Multidimensional chemical control of CRISPR–Cas9

Cas9-based technologies have transformed genome engineering and the interrogation of genomic functions, but methods to control such technologies across numerous dimensions-including dose, time, specificity, and mutually exclusive modulation of multiple genes-are still lacking. We conferred such multidimensional controls to diverse Cas9 systems by leveraging small-molecule-regulated protein degron domains. Application of our strategy to both Cas9-mediated genome editing and transcriptional activities opens new avenues for systematic genome interrogation

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 n-mers). 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

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

Advances in the molecular design of potential anticancer agents via targeting of human telomeric DNA

Telomerases are an attractive drug target to develop new generation drugs against cancer. A telomere appears from the chromosomal termini and protects it from double-stranded DNA degradation. A short telomere promotes genomic instability, like end-to-end fusion and regulates the over-expression of the telomere repairing enzyme, telomerase. The telomerase maintains the telomere length, which may lead to genetically abnormal situations, leading to cancer. Thus, the design and synthesis of an efficient telomerase inhibitor is a viable strategy toward anticancer drugs development. Accordingly, small molecule induced stabilization of the G-quadruplex structure, formed by the human telomeric DNA, is an area of contemporary scientific art. Several such compounds efficiently stabilize the G-quadruplex forms of nucleic acids, which often leads to telomerase inhibition. This Feature article presents the discovery and development of the telomere structure, function and evolution in telomere targeted anticancer drug design and incorporates the recent advances in this area, in addition to discussing the advantages and disadvantages in the methods, and prospects for the future

Role of pH controlled DNA secondary structures in the reversible dispersion/precipitation and separation of metallic and semiconducting single-walled carbon nanotubes

Single-stranded DNA (ss-DNA) oligomers (dA(20), d(C(3)TA(2))(3)C-3] or dT(20)) are able to disperse single-walled carbon nanotubes (SWNTs) in water at pH 7 through non-covalent wrapping on the nanotube surface. At lower pH, an alteration of the DNA secondary structure leads to precipitation of the SWNTs from the dispersion. The structural change of dA(20) takes place from the single-stranded to the A-motif form at pH 3.5 while in case of d(C(3)TA(2))(3)C-3] the change occurs from the single-stranded to the i-motif form at pH 5. Due to this structural change, the DNA is no longer able to bind the nanotube and hence the SWNT precipitates from its well-dispersed state. However, this could be reversed on restoring the pH to 7, where the DNA again relaxes in the single-stranded form. In this way the dispersion and precipitation process could be repeated over and over again. Variable temperature UV-Vis-NIR and CD spectroscopy studies showed that the DNA-SWNT complexes were thermally stable even at similar to 90 degrees C at pH 7. Broadband NIR laser (1064 nm) irradiation also demonstrated the stability of the DNA-SWNT complex against local heating introduced through excitation of the carbon nanotubes. Electrophoretic mobility shift assay confirmed the formation of a stable DNA-SWNT complex at pH 7 and also the generation of DNA secondary structures (A/i-motif) upon acidification. The interactions of ss-DNA with SWNTs cause debundling of the nanotubes from its assembly. Selective affinity of the semiconducting SWNTs towards DNA than the metallic ones enables separation of the two as evident from spectroscopic as well as electrical conductivity studies

Motion-Induced Changes in Emission as an Effective Strategy for the Ratiometric Probing of Human Serum Albumin and Trypsin in Biological Fluids

Herein, we report the formation of a highly luminescent, pH-sensitive, thermoreversible nanoaggregate in pure aqueous medium through the self-agglomeration of carbazole-based amphiphiles. The self-assembly process restricted the intramolecular motion of the molecules and induced a change in its emission signal from blue to cyan, owing to an aggregation-induced emission (AIE) effect. A similar type of ratiometric response was also observed in the presence of human serum albumin (HSA). However, in this case, the molecular motion of the flexible fluorescent probe was restricted by its embedded microenvironment, owing to a motion-induced change in emission (MICE) effect, not by aggregation. Moreover, the probe showed quite high selectivity for HSA over other serum albumin proteins. Our carbazole-based fluorescent probes are a unique example of the ratiometric sensing of HSA through the sole involvement of reversible noncovalent interactions. Considering the important of HSA in clinical diagnosis, a wide range of biological fluids, such as human urine, saliva, and plasma, were screened to analyze their HSA content. In addition, this system was also employed for the detection of trypsin at subnanomolar concentrations through the digestion of HSA

New dimeric carbazole-benzimidazole mixed ligands for the stabilization of human telomeric G-quadruplex DNA and as telomerase inhibitors. A remarkable influence of the spacer

for selectively targeting cancer cells. Herein, we report the design and evolution of a new kind of carbazole-based benzimidazole dimers for their efficient telomerase inhibition activity. Spectroscopic titrations reveal the ligands high affinity toward the G4 DNA with significantly higher selectivity over duplex-DNA. The electrophoretic mobility shift assay shows that the ligands efficiently promote the formation of 04 DNA even at a lower concentration of the stabilizing K+ ions. The TRAP-LIG assay demonstrates the ligand's potential telomerase inhibition activity and also establishes that the activity proceeds via G4 DNA stabilization. An efficient nuclear internalization of the ligands in several common cancer cells (HeLa, HT1080, and A549) also enabled differentiation between normal HFF cells in co-cultures of cancer and normal ones. The ligands induce significant apoptotic response and antiproliferative activity toward cancer cells selectively when compared to the normal cells

A Versatile Probe for Caffeine Detection in Real-Life Samples via Excitation-Triggered Alteration in the Sensing Behavior of Fluorescent Organic Nanoaggregates

Excitation triggered alteration in the sensing behavior of fluorescent nanoaggregates was explored in water, considering caffeine as the “target analyte”. Merely by changing the excitation wavelength, we could specifically excite either the monomeric species or the fluorescent nanoaggregates. The monomer showed highly sensitive interaction with caffeine despite poor selectivity, while the “strongly associated” fluorescent nanoaggregates displayed relatively high selectivity with low sensitivity. In addition, the extent of self-aggregation was also found to be influenced by the micropolarity of the local surroundings and the electronics of the core carbazole unit. Furthermore, the present protocol was utilized for the estimation of caffeine in different beverages and biological fluids with reasonably high accuracy. Inexpensive, portable paper strips were designed for a rapid, on-site detection of caffeine without involving sophisticated instruments or trained technicians

Design and Synthesis of New Benzimidazole-Carbazole Conjugates for the Stabilization of Human Telomeric DNA, Telomerase Inhibition, and Their Selective Action on Cancer Cells

Cell-permeable small molecules that enhance the stability of the G-quadruplex (G4) DNA structures are currently among the most intensively pursued ligands for inhibition of the telomerase activity. Herein we report the design and syntheses of four novel benzimidazole carbazole conjugates and demonstrate their high binding affinity to G4 DNA. Si nuclease assay confirmed the ligand mediated G-quadruplex DNA protection. Additional evidence from Telomeric Repeat Amplification Protocol (TRAP-LIG) assay demonstrated efficient telomerase inhibition activity by the ligands. Two of the ligands showed IC50 values in the sub-micromolar range in the TRAP-LIG assay, which are the best among the benzimidazole derivatives reported so far. The ligands also exhibited cancer cell selective nuclear internalization, nuclear condensation, fragmentation, and eventually antiproliferative activity in long-term cell viability assays. Annexin V-FITC/PI staining assays confirm that the cell death induced by the ligands follows an apoptotic pathway. An insight into the mode of ligand binding was obtained from the molecular dynamics simulations

Synthesis of nanocrystalline and mesoporous zinc sulphide from a single precursor Zn(SOCCH(3))(2)Lut(2) complex

We report the formation of mesoporous zinc sulphide, composed by the fine network of nanoparticles, which was formed via a single precursor Zn(SOCCH(3))(2)Lut(2) complex. The complex was chemically synthesized using zinc carbonate basic, 3,5-lutidine and thioacetic acid, in air. The metal precursor complex was characterized using different conventional techniques. Thermogravimetric analysis (TGA) result indicates that the decomposition of the complex starts at 100 degrees C and continues up to 450 degrees C, finally yielding ZnS. ZnS nanocrystals were characterized by powder X-ray diffraction (XRD) technique, field emission scanning electron microscopy (FESEM). N(2)-sorption isotherm, UV-vis spectroscopy and photoluminescence (PL) spectroscopy. The grain diameter of nanocrystals was found to be 4-5 nm. The material followed Type-IV N(2)-sorption isotherm, which is the characteristic of mesoporous materials. The band gap energy, as obtained from optical measurements was around 3.8 eV. (C) 2011 Elsevier Ltd. All rights reserved