Symmetrical Bisbenzimidazoles with Benzenediyl Spacer: The Role of the Shape of the Ligand on the Stabilization and Structural Alterations in Telomeric G-Quadruplex DNA and Telomerase Inhibition

The extremities of chromosomes end in a G-rich single-stranded overhang that has been implicated in the onset of the replicate senescence. The repeated sequence forming a G-overhang is able to adopt a four-stranded DNA structure called G-quadruplex, which is a poor substrate for the enzyme telomerase. Small molecule based ligands that selectively stabilize the telomeric G-quadruplex DNA, induce telomere shortening eventually leading to cell death. Herein, we have investigated the G-quadruplex DNA interaction with two isomeric bisbenzimidazole-based compounds that differ in terms of shape (V-shaped angular vs linear).While the linear isomer induced some stabilization of the intramolecular G-quadruplex structure generated in the presence of Na+ the other, having V-shaped central planar core, caused a dramatic structural alteration of the latter, above a threshold concentration. This transition was evident from the pronounced changes observed in the circular dichroism spectra and from the get mobility shift assa involving the G-quadruples DNA. Notably, this angular isomer could also induce the G-quadruplex formation in the absence of any added cation. The ligand-quadruples complexes were investigated by computational molecular modeling, providing further information on structure-activity relationships. Finally, TRAP (telomerase repeat amplification protocol) experiments demonstrated that the angular isomer is selective toward the inhibition of telomerase activity.

Interaction of G-Quadruplexes with Nonintercalating Duplex-DNA Minor Groove Binding Ligands

The enzyme telomerase synthesizes the G-rich DNA strands of the telomere and its activity is often associated with cancer. The telomerase may be therefore responsible for the ability of a cancer cell-to escape apoptosis. The G-rich DNA sequences often adopt tetra-stranded structure, known as the G-quadruplex DNA (G4-DNA). The stabilization of the telomeric DNA into the G4-DNA structures by small molecules has been the focus of many researchers for the design and development of new anticancer agents. The compounds which stabilize the G-quadruplex in the telomere inhibit the telomerase activity. Besides telomeres, the G4-DNA forming sequences are present in the genomic regions of biological significance including the transcriptional regulatory and promoter regions of several oncogenes. Inducing a G-quadruplex structure within the G-rich promoter sequences is a potential way of achieving selective gene regulation. Several G-quadruplex stabilizing ligands are known. Minor groove binding ligands (MGBLs) interact with the double-helical DNA through the minor grooves sequence-specifically and interfere with several DNA associated processes. These MGBLs when suitably modified switch their preference sometimes from the duplex DNA to G4-DNA and stabilize the G4-DNA as well. Herein, we focus on the recent advances in understanding the G-quadruplex structures, particularly made by the human telomeric ends, and review the results of various investigations of the interaction of designed organic ligands with the G-quadruplex DNA while highlighting the importance of MGBL-G-quadruplex interactions.

Recent Developments in the Chemistry and Biology of G-Quadruplexes with Reference to the DNA Groove Binders

DNA is the chemotherapeutic target for treating diseases of genetic origin. Besides well-known double-helical structures (A, B, Z, parallel stranded-DNA etc.), DNA is capable of forming several multi-stranded structures (triplex, tetraplex, i-motif etc.) which have unique biological significance. The G-rich 3'-ends of chromosomes, called telomeres, are synthesized by telomerase, a ribonucleoprotein, and over-expression of telomerase is associated with cancer. The activity of telomerase is suppressed if the G-rich region is folded into the four stranded structures, called G-quadruplexes (G4-DNAs) using small synthetic ligands. Thus design and synthesis of new G4-DNA ligands is an attractive strategy to combat cancer. G4-DNA forming sequences are also prevalent in other genomic regions of biological significance including promoter regions of several oncogenes. Effective gene regulation may be achieved by inducing a G4-DNA structure within the G-rich promoter sequences. To date, several G4-DNA stabilizing ligands are known. DNA groove binders interact with the duplex B-DNA through the grooves (major and minor groove) in a sequence-specific manner. Some of the groove binders are known to stabilize the G4-DNA. However, this is a relatively under explored field of research. In this review, we focus on the recent advances in the understanding of the G4-DNA structures, particularly made from the human telomeric DNA stretches. We summarize the results of various investigations of the interaction of various organic ligands with the G4-DNA while highlighting the importance of groove binder-G4-DNA interactions.

Identification of putative regulatory motifs in the upstream regions of co-expressed functional groups of genes in Plasmodium falciparum

Background: Regulation of gene expression in Plasmodium falciparum (Pf) remains poorly understood. While over half the genes are estimated to be regulated at the transcriptional level, few regulatory motifs and transcription regulators have been found. Results: The study seeks to identify putative regulatory motifs in the upstream regions of 13 functional groups of genes expressed in the intraerythrocytic developmental cycle of Pf. Three motif-discovery programs were used for the purpose, and motifs were searched for only on the gene coding strand. Four motifs – the 'G-rich', the 'C-rich', the 'TGTG' and the 'CACA' motifs – were identified, and zero to all four of these occur in the 13 sets of upstream regions. The 'CACA motif' was absent in functional groups expressed during the ring to early trophozoite transition. For functional groups expressed in each transition, the motifs tended to be similar. Upstream motifs in some functional groups showed 'positional conservation' by occurring at similar positions relative to the translational start site (TLS); this increases their significance as regulatory motifs. In the ribonucleotide synthesis, mitochondrial, proteasome and organellar translation machinery genes, G-rich, C-rich, CACA and TGTG motifs, respectively, occur with striking positional conservation. In the organellar translation machinery group, G-rich motifs occur close to the TLS. The same motifs were sometimes identified for multiple functional groups; differences in location and abundance of the motifs appear to ensure different modes of action. Conclusion: The identification of positionally conserved over-represented upstream motifs throws light on putative regulatory elements for transcription in Pf.

Conformational Polymorphism in G-tetraplex Structures: Strand Reversal by Base Flipover or Sugar Flipover

Guanine rich sequences adopt a variety of four stranded structures, which differ in strand orientation and conformation about the glycosidic bond even though they are all stabilised by Hoogsteen hydrogen bonded guanine tetrads. Detailed model building and molecular mechanics calculations have been carried out to investigate various possible conformations of guanines along a strand and different possible orientations of guanine strands in a G-tetraplex structure. It is found that for an oligo G stretch per se, a parallel four stranded structure with all guanines in anti conformation is favoured over other possible tetraplex structures. Hence an alternating syn-anti arrangement of guanines along a strand is likely to occur only in folded back tetraplex structures with antiparallel G strands. Our study provides a theoretical rationale for the observed alternation of glycosidic conformation and the inverted stacking arrangement arising from base flipover, in antiparallel G-tetraplex structures and also highlights the various structural features arising due to different types of strand orientations. The molecular mechanics calculations help in elucidating the various interactions which stabilize different G-tetraplex structures and indicate that screening of phosphate charge by counterions could have a dramatic effect on groove width in these four stranded structures.

Conformational polymorphism in G-tetraplex structures: strand reversal by base flipover or sugar flipover

Guanlne rich sequences adopt a variety of four stranded structures, which differ in strand orientation and conformation about the glycosldic bond even though they are all stabilised by Hoogsteen hydrogen bonded guanlne tetrads. Detailed model building and molecular mechanics calculations have been carried out to investigate various possible conformations of guanlnes along a strand and different possible orientations of guanlne strands In a G-tetraplex structure. It is found that for an ollgo G stretch per se, a parallel four stranded structure with all guanines In anti conformation is favoured over other possible tetraplex structures. Hence an alternating syn-anti arrangement of guanlnes along a strand is likely to occur only in folded back tetraplex structures with antiparallel G strands. Our study provides a theoretical rationale for the observed alternation of glycosldic conformation and the inverted stacking arrangement arising from base filpover, In antlparallel G-tetraplex structures and also highlights the various structural features arising due to different types of strand orientations. The molecular mechanics calculations help in elucidating the various interactions which stabilize different G-tetraplex structures and indicate that screening of phosphate charge by counterions could have a dramatic effect on groove width in these four stranded structures.

Caryophyllene-Rich Essential Oil of Didymocarpus tomentosa: Chemical Composition and Cytotoxic Activity

The essential oil from the leaves of Didymocarpus tomentosa was extracted by hydrodistillation and analyzed by GC/FID and GC/MS. Twenty five constituents amounting to 81.6% of the oil were identified. The leaf oil contained 78.7% sesquiterpenes and 2.9% monoterpenes. The leaf essential oil of D. tomentosa is a unique caryophyllene-rich natural source containing beta-caryophyllene, caryophyllene oxide, alpha-humulene and humulene oxide. The cytotoxic activity of the oil was determined by the BSLT using shrimp larva and the MTT assay using HeLa tumor cell line. The oil showed significant cytotoxic activity with LC50 and IC50 values of 12.26 and 11.4 mu g/mL, respectively. This is the first report on the chemical composition and cytotoxic activity of the essential oil of D. tomentosa.

Li3MRuO5 (M = Co, Ni), new lithium-rich layered oxides related to LiCoO2: promising electrochemical performance for possible application as cathode materials in lithium ion batteries

We describe the synthesis and crystal structure of Li3MRuO5 (M = Co and Ni), new rock salt related oxides. Both the oxides crystallize in the layered LiCoO2 (alpha-NaFeO2) structure, as revealed by powder XRD data. Magnetic susceptibility data suggest that the oxidation states of transition metals are Li3Co3+(ls)Ru4+(ls) O-5 (ls = low spin) for the M = Co compound and Li3Ni2+Ru5+O5 for the M = Ni compound. Electrochemical investigations of lithium deintercalation-intercalation behaviour reveal that both Co and Ni phases exhibit attractive specific capacities of ca. 200 mA h g(-1) at an average voltage of 4 V that has been interpreted as due to the oxidation of Co3+ and Ru4+ in Li3CoRuO5 and Ni2+ to Ni4+ in the case of Li3NiRuO5. Thus, a different role of Ru ions is played in the isostructural oxides. Finally, in both cases evidence of irreversible behaviour above 4.2 V is observed and interpreted as formation of high valent ions or alternatively oxidation of oxide ions.

Biological sulfate reduction of a sulfate-rich industrial waste liquor using sulfate reducing bacteria

An industrial waste liquor having high sulfate concentrations was subjected to biological treatment using the sulfate-reducing bacteria (SRB) Desulfovibrio desulfuricans. Toxicity levels of different sulfate, cobalt and nickel concentrations toward growth of the SRB with respect to biological sulfate reduction kinetics was initially established. Optimum sulfate concentration to promote SRB growth amounted to 0.8 - 1 g/L. The strain of D. desulfuricans used in this study initially tolerated up to 4 -5 g/L of sulfate or 50 mg/L of cobalt and nickel, while its tolerance could be further enhanced through adaptation by serial subculturing in the presence of increasing concentrations of sulfate, cobalt and nickel. From the waste liquor, more than 70% of sulfate and 95% of cobalt and nickel could be precipitated as sulfides, using a preadapted strain of D. desulfuricans. Probable mechanisms involving biological sulfide precipitation and metal adsorption onto precipitates and bacterial cells are discussed.

Oxy-steam gasification of biomass for hydrogen rich syngas production using downdraft reactor configuration

The paper focuses on the use of oxygen and steam as the gasification agents in the thermochemical conversion of biomass to produce hydrogen rich syngas, using a downdraft reactor configuration. Performance of the reactor is evaluated for different equivalence ratios (ER), steam to biomass ratios (SBR) and moisture content in the fuel. The results are compared and evaluated with chemical equilibrium analysis and reaction kinetics along with the results available in the literature. Parametric study suggests that, with increase in SBR, hydrogen fraction in the syngas increases but necessitates an increase in the ER to maintain reactor temperature toward stable operating conditions. SBR is varied from 0.75 to 2.7 and ER from 0.18 to 0.3. The peak hydrogen yield is found to be 104g/kg of biomass at SBR of 2.7. Further, significant enhancement in H-2 yield and H-2 to CO ratio is observed at higher SBR (SBR=1.5-2.7) compared with lower range SBR (SBR=0.75-1.5). Experiments were conducted using wet wood chips to induce moisture into the reacting system and compare the performance with dry wood with steam. The results clearly indicate the both hydrogen generation and the gasification efficiency ((g)) are better in the latter case. With the increase in SBR, gasification efficiency ((g)) and lower heating value (LHV) tend to reduce. Gasification efficiency of 85.8% is reported with LHV of 8.9MJNm(-3) at SBR of 0.75 compared with 69.5% efficiency at SBR of 2.5 and lower LHV of 7.4 at MJNm(-3) at SBR of 2.7. These are argued on the basis of the energy required for steam generation and the extent of steam consumption during the reaction, which translates subsequently in the LHV of syngas. From the analysis of the results, it is evident that reaction kinetics plays a crucial role in the conversion process. The study also presents the importance of reaction kinetics, which controls the overall performance related to efficiency, H-2 yield, H-2 to CO fraction and LHV of syngas, and their dependence on the process parameters SBR and ER. Copyright (c) 2013 John Wiley & Sons, Ltd.

Porous lithium rich Li1.2Mn0.54Ni0.22Fe0.04O2 prepared by microemulsion route as a high capacity and high rate capability positive electrode material

A porous layered composite of Li2MnO3 and LiMn0.35Ni0.55Fe0.1O2 (composition:Li1.2Mn0.54Ni0.22Fe0.04O2) is prepared by inverse microemulsion method and studied as a positive electrode material. The precursor is heated at several temperatures between 500 and 900 degrees C. The X-ray diffraction, scanning electron microscopy, and transmission electron microscopy studies suggested that well crystalline submicronsized particles are obtained. The product samples possess mesoporosity with broadly distributed pores around 10 similar to 50 nm diameter. Pore volume and surface area decrease by increasing the temperature of preparation. However, the electrochemical activity of the composite samples increases with an increase in temperature. The discharge capacity values of the samples prepared at 900 degrees C are about 186 mAh g(-1) at a specific current of 25 mA g(-1) with an excellent cycling stability. The composite sample also possesses high rate capability. The high rate capability is attributed to the porous nature of the material. (C) 2014 Elsevier Ltd. All rights reserved.

Oxygen-participated electrochemistry of new lithium-rich layered oxides Li3MRuO5 M = Mn, Fe)

We describe the synthesis, crystal structure and lithium deinsertion-insertion electrochemistry of two new lithium-rich layered oxides, Li3MRuO5 (M = Mn, Fe), related to rock salt based Li2MnO3 and LiCoO2. The Li3MnRuO5 oxide adopts a structure related to Li2MnO3 (C2/m) where Li and (Li0.2Mn0.4Ru0.4) layers alternate along the c-axis, while the Li3FeRuO5 oxide adopts a near-perfect LiCoO2 (R (3) over barm) structure where Li and (Li0.2Fe0.4Ru0.4) layers are stacked alternately. Magnetic measurements indicate for Li3MnRuO5 the presence of Mn3+ and low spin configuration for Ru4+ where the itinerant electrons occupy a pi*-band. The onset of a net maximum in the chi vs. T plot at 9.5 K and the negative value of the Weiss constant (theta) of -31.4 K indicate the presence of antiferromagnetic superexchange interactions according to different pathways. Lithium electrochemistry shows a similar behaviour for both oxides and related to the typical behaviour of Li-rich layered oxides where participation of oxide ions in the electrochemical processes is usually found. A long first charge process with capacities of 240 mA h g(-1) (2.3 Li per f.u.) and 144 mA h g(-1) (1.38 Li per f.u.) is observed for Li3MnRuO5 and Li3FeRuO5, respectively. An initial sloping region (OCV to ca. 4.1 V) is followed by a long plateau (ca. 4.3 V). Further discharge-charge cycling points to partial reversibility (ca. 160 mA h g(-1) and 45 mA h g(-1) for Mn and Fe, respectively). Nevertheless, just after a few cycles, cell failure is observed. X-ray photoelectron spectroscopy (XPS) characterisation of both pristine and electrochemically oxidized Li3MRuO5 reveals that in the Li3MnRuO5 oxide, Mn3+ and Ru4+ are partially oxidized to Mn4+ and Ru5+ in the sloping region at low voltage, while in the long plateau, O2- is also oxidized. Oxygen release likely occurs which may be the cause for failure of cells upon cycling. Interestingly, some other Li-rich layered oxides have been reported to cycle acceptably even with the participation of the O2- ligand in the reversible redox processes. In the Li3FeRuO5 oxide, the oxidation process appears to affect only Ru (4+ to 5+ in the sloping region) and O2- (plateau) while Fe seems to retain its 3+ state.

Improved capacity and stability of integrated Li and Mn rich layered-spinel Li1.17Ni0.25Mn1.08O3 cathodes for Li-ion batteries

A Li-rich layered-spinel material with a target composition Li1.17Ni0.25Mn1.08O3 (xLiLi1/3Mn2/3]O-2.(1 - x) LiNi0.5Mn1.5O4, (x = 0.5)) was synthesized by a self-combustion reaction (SCR), characterized by XRD, SEM, TEM, Raman spectroscopy and was studied as a cathode material for Li-ion batteries. The Rietveld refinement results indicated the presence of monoclinic (LiLi1/3Mn2/3]O-2) (52%), spinel (LiNi0.5Mn1.5O4) (39%) and rhombohedral LiNiO2 (9%). The electrochemical performance of this Li-rich integrated cathode material was tested at 30 degrees C and compared to that of high voltage LiNi0.5Mn1.5O4 spinel cathodes. Interestingly, the layered-spinel integrated cathode material exhibits a high specific capacity of about 200 mA h g(-1) at C/10 rate as compared to 180 mA h g(-1) for LiNi0.5Mn1.5O4 in the potential range of 2.4-4.9 V vs. Li anodes in half cells. The layered-spinel integrated cathodes exhibited 92% capacity retention as compared to 82% for LiNi0.5Mn1.5O4 spinel after 80 cycles at 30 degrees C. Also, the integrated cathode material can exhibit 105 mA h g(-1) at 2 C rate as compared to 78 mA h g(-1) for LiNi0.5Mn1.5O4. Thus, the presence of the monoclinic phase in the composite structure helps to stabilize the spinel structure when high specific capacity is required and the electrodes have to work within a wide potential window. Consequently, the Li1.17Ni0.25Mn1.08O3 composite material described herein can be considered as a promising cathode material for Li ion batteries.

Evaluation of CaO-CeO2-partially stabilized zirconia thermal barrier coatings

Plasma sprayable powders were prepared from ZrO2-CaO-CeO2 system using an organic binder and coated onto stainless steel substrates previously coated by a bond coat (Ni 22Cr 20Al 1.0Y) using plasma spraying. The coatings exhibited good thermal barrier characteristics and excellent resistance to thermal shock at 1000 degrees C under simulated laboratory conditions (90 half hour cycles without failure) and at 1200 degrees C under accelerated burner rig test conditions (500 2 min cycles without failure). No destabilization of cubic/tetragonal ZrO2 phase fraction occured either during the long hours (45 h cumulative) or the large number of thermal shock tests. Growth of a distinct SiO2 rich region within the ceramic was observed in the specimens thermal shock cycled at 1000 degrees C apart from mild oxidation of the bond coat. The specimens tested at 1200 degrees C had a glassy appearance on the top surface and exhibited severe oxidation of the bond coat at the ceramic-bond coat interface. The glassy appearance of the surface is due to the formation of a liquid silicate layer attributable to the impurity phase present in commercial grade ZrO2 powder. These observations are supported by SEM analysis and quantitative EDAX data.

Structural correlations in GexSe1-x glasses - a neutron diffraction study

Neutron diffraction measurement is carried out on GexSe1-x glasses, where 0.1 less than or equal to x less than or equal to 0.4, in a Q interval of 0.55-13.8 Angstrom(-1). The first sharp diffraction peak (FSDP) in the structure factor, S(Q), shows a systematic increase in the intensity and shifts to a lower Q with increasing Ge concentration. The coherence length of FSDP increases with x and becomes maximum for 0.33 less than or equal to x less than or equal to 0.4. The Monte-Carlo method, due to Soper, is used to generate S(Q) and also the pair correlation function, g(r). The generated S(Q) is in agreement with the experimental data for all x. Analysis of the first four peaks in the total correlation function, T(r), shows that the short range order in GeSe2 glass is due to Ge(Se-1/2)(4) tetrahedra, in agreement with earlier reports. Se-rich glasses contain Se-chains which are cross-linked with Ge(Se-1/2)(4) tetrahedra. Ge-2(Se-1/2)(6) molecular units are the basic structural units in Ge-rich, x = 0.4, glass. For x = 0.2, 0.33 and 0.4 there is evidence for some of the tetrahedra being in an edge-shared configuration. The number of edge-shared tetrahedra in these glasses increase with increasing Ge content.