Dynamic quenching study of 2-amino-3-bromo-1,4-naphthoquinone by titanium dioxide nano particles in solution (methanol)

Single-nucleobase resolution of a surface energy transfer nanoruler for in situ measurement of aptamer binding at the receptor subunit level in living cells

In situ identification of aptamer-binding targets on living cell membrane surfaces is of considerable interest, but a major challenge, specifically, when advancing recognition to the level of membrane receptor subunits. Here we propose a novel nanometal surface energy transfer (NSET) based nanoruler with a single-nucleobase resolution (SN-nanoruler), in which FAM-labeled aptamers and single-sized gold nanoparticle (GNP) antibody conjugates act as a donor and an acceptor. A single nucleobase resolution of the SN-nanoruler was experimentally illustrated by molecular size, orientation, quenching nature, and other dye-GNP pairs. The SN-nanoruler provides high reproducibility and precision for measuring molecule distance on living cell membranes at the nanometer level owing to only the use of single-sized antibody-capped GNPs. In situ identification of the aptamer binding site was advanced to the protein subunit level on the living cell membrane for the utilization of this SN-nanoruler. The results suggest that the proposed strategy is a solid step towards the wider application of optical-based rulers to observe the molecular structural configuration and dynamic transitions on the membrane surface of living cells.

Insights into the Binding Interaction of Catechol 1,2-Dioxygenase with Catechol in Achromobacter xylosoxidans DN002

Microbial remediation has become one of the promising ways to eliminate polycyclic aromatic hydrocarbons (PAHs) pollution due to its efficient enzyme metabolism system. Catechol 1,2-dioxygenase (C12O) is a crucial rate-limiting enzyme in the degradation pathway of PAHs in Achromobacter xylosoxidans DN002 that opens the benzene ring through the ortho-cleavage pathway. However, little attention has been given to explore the interaction mechanism of relevant enzyme-substrate. This study aims to investigate the binding interaction between C12O of strain DN002 and catechol by means of a molecular biological approach combined with homology modeling, molecular docking, and multiple spectroscopies. The removal rate of catechol in the mutant strain of cat A deletion was only 12.03%, compared to the wild-type strain (54.21%). A Ramachandran plot of active site regions of the primary amino acid sequences in the native enzyme showed that 93.5% sequences were in the most favored regions on account of the results of homology modeling, while an additional 6.2% amino acid sequences were found in conditionally allowed regions, and 0.4% in generously allowed regions. The binding pocket of C12O with catechol was analyzed to obtain that the catalytic trimeric group of Tyr164-His224-His226 was proven to be great vital for the ring-opening reaction of catechol by molecular docking. In the native enzyme, binding complexes were spontaneously formed by hydrophobic interactions. Binding constants and thermodynamic potentials from fluorescence spectra indicated that catechol effectively quenched the intrinsic fluorescence of C12O in the C12O/catechol complex via conventional static and dynamic quenching mechanisms of C12O. The results of ultraviolet and visible (UV) spectra, synchronous fluorescence, and circular dichroism (CD) spectra revealed conspicuous changes in the local conformation, and site-directed mutagenesis confirmed the role of predicted key residues during catalysis, wherein His₂₂₆ had a significant effect on catechol utilization by C12O. This is the first report to reveal interactions of C12O with substrate from the molecular docking results, providing the mechanistic understanding of representative dioxygenases involved in aromatic compound degradation, and a solid foundation for further site modifications as well as strategies for the directed evolution of this enzyme.

Spectroscopic investigation, photophysical parameters and DFT calculations of 4,4'-(1E,1'E)-2,2'-(pyrazine-2,5-diyl)bis(ethene-2,1-diyl)bis(N,N-dimethylaniline) (PENDA) in different solvents

A comprehensive investigation on the photophysics of a π-conjugated potential push-pull chromophore system 4,4'-(1E,1'E)-2,2'-(Pyrazine-2,5-diyl)bis(ethene-2,1-diyl)bis(N,N-dimethylaniline) (PENDA) has been carried out spectroscopically. The optical absorption and emission properties of this molecule have been studied in different solvents. The molecule PENDA shows strong solvatochromic emission upon changing the solvent polarity from nonpolar to polar; indicating that emission state is of intramolecular charge transfer (ICT) character. The solvent effect on the spectral properties such as singlet absorption, molar absorptivity, oscillator strength, dipole moment and fluorescence quantum yield of PENDA have been studied in detail. Lippert-Mataga and Reichardt correlations were used to estimate the difference between the excited and ground state dipole moments (Δμ). Ground and electronic excited states geometric optimizations were performed using density functional theory (DFT) and time-dependent density functional theory (TDDFT), respectively, with the Gaussian 09 package. A solution of (8×10(-5) M) PENDA in THF, dioxane, CH3CN and CHCl3 gives laser emission when pumped by a nitrogen laser pulse (λex=337.1 nm) of 800 ps duration and 1.48 mJ pulse energy. PENDA dye displays fluorescence quenching by colloidal silver nanoparticles (Ag NPs) in ethanol. The fluorescence data reveal that dynamic quenching and energy transfer play a major role in the fluorescence quenching mechanism.

The quenching effect of silver nanoparticles on 2-amino-3-bromo-1, 4-naphthoquinone using fluorescence spectroscopy

Nanoparticles of noble metals belong to the most extensively studied colloidal systems in the field of nanoscience and nanotechnology. Silver nanoparticles of different sizes have been prepared with the chemical reduction method using sodium borohydride and characterized using optical absorption technique. Using optical absorption and fluorescence emission studies, the photo physical properties of 2-amino-3-bromo1, 4-naphthoquinone (ABNQ) on silver nanoparticle have been studied. Concentration of the silver nanoparticle has been evaluated and the particle size dependent interaction between silver nanoparticles and ABNQ has been studied. The fluorescence quantum yield of ABNQ with and without silver nanoparticles has been calculated. The Stern-Volmer quenching constants and the molar absorptivity have been evaluated.