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DNA intercalation

K Singaravelan, A Chandramohan, M Saravanabhavan, I V Muthu Vijayan Enoch, V S Suganthi
Radical scavenging activity against DPPH radical and binding properties of a hydrogen bonded charge transfer molecular salt 4-chloro anilinium-3-nitrophthalate(CANP) with calf thymus DNA has been studied by electronic absorption and emission spectroscopy. The molecular structure and crystallinity of the CANP salt have been established by carried out powder and single crystal X-ray diffraction analysis which indicated that cation and anion are linked through strong N(+)H(…)O(-) type of hydrogen bond. FTIR spectroscopic study was carried out to know the various functional groups present in the crystal...
May 10, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
Priya Singh, Susobhan Choudhury, Shreyasi Dutta, Aniruddha Adhikari, Siddhartha Bhattacharya, Debasish Pal, Samir Kumar Pal
The jam-packed intracellular environments differ the activity of a biological macromolecule from that in laboratory environments (in vitro) through a number of mechanisms called molecular crowding related to structure, function and dynamics of the macromolecule. Here, we have explored the structure, function and dynamics of a model enzyme protein DNase I in molecular crowing of polyethylene glycol (PEG; MW 3350). We have used steady state and picosecond resolved dynamics of a well-known intercalator ethidium bromide (EB) in a 20-mer double-stranded DNA (dsDNA) to monitor the DNA-cleavage by the enzyme in absence and presence PEG...
May 15, 2017: International Journal of Biological Macromolecules
Alexandre Antunes Brum, Andrea de Fatima Silva Rezende, Francisco Silvestre Brilhante, Thais Collares, Karine Begnine, Fabiana Kommling Seixas, Tiago Veiras Collares, Odir Antônio Dellagostin, Vasco Azevedo, Anderson Santos, Ricardo Wagner Portela, Sibele Borsuk
PURPOSE: We tested the efficacy of the esterase encoded by cp1002_RS09720 from Corynebacteriumpseudotuberculosis in recombinant subunit and DNA caseous lymphadenitis (CLA) vaccines. This target was predicted as one of the best CLA vaccine candidates by mature epitope density analysis. METHODOLOGY: Gene cp1002_RS09720 was cloned into two different vectors (pAE for subunit vaccine and pTARGET for DNA vaccine). Four groups of 15 mice each were immunized with the recombinant esterase rCP09720 associated with aluminium hydroxide adjuvant (G1), pTARGET/cp09720 DNA vaccine (G2), a naked pTARGET (G3) or PBS as a negative control (G4)...
May 2017: Journal of Medical Microbiology
V Violet Dhayabaran, T Daniel Prakash
A novel Schiff base, (S,Z)-4-(methylthio)-2-((3-oxo-2,3-dihydro-1H-inden-1-ylidene)amino)butanoic acid (L) and four M(II) complexes (where M = Co, Cu, Ni and Zn) were synthesized and characterized. The DNA-binding characteristics of the complexes were investigated using various spectroscopic methods and viscosity measurements. Analysis of the results suggests that all the complexes bind to calf thymus DNA via intercalation. Among the four, Cu(II) complex was found to promote the photocleavage of plasmid DNA pBR322 under irradiation at 365 nm...
May 18, 2017: Luminescence: the Journal of Biological and Chemical Luminescence
Yan Zhao, Shichao Hu, Huaming Wang, Kaiwen Yu, Yan Guan, Xiaoyun Liu, Na Li, Feng Liu
We develop a DNA dendrimer-streptavidin (SA) nanocomplex as a novel signal amplifier to create biosensing platforms for disease-related species. The DNA dendrimer-SA nanocomplex is fabricated by crosslinking the nonlinear hybridization chain reaction based DNA dendrimer with the SA-coupled linker DNA, and possesses multiple sticky ends, a high molecular weight, and a hyperbranched nanostructure with large numbers of DNA duplexes. Taking advantages of the DNA dendrimer-SA nanocomplex and a label-free quartz crystal microbalance (QCM) technology, we first construct a mass-sensitive QCM biosensing platform for nucleic acids, which displays high selectivity and sensitivity with the detection limit of 0...
May 18, 2017: Analytical Chemistry
Milena Balazy, Alejandra Fausto, Christina Voskanian, Bianca Chavez, Harmanpreet Panesar, Thomas G Minehan
To explore the utility of the azinomycin B chromophore as a platform for the development of major-groove binding small molecules, we have prepared a series of 3-methoxy-5-methylnaphthalene derivatives containing diamine, triamine, and carbohydrate linker moieties. All bis- and tris-azinomycin derivatives are intercalators that display submicromolar binding affinities for calf-thymus DNA, as revealed by viscometry measurements and fluorescent intercalator displacement (FID) assays, respectively. Although the tightest binding ligand 1d (Ka = 2...
May 17, 2017: Organic & Biomolecular Chemistry
Romana Smolková, Vladimír Zeleňák, Lukáš Smolko, Juraj Kuchár, Miroslava Rabajdová, Michaela Ferenčáková, Mária Mareková
Three novel Zn(II) complexes of NSAID niflumic acid (Hnif) were prepared and studied, namely; [Zn(MeOH)4(nif)2] (1), [Zn(cyclam)(nif)2] (2) and [Zn(nif)2(tmen)] (3), where nif is deprotonated niflumic acid, cyclam is 1,4,8,11-Tetraazacyclotetradecane and tmen is N,N,N',N'-Tetramethylethylenediamine. The complexes have been characterized by infrared spectroscopy, elemental and thermal analysis and single-crystal X-ray structure analysis. All three complexes contain two deprotonated niflumato anions monodentately coordinated via carboxylato groups...
May 5, 2017: European Journal of Medicinal Chemistry
Wen-Jun Song
A new fluorescent sensing platform based on ultrathin metal-organic framework (MOF) nanosheets (MnDMS) was prepared from the flexible ligand 2,2-dimethylsuccinate and Mn ions. The MnDMS nanoparticles can be obtained by simply ultrasonication of the MnDMS crystal, and then can be exfoliated into nanosheets by Li-intercalation method. The MnDMS nanosheets can be easily assembled with biological probes, leading to efficient fluorescence quenching of the fluorophore tagged ssDNA and microRNA (miRNA). By using a hybridization chain reaction (HCR) strategy, the fluorescence signal can be obviously amplified...
August 1, 2017: Talanta
Hui-Zhen Zhang, Shi-Chao He, Yan-Jun Peng, Hai-Juan Zhang, Lavanya Gopala, Vijai Kumar Reddy Tangadanchu, Lin-Ling Gan, Cheng-He Zhou
A novel series of benzimidazole-incorporated sulfonamide analogues were designed and synthesized with an effort to overcome the increasing antibiotic resistance. Compound 5c gave potent activities against Gram-positive bacteria and fungi, and 2,4-dichlorobenzyl derivative 5g showed good activities against Gram-negative bacteria. Both of these two active molecules 5c and 5g could effectively intercalate into calf thymus DNA to form compound-DNA complex respectively, which might block DNA replication to exert their powerful antimicrobial activity...
May 2, 2017: European Journal of Medicinal Chemistry
Tingxiao Qin, Kunhui Liu, Di Song, Chunfan Yang, Hongmei Su
G-rich and C-rich DNA can fold into the tetrastranded helical structures G-quadruplex or C-quadruplex (i-motif) that are considered as specific drug targets for cancer therapy. A large number of small molecules (the so-called ligands), which could bind and modulate the stability of G-quadruplexes structures, have been widely examined. Hitherto, much less is known for the ligand binding interactions with the relatively young C-quadruplex (i-motif). Here by combining steady-state measurements (UV-vis, fluorescence, and ICD) with time-resolved laser flash photolysis spectroscopy, we study the binding interactions of cationic porphyrin (TMPyP4) with i-motifs (C₃TA₂)₃C₃T and (C₄A₄C₄)2...
May 9, 2017: Chemistry, An Asian Journal
Priyaranjan Kumar, Srikanth Dasari, Ashis K Patra
Ruthenium complexes trans-[Ru(sac)2(dpq)2] (1) and trans-[Ru(sac)2(dppz)2] (2) where sac is artificial sweetener saccharin (o-sulfobenzimide; 1,2-benzothiazole-3(2H)-one1,1-dioxide (Hsac)), dpq = dipyrido[3,2-d:2',3'-f]quinoxaline and dppz = dipyrido[3,2-a:2',3'-c]phenazine have been synthesized and thoroughly characterized using various analytical and spectral techniques. Saccharin known to act as carbonic anhydrase IX (CA IX) inhibitor which is a biomarker for highly aggressive and proliferative tumor in hypoxic stress, so inhibition of CA IX is a potential strategy for anticancer chemotherapy...
May 3, 2017: European Journal of Medicinal Chemistry
Wanbo Liu, Siwen Wang, Irina A Dotsenko, Vyacheslav V Samoshin, Liang Xue
Guanine-rich DNA sequences can undergo self-assembly into unique G-quadruplex structures that interfere with the binding of proteins to the same DNA region. The formation of DNA G-quadruplexes requires monovalent cations (Na(+) and K(+)) or small molecules known as G-quadruplex (G4) ligands. Phenanthroline is a type of G4 ligand scaffold known for its coordination with metal ions to form complexes with a large aromatic surface area, which aptly stack with G-quartets. In this report, we have investigated the side chain effect on G-quadruplex recognition by evaluating a series of 5-substituted phenanthroline-based metal complexes (Phen-Ni) binding to telomeric G-quadruplex DNA...
April 27, 2017: Journal of Inorganic Biochemistry
V M Manikandamathavan, M Thangaraj, T Weyhermuller, R P Parameswari, V Punitha, N Narasimha Murthy, Balachandran Unni Nair
Two mononuclear copper (II) terpyridine complexes namely, [Cu(Btptpy) (ClO4)](ClO4) 1, and [Cu(Bttpy) (ClO4)](ClO4) 2, (Btptpy (L1) = 4'-(Benzothiophene)-2,2':6',2″-terpyridine, Bttpy (L2) = 4'-(Benzylthiazolyl)-2,2':6',2″-terpyridine) have been synthesized and characterized. Single crystal X-ray diffraction shows that, both ligands belong to monoclinic crystal system with space group P21/c (L1) and P21/n (L2). Absorption spectral titration, DNA melting study, circular dichroism and viscosity measurement reveal that, complex 1 and 2 bind with DNA through intercalation...
April 15, 2017: European Journal of Medicinal Chemistry
Chang Su, Dongjian Zhang, Na Bao, Aiyan Ji, Yuanbo Feng, Li Chen, Yicheng Ni, Jian Zhang, Zhiqi Yin
PURPOSE: Identifying necrotic myocardium in ischemic regions is of great importance for risk stratification and clinical decision-making. However, rapid noninvasive imaging of necrotic myocardium is still challenging. This study sought to evaluate the potential of 1,4-naphthoquinones to rapidly visualize necrotic myocardium and the possible mechanisms of necrosis avidity. PROCEDURES: Six 1,4-naphthoquinones were radiolabeled with iodine-131 and the necrosis avidity was estimated in mouse models with muscular necrosis by gamma counting and autoradiography...
May 3, 2017: Molecular Imaging and Biology: MIB: the Official Publication of the Academy of Molecular Imaging
Díaz-Gómez G Dalia, Galindo-Murillo Rodrigo, Fernando Cortes-Guzman
Molecular recognition between ligands and nucleic acids is one of the key roles in therapeutic activity. Some molecules interact with DNA in a non-bonded manner via intercalation or through the grooves. The recognition of minor groove binders is attributed to a set of H-bonding interactions between the binders and the hydrogen-bond acceptor groups at the groove floor and walls. Commonly it is considered that interactions with the sugar groups of the DNA backbone are insignificant and do not contribute to the binding affinity or the specificity...
May 2, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Angus Beane, Bill R Miller, Carol A Parish
Dynemicin A has the ability to undergo the Bergman cyclization, forming a para-benzyne moiety with the ability to induce DNA strand scission. This property of dynemicin A makes it a promising anti-tumor agent. Past research has shown conclusively that dynemicin A binds to and abstracts a hydrogen atom (H5') from the DNA backbone, but the molecular mechanism of the binding event is not fully understood. We have used AMBER Molecular Dynamics simulations to investigate the dynamics associated with the reaction mechanisms...
April 11, 2017: Journal of Molecular Graphics & Modelling
Laila H Abdel-Rahman, Ahmed M Abu-Dief, Moustafa O Aboelez, Azza A Hassan Abdel-Mawgoud
The present study was conducted to synthesis of some new imine Cr(III), VO(II), Mn(II) and Ni(II) complexes derived from the condensation of 2-amino phenol with 2-hydroxynapthaldehyde were synthesized. The prepared HNPN imine ligand was analyzed by its melting point, IR, (1)H NMR and (13)C NMR spectroscopies. The investigated HNPN imine complexes were characterized by elemental analysis, FT IR, UV-vis and thermal analysis (TGA) under nitrogen atmosphere from ambient temperature to 750°C. The experimental results revealed that the investigated complexes contain hydrated water molecules...
April 9, 2017: Journal of Photochemistry and Photobiology. B, Biology
Asmita Das, Debashis Majumder, Chabita Saha
Flavonoids are dietary intakes which are bestowed with several health benefits. The most studied property of flavonoids is their antioxidant efficacy. Among the chosen flavonoids Quercetin, Kaempferol and Myricetin is catagorized as flavonols whereas Apigenin and Luteolin belong to the flavone group. In the present study anti-cancer properties of flavonoids are investigated on the basis of their binding efficacy to ct-DNA and their ability to induce cytotoxicity in K562 leukaemic cells. The binding affinities of the flavonoids with calf thymus DNA (ct-DNA) are in the order Quercetin>Myricetin>Luteolin>Kaempferol>Apigenin...
April 19, 2017: Journal of Photochemistry and Photobiology. B, Biology
Ádám Orosz, Szilvai Bősze, Gábor Mező, Ildikó Szabó, Levente Herényi, Gabriella Csík
Recently, we have characterized the DNA and nucleoprotein (NP) binding of bis(4-N-methylpyridyl)-15,20-di(4-carboxyphenyl)porphyrin (BMPCP) and meso-tri(4-N-methylpyridyl)-mono(4-carboxyphenyl)porphyrin (TMPCP) and their tetrapeptide conjugates (BMPCP-4P2 and TMPCP-4P, respectively). In this work, we investigated the interaction of TMPCP conjugated to the tetrapeptide branches of branched chain polymeric polypeptide with poly-L-lysine backbone (AK) with DNA or NP using spectroscopic methods. Analysis of absorption spectra revealed the external binding but no intercalation of TMPCP-AK to DNA...
April 27, 2017: Amino Acids
Sara Bonetta, Cristina Pignata, Silvia Bonetta, Lorenza Meucci, Donatella Giacosa, Elena Marino, Giorgio Gilli, Elisabetta Carraro
Legionella pneumophila is a ubiquitous microorganism widely distributed in aquatic environments and can cause Legionellosis in humans. A promising approach to detect viable cells in water samples involves the use of quantitative polymerase chain reaction (qPCR) in combination with photoactivatable DNA intercalator propidium monoazide (PMA). However, the PMA efficiency could be different depending on the experimental conditions used. The aim of this study was to compare two PMA exposure protocols: (A) directly on the membrane filter or (B) in liquid after filter washing...
April 27, 2017: International Journal of Environmental Research and Public Health
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