Ultrafast electron transfer in the recognition of different DNA sequences by a DNA-binding protein with different dynamical conformations

<div><p>Ultrafast electron transfer (ET) phenomenon in protein and protein–DNA complex is very much crucial and often leads to the regulation of various kinds of redox reactions in biological system. Although, the conformation of the protein in protein–DNA complex is concluded to play the key role in the ET process, till date very little evidences exist in the literature. λ-repressor–operator DNA interaction, particularly O_R1 and O_R2, is a key component of the λ-genetic switch and is a model system for understanding the chemical principles of the conformation-dependent ET reaction, governed by differential protein dynamics upon binding with different DNA target sequences. Here, we have explored the photoinduced electron transfer from the tryptophan moieties of the protein λ-repressor to two operators DNA of different sequences (O_R1 and O_R2) using picosecond-resolved fluorescence spectroscopy. The enhanced flexibility and different conformation of the C-terminal domain of the repressor upon complexation with O_R1 DNA compared to O_R2 DNA are found to have pronounced effect on the rate of ET. We have also observed the ET phenomenon from a dansyl chromophore, bound to the lysine residue, distal from the DNA-binding domain of the protein to the operator DNA with a specific excitation at 299 nm wavelength. The altered ET dynamics as a consequence of differential protein conformation upon specific DNA sequence recognition may have tremendous biological implications.</p> </div

MoS₂ Nanocrystals Confined in a DNA Matrix Exhibiting Energy Transfer

We report the wet chemical synthesis of MoS₂ nanocrystals (NCs), a transition-metal dichalcogenide, using DNA as a host matrix. As evidenced from transmission electron microscopy (TEM), the NCs are highly crystalline, with an average diameter of ∼5 nm. Ultraviolet–visible (UV–vis) absorption studies along with band gap calculations confirm that NCs are in quantum confinement. A prominent red shift of the optical absorption bands has been observed upon formation of the thin film using hexadecyltrimethylammonium chloride (CTAC), i.e., in the case of MoS₂@DNA–CTAC. In the thin film, strong electron–phonon coupling arises because of the resonance effect, which is reflected from the emergence of intense first-, second-, and third-order Raman peaks, whenever excited with the 488 nm line. We have established that our as-synthesized MoS₂ NCs quench the fluorescence of a well-known DNA minor groove binding probe, Hoechst 33258. Unprecedented fluorescence quenching (94%) of donor (Hoechst 33258) emission and efficient energy transfer (89%) between Hoechst 33258 and MoS₂ NCs (acceptor) are obtained. The donor–acceptor distance of these conjugates has been described by a Förster resonance energy transfer (FRET)-based model. Furthermore, employing a statistical method, we have estimated the probability of the distance distribution between the donor and acceptor. We believe that the study described herein may enable substantial advances in fields of optoelectronics, photovoltaics, catalysis, and many others

Protein-Mediated Synthesis of Nanosized Mn-Doped ZnS: A Multifunctional, UV-Durable Bio-Nanocomposite

The design of synthetic nanoparticles (NPs) capable of recognizing given chemical entities in a specific and predictable manner is of great fundamental and practical importance. Herein, we report a simple, fast, water-soluble, and green phosphine free colloidal synthesis route for the preparation of multifunctional enzyme-capped ZnS bionanocomposites (BNCs) with/without transitional metal-ion doping. The enzymes α-Chymotrypsin (CHT), associated with the NPs, are demonstrated as an effectual host for organic dye Methylene Blue (MB) revealing the molecular recognition of such dye molecules by the BNCs. An effective hosting of MB in the close proximity of ZnS NPs (with ∼3 nm size) leads to photocatalysis of the dyes which has further been investigated with doped-semiconductors. The NP-associated enzyme α-CHT is found to be active toward a substrate (Ala-Ala-Phe-7-amido-4-methyl-coumarin), hence leads to significant enzyme catalysis. Irradiation induced luminescence enhancement (IILE) measurements on the BNCs clearly interpret the role of surface capping agents which protect against deep UV damaging of ZnS NPs

Modulation of Environmental Dynamics at the Active Site and Activity of an Enzyme under Nanoscopic Confinement: Subtilisin Carlsberg in Anionic AOT Reverse Micelle

Hydration dynamics plays a crucial role in determining the structure, function, dynamics, and stability of an enzyme. These dynamics involve the trapped-water motions within small distance along with the total protein dynamics. However, the exact molecular basis for the induction of enzyme function by water dynamics is still remain unclear. Here, we have studied both enzymatic activity and environmental dynamics at the active site of an enzyme, Subtilisin Carlsberg (SC), under confined environment of the reverse micelle (RM) retaining the structural integrity of the protein. Kinetic measurements show that enzymatic activity increases with increasing the water content of the RM. The picosecond-resolved fluorescence Stokes shift studies indicate faster hydration dynamics at the active site of the enzyme with increasing the water content in the RM (<i>w</i>₀ values). Temperature-dependent hydration dynamics studies demonstrate the increased flexibility of the protein at higher temperature under confinement. From temperature-dependent solvation dynamics study, we have also calculated the activation energy that has to be overcome for full orientational freedom to the water molecules from bound to free-state. The results presented here establish a correlation between the enzymatic activity and dynamics of hydration of the encapsulated protein SC in cell-like confined environment within the structural integrity of the enzyme

Microstructure, Morphology, and Ultrafast Dynamics of a Novel Edible Microemulsion

An edible microemulsion (ME) composed of Tween 80/butyl lactate/isopropyl myristate (IPM)/water has been formulated. Pseudoternary phase diagram of the system contains a large single isotropic region. The phase behavior of the system is also studied at low pH (2.6) and in 0.9% NaCl solution. Conductivity, viscosity, ultrasonic velocity, and compressibility studies find consistent results in the structural transition (from water-in-oil (w/o) to bicontinuous, and from bicontinuous to oil-in-water (o/w)) behavior of the ME. Dynamic light scattering studies reveal the size of the MEs. The absorption and steady state emission spectra of 4-(dicyanomethylene)-2-methyl-6-(p-dimethylamino-styryl)-4H-pyran (DCM) successfully probe the polarity of the ME at its solvation shell and shows the efficacy of hosting model drug molecules. The rotational anisotropy of the dye has been studied to ascertain the geometrical restriction of the probe molecule. Picosecond-resolved fluorescence spectroscopy applies well to study the relaxation dynamics of water in the solvation shell of the MEs. The study finds strong correlation in the relaxation dynamics of water with the structure of host assembly and offers an edible ME system which could act as a potential drug delivery system and nontoxic nanotemplate for other applications

Facile synthesis of reduced graphene oxide–gold nanohybrid for potential use in industrial waste-water treatment

<p>Here, we report a facile approach, by the photochemical reduction technique, for <i>in situ</i> synthesis of Au-reduced graphene oxide (Au-RGO) nanohybrids, which demonstrate excellent adsorption capacities and recyclability for a broad range of dyes. High-resolution transmission electron microscopy (HRTEM), X-ray diffraction (XRD), and X-ray photoelectron spectroscopy (XPS) data confirm the successful synthesis of Au-RGO nanohybrids. The effect of several experimental parameters (temperature and pH) variation can effectively control the dye adsorption capability. Furthermore, kinetic adsorption data reveal that the adsorption process follows a pseudo second-order model. The negative value of Gibbs free energy (ΔG⁰) confirms spontaneity while the positive enthalpy (ΔH⁰) indicates the endothermic nature of the adsorption process. Picosecond resolved fluorescence technique unravels the excited state dynamical processes of dye molecules adsorbed on the Au-RGO surface. Time resolved fluorescence quenching of Rh123 after adsorption on Au-RGO nanohybrids indicates efficient energy transfer from Rh123 to Au nanoparticles. A prototype device has been fabricated using Au-RGO nanohybrids on a syringe filter (pore size: 0.220 μm) and the experimental data indicate efficient removal of dyes from waste water with high recyclability. The application of this nanohybrid may lead to the development of an efficient reusable adsorbent in portable water purification.</p