 2, [Zn(nif-O)(nif-O,O')2(bipyam)], 3, [Zn(nif-O,O')2(phen)], 4 and [Zn(nif-O)2(Hpko-N,N')2], 5 were formed, respectively...
September 1, 2017: Journal of Inorganic Biochemistry
Ye Sol Oh, Jin Ha Park, Sung Wook Han, Seog K Kim, Young-Ae Lee
Meso-tetrakis(N-methyl pyridinium-4-yl)porphyrin (TMPyP) intercalates between the base-pairs of DNA at a low [TMPyP]/[DNA base] ratio in aqueous solutions and molecular crowding conditions, which is induced by the addition of poly(ethylene glycol) (PEG). Studied DNA binding drugs, including TMPyP, 9-AA(Aminoacridine), EB(Ethidium Bromide) and DAPI(4', 6-diamidino-2-phenylindole) showed similar binding properties in the presence or absence of PEG molecules which is examined by circular and linear dichroism. According to the LD(r) (Reduced Linear Dichroism) results of the binding drugs examined in this work, PEG molecules induced no significant change compared to their binding properties in aqueous buffering systems...
September 6, 2017: Journal of Biomolecular Structure & Dynamics
Takanori Harashima, Chie Kojima, Shintaro Fujii, Manabu Kiguchi, Tomoaki Nishino
The single-molecule conductance of DNA was found to increase by over four fold upon intercalation, while the conductance nearly unaltered upon groove-binding. These effects are interpreted on the basis of the electronic interaction of the DNA-binding molecules with the stacked DNA bases.
September 19, 2017: Chemical Communications: Chem Comm
Kevin D Dorfman
The development of bright bis-intercalating dyes for DNA in the 1990s, most notably YOYO-1, revolutionized the field of polymer physics in the ensuing years. These dyes, in conjunction with modern molecular biology techniques, permit the facile observation of polymer dynamics via fluorescence microscopy, and thus direct tests of different theories of polymer dynamics. At the same time, they have played a key role in advancing an emerging next-generation method known as genome mapping in nanochannels. The effect of intercalation on the bending energy of DNA, as embodied by a change in its statistical segment length (or, alternatively, its persistence length) has been the subject of significant controversy...
August 31, 2017: Journal of Biomechanical Engineering
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