Topologically-Interlocked Minicircles as Probes of DNA Topology and DNA-Protein Interactions

DNA minicircles exist in biological contexts, such as kinetoplast DNA, and are promising components for creating functional nanodevices. They have been used to mimic the topological features of nucleosomal DNA and to probe DNA-protein interactions such as HIV-1 and PFV integrases, and DNA gyrase. Here, we synthesized the topologically-interlocked minicircle rotaxane and catenane inside a frame-shaped DNA origami. These minicircles are 183 bp in length, constitute six individual single-stranded DNAs that are ligated to realize duplex interlocking, and adopt temporary base pairing of single strands for interlocking. To probe the DNA-protein interactions, restriction reactions were carried out on DNAs with different topologies such as free linear duplex or duplex constrained inside origami and free or topologically-interlocked minicircles. Except the free linear duplex, all tested structures were resistant to restriction digestion, indicating that the topological features of DNA, such as flexibility, curvature, and groove orientation, play a major role in DNA-protein interactions.     

Solvent-free synthesis of dibenzo[b,j][1,10]phenanthroline derivatives using Eaton’s reagent as catalyst

A new class of dibenzo[b,j][1,10]phenanthrolines has been prepared. The synthon acridones were achieved in very good yield by a one-pot reaction of 2-amino-5-chloro or 2′-chloro/flouro-substituted benzophenones with 1,2-cyclohexanedione in the presence of freshly prepared Eaton’s reagent (phosphorus pentoxide–methanesulfonic acid) without solvent, through Friedländer synthesis. Then these intermediates were reacted with 2-amino-3,5-dibromobenzaldehyde to afford 1,3-dibromo-10-chloro-8-aryl-6,7-dihydrodibenzo[b,j][1,10]phenanthroline. Also an one-pot reaction between 2?mol of 2-amino-5-chloro aryl benzophenones with 1?mol of 1,2-cyclohexanedione to get 3,10-dichloro-5,8-diaryl-6,7-dihydrodibenzo[b,j][1,10]phenanthroline has also been reported. The newly synthesized structures of the compounds were deduced by spectroscopic techniques.     

Synthesis of Zinc Oxide Nanoparticles Using Rubus fairholmianus Root Extract and Their Activity against Pathogenic Bacteria

Recently, the biosynthesis of zinc oxide nanoparticles (ZnO NPs) from crude extracts and phytochemicals has attracted much attention. Green synthesis of NPs is cost-effective, eco-friendly, and is a promising alternative for chemical synthesis. This study involves ZnO NPs synthesis using Rubus fairholmianus root extract (RE) as an efficient reducing agent. The UV spectrum of RE-ZnO NPs exhibited a peak at 357 nm due to intrinsic bandgap absorption and an XRD pattern that matches the ZnO crystal structure (JCPDS card no: 36-1451). The average particle size calculated from the Debye–Scherrer equation is 11.34 nm. SEM analysis showed that the RE-ZnO NPs spherical in shape with clusters (1–100 nm). The antibacterial activity of the NPs was tested against Staphylococcus aureus using agar well diffusion, minimum inhibitory concentration, and bacterial growth assay. The R. fairholmianus phytochemicals facilitate the synthesis of stable ZnO NPs and showed antibacterial activity.     

Immunomagnetic nanoparticle based quantitative PCR for rapid detection of Salmonella

We have developed a rapid and sensitive method for immunomagnetic separation (IMS) of Salmonella along with their real time detection via PCR. Silica-coated magnetic nanoparticles were functionalized with carboxy groups to which anti-Salmonella antibody raised against heat-inactivated whole cells of Salmonella were covalently attached. The immuno-captured target cells were detected in beverages like milk and lemon juice by multiplex PCR and real time PCR with a detection limit of 10⁴ cfu.mL^?1 and 10³ cfu.mL^?1, respectively. We demonstrate that IMS can be used for selective concentration of target bacteria from beverages for subsequent use in PCR detection. PCR also enables differentiation of Salmonella typhi and Salmonella paratyphi A using a set of four specific primers. In addition, IMS—PCR can be used as a screening tool in the food and beverage industry for the detection of Salmonella within 3–4 h which compares favorably to the time of several days that is needed in case of conventional detection based on culture and biochemical methods.

Towards Photochromic Azobenzene-Based Inhibitors for Tryptophan Synthase

Light regulation of drug molecules has gained growing interest in biochemical and pharmacological research in recent years. In addition, a serious need for novel molecular targets of antibiotics has emerged presently. Herein, the development of a photocontrollable, azobenzene-based antibiotic precursor towards tryptophan synthase (TS), an essential metabolic multienzyme complex in bacteria, is presented. The compound exhibited moderately strong inhibition of TS in its E configuration and five times lower inhibition strength in its Z configuration. A combination of biochemical, crystallographic, and computational analyses was used to characterize the inhibition mode of this compound. Remarkably, binding of the inhibitor to a hitherto-unconsidered cavity results in an unproductive conformation of TS leading to noncompetitive inhibition of tryptophan production. In conclusion, we created a promising lead compound for combatting bacterial diseases, which targets an essential metabolic enzyme, and whose inhibition strength can be controlled with light.     

Tuning the Reactivity of a Substrate for SNAP-Tag Expands Its Application for Recognition-Driven DNA-Protein Conjugation

Recognition-driven modification has been emerging as a novel approach to modifying biomolecular targets of interest site-specifically and efficiently. To this end, protein modular adaptors (MAs) are the ideal reaction model for recognition-driven modification of DNA as they consist of both a sequence-specific DNA-binding domain (DBD) and a self-ligating protein-tag. Coupling DNA recognition by DBD and the chemoselective reaction of the protein tag could provide a highly efficient sequence-specific reaction. However, combining an MA consisting of a reactive protein-tag and its substrate, for example, SNAP-tag and benzyl guanine (BG), revealed rather nonselective reaction with DNA. Therefore new substrates of SNAP-tag have been designed to realize sequence-selective rapid crosslinking reactions of MAs with SNAP-tag. The reactions of substrates with SNAP-tag were verified by kinetic analyses to enable the sequence-selective crosslinking reaction of MA. The new substrate enables the distinctive orthogonality of SNAP-tag against CLIP-tag to achieve orthogonal DNA-protein crosslinking by six unique MAs.     

Experimental analysis of tamarind seed powder-based flash powder composition for eco-friendly firecrackers

Journal of Thermal Analysis and Calorimetry - In this work, considering the various practical concerns during storage, processing, handling and emission of flash powder used for making firecracker,...     

Bifunctional coordination polymers as efficient catalysts for carbon dioxide conversion

The multidentate ligand H₂ L upon complexation with Zn (II) and Cd (II) provide a one‐dimensional polymeric networks. These coordination polymers (CPs) CP‐1 and CP‐2 containing Zn (II) and Cd (II) metals respectively are well characterized. The single crystal structural analysis confirms the formation of one‐dimensional coordination polymer with zigzag fashion in CP‐1 and ladder chain CP‐2 . Both the CPs are applied as catalysts to synthesize various cyclic carbonates from epoxides and carbon dioxide. The catalysts are giving better conversion under solvent‐free and additive‐free condition using 10 bar CO₂ and 100 °C as optimized pressure and temperature. The detailed kinetic experiments suggesting the first order kinetics, the energy of activation (Ea) is calculated for this catalytic conversion.     

Nonspecific Effect of Double-Stranded (ds) RNA on Prophenoloxidase (proPO) Expression in Penaeus monodo n

RNA interference-mediated silencing is an effective way of controlling white spot syndrome virus (WSSV). However, the effect of RNAi on the innate immune mechanism is not well understood. Prophenoloxidase (proPO) is an important component of the shrimp innate immunity. In the present study, nonspecific effect of two double-stranded (ds)RNA-expressing constructs, one targeting vp28 gene of WSSV (pCMV-VP28-LH) and another targeting green fluorescent protein (GFP) (pCMV-GFP-LH) on proPO2 gene expression, is investigated. mRNA expression levels of proPO2 in hemocytes of DNA construct-injected shrimp were estimated using real-time PCR with elongation factor 1-α as internal control. Empty vector (pcDNA)-injected shrimp were used as experimental control. In pCMV-VP28-LH-injected shrimp, proPO2 showed significant upregulation until 48 h post-injection (p.i.). Similarly, pCMV-GFP-LH-injected animals showed high levels of expression until 72 h p.i. WSSV-challenged animals, compared to pcDNA-injected control group, showed no significant change in expression of the gene until 24 h. However, an increased expression was noticed at 48 h p.i. Our results suggest that neither the plasmids nor the long hairpin RNA expressed by the constructs has any nonspecific silencing effect on the proPO2 expression. On the contrary, the consistent upregulation of proPO2 observed in shrimp injected with dsRNA at early time-points indicates the possibility of nonspecific protection against WSSV infection.