Fluorescence enhancement of europium (III) perchlorate by 1,10‐phenanthroline on the 1‐(naphthalen‐2‐yl)‐2‐(phenylsulthio)ethanone complex and luminescence mechanism

A novel ligand, 1‐(naphthalen‐2‐yl)‐2‐(phenylsulthio)ethanone was synthesized using a new method and its two europium (Eu) (III) complexes were synthesized. The compounds were characterized by elemental analysis, coordination titration analysis, molar conductivity, infrared, thermo gravimetric analyzer‐differential scanning calorimetry (TGA‐DSC), ¹H NMR and UV spectra. The composition was suggested as EuL₅ · (ClO₄)₃ · 2H₂O and EuL₄ · phen(ClO₄)₃ · 2H₂O (L = C₁₀H₇COCH₂SOC₆H₅). The fluorescence spectra showed that the Eu(III) displayed strong characteristic metal‐centered fluorescence in the solid state. The ternary rare earth complex showed stronger fluorescence intensity than the binary rare earth complex in such material. The strongest characteristic fluorescence emission intensity of the ternary system was 1.49 times as strong as that of the binary system. The phosphorescence spectra were also discussed. Copyright © 2014 John Wiley & Sons, Ltd.     

Diverse modes of 5′‐[4‐(aminoiminomethyl)phenyl]‐[2,2′‐bifuran]‐5‐carboximidamide (DB832) interaction with multi‐stranded DNA structures

The modes of binding of 5′‐[4‐(aminoiminomethyl)phenyl]‐[2,2′‐Bifuran]‐5‐carboximidamide (DB832) to multi‐stranded DNAs: human telomere quadruplex, monomolecular R‐triplex, pyr/pur/pyr triplex consisting of 12 T*(T·A) triplets, and DNA double helical hairpin were studied. The optical adsorption of the ligand was used for monitoring the binding and for determination of the association constants and the numbers of binding sites. CD spectra of DB832 complexes with the oligonucleotides and the data on the energy transfer from DNA bases to the bound DB832 assisted in elucidating the binding modes. The affinity of DB832 to the studied multi‐stranded DNAs was found to be greater (K_ass ≈ 10⁷M^?1) than to the duplex DNA (K_ass ≈ 2 × 10⁵M^?1). A considerable stabilizing effect of DB832 binding on R‐triplex conformation was detected. The nature of the ligand tight binding differed for the studied multi‐stranded DNA depending on their specific conformational features: recombination‐type R‐triplex demonstrated the highest affinity for DB832 groove binding, while pyr/pur/pyr TTA triplex favored DB832 intercalation at the end stacking contacts and the human telomere quadruplex d[AG₃(T₂AG₃)₃] accommodated the ligand in a capping mode. Additionally, the pyr/pur/pyr TTA triplex and d[AG₃(T₂AG₃)₃] quadruplex bound DB832 into their grooves, though with a markedly lesser affinity. DB832 may be useful for discrimination of the multi‐sranded DNA conformations and for R‐triplex stabilization. © 2009 Wiley Periodicals, Inc. Biopolymers 93: 8–20, 2010. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

Enzyme Kinetics of an Alternative Splicing Isoform of Mitochondrial 8‐Oxoguanine DNA Glycosylase,OGG1‐1b,and Compared with the Nuclear OGG1‐1a

Eight alternatively spliced isoforms of human 8‐oxoguanine DNA glycosylase (OGG1) (OGG1‐1a to ‐1c and ‐2a to ‐2e) are registered in the National Center for Biotechnology Information. OGG1(s) in mitochondria have not yet been fully characterized biochemically. In this study, we purified mitochondrial recombinant OGG1‐1b protein and compared its activity with nuclear OGG1‐1a protein. The reaction rate constant (k_g) of the 7,8‐dihydro‐8‐oxoguanine (8‐oxoG) glycosylase activity of OGG1‐1b was 8‐oxoG:C >> 8‐oxoG:T >> 8‐oxoG:G > 8‐oxoG:A (7.96, 0.805, 0.070, and 0.015 min^?1, respectively) and that of the N‐glycosylase/DNA lyase activity (k_gl) of OGG1‐1b was 8‐oxoG:C > 8‐oxoG:T ?8‐oxoG:G >> 8‐oxoG:A (0.286, 0.079, 0.040, and negligible min^?1, respectively). These reaction rate constants were similar to those of OGG1‐1a except for k_gl against 8‐oxoG:A. APEX nuclease 1 was required to promote DNA strand breakage by OGG1‐1b. These results suggest that OGG1‐1b is associated with 8‐oxoG cleavage in human mitochondria and that the mechanism of this repair is similar to that of nuclear OGG1‐1a.     

N‐[2‐[(3‐Chlorophenyl)amino]‐phenyl]‐3‐(difluoromethyl)‐1‐methyl‐1H‐pyrazole‐4‐carboxamide: Synthesis,Crystal Structure,Molecular Docking and Biological Activities

In continuation of our previous research on the development of novel pyrazole‐4‐carboxamide with potential antifungal activity, compound SCU2028 , namely N‐[2‐[(3‐chlorophenyl)amino]phenyl]‐3‐(difluoromethyl)‐1‐methyl‐1H‐pyrazole‐4‐carboxamide, was synthesized by new method, structurally characterized by IR, HR‐ESI‐MS, ¹H‐ and ¹³C‐NMR spectra and further identified by single‐crystal X‐ray diffraction. In pot tests, compound SCU2028 showed good in vivo antifungal activity against Rhizoctonia solani (R. solani) and IC₅₀ value of it was 7.48 mg L^?1. In field trials, control efficacy of compound SCU2028 at 200 g.a.i. ha^?1 was 42.30 % on the 7^th day after the first spraying and 68.10 % on the 14^th day after the second spraying, only slightly lower than that of thifluzamide (57.20 % and 71.40 %, respectively). Further in vitro inhibitory activity showed inhibitory ability of compound SCU2028 was 45‐fold higher than that of bixafen and molecular docking of compound SCU2028 to SDH predicted its binding orientation in the active site of the target protein SDH. These results suggested that compound SCU2028 was a potential fungicide for control of rice sheath blight.     

Synthesis,in vitro stability,and antiproliferative effect of d‐cysteine modified GnRH‐doxorubicin conjugates

Overexpression of gonadotropin‐releasing hormone (GnRH) receptor in many tumors but not in normal tissues makes it possible to use GnRH analogs as targeting peptides for selective delivery of cytotoxic agents, which may help to enhance the uptake of anticancer drugs by cancer cells and reduce toxicity to normal cells. The GnRH analogs [d ‐Cys⁶, desGly¹⁰, Pro⁹‐NH₂]‐GnRH, [d ‐Cys⁶, desGly¹⁰, Pro⁹‐NHEt]‐GnRH, and [d ‐Cys⁶, α‐aza‐Gly¹⁰‐NH₂]‐GnRH were conjugated with doxorubicin (Dox), respectively, through N‐succinimidyl‐3‐maleimidopropionate as a linker to afford three new GnRH‐Dox conjugates. The metabolic stability of these conjugates in human serum was determined by RP‐HPLC. The antiproliferative activity of the conjugates was examined in GnRH receptor‐positive MCF‐7 human breast cancer cell line by MTT assay. The three GnRH‐Dox conjugates showed improved metabolic stability in human serum in comparison with AN‐152. The antiproliferative effect of conjugate II ([d ‐Cys⁶, desGly¹⁰, Pro⁹‐NHEt]‐GnRH‐Dox) on MCF‐7 cells was higher than that of conjugate I ([d ‐Cys⁶, desGly¹⁰, Pro⁹‐NH₂]‐GnRH‐Dox) and conjugate III ([d ‐Cys⁶, α‐aza‐Gly¹⁰‐NH₂]‐GnRH‐Dox), and the cytotoxicity of conjugate II against GnRH receptor‐negative 3T3 mouse embryo fibroblast cells was decreased in comparison with free Dox. GnRH receptor inhibition test suggested that the antiproliferative activity of conjugate II might be due to the cellular uptake mediated by the targeting binding of [d ‐Cys⁶‐des‐Gly¹⁰‐Pro⁹‐NHEt]‐GnRH to GnRH receptors. Our study indicates that targeting delivery of conjugate II mediated by [d ‐Cys⁶‐des‐Gly¹⁰‐Pro⁹‐NHEt]‐GnRH is a promising strategy for chemotherapy of tumors that overexpress GnRH receptors.     

Purification,crystal structure and antimicrobial activity of phenazine‐1‐carboxamide produced by a growth‐promoting biocontrol bacterium,Pseudomonas aeruginosa MML2212

Aim: To purify and characterize an antimicrobial compound produced by a biocontrol bacterium, Pseudomonas aeruginosa MML2212, and evaluate its activity against rice pathogens, Rhizoctonia solani and Xanthomonas oryzae pv. oryzae. Methods and Results: Pseudomonas aeruginosa strain MML2212 isolated from the rice rhizosphere with wide‐spectrum antimicrobial activity was cultured in Kings’B broth using a fermentor for 36 h. The extracellular metabolites were isolated from the fermented broth using ethyl acetate extraction and purified by two‐step silica‐gel column chromatography. Three fractions were separated, of which a major compound was obtained in pure state as yellow needles. It was crystallized after dissolving with chloroform followed by slow evaporation. It is odourless with a melting point of 220–222°C. It was soluble in most of the organic solvents and poorly soluble in water. The molecular mass of purified compound was estimated as 223·3 by mass spectral analysis. Further, it was characterized by IR, ¹H and ¹³C NMR spectral analyses. The crystal structure of the compound was elucidated for the first time by X‐ray diffraction study and deposited in the Cambridge Crystallographic Data Centre ( http://www.ccde.com.ac.uk ) with the accession no. CCDC 617344 . Conclusion: The crystal compound was undoubtedly identified as phenazine‐1‐carboxamide (PCN) with the empirical formula of C₁₃H₉N₃O. Significance and Impact of the Study: As this is the first report on the crystal structure of PCN, it provides additional information to the structural chemistry. Furthermore, the present study reports the antimicrobial activity of purified PCN on major rice pathogens, R. solani and X. oryzae pv. oryzae. Therefore, the PCN can be developed as an ideal agrochemical candidate for the control of both sheath blight and bacterial leaf blight diseases of rice.     

Synthesis and Crystal Structure of Binuclear Copper(II) Complex Bridged by N‐(2‐Hydroxyphenyl)‐N′‐[3‐(diethylamino)propyl]oxamide: In Vitro Anticancer Activity and Reactivity Toward DNA and Protein

A new oxamido‐bridged bicopper(II) complex, [Cu₂(pdpox)(bpy)(CH₃OH)](ClO₄), where H₃pdpox and bpy stand for N‐(2‐hydroxyphenyl)‐N′‐[3‐(diethylamino)propyl]oxamide and 2,2′‐bipyridine, respectively, has been synthesized and characterized by elemental analyses, molar conductivity measurements, infrared and electronic spectra studies, and X‐ray single crystal diffraction. In the crystal structure, the pdpox^3? ligand bridges two copper(II) ions as cisoid conformation. The inner copper(II) ion has a {N₃O} square‐planar coordination geometry, while the exo‐ one is in a {N₂O₃} square‐pyramidal environment. There are two sets of interpenetrating two‐dimensional hydrogen bonding networks parallel to the planes (2 1 0) and (), respectively, to form a three‐dimensional supramolecular structure. The bicopper(II) complex exhibits cytotoxic activity against the SMMC7721 and A549 cell lines. The reactivity toward herring sperm DNA and bovine serum albumin revealed that the bicopper(II) complex can interact with the DNA by intercalation mode, and the complex binds to protein BSA responsible for quenching of tryptophan fluorescence by static quenching mechanism. © 2013 Wiley Periodicals, Inc. J BiochemMol Toxicol 27:412‐424, 2013; View this article online at wileyonlinelibrary.com . DOI 10.1002/jbt.21504     

In Vitro and In Vivo Evaluation of N‐{2‐[4‐(3‐Cyanopyridin‐2‐yl)piperazin‐1‐yl]ethyl}‐3‐[11C]methoxybenz­amide,a Positron Emission Tomography (PET) Radioligand for Dopamine D4 Receptors,in Rodents

The D₄ dopamine receptor belongs to the D₂‐like family of dopamine receptors, and its exact regional distribution in the central nervous system is still a matter of considerable debate. The availability of a selective radioligand for the D₄ receptor with suitable properties for positron emission tomography (PET) would help resolve issues of D₄ receptor localization in the brain, and the presumed diurnal change of expressed protein in the eye and pineal gland. We report here on in vitro and in vivo characteristics of the high‐affinity D₄ receptor‐selective ligand N‐{2‐[4‐(3‐cyanopyridin‐2‐yl)piperazin‐1‐yl]ethyl}‐3‐[¹¹C]methoxybenzamide ([¹¹C] 2 ) in rat. The results provide new insights on the in vitro properties that a brain PET dopamine D₄ radioligand should possess in order to have improved in vivo utility in rodents.     

Nucleosomal arrays self‐assemble into supramolecular globular structures lacking 30‐nm fibers

The existence of a 30‐nm fiber as a basic folding unit for DNA packaging has remained a topic of active discussion. Here, we characterize the supramolecular structures formed by reversible Mg²⁺‐dependent self‐association of linear 12‐mer nucleosomal arrays using microscopy and physicochemical approaches. These reconstituted chromatin structures, which we call “oligomers”, are globular throughout all stages of cooperative assembly and range in size from ~50 nm to a maximum diameter of ~1,000 nm. The nucleosomal arrays were packaged within the oligomers as interdigitated 10‐nm fibers, rather than folded 30‐nm structures. Linker DNA was freely accessible to micrococcal nuclease, although the oligomers remained partially intact after linker DNA digestion. The organization of chromosomal fibers in human nuclei in situ was stabilized by 1 mM MgCl₂, but became disrupted in the absence of MgCl₂, conditions that also dissociated the oligomers in vitro. These results indicate that a 10‐nm array of nucleosomes has the intrinsic ability to self‐assemble into large chromatin globules stabilized by nucleosome–nucleosome interactions, and suggest that the oligomers are a good in vitro model for investigating the structure and organization of interphase chromosomes.     

Binding Pockets and Permeation Channels for Dioxygen through Cofactorless 3‐Hydroxy‐2‐methylquinolin‐4‐one 2,4‐Dioxygenase in Association with Its Natural Substrate, 3‐Hydroxy‐2‐methylquinolin‐4(1H)‐one. A Perspective from Molecular Dynamics Simulations

This work describes an investigation of pathways and binging pockets (BPs) for dioxygen (O₂) through the cofactorless oxygenase 3‐hydroxy‐2‐methylquinolin‐4‐one 2,4‐dioxygenase in complex with its natural substrate, 3‐hydroxy‐2‐methylquinolin‐4(1H)‐one, in aqueous solution. The investigation tool was random‐acceleration molecular dynamics (RAMD), whereby a tiny, randomly oriented external force is applied to O₂ in order to accelerate its movements. In doing that, care was taken that the external force only continues, if O₂ moves along a direction for a given period of time, otherwise the force changed direction randomly. Gates for expulsion of O₂ from the protein, which can also be taken as gates for O₂ uptake, were found throughout almost the whole external surface of the protein, alongside a variety of BPs for O₂. The most exploited gates and BPs were not found to correspond to the single gate and BP proposed previously from the examination of the static model from X‐ray diffraction analysis of this system. Therefore, experimental investigations of this system that go beyond the static model are urgently needed.     

Role of AP‐endonuclease (Ape1) active site residues in stabilization of the reactant enzyme‐DNA complex

Apurinic/apyrimidinic endonuclease 1 (Ape1) is an important metal‐dependent enzyme in the base excision repair mechanism, responsible for the backbone cleavage of abasic DNA through a phosphate hydrolysis reaction. Molecular dynamics simulations of Ape1 complexed to its substrate DNA performed for models containing 1 or 2 Mg²⁺‐ions as cofactor located at different positions show a complex with 1 metal ion bound on the leaving group site of the scissile phosphate to be the most likely reaction‐competent conformation. Active‐site residue His309 is found to be protonated based on pKa calculations and the higher conformational stability of the Ape1‐DNA substrate complex compared to scenarios with neutral His309. Simulations of the D210N mutant further support the prevalence of protonated His309 and strongly suggest Asp210 as the general base for proton acceptance by a nucleophilic water molecule.     

Luminescence study and dosimetry approach of Ce on an α‐Sr2P2O7 phosphor synthesized by a high‐temperature combustion method

We report synthesis of a cerium‐activated strontium pyrophosphate (Sr₂P₂O₇) phosphor using a high‐temperature combustion method. Samples were characterized by X‐ray diffraction (XRD), Fourier transform infrared spectroscopy (FT‐IR), photoluminescence (PL) and thermoluminescence (TL). The XRD pattern reveals that Sr₂P₂O₇ has an α‐phase with crystallization in the orthorhombic space group of Pnam. The IR spectrum of α‐Sr₂P₂O₇ displays characteristic bands at 746 and 1190 cm^‐1 corresponding to the absorption of (P₂O₇)^‐4. PL emission spectra exhibit a broad emission band around 376 nm in the near‐UV region due to the allowed 5d–4f transition of cerium and suggest its applications in a UV light‐emitting diode (LED) source. PL also reveals that the emission originates from 5d–4f transition of Ce³⁺ and intensity increases with doping concentration. TL measurements made after X‐ray irradiation, manifest a single intense glow peak at around 192°C, which suggests that this is an outstanding candidate for dosimetry applications. The kinetic parameters, activation energy and frequency factor of the glow curve were calculated using different analysis methods. Copyright © 2014 John Wiley & Sons, Ltd.     

Structure and DNA binding characteristics of the three‐Cys2His2 domain of mouse testis zinc finger protein

The C‐terminal three‐Cys₂His₂ zinc‐finger domain (TZD) of mouse testis zinc‐finger protein binds to the 5′‐TGTACAGTGT‐3′ at the Aie1 (aurora‐C) promoter with high specificity. Interestingly, the primary sequence of TZD is unique, possessing two distinct linkers, TGEKP and GAAP, and distinct residues at presumed DNA binding sites at each finger, especially finger 3. A K_d value of ～10^?8 M was obtained from surface plasmon resonance analysis for the TZD‐DNA complex. NMR structure of the free TZD showed that each zinc finger forms a typical ββα fold. On binding to DNA, chemical shift perturbations and the R₂ transverse relaxation rate in finger 3 are significantly smaller than those in fingers 1 and 2, which indicates that the DNA binding affinity in finger 3 is weaker. Furthermore, the shift perturbations between TZD in complex with the cognate DNA and its serial mutants revealed that both ADE7 and CYT8, underlined in 5′‐ATATGTACAGTGTTAT‐3′, are critical in specific binding, and the DNA binding in finger 3 is sequence independent. Remarkably, the shift perturbations in finger 3 on the linker mutation of TZD (GAAP mutated to TGEKP) were barely detected, which further indicates that finger 3 does not play a critical role in DNA sequence‐specific recognition. The complex model showed that residues important for DNA binding are mainly located on positions ?1, 2, 3, and 6 of α‐helices in fingers 1 and 2. The DNA sequence and nonsequence‐specific bindings occurring simultaneously in TZD provide valuable information for better understanding of protein–DNA recognition. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

Structural transition from dimeric to tetrameric i‐motif,caused by the presence of TAA at the 3′‐end of human telomeric C‐rich sequence

Widely dispersed in genomic DNA, the tandem C‐rich repetitive stretches may fold below physiological pH, into i‐motif structures, stabilized by C·C⁺ pairing. Herein, structural status of a 9‐mer stretch d(CCCTAACCC), [the truncated double repeat of human telomeric sequence], and its extended version, comprising of additional ? TAA segment at the 3′‐end, representing the complete double repeat d(CCCTAACCCTAA), has been investigated. The pH dependent monophasic UV‐melting, Gel and CD data suggested that while the truncated version adopts a bimolecular i‐motif structure, its complete double repeat (12‐mer) sequence exists in two (bimolecular and tetramolecular) forms. A model is proposed for the tetramolecular i‐motif with conventional C · C⁺ base pairs, additionally stabilized by asymmetric A · A base pairs at the ?3′ TAA flanking ends and Watson–Crick A · T hydrogen bonding between intervening bases on antiparallel strands. Expanding the known topologies of DNA i‐motifs, such atypical geometries of i‐motifs may have implications in their recognition by proteins. © 2009 Wiley Periodicals, Inc. Biopolymers 93: 150–160, 2010. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

Synthesis,crystal structure and fluorescence properties of terbium complexes with phenoxyacetic acid and 2,4,6‐tris‐(2‐pyridyl)‐s–triazine

Two complexes of Tb³⁺, Gd³⁺/Tb³⁺ and one heteronuclear crystal Gd³⁺/Tb³⁺ with phenoxyacetic acid (HPOA) and 2,4,6‐tris‐(2‐pyridyl)‐s–triazine (TPTZ) have been synthesized. Elemental analysis, rare earth coordination titration, inductively coupled plasma atomic emission spectrometry (ICP‐AES) and thermogravimetric analysis‐differential scanning calorimetry (TG‐DSC) analysis show that the two complexes are Tb₂(POA)₆(TPTZ)₂·6H₂O and TbGd(POA)₆(TPTZ)₂·6H₂O, respectively. The crystal structure of TbGd(POA)₆(TPTZ)₂·2CH₃OH was determined using single‐crystal X‐ray diffraction. The monocrystal belongs to the triclinic system with the P‐1 space group. In particular, each metal ion is coordinately bonded to three nitrogen atoms of one TPTZ and seven oxygen atoms of three phenoxyacetic ions. Furthermore, there exist two coordinate forms between C₆H₅OCH₂COO^– and the metal ions in the crystal. One is a chelating bidentate, the other is chelating and bridge coordinating. Fluorescence determination shows that the two complexes possess strong fluorescence emissions. Furthermore, the fluorescence intensity of the Gd³⁺/Tb³⁺ complex is much stronger than that of the undoped complex, which may result from a decrease in the concentration quench of Tb³⁺ ions, and intramolecular energy transfer from the ligands coordinated with Gd³⁺ ions to Tb³⁺ ions. Copyright © 2015 John Wiley & Sons, Ltd.     

Antioxidation and DNA‐Binding Properties of Binuclear Lanthanide(III) Complexes with a Schiff Base Ligand Derived from 8‐Hydroxyquinoline‐7‐carboxaldehyde and Benzoylhydrazine

8‐Hydroxyquinoline‐7‐carboxaldehyde (8‐HQ‐7‐CA), Schiff‐base ligand 8‐hydroxyquinoline‐7‐carboxaldehyde benzoylhydrazone, and binuclear complexes [LnL(NO₃)(H₂O)₂]₂ were prepared from the ligand and equivalent molar amounts of Ln(NO₃)?6 H₂O (Ln=La³⁺, Nd³⁺, Sm³⁺, Eu³⁺, Gd³⁺, Dy³⁺, Ho³⁺, Er³⁺, Yb³⁺, resp.). Ligand acts as dibasic tetradentates, binding to Ln^III through the phenolate O‐atom, N‐atom of quinolinato unit, and C?N and ? O? C?N? groups of the benzoylhydrazine side chain. Dimerization of this monomeric unit occurs through the phenolate O‐atoms leading to a central four‐membered (LnO)₂ ring. Ligand and all of the Ln^III complexes can strongly bind to CT‐DNA through intercalation with the binding constants at 10⁵–10⁶ M ^?1. Moreover, ligand and all of the Ln^III complexes have strong abilities of scavenging effects for hydroxyl (HO^.) radicals. Both the antioxidation and DNA‐binding properties of Ln^III complexes are much better than that of ligand.