Single-molecule Förster resonance energy transfer reveals an innate fidelity checkpoint in DNA polymerase I

Enzymatic reactions typically involve complex dynamics during substrate binding, conformational rearrangement, chemistry, and product release. The noncovalent steps provide kinetic checkpoints that contribute to the overall specificity of enzymatic reactions. DNA polymerases perform DNA replication with outstanding fidelity by actively rejecting noncognate nucleotide substrates early in the reaction pathway. Substrates are delivered to the active site by a flexible fingers subdomain of the enzyme, as it converts from an open to a closed conformation. The conformational dynamics of the fingers subdomain might also play a role in nucleotide selection, although the precise role is currently unknown. Using single-molecule F?rster resonance energy transfer, we observed individual Escherichia coli DNA polymerase I (Klenow fragment) molecules performing substrate selection. We discovered that the fingers subdomain actually samples through three distinct conformations--open, closed, and a previously unrecognized intermediate conformation. We measured the overall dissociation rate of the polymerase-DNA complex and the distribution among the various conformational states in the absence and presence of nucleotide substrates, which were either correct or incorrect. Correct substrates promote rapid progression of the polymerase to the catalytically competent closed conformation, whereas incorrect nucleotides block the enzyme in the intermediate conformation and induce rapid dissociation from DNA. Remarkably, incorrect nucleotide substrates also promote partitioning of DNA to the spatially separated 3'-5' exonuclease domain, providing an additional mechanism to prevent misincorporation at the polymerase active site. These results reveal the existence of an early innate fidelity checkpoint, rejecting incorrect nucleotide substrates before the enzyme encloses the nascent base pair.     

Aza-Michael addition of 1,2-diazoles to structurally diverse enones: Efficient methods toward β-amino ketones

An efficient and mild protocol was realized using 1,2-diazoles and related heterocycles with cyclic and acyclic enones in presence of T3P (2,4,6-tripropyl-1,3,5,2,4,6-trioxatriphosphorinane-2,4,6-trioxide) toward the regioselective formation of N-cycloalkyl heterocycles at room temperature. The developed reaction conditions showcased good selectivity over a wide range of 1,2-diazoles and enones by delivering N-cycloalkyl heterocycles in excellent yields.     

Study on the Synthesis of ZnO Nanoparticles Using Azadirachta indica Extracts for the Fabrication of a Gas Sensor

This paper compared the effects of A. indica plant proteins over chemical methods in the morphology of zinc oxide nanoparticles (ZnO NPs) prepared by a co-precipitation method, and ethanol sensing performance of prepared thin films deposited over a fluorene-doped tin oxide (FTO) bind glass substrate using spray pyrolysis technique. The average crystallite sizes and diameters of the grain-sized cluster ZnO NPs were 25 and (701.79 ± 176.21) nm for an undoped sample and 20 and (489.99 ± 112.96) nm for A. india dye-doped sample. The fourier transform infrared spectroscopy (FTIR) analysis confirmed the formation of the Zn–O bond at 450 cm⁻¹, and also showed the presence of plant proteins due to A. indica dye extracts. ZnO NPs films exhibited good response (up to 51 and 72% for without and with A. indica dye-doped extracts, respectively) toward ethanol vapors with quick response-recovery characteristics at a temperature of 250 °C for undoped and 225 °C for A. indica dye-doped ZnO thin films. The interaction of A. indica dye extracts helps to decrease the operating temperature and increased the response and recovery rates of the sensor, which may be due to an increase in the specific surface area, resulting in adsorption of more oxygen and hence high response results.     

Comparative Study on Co-Ground Products of Rofecoxib with β-Cyclodextrin and Its Sulfobutyl Ether-7 Derivative in Solution and in the Solid State

The inclusion behavior of sulfobutyl ether-7 derivative ofβ-cyclodextrin (SBE7βCD), in solution and solidstate was compared with that of natural β-cyclodextrin(βCD) toward a poorly water-soluble anti-inflammatoryagent, rofecoxib (ROFX), chemically 4[4-(methylsulfonyl)phenyl]-3-phenyl-2 (5H)-furazone. Drug-cyclodextrin solidsystems were prepared by cogrinding in a ball mill. A phasesolubility method was used to evaluate the stoichiometries andstability constants of ROFX-βCD (1 : 1 and 62 M^-1)and ROFX-SBE7βCD (1 : 1 and 132 M^-1) complexes.The formation of inclusion complexes with βCD andSBE7βCD in the solid state were confirmed by infraredspectroscopy, differential scanning calorimetry, X-ray diffractometry,scanning electron microscopy and in the liquid state by phasesolubility analysis, nuclear magnetic resonance spectroscopy andcircular dichroism studies. Dissolution studies using the USP paddlemethod were carried out in phosphate buffer pH 7.2 at 37 °Cfor both βCD and SBE7βCD complexes of rofecoxib.Solubility enhancement was much greater for the rofecoxib-SBE7βCDcomplex compared to drug-βCD complex. The stability constantobtained for the SBE7βCD inclusion complex of rofecoxib wasthe highest. Finally, dissolution profiles obtained suggest thatSBE7βCD is more effective than β-cyclodextrin inimproving the pharmaceutical properties of rofecoxib.     

FTIR and Raman microspectroscopy of normal,benign, and malignant formalin-fixed ovarian tissues

Ovarian cancer is the sixth most common cancer among women worldwide, and mortality rates from this cancer are higher than for other gynecological cancers. This is attributed to a lack of reliable screening methods and the inadequacy of treatment modalities for the advanced stages of the disease. FTIR and Raman spectroscopic studies of formalin-fixed normal, benign, and malignant ovarian tissues have been undertaken in order to investigate and attempt to understand the underlying biochemical changes associated with the disease, and to explore the feasibility of discriminating between these different tissue types. Raman spectra of normal tissues indicate the dominance of proteins and lower contents of DNA and lipids compared to malignant tissues. Among the pathological tissues studied, spectra from benign tissues seem to contain more proteins and less DNA and lipids compared to malignant tissue spectra. FTIR studies corroborate these findings. FTIR and Raman spectra of both normal and benign tissues showed more similarities than those of malignant tissues. Cluster analysis of first-derivative Raman spectra in the 700–1700 cm⁻¹ range gave two clear groups, one corresponding to malignant and the other to normal+benign tissues. At a lower heterogeneity level, the normal+benign cluster gave three nonoverlapping subclusters, one corresponding to normal and two for benign tissues. Cluster analysis of second-derivative FTIR spectra in the combined spectral regions of 1540–1680 and 1720–1780 cm⁻¹ resulted into two clear clusters corresponding to malignant and normal+benign tissues. The cluster corresponding to normal+benign tissues produced nonoverlapping subclusters for normal and benign tissues at a lower heterogeneity level. The findings of this study demonstrate the feasibility of Raman and FTIR microspectroscopic discrimination of formalin-fixed normal, benign, and malignant ovarian tissues.     

Convergence in the incompressible limit of finite element approximations based on the Hu-Washizu formulation

The classical Hu–Washizu mixed formulation for plane problems in elasticity is examined afresh, with the emphasis on behavior in the incompressible limit. The classical continuous problem is embedded in a family of Hu–Washizu problems parametrized by a scalar α for which corresponds to the classical formulation, with λ and μ being the Lamé parameters. Uniform well- posedness in the incompressible limit of the continuous problem is established for α ≠ − 1. Finite element approximations are based on the choice of piecewise bilinear approximations for the displacements on quadrilateral meshes. Conditions for uniform convergence are made explicit. These conditions are shown to be met by particular choices of bases for stresses and strains, and include bases that are well known, as well as newly constructed bases. Though a discrete version of the spherical part of the stress exhibits checkerboard modes, it is shown that a λ-independent a priori error estimate for the displacement can be established. Furthermore, a λ-independent estimate is established for the post-processed stress. The theoretical results are explored further through selected numerical examples.     

Structure and synthesis of hypophyllanthin,nirtetralin, phyltetralin and lintetralin

Structures propounded for the four aryltetralin lignan constituents isolated from $\text{Phyllanthus niruri}$ Linn. are confirmed by syntheses of their (±)-forms.     

N,N′-Bis(2-hydroxybenzyl)ethylenediamine-N,N′-dipropionic acid. A new chelating ligand for iron(III)

A new potentially chelating ligandN,N′-bis(2-hydroxybenzyl)ethylenediamine-N,N′-dipropionic acid, (HBEP) has been prepared in high yield and its ionization constants have been determined by potentiometric and spectrophotometric methods. The stability constant for the Fe^III-HBEP chelate has been determined spectrophotometrically, and the ligational behaviour of HBEP with iron(III) compared with that of its homologue, HBED (N,N′-bis(2-hydroxybenzyl)ethylenediamine-N,N′-diacetic acid). IPCL Communication No. 169.     

Catalytic tail-to-tail dimerization of methyl acrylate using bis(triphenylphosphine)tricarbonyl ruthenium(0)

The complex Ru(CO)₃(PPh₃)₂ catalyzes the dimerization of methyl acrylate at 120–140°C to give tail-to-tail dimers containing predominantly dimethyl (E)-2-hexene-1,6-dioate together with small amounts of trimers and polymer. The reaction under hydrogen atmosphere selectively gave tail-to-tail dimers in improved yield without formation of trimers and polymer. Under these conditions a catalyst turnover number of 246 was obtained at 130°C in 6 h.