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.     

Tuning the properties of a black TiO2-Ag visible light photocatalyst produced by a rapid one-pot chemical reduction

A highly efficient black TiO₂-Ag photocatalytic nanocomposite, active under both UV and visible light illumination, was synthesized by decorating the surface of 25 nm TiO₂ particles with Ag nanoparticles. The material was obtained via a rapid, one-pot, simple (surfactant and complexing agent free) chemical reduction method using silver nitrate and formaldehyde as a metal salt and reducing agent, respectively. The nanocomposite shows an increase of over 800% in the rate of photocatalytic methylene blue dye degradation, compared to commercial unmodified TiO_2, under UV-VIS illumination. Unlike pure TiO₂, the nanocomposite exhibits visible light activation, with a corresponding drop in optical reflectance from 100% to less than 10%. The photocatalytic properties were shown to be strongly enhanced by post-reduction annealing heat treatments in air, which were observed to decrease, rather than coarsen, silver particle size, and increase particle distribution. This, accompanied by a variation in the silver surface oxidation states, appear to dramatically affect the photocatalytic efficiency under both UV and visible light. This highly active photocatalyst could have wide ranging applications in water and air pollution remediation and solar fuel production.     

Study of basic patterns of light scattering in aqueous solution of milling yellow

Basic characteristics of light scattering in an aqueous solution of milling yellow are presented in a form of relations between the scattered radiant power, states of polarization of primary radiation and scattered radiation, observation angle and azimuthal angle.It is found that the state of polarization of the scattered light in milling-yellow solution can be utilized as a foundation of reliable photoelastic scattered-light techniques for flow analysis. However, Rayleight's model of scattering is nnt directly applicable.Paper contains data on major parameters of light scattering, knowledge of which is necessary to correctly design flowbirefringence experiments. In particular, these data can be used to develop a set of conditions and constraints for designing of particular scattered-light flow-birefringence experiments, and of corresponding transfer functions.     

Characteristic relations of flow birefringence

This is the first of two closely related papers on the flow-birefringence response to the velocity vector field of a particular liquid representing a certain class of birefringent bodies.^* The flowing material under study was the aqueous solution of the compound known under the name NGS 1828 and commonly known as “milling yellow” or “acid yellow”. This solution appears to exhibit all three major mechanisms of birefringence. The physical parameters characterizing this material depend strongly on temperature, concentration and age and, therefore, it can be considered as representing a typical class of liquids used in flow-model experiments. The paper presents the experimental evidence that the flow birefringence cannot be explained and described by the simple mathematical model of birefringence in solid continuum which relates the changes of the components of dielectric tensor to the components of stress and strain tensors, or their derivatives, and which neglects the influence of the spectral frequency (wavelength of radiation). Results are presented for transmission birefringence (and for scattered-light birefringence in the second paper) in the visible and the infrared bands of radiation. It is shown that:

- the amount of birefringence depends strongly and non-monotonically on wavelength of radiation;

- the linear range of optical response to shear-strain rate depends on wavelengths of radiation;

- the directions of optic axes strongly depend both on the shear-strain rate and on the wavelength of radiation, even in the linear range of mechanical response.

It is further shown that there exists a relation between the absorption bands, the maximum transmittance, the dispersion of birefringence, the spectral dependence of optic-axes direction, and the linear range of optical response. Within the maximum transmittance band and the linear range of mechanical response the linear range of birefringence is maximum and the dispersion of birefringence is minimum with respect to the shear-strain rate; the corresponding dispersion of optic axis is also minimum. Samples of typical recordings are given in the visible and the infrared radiation for typical flow patterns. One of the practical conclusions is that to optimize the flow-birefringence studies of engineering problems it is advisable to choose the radiation in the near-infrared range. The evidence presented shows that the common trend in engineering research toward simplification of the model of the flow-birefringence response is not necessary.     

Methanolysis of (Triphenyl Phosphazenyl) Celoro and Fluorocyclotriphosphazenes

Abstract

The different mechanistic features involved in the replacement of chlorine and fluorine atoms from N₃P₃ (NPPh₃)X₅[X [dbnd] Cl(I) or F(II)] by methoxide have been identified. An oxophosphazadiene derivative is also isolated.     

Synthesis of Peptide Cysteine Dimedone Using Fmoc-Cys(Dmd)-OH: Glutathione Cysteine Dimedone as a Probe in Investigating the Sulfenic Acid Mediated Oxidation of Glutathione

Dimedone is the most widely used chemical probe for detection of cysteine sulfenic acid in peptides and proteins. The reaction of dimedone with cysteine sulfenic acid results in the formation of unique cysteine dimedone motif containing thioether bridge. Based on the structure of cysteine dimedone residue in polypeptide, a new building block of Fmoc-Cys(Dmd)-OH was developed for solid phase synthesis of peptide cysteine dimedone. Mass spectrometric sequencing of synthetic peptides have confirmed successful incorporation of cysteine dimedone in peptide chain using HBTU/HOBt as a coupling agent. The new method permits synthesis of peptides containing both cysteine thiol and cysteine dimedone in the same sequence which was difficult to achieve by conventional methods. The synthetic peptide of glutathione cysteine dimedone was used as a standard in probing the air-mediated oxidation of thiol to disulfide form of glutathione. The co-elution of standard peptide and reaction mixture of oxidation of glutathione in presence of dimedone using RP-HPLC have confirmed the formation of glutathione cysteine sulfenic as an intermediate in the air-mediated oxidation of glutathione. The synthetic peptides of cysteine dimedone may find application in the field of redox proteomics and generation of antibodies against modified cysteine residue.     

A Plausible Simultaneous Synthesis of Amino Acids and Simple Peptides on the Primordial Earth

Following his seminal work in 1953, Stanley Miller conducted an experiment in 1958 to study the polymerization of amino acids under simulated early Earth conditions. In the experiment, Miller sparked a gas mixture of CH₄, NH₃, and H₂O, while intermittently adding the plausible prebiotic condensing reagent cyanamide. For unknown reasons, an analysis of the samples was not reported. We analyzed the archived samples for amino acids, dipeptides, and diketopiperazines by liquid chromatography, ion mobility spectrometry, and mass spectrometry. A dozen amino acids, 10 glycine‐containing dipeptides, and 3 glycine‐containing diketopiperazines were detected. Miller’s experiment was repeated and similar polymerization products were observed. Aqueous heating experiments indicate that Strecker synthesis intermediates play a key role in facilitating polymerization. These results highlight the potential importance of condensing reagents in generating diversity within the prebiotic chemical inventory.     

BiVO4/TiO2 core-shell heterostructure: wide range optical absorption and enhanced photoelectrochemical and photocatalytic performance

In the present study, pristine BiVO₄, TiO₂ and BiVO₄/TiO₂ core-shell heterostructured nanoparticles are prepared by hydrothermal methods and studied for structural, morphological, optical, photoelectrochemical water splitting and photocatalytic degradation of methylene blue as an organic pollutant. Both pristine BiVO₄ and TiO₂ exhibit poor PEC and PC performance under visible light illumination. However, an enhanced PEC and PC activity in BiVO₄/TiO₂ core-shell heterostructure is observed due to high solar energy absorption and superior charge separation properties in core-shell nanoparticles. The photoelectrode prepared using BiVO₄/TiO₂ core-shell nanoparticles exhibit a photocathode behavior and produced cathodic photocurrent, however, the pristine BiVO₄ and TiO₂ photoelectrodes act as photoanode and produced anodic photocurrent. This behavior of change in current direction is also observe in the Mott-Schottky analysis where the BiVO₄/TiO₂ core-shell nanoparticles photoelectrode exhibits the positive slow showing p-type semiconducting behavior. The change in cathodic photoresponse in core-shell nanoparticles in comparison to anodic photoresponse of BiVO₄ and TiO₂ nanoparticles is explained in terms of the variations in the work function values. These results highlight the advantages of core-shell nanoparticle of suitable materials for photocatalytic and photoelectrochemical applications.