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DNA intercalation

Joseph D Kimball, Badri Maliwal, Sangram L Raut, Hung Doan, Zhangatay Nurekeyev, Ignacy Gryczynski, Zygmunt Gryczynski
Fluorescence signal enhancement induced by the binding of intercalators to DNA has been broadly utilized in various DNA detection methods. In most instances the increase in fluorescence intensity is associated with a concomitant increase of fluorescence lifetime. This increase of the fluorescence lifetime presents an additional opportunity to increase detection sensitivity. In this paper, we present a new approach to significantly enhance the sensitivity in detecting minute DNA concentrations. The approach is based on simultaneous use of time-gated detection and multi-pulse pumping...
May 18, 2018: Analyst
Indranil Roy, Sharan Bobbala, Jiawang Zhou, Minh T Nguyen, Siva Krishna Mohan Nalluri, Yilei Wu, Daniel Ferris, Evan Alexander Scott, Michael R Wasielewski, J Fraser Stoddart
The ideal fluorescent probe for live-cell imaging is bright, non-cytotoxic and can be delivered easily into the living cells in an efficient manner. The design of synthetic fluorophores, having all three of these properties, however, has proved to be challenging. Here, we introduce a simple, yet effective, strategy based on well-established chemistry for designing a new class of fluorescent probes for live-cell imaging. A box-like hybrid cyclophane, namely ExTzBox•4X (6•4X, X = PF6 - , Cl- ), has been synthesized by connecting an extended viologen (ExBIPY) and a dipyridyl thiazolothiazole (TzBIPY) unit in an end-to-end fashion with two p-xylylene ( p-Xy) linkers...
May 17, 2018: Journal of the American Chemical Society
Seyed Morteza Seifati, Navid Nasirizadeh, Mostafa Azimzadeh
Phenylketonuria (PKU)-associated DNA mutation in newborn children can be harmful to his health and early detection is the best way to inhibit consequences. A novel electrochemical nano-biosensor was developed for PKU detection, based on signal amplification using nanomaterials, e.g. gold nanoparticles (AuNPs) decorated on the reduced graphene oxide sheet on the screen-printed carbon electrode. The fabrication steps were checked by field emission scanning electron microscope imaging as well as cyclic voltammetry analysis...
June 2018: IET Nanobiotechnology
Jaroslav Malina, Nicholas P Farrell, Viktor Brabec
The formation of triple-helical DNA is implicated in the regulation of gene expression. The triplexes are, however, unstable under physiological conditions so that effective stabilizers for the triplex formation are needed. Here, we describe a new strategy for stabilization of the triplexes based on the antitumor substitution-inert polynuclear platinum complexes (SI-PPCs). These compounds were shown previously to bind to DNA through the phosphate clamp - a discrete mode of DNA-ligand recognition distinct from the canonical intercalation and minor-groove binding...
May 16, 2018: Angewandte Chemie
Hongmei Yang, Yihan Wang, Wenjing Yu, Lei Shi, Hongfeng Wang, Rui Su, Changbao Chen, Shuying Liu
The identification and screening of triplex DNA binders are important because these compounds, in many cases, are potential anticancer agents as well as promising drug candidates. Therefore, the ability to screen for these compounds in a high-throughput mode could dramatically improve the drug screening process. A method involving a combination of 96-well plate format and peak area-fading ultra high performance liquid chromatography coupled with Orbitrap mass spectrometry was employed for screening bioactive compounds binding to the triplex DNA from the extracts of Stephania tetrandra S...
May 15, 2018: Journal of Separation Science
Cristiano Ceron Jayme, Italo Rodrigo Calori, Elise Marques Freire Cunha, Antonio Claudio Tedesco
The aim of this study was to evaluate the interaction of aluminum phthalocyanine chloride (AlClPc) with double-stranded DNA. Absorption and fluorescence spectra, resonance light scattering, and circular dichroism were evaluated in water and water/ethanol mixtures with different concentrations of DNA or AlClPc. AlClPc showed a high ability to bind to DNA in both water and 4/6 water/ethanol mixture (v/v), with a majority of monomeric and aggregated initial forms of AlClPc, respectively. In this interaction, AlClPc bound preferentially to the grooves of DNA...
May 5, 2018: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
Pei-Ching Wu, Shu-Ling Tzeng, Chung-Ke Chang, Ya-Fen Kao, Michael J Waring, Ming-Hon Hou
Small-molecule compounds that target mismatched base pairs in DNA offer a novel prospective for cancer diagnosis and therapy. The potent anticancer antibiotic echinomycin functions by intercalating into DNA at CpG sites. Surprisingly, we found that the drug strongly prefers to bind to consecutive CpG steps separated by a single T:T mismatch. The preference appears to result from enhanced cooperativity associated with the binding of the second echinomycin molecule. Crystallographic studies reveal that this preference originates from the staggered quinoxaline rings of the two neighboring antibiotic molecules that surround the T:T mismatch forming continuous stacking interactions within the duplex...
May 8, 2018: Nucleic Acids Research
Qian Zhou, Chaoqun You, Cong Zheng, Yawen Gu, Hongchao Gu, Rui Zhang, Hongshuai Wu, Baiwang Sun
DNA is considered to be one of the most promising targets for anticancer agents. Acridine analogues have anticancer activity based on DNA binding and topoisomerases inhibition. However, due to the side effects, resistance and low bioavailability, a few have entered into clinical usage and the mechanisms of action are not fully understood. Novel acridine derivatives are needed for effective cancer therapy. A series of novel 3-nitroacridine-based derivatives were synthesized, their DNA binding and anticancer activities were evaluated...
May 5, 2018: Life Sciences
Guo-Lan Ma, Xu-Dan Bi, Feng Gao, Zheng Feng, Dong-Chun Zhao, Feng-Jie Lin, Ru Yan, Dandan Liu, Peng Liu, Jingbo Chen, Hongbin Zhang
Six novel polypyridyl ruthenium complexes with (E)-2-styryl-1H- imidazo[4,5-f][1,10]phenanthroline ligand and its analogues have been designed to enhance the DNA intercalation ability of their model compound [Ru(bpy)2 (pip)]2+ (bpy = 2,2'-bipyridine, pip = 2-phenyl-1H-imidazo[4,5-f][1,10]phenanthroline). As shown in the optimized geometry of the complexes, the introduction of styryl group not only extended the conjugated area of the intercalative ligand, but also retained the excellent planarity. These two merits have been proven to be beneficial for their DNA intercalation, thus greatly improved their inhibition activity towards DNA transcription by RNA polymerase and DNA topoisomerase, two enzymes closely related to both DNA and tumor cell growth...
May 2, 2018: Journal of Inorganic Biochemistry
A G Bharathi Dileepan, T Daniel Prakash, A Ganesh Kumar, P Shameela Rajam, V Violet Dhayabaran, R Rajaram
In the present work, five macrocyclic compounds, C18 H12 N2 O4 (1), C38 H24 N8 O6 (1a), C38 H24 N8 O4 S2 (1b), C40 H32 N8 O4 (2a) and C48 H32 N8 O4 (2b) have been synthesized and thoroughly characterized by elemental analysis, FT-IR, 1D & 2D NMR and electron spray ionization mass spectral analysis. The DNA binding ability of these compounds were investigated in vitro by UV-Visible, fluorescence, circular dichroism (CD) spectroscopy and viscosity measurements. The results indicate that these compounds possess strong DNA binding affinity via intercalation, while the order of binding strength followed the trend 2b (1...
April 21, 2018: Journal of Photochemistry and Photobiology. B, Biology
Vlasta Bonacic-Koutecky, Martina Perić, Zeljka Sanader
Our investigation of one-photon absorption (OPA) and nonlinear optical (NLO) properties such as two-photon absorption (TPA) of silver trimer intercalated in DNA based on TDDFT approach allowed us to propose mechanism responsible for large TPA cross sections of such NLO-phores. We present concept which illustrates key role of quantum cluster as well as of nucleotide bases from immediate neighborhood. For this purpose, different surroundings consisting of Guanine-Cytosine and Adenine-Thymine such as (GCGC) and (ATAT) have been investigated which are exhibiting substantially different values of TPA cross sections...
May 1, 2018: Journal of Physical Chemistry Letters
Katarzyna Malarz, Anna Mrozek-Wilczkiewicz, Maciej Serda, Marta Rejmund, Jaroslaw Polanski, Robert Musiol
Thiosemicarbazones are chelators of transition metals such as iron or copper whose anticancer potency is intensively investigated. Although two compounds from this class have entered clinical trials, their precise mechanism of action is still unknown. Recent studies have suggested the mobilization of the iron ions from a cell, as well as the inhibition of ribonucleotide reductase, and the formation of reactive oxygen species. The complexity and vague nature of this mechanism not only impedes a more rational design of novel compounds, but also the further development of those that are highly active that are already in the preclinical phase...
April 3, 2018: Oncotarget
Min Wei, Wenyang Zhang
In this work, a novel aptamer-based electrochemical biosensor was developed for the determination of Ochratoxin A (OTA) by using carbon aerogels (CAs) and methylene blue (MB) as signal amplification strategy. CAs was used as carrier to load the abundant of complementary DNA (cDNA), which could enhance the hybridization between CAs-cDNA and aptamer immobilized on the electrode surface, thus provide more double-stranded DNA for MB intercalation. The current of MB on the CAs-cDNA/apt/AuE sensor was twice that on the cDNA/apt/AuE sensor, which indicated that the CAs with high surface area enabled a higher loading of the cDNA and absorbed more MB, thus realized the signal amplification strategy...
April 25, 2018: Chemistry Central Journal
Jan Hormann, Jaroslav Malina, Oliver Lemke, Max J Hülsey, Stefanie Wedepohl, Jan Potthoff, Claudia Schmidt, Ingo Ott, Bettina G Keller, Viktor Brabec, Nora Kulak
Many drugs that are applied in anticancer therapy such as the anthracycline doxorubicin contain DNA-intercalating 9,10-anthraquinone (AQ) moieties. When Cu(II) cyclen complexes were functionalized with up to three (2-anthraquinonyl)methyl substituents, they efficiently inhibited DNA and RNA synthesis resulting in high cytotoxicity (selective for cancer cells) accompanied by DNA condensation/aggregation phenomena. Molecular modeling suggests an unusual bisintercalation mode with only one base pair between the two AQ moieties and the metal complex as a linker...
April 23, 2018: Inorganic Chemistry
Siffeen Zehra, Mohammad Shavez Khan, Iqbal Ahmad, Farukh Arjmand
New tailored Cu(II) & Zn(II) metal-based antitumor drug entities were synthesized from substituted benzothiazole o‒vanillin Schiff base ligands. The complexes were thoroughly characterized by elemental analysis, spectroscopic studies {IR, 1 H & 13 C NMR, ESI-MS, EPR} and magnetic susceptibility measurements. The structure activity relationship (SAR) studies of benzothiazole Cu(II) & Zn(II) complexes having molecular formulas [C30 H22 CuN5 O7 S2 ], [C30 H20 Cl2 CuN5 O7 S2 ], [C30 H20 CuF2 N5 O7 S2 ], [C30 H22 N4 O4 S2 Zn], [C30 H20 Cl2 N4 O4 S2 Zn] and [C30 H20 F2 N5 O7 S2 Zn], with CT‒DNA were performed by employing absorption, emission titrations and hydrodynamic measurements...
April 20, 2018: Journal of Biomolecular Structure & Dynamics
Jie Kang, Lavanya Gopala, Vijai Kumar Reddy Tangadanchu, Wei-Wei Gao, Cheng-He Zhou
AIM: The increasing emergence of resistant bacteria imposed an urgent request to discover novel antibacterial agents. This work was to develop naphthalimide nitroimidazoles as potentially antibacterial agents. Results/methodology: Compound 9e showed the strong antibacterial activity (minimal inhibitory concentration = 0.013 μmol/ml) against resistant Acinetobacter baumannii (A. baumannii) with rapid killing effect and no obvious triggering of the development of resistance. Its combination use with chloromycin, norfloxacin or clinafloxacin improved the antibacterial potency...
April 19, 2018: Future Medicinal Chemistry
Ufuk Yildiz, Burak Coban
A new derivate of 4-bromo-1,8-naphthalic anhydride and its quaternized analogue have been prepared and characterized. The interactions of both derivatives with human telomere quadruplex-DNA and ds-DNA have been comparatively studied by UV-visible (UV-Vis), fluorescent intercalator displacement assays, competition dialysis, circular dichroism (CD), agarose gel electrophoresis, and polyacrylamide gel electrophoresis. The results show that both derivatives can stabilize G-quadruplexes DNA, and they show different binding affinities for G-quadruplexes-DNA and ds-DNA...
April 19, 2018: Applied Biochemistry and Biotechnology
Alakesh Bera, Sajal Biring
Different studies indicated that the prion protein induces hybridization of complementary DNA strands. Cell culture studies showed that the scrapie isoform of prion protein remained bound with the chromosome. In present work, we used an oxazole dye, YOYO, as a reporter to quantitative characterization of the DNA condensation by prion protein. We observe that the prion protein induces greater fluorescence quenching of YOYO intercalated in DNA containing only GC bases compared to the DNA containing four bases whereas the effect of dye bound to DNA containing only AT bases is marginal...
2018: Journal of Nucleic Acids
Jelena Petronijević, Nenad Janković, Tatjana P Stanojković, Nenad Joksimović, Nađa Đ Grozdanić, Milan Vraneš, Aleksandar Tot, Zorica Bugarčić
In order to investigate new potential therapeutically active agents, we investigated the biological properties of two small libraries of quinoxalinones and 1,4-benzoxazin-2-ones. The results obtained showed that compounds 5, 9-11 have good cytotoxic activity against HeLa cells where the lowest IC50 value (10.46 ± 0.82 μM/mL) was measured for compound 10. Additionally, the most active compounds (5, 9-11) showed much better selectivity for MRC-5 cells (up to 17.4) compared to cisplatin. In vitro evaluation of the inhibition of the enzyme α-glucosidase showed that compounds 10 and 11 exert significant inhibition of the enzyme at 52...
April 14, 2018: Archiv der Pharmazie
Raquel Ciuvalschi Maia, Michelle X G Pereira, Amanda S O Hammes, Flavia C Vasconcelos, Aline R Pozzo, Thais Hancio Pereira, Ernesto R Caffarena, Cerli R Gattass
BACKGROUND: Acute myeloid leukemia (AML) represent the largest number of annual deaths from hematologic malignancy. In the United-States, it is estimated that 21.380 individuals will be diagnosed with AML and 49.5% of patients will die in 2017. Therefore, the searching for novel compounds capable of increasing the overall survival rate to the treatment of AML cells is urgent. OBJECTIVES: To investigate the cytotoxicity effect of the natural compound PA and to explore the mechanism of action of PA in AML cell lines with different phenotypes...
April 12, 2018: Anti-cancer Agents in Medicinal Chemistry
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