Computational studies on the molecular insights of aptamer induced poly(N-isopropylacrylamide)-graft-graphene oxide for on/off- switchable whole-cell cancer diagnostics.

This work deals with first-principles and in silico studies of graphene oxide-based whole-cell selective aptamers for cancer diagnostics utilising a tunable-surface strategy. Herein, graphene oxide (GO) was constructed as a surface-based model with poly(N-isopropylacrylamide) (PNIPAM) covalently grafted as an "on/off"-switch in triggering interactions with the cancer-cell protein around its lower critical solution temperature. The atomic building blocks of the aptamer and the PNIPAM adsorbed onto the GO was investigated at the density functional theory (DFT) level. The presence of the monomer of PNIPAM stabilised the system's π-π interaction between GO and its nucleobases as confirmed by higher bandgap energy, satisfying the eigenvalues of the single-point energy observed rather than the nucleobase and the GO complex independently. The unaltered geometrical structures of the surface emphasise the physisorption type interaction between the nucleobase and the GO/NIPAM surface. The docking result for the aptamer and the protein, highlighted the behavior of the PNIPAM-graft-GO  is exhibiting globular and extended conformations, further supported by molecular dynamics (MD) simulations. These studies enabled a better understanding of the thermal responsive behavior of the polymer-enhanced GO complex for whole-cell protein interactions through computational methods.

Light induced DNA-functionalized TiO2 nanocrystalline interface: Theoretical and experimental insights towards DNA damage detection.

Owing to the emerging applications of DNA-functionalized TiO2 nanocrystals towards DNA damage detection, it is inevitable to understand the better chemistry as well as in-depth molecular interaction phenomena. Fundamentally, energy difference underlies the layer-by-layer construction, resulted in the increase of the interaction energy and thus, altering the electrochemical behavior. Herein, Density functional theory (DFT) calculations were performed using DMol3 and DFTB+ codes successfully to elucidate the structural, electronics, and vibrational properties of the layer-by-layer components composing ss-DNA/dopamine/TiO2/FTO. The obtained results are in good agreement with the experimental findings. The band gaps of FTO and TiO2 were computationally obtained at 3.335 and 3.136 eV which are comparable with the experimental data (3.500 eV; FTO and 3.200 eV; TiO2). Frontier orbital analysis is also considered to elucidate their electron transfer phenomena. Further, a 100 ns MD simulations are carried out using canonical ensemble embedded with COMPASS-Universal Forcefields generating useful thermodynamics parameters. Binding energies indicate increasing interaction energies for the layer-by-layer nanosystem, in agreement with the increasing diameter of electrochemical impedance spectroscopy (EIS) semicircle. Our results reveal the fundamental understanding of the DNA-functionalized TiO2 nanocrystals down to molecular and electronic level and further, paving a way of its application towards nanoelectrochemical DNA biosensors.

Smartphone based bioanalytical and diagnosis applications: A review.

A smartphone is a facile, handy-analytical device that makes our lives comfortable and stress-free in terms of health care diagnostic assessments. Due to recent advancements in the technology and the introduction of user friendly operating systems and applications, the smartphones have replaced laptops and desktop computers. Taking this fact into account, researchers have designed sensing systems which are more compatible with smartphones. Consequently, these devices are attracting the attention of researchers from fields such as telemedicine, biotechnology, chemical sciences and environmental sciences. In this review, our focus is on recent advances on smartphone based sensing and diagnosis applications.

One-pot biosynthesis of silver nanoparticles using Iboza Riparia and Ilex Mitis for cytotoxicity on human embryonic kidney cells.

Plant extracts continue gaining significant prominence in green synthesis of silver nanoparticles (AgNPs), due to their potential applications in nano-medicine and material engineering. This work reports on green synthesis of silver nanoparticles (AgNPs) from aqueous extracts of Iboza Riparia leaf and Ilex Mitis root bark with diterpenes (DTPs) and saponins (SPNs) as major components. After TEM, DLS, TGA/DSC, ATR, XRD and UV-Vis characterization, the relevant cytotoxicity studies were conducted with the MTT assay on human embryonic kidney cells (HEK293T) followed by antioxidant activity with ABTS. Overall, the AgNPs-DTPs (156nm) were found to be less toxic with 49.7% cell viability, while AgNPs-SPNs (50nm) and AgNPs-PVA (44nm) had cell viability of 40.8 and 28.0% respectively at 400µM. Based on the cytotoxicity and antioxidant activity, it is fair to report that these plant extracts have potential reducing and capping agents as they retain chemical properties on the surface of the nanoparticles.

Biosynthesis of ZnO nanoparticles using Jacaranda mimosifolia flowers extract: Synergistic antibacterial activity and molecular simulated facet specific adsorption studies.

The naturally occurring biomolecules present in the plant extracts have been identified to play an active role in the single step formation of nanoparticles with varied morphologies and sizes which is greener and environmentally benign. In the present work, spherical zinc oxide nanoparticles (ZnO NPs) of 2-4nm size were synthesized using aqueous extract of fallen Jacaranda mimosifolia flowers (JMFs), treated as waste. The microwave assisted synthesis was completed successfully within 5min. Thereafter, phase identification, morphology and optical band gap of the synthesized ZnO NPs were done using X-ray diffraction (XRD), high resolution transmission electron microscopy (HRTEM) and UV-Visible spectroscopy techniques. The composition of JMFs extract was analyzed by gas chromatography-mass spectrometry (GC-MS) and the ZnO NPs confirmation was further explored with fourier transform infrared spectroscopy (FTIR). The GC-MS results confirmed the presence of oleic acid which has high propensity of acting as a reducing and capping agent. The UV-Visible data suggested an optical band gap of 4.03eV for ZnO NPs indicating their small size due to quantum confinement. Further, facet specific adsorption of oleic acid on the surface of ZnO NPs was studied computationally to find out the impact of biomolecules in defining the shape and size of NPs. The viability of gram negative Escherichia coli and gram positive Enterococcus faecium bacteria was found to be 48% and 43%, respectively at high concentration of NPs.

Electrochemical sensing platform amplified with a nanobiocomposite of L-phenylalanine ammonia-lyase enzyme for the detection of capsaicin.

The present study involves the development of a sensitive electrochemical biosensor for the determination of capsaicin extracted from chilli fruits, based on a novel signal amplification strategy using enzyme technology. For the first time, platinum electrode modified with multiwalled carbon nanotubes where phenylalanine ammonia-lyase enzyme was immobilized using nafion was characterized by attenuated total reflectance infrared spectroscopy, transmittance electron microscopy and thermo-gravimetric analysis supported by computational methods. Cyclic and differential pulse voltammetry measurements were performed to better understand the redox mechanism of capsaicin. The performance of the developed electrochemical biosensor was tested using spiked samples with recoveries ranging from 98.9 to 99.6%. The comparison of the results obtained from bare and modified platinum electrodes revealed the sensitivity of the developed biosensor, having a detection limit (S/N=3) of 0.1863µgmL(-1) and electron transfer rate constant (ks) of 3.02s(-1). Furthermore, adsorption and ligand-enzyme docking studies were carried out to better understand the redox mechanisms supported by density functional theory calculations. These results revealed that capsaicin forms hydrogen bonds with GLU355, GLU541, GLU586, ARG and other amino acids of the hydrophobic channel of the binding sites thereby facilitating the redox reaction for the detection of capsaicin.

An ultrasensitive performance enhanced novel cytochrome c biosensor for the detection of rebaudioside A.

In this study a novel cyctochrome c modified nanocomposite electrochemical biosensor was developed for the electrochemical determination of rebaudioside A in different food samples. The electrode surface was fabricated with graphene oxide assimilated with gold nanoparticles decorated on multiwalled carbon nanotubes/cytochrome c. The developed biosensor exhibited a 10-fold enhancement in the differential pulse voltammetry signal carried out at pH 11.0 in a 0.1M borate buffer. Under the optimized conditions, Ip (µA) was proportional to the rebaudioside A concentration in the range of 0.001-0.05 mM (R(2)=0.8308) and 0.075-1.25 mM (R(2)=0.9920) with a detection limit (S/N=3) of 0.264 µM. Results of this study revealed that cyctochrome c was adsorbed tightly onto the surface of the modified electrode and showed an enzymatic catalytic activity towards the quasi-reversible reduction of rebaudioside A at -0.1 V (vs Ag/AgCl). The direct electron transfer by cytochrome c was further supported by HOMO-LUMO calculations performed at the density functional theory level. Additionally, the molecular docking simulations predicted a stronger binding affinity of rebaudioside A towards cytochrome c, thus supporting their host-guest relationship. The use of novel electrode materials in this study demonstrates the application of the electrochemical biosensor in the food industry.

Fabrication of copper nanoparticles decorated multiwalled carbon nanotubes as a high performance electrochemical sensor for the detection of neotame.

A highly sensitive and novel electrochemical sensor for the detection of neotame using differential pulse voltammetry with a modified glassy carbon electrode is presented. The method was further customized by the fabrication of the electrode surface with copper nanoparticles-ammonium piperidine dithiocarbamate-mutiwalled carbon nanotubes assimilated with ß-cyclodextrin. The multiwalled carbon nanotubes assimilated with ß-cyclodextrin/glassy carbon electrode exhibited catalytic activity towards the oxidation of neotame at a potential of 1.3 V at pH 3.0. The transmission electron microscopy, thermogravimetric analysis, frontier transform infrared spectroscopy and cyclic voltammetry were employed to characterize the electrochemical sensor. The sensitivity and detection limits of the electrode increased two-fold in contrast to the ß-CD-MWCNTs/GCE sensor. The developed method was successfully applied for the determination of neotame in food samples, with results similar to those achieved by our modified capillary electrophoresis method with a 96% confidence level.