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DNA intercalation

Masashi Kitamura, Seiji Kubo, Jin Tanaka, Tatsushi Adachi
Screening for male-derived biological material from collected samples plays an important role in criminal investigations, especially those involving sexual assaults. We have developed a loop-mediated isothermal amplification (LAMP) assay targeting multi-repeat sequences of the Y chromosome for detecting male DNA. Successful amplification occurred with 0.5 ng of male DNA under isothermal conditions of 61 to 67 °C, but no amplification occurred with up to 10 ng of female DNA. Under the optimized conditions, the LAMP reaction initiated amplification within 10 min and amplified for 20 min...
August 12, 2017: International Journal of Legal Medicine
Eimer Mary Tuite, Bengt Nordén
The binding mode of thionine (3,7-diamino-5-phenothiazinium) with alternating and non-alternating DNA polynucleotides at low binding ratios was conclusively determined using linear and circular dichroism spectroscopies. The binding to [poly(dG-dC)]2 and poly(dG)·poly(dC) was purely intercalative and was insensitive to ionic strength. Intercalative binding to [poly(dA-dT)]2 is observed at low ionic strength, but a shift of some dye to an non-intercalative mode is observed as the background salt concentration increases...
August 1, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
Ri Zhou, Zai-Qun Liu
To overcome the problem on the relationship of antioxidative effect with the branch number in a tetramer, we herein designed a series of antioxidants with pentaerythritol, glycerol, and ethylene glycol as the cores, and gallic, ferulic, caffeic, and p-hydroxybenzoic acids as the antioxidative moieties. In the case of DNA oxidation mediated by 2,2'-azobis(2-amidinopropane hydrochloride, AAPH), it was found that the stoichiometric factor (n) of a carboxylic acid increased rapidly when the acid was esterified with ethylene glycol, glycerol, and pentaerythritol to form a dimer, trimer, and tetramer, respectively...
August 5, 2017: Archives of Biochemistry and Biophysics
Paul D Cunningham, William P Bricker, Sebastián A Díaz, Igor L Medintz, Mark Bathe, Joseph S Melinger
Sequence-selective bis-intercalating dyes exhibit large increases in fluorescence in the presence of specific DNA sequences. This property makes this class of fluorophore of particular importance to biosensing and super-resolution imaging. Here we report ultrafast transient anisotropy measurements of resonance energy transfer (RET) between thiazole orange (TO) molecules in a complex formed between the homodimer TOTO and double-stranded (ds) DNA. Biexponential homo-RET dynamics suggest two subpopulations within the ensemble: 80% intercalated and 20% non-intercalated...
August 7, 2017: Journal of Chemical Physics
Yellaiah Tangella, Kesari Lakshmi Manasa, V Laxma Nayak, Manda Sathish, B Sridhar, Abdullah Alarifi, Narayana Nagesh, Ahmed Kamal
An operationally facile and high yielding one-pot, three-component protocol has been developed for the preparation of selectively trans-2,3-dihydrofuro[3,2-c]coumarins and trans-1,2-dihydrobenzo[h]furo[3,2-c]quinolinones. This protocol proceeds through a domino Knoevenagel condensation, a Michael addition followed by intramolecular SN2 cyclisation. All the synthesized compounds have been evaluated for their in vitro cytotoxic activity against selected human cancer cell lines. Interestingly, most of the compounds have exhibited considerable cytotoxicity with IC50 values <10 μM in all the tested cell lines...
August 16, 2017: Organic & Biomolecular Chemistry
L Parisi, C Galli, A Bianchera, P Lagonegro, L Elviri, A Smerieri, S Lumetti, E Manfredi, R Bettini, G M Macaluso
The aim of the present study was to investigate how the enrichment of chitosan films with anti-fibronectin aptamers could enhance scaffold colonization by osteoblasts, by improving their adhesion and accelerating their proliferation. Chitosan discs were enriched with excess of anti-fibronectin aptamer. Aptamer adsorption on chitosan was monitored by measuring aptamer concentration in the supernatant by spectrophotometry, as well as its release, while functionalization was confirmed by labelling aptamers with a DNA intercalating dye...
September 2017: Journal of Materials Science. Materials in Medicine
Alaa S Gouda, Mahasen S Amine, Erik B Pedersen
In order to gain insight into how to improve thermal stability of i-motifs when used in the context of biomedical and nanotechnological applications, novel anthraquinone-modified i-motifs were synthesized by insertion of 1,8-, 1,4-, 1,5- and 2,6-disubstituted anthraquinone monomers into the TAA loops of a 22mer cytosine-rich human telomeric DNA sequence. The influence of the four anthraquinone linkers on the i-motif thermal stability was investigated at 295 nm and pH 5.5. Anthraquinone monomers modulate the i-motif stability in a position-depending manner and the modulation also depends on the substitution pattern of the anthraquinone...
August 9, 2017: Organic & Biomolecular Chemistry
Jenna M Hendershot, Patrick J O'Brien
DNA repair enzymes recognize and remove damaged bases that are embedded in the duplex. To gain access, most enzymes use nucleotide flipping , whereby the target nucleotide is rotated 180 degree into the active site. In human alkyladenine DNA glycosylase (AAG), the enzyme that initiates base excision repair of alkylated bases, the flipped-out nucleotide is stabilized by intercalation of the side chain of tyrosine 162 that replaces the lesion nucleobase. Previous kinetic studies provided evidence for the formation of a transient complex that precedes the stable flipped-out complex, but it is not clear how this complex differs from nonspecific complexes...
July 26, 2017: Journal of Biological Chemistry
Kranthikumar Yadav, Penchala Narasimha Rao Meka, Sudeshna Sadhu, Sravanthi Devi Guggilapu, Jeshma Kovvuri, Ahmed Kamal, Ragampeta Srinivas, Panuganti Devayani, Bathini Nagendra Babu, Narayana Nagesh
Guanine rich regions in DNA, which can form highly stable secondary structures, namely, G-quadruplex or G4 DNA structures, affect DNA replication and transcription. Molecules that stabilize G4 DNA have become important in recent years. In this study, G4 DNA stabilization, inhibition of telomerase, and anticancer activity of synthetic β-carboline-benzimidazole derivatives (5a, 5d, 5h, and 5r) were studied. Among them, derivatives containing a 4-methoxyphenyl ring at C1 and a 6-methoxy-substituted benzimidazole at C3 (5a) were found to stabilize telomeric G-quadruplex DNA efficiently...
August 10, 2017: Biochemistry
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
Maximilian 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 27, 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...
August 25, 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 ((3)MLCT) state that is equilibrium with an intraligand ((3)IL) state...
July 25, 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
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