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.

Dimeric 1,3-Phenylene-bis(piperazinyl benzimidazole)s: Synthesis and Structure-Activity Investigations on their Binding with Human Telomeric G-Quadruplex DNA and Telomerase Inhibition Properties

Ligand-induced stabilization of G-quadruplex structures formed by the human telomeric DNA is an active area of research. The compounds which stabilize the G-quadruplexes often lead to telomerase inhibition. Herein we present the results of interaction of new monomeric and dimeric ligands having 1,3-phenylene-bis(piperazinyl benzimidazole) unit with G-quadruplex DNA (G4DNA) formed by human telomeric repeat d(G(3)T(2)A)(3)G(3)]. These ligands efficiently stabilize the preformed G4DNA in the presence of 100 mM monovalent alkali metal ions. Also, the G4DNA formed in the presence of low concentrations of ligands in 100 mM K+ adopts a highly stable parallel-stranded conformation. The G-quadruplexes formed in the presence of the dimeric compound are more stable than that induced by the corresponding monomeric counterpart. The dimeric ligands having oligo-oxyethylene spacers provide much higher stability to the preformed G4DNA and also exert significantly higher telomerase inhibition activity. Computational aspects have also been discussed.

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.

Binding of Gemini Bisbenzimidazole Drugs with Human Telomeric G-Quadruplex Dimers: Effect of the Spacer in the Design of Potent Telomerase Inhibitors

The study of anticancer agents that act via stabilization of telomeric G-quadruplex DNA (G4DNA) is important because such agents often inhibit telomerase activity. Several types of G4DNA binding ligands are known. In these studies, the target structures often involve a single G4 DNA unit formed by short DNA telomeric sequences. However, the 3'-terminal single-stranded human telomeric DNA can form higher-order structures by clustering consecutive quadruplex units (dimers or nmers). Herein, we present new synthetic gemini (twin) bisbenzimidazole ligands, in which the oligo-oxyethylene spacers join the two bisbenzimidazole units for the recognition of both monomeric and dimeric G4DNA, derived from d(T2AG3)4 and d(T2AG3) 8 human telomeric DNA, respectively. The spacer between the two bisbenzimidazoles in the geminis plays a critical role in the G4DNA stability. We report here (i) synthesis of new effective gemini anticancer agents that are selectively more toxic towards the cancer cells than the corresponding normal cells; (ii) formation and characterization of G4DNA dimers in solution as well as computational construction of the dimeric G4DNA structures. The gemini ligands direct the folding of the single-stranded DNA into an unusually stable parallel-stranded G4DNA when it was formed in presence of the ligands in KCl solution and the gemini ligands show spacer length dependent potent telomerase inhibition properties.

Potential G-quadruplex formation at breakpoint regions of chromosomal translocations in cancer may explain their fragility

Genetic alterations like point mutations, insertions, deletions, inversions and translocations are frequently found in cancers. Chromosomal translocations are one of the most common genomic aberrations associated with nearly all types of cancers especially leukemia and lymphoma. Recent studies have shown the role of non-B DNA structures in generation of translocations. In the present study, using various bioinformatic tools, we show the propensity of formation of different types of altered DNA structures near translocation breakpoint regions. In particular, we find close association between occurrence of G-quadruplex forming motifs and fragile regions in almost 70% of genes involved in rearrangements in lymphoid cancers. However, such an analysis did not provide any evidence for the occurrence of G-quadruplexes at the close vicinity of translocation breakpoint regions in nonlymphoid cancers. Overall, this study will help in the identification of novel non-B DNA targets that may be responsible for generation of chromosomal translocations in cancer. (C) 2012 Elsevier Inc. All rights reserved.

Stabilization and Structural Alteration of the G-Quadruplex DNA Made from the Human Telomeric Repeat Mediated by Troger's Base Based Novel Benzimidazole Derivatives

Ligand-induced stabilization of the G-quadruplex DNA structure derived from the single-stranded 3'-overhang of the telomeric DNA is an attractive strategy for the inhibition of the telomerase activity. The agents that can induce/stabilize a DNA sequence into a G-quadruplex structure are therefore potential anticancer drugs. Herein we present the first report of the interactions of two novel bisbenzimidazoles (TBBz1 and TBBz2) based on Troger's base skeleton with the G-quadruplex DNA (G4DNA). These Troger's base molecules stabilize the G4DNA derived from a human telomeric sequence. Evidence of their strong interaction with the G4DNA has been obtained from CD spectroscopy, thermal denaturation, and UV-vis titration studies. These ligands also possess significantly higher affinity toward the G4DNA over the duplex DNA. The above results obtained are in excellent agreement with the biological activity, measured in vitro using a modified TRAP assay. Furthermore, the ligands are selectively more cytotoxic toward the cancerous cells than the corresponding noncancerous cells. Computational studies suggested that the adaptive scaffold might allow these ligands to occupy not only the G-quartet planes but also the grooves of the G4DNA.

Evaluation of Fracture Parameters by Double-G, Double-K Models and Crack Extension Resistance for High Strength and Ultra High Strength Concrete Beams

This paper presents the advanced analytical methodologies such as Double- G and Double - K models for fracture analysis of concrete specimens made up of high strength concrete (HSC, HSC1) and ultra high strength concrete. Brief details about characterization and experimentation of HSC, HSC1 and UHSC have been provided. Double-G model is based on energy concept and couples the Griffith's brittle fracture theory with the bridging softening property of concrete. The double-K fracture model is based on stress intensity factor approach. Various fracture parameters such as cohesive fracture toughness (4), unstable fracture toughness (K-Ic(c)), unstable fracture toughness (K-Ic(un)) and initiation fracture toughness (K-Ic(ini)) have been evaluated based on linear elastic fracture mechanics and nonlinear fracture mechanics principles. Double-G and double-K method uses the secant compliance at the peak point of measured P-CMOD curves for determining the effective crack length. Bi-linear tension softening model has been employed to account for cohesive stresses ahead of the crack tip. From the studies, it is observed that the fracture parameters obtained by using double - G and double - K models are in good agreement with each other. Crack extension resistance has been estimated by using the fracture parameters obtained through double - K model. It is observed that the values of the crack extension resistance at the critical unstable point are almost equal to the values of the unstable fracture toughness K-Ic(un) of the materials. The computed fracture parameters will be useful for crack growth study, remaining life and residual strength evaluation of concrete structural components.

Molecular Design of Synthetic Benzimidazoles for the Switchover of the Duplex to G-quadruplex DNA Recognition

Benzimidazole derivatives are well known for their antibacterial, antiviral, anticonvulsant, antihistaminic, anthelmintic and antidepressant activities. Benzimidazole's unique base-selective DNA recognition property has been studied widely. However, most of the early benzimidazole systems have been targeted towards the binding of duplex DNA. Here we have shown the evolution and progress of the design and synthesis of new benzimidazole systems towards selective recognition of the double-stranded DNA first. Then in order to achieve selective recognition of the G-quadruplex DNA and utilize their potential as future anti-cancer drug candidates, we have demonstrated their selective cytotoxicity towards the cancer cells and potent telomerase inhibition ability.

Fretting wear behaviour of hydroxyapatite-titanium composites in simulated body fluid, supplemented with 5 g l(-1) bovine serum albumin

Damaged articulating joints can be repaired or replaced with synthetic biomaterials, which can release wear debris due to articulation, leading to the osteolysis. In a recent work, it has been shown that it is possible to achieve a better combination of flexural strength/fracture toughness as well as in vitro bioactivity and cytocompatibility properties in spark plasma sintered hydroxyapatite-titanium (HA-Ti) composites. Although hydroxyapatite and titanium are well documented for their good biocompatibility, nanosized hydroxyapatite (HA) and titanium (Ti) particles can cause severe toxicity to cells. In order to address this issue, fretting wear study of HA-Ti composites under dry and wet (1x SBF, supplemented with 5 g l(-1) bovine serum albumin (BSA)) condition was performed to assess the wear resistance as well as wear debris formation, in vitro. The experimental results reveal one order of magnitude lower wear rate for HA-10 wt% Ti (7.5 x 10(-5) mm(3) N-1 m(-1)) composite than monolithic HA (3.9 x 10(-4) mm(3) N-1 m(-1)) in simulated body fluid. The difference in the tribological properties has been analyzed in the light of phase assemblages and mechanical properties. Overall, the results suggest the potential use of HA-Ti composites over existing HA-based biocomposites in orthopedic as well as dental applications.

G-Quadruplex Structures Formed at the HOX11 Breakpoint Region Contribute to Its Fragility during t(10;14) Translocation in T-Cell Leukemia

The t(10;14) translocation involving the HOX11 gene is found in several T-cell leukemia patients. Previous efforts to determine the causes of HOX11 fragility were not successful. The role of non-B DNA structures is increasingly becoming an important cause of genomic instability. In the present study, bioinformatics analysis revealed two G-quadruplex-forming motifs at the HOX11 breakpoint cluster. Gel shift assays showed formation of both intra- and intermolecular G-quadruplexes, the latter being more predominant. The structure formation was dependent on four stretches of guanines, as revealed by mutagenesis. Circular dichroism analysis identified parallel conformations for both quadruplexes. The non-B DNA structure could block polymerization during replication on a plasmid, resulting in consistent K K+-dependent pause sites, which were abolished upon mutation of G-motifs, thereby demonstrating the role of the stretches of guanines even on double-stranded DNA. Extrachromosomal assays showed that the G-quadruplex motifs could block transcription, leading to reduced expression of green fluorescent protein (GFP) within cells. More importantly, sodium bisulfite modification assay showed the single-stranded character at regions I and II of HOX11 in the genome. Thus, our findings suggest the occurrence of G-quadruplex structures at the HOX11 breakpoint region, which could explain its fragility during the t(10;14) translocation.

Morphological Effects of G-Quadruplex Stabilization Using a Small Molecule in Zebrafish

Zebrafish (Danio rerio) embryos are transparent and advantageous for studying early developmental changes due to ex utero development, making them an appropriate model for studying gene expression changes as a result of molecular targeting. Zebrafish embryos were injected with a previously reported G-quadruplex selective ligand, and the phenotypic changes were recorded. We report marked discrepancies in the development of intersegmental vessels. In silico analysis determined that the putative G-quadruplex motif occur in the upstream promoter region of the Cdh5 (N-cadherin) gene. A real-time polymerase chain reaction-based investigation indicated that in zebrafish, CDH-2 (ZN-cad) was significantly downregulated in the ligand-treated embryos. Biophysical characterization of the interaction of the ligand with the G-quadruplex motif found in this promoter yielded strong binding and stabilization of the G-quadruplex with this ligand. Hence, we report for the first time the phenotypic impact of G-quadruplex targeting with a ligand in a vertebrate organism. This study has unveiled not only G-quadruplex targeting in non-human animal species but also the potential that G-quadruplexes can provide a ready tool for understanding the phenotypic effects of targeting certain important genes involved in differentiation and developmental processes in a living eukaryotic organism.

Two-pion low-energy contribution to the muon g-2 with improved precision from analyticity and unitarity

The two-pion contribution from low energies to the muon magnetic moment anomaly, although small, has a large relative uncertainty since in this region the experimental data on the cross sections are neither sufficient nor precise enough. It is therefore of interest to see whether the precision can be improved by means of additional theoretical information on the pion electromagnetic form factor, which controls the leading-order contribution. In the present paper, we address this problem by exploiting analyticity and unitarity of the form factor in a parametrization-free approach that uses the phase in the elastic region, known with high precision from the Fermi-Watson theorem and Roy equations for pi pi elastic scattering as input. The formalism also includes experimental measurements on the modulus in the region 0.65-0.70 GeV, taken from the most recent e(+)e(-) ->pi(+)pi(-) experiments, and recent measurements of the form factor on the spacelike axis. By combining the results obtained with inputs from CMD2, SND, BABAR, and KLOE, we make the predictions a(mu)(pi pi,LO)2m(pi), 0.30 GeV] = (0.553 +/- 0.004) x 10(-10) and a(mu)(pi pi,LO)0.30 GeV; 0.63 GeV] = (133.083 +/- 0.837) x 10(-10). These are consistent with the other recent determinations and have slightly smaller errors.

The influence of mesoporous silica in low T-g cyclic olefin copolymer nanocomposite films: Mechanical and moisture barrier studies

In this study, mesoporous silica-cyclic olefin copolymer nanocomposite films were fabricated by solution casting. With an increase in silica loading, the stiffness of the matrix increased. The nanocomposite film shows increased strain to failure with moisture after aging by matrix plasticization. The storage modulus and loss factor for samples with silica content show better results compared with pristine polymer, as indicated by dynamic mechanical analysis. The interaction between filler-polymer chain exhibit hydrophobicity compared to the neat polymer. Water absorption studies at room temperature and near the T-g of the polymer (similar to 64 degrees C) were carried out. The nanocomposites up to 4 wt% filler reduces the water diffusion by forming hydrogen and chemical bonding. The result by calcium degradation test method for moisture permeability and Schottky structured organic device encapsulation under weathering condition confirms the effective reinforcement effect of silica particles in the matrix. (C) 2014 Elsevier Ltd. All rights reserved.