A hybrid foldamer with unique architecture from conformationally constrained aliphatic-aromatic amino acid conjugate

In this paper, we describe the design and synthesis of a novel hybrid foldamer, derived from a conformationally constrained aliphatic-aromatic amino acid conjugate that adopts a well-defined, compact, three-dimensional structure, governed by a combined conformational restriction imposed by the individual amino acids from which the foldamer is composed. Conformational investigations confirmed the prevalence of a unique doubly bent conformation for the foldamer, in both solid and solution states, as evidenced from single crystal X-ray and 2D NOESY studies, respectively. The findings suggest that constrained aliphatic-aromatic amino acid conjugates offer new avenues for the de novo design of hybrid foldamers with distinctive structural architectures. Furthermore, the de novo design strategy disclosed herein has the potential for significantly augmenting the ‘tool-box’ of the modern day peptidomimetic chemist, as well as providing a novel approach to the field of rational design.     

Phase diagrams and dielectric studies of binary mixtures exhibiting intermediate nematic and induced smectic phases

Investigations on the phase diagrams of two bi-component mixtures of liquid crystals are presented. Whereas in one of the bi-component systems, smectic A (SmA) phase is seen to be induced, in the other case the so-called nematic “island” has been observed. The dielectric properties of magnetically oriented sample forming nematic phase and induced smectic phase in one of the mixtures, and a nematic “island” and SmA phase in the other mixture, were measured in the frequency range from 1?Hz to 10?MHz at different temperatures. The transition temperatures obtained from the polarizing microscope and differential scanning calorimeter measurements agree well with the dielectric relaxation data.     

Analyses of Lattice Traffic Flow Model on a Gradient Highway

The optimal current difference lattice hydrodynamic model is extended to investigate the traffic flow dynamics on a unidirectional single lane gradient highway. The effect of slope on uphill/downhill highway is examined through linear stability analysis and shown that the slope significantly affects the stability region on the phase diagram.Using nonlinear stability analysis, the Burgers, Korteweg-deVries(KdV) and modified Korteweg-deVries(mKdV) equations are derived in stable, metastable and unstable region, respectively. The effect of reaction coefficient is examined and concluded that it plays an important role in suppressing the traffic jams on a gradient highway. The theoretical findings have been verified through numerical simulation which confirm that the slope on a gradient highway significantly influence the traffic dynamics and traffic jam can be suppressed efficiently by considering the optimal current difference effect in the new lattice model.     

Changes in dynamics of SRE-RNA on binding to the VTS1p-SAM domain studied by 13C NMR relaxation

RNA recognition by proteins is often accompanied by significant changes in RNA dynamics in addition to conformational changes. However, there are very few studies which characterize the changes in molecular motions in RNA on protein binding. We present a quantitative (13)C NMR relaxation study of the changes in RNA dynamics in the pico-nanosecond time scale and micro-millisecond time scale resulting from interaction of the stem-loop SRE-RNA with the VTS1p-SAM domain. (13)C relaxation rates of the protonated carbons of the nucleotide base and anomeric carbons have been analyzed by employing the model-free formalism, for a fully (13)C/(15)N-labeled sample of the SRE-RNA in the free and protein-bound forms. In the free RNA, the nature of molecular motions are found to be distinctly different in the stem and the loop region. On binding to the protein, the nature of motions becomes more homogeneous throughout the RNA, with many residues showing increased flexibility at the aromatic carbon sites, while the anomeric carbon sites become more rigid. Surprisingly, we also observe indications of a slow collective motion of the RNA in the binding pocket of the protein. The observation of increased motions on binding is interesting in the context of growing evidence that binding does not always lead to motional restrictions and the resulting entropy gain could favor the free energy of association.     

Towards CRISPR powered electrochemical sensing for smart diagnostics

Even though global health has been steadily improved, the global disease burden associated with communicable and non-communicable diseases extensively increased healthcare expenditure. The present COVID-19 pandemic scenario has again ascertained the importance of clinical diagnostics as a basis to make life-saving decisions. In this context, there is a need for developing next-generation integrated smart real-time responsive biosensors with high selectivity and sensitivity. The emergence of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas biosensing systems has shown remarkable potential for developing next-generation biosensors. CRISPR/Cas integrated electrochemical biosensors (E-CRISPR) stands out with excellent properties. In this opinionated review, we illustrate the rapidly evolving applications for E-CRISPR-integrated detection systems towards biosensing and the future scope associated with E-CRISPR based diagnostics.     

An extensive study on isosorbide-5-mononitrate acid adducts for quantification in human plasma using liquid chromatography/electrospray ionization tandem mass spectrometry and its application to bioequivalence sample analysis

A rapid and sensitive liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) method for the determination of isosorbide-5-mononitrate (5-ISMN), used in the treatment of angina pectoris, in human plasma is described. The quantification of 5-ISMN was performed via stable acetate adduct formation with a high relative abundance. The plasma filtrate obtained after solid-phase extraction (SPE), using a polymer based, hydrophilic-lipophilic balanced (HLB) cartridge, was submitted directly to reversed-phase high-performance liquid chromatography separation followed by ESI and detection of the resulting ions using triple-quadrupole mass spectrometry in selected reaction monitoring (SRM) mode. There was no significant matrix effect on the analysis. For validation of the method, the recovery of the free analyte response was compared to that obtained from an optimized extraction method. The analyte stability was examined under conditions mimicking the sample storage, handling, and analytical procedures. The extraction procedure yielded extremely clean extracts with a recovery of 95.51% and 93.98% for iossorbide-5-mononitrate and topiramate (internal standard (IS)), respectively. The calibration curves were linear for the dynamic range of 10.0 to 1000.0 ng/mL with a correlation coefficient r > or = 0.9985. The intra-assay and inter-assay precision for the samples at the lower limit of quantification (LLOQ) were 9.02 and 13.30%, respectively. The intra-assay accuracies at LLOQ, LQC, MQC and HQC levels varied from 98.13 to 118.15, 102.34 to 105.21, 100.69 to 109.68, and 95.76 to 102.92%, respectively, while the inter-assay accuracies ranged from 93.10 to 118.15, 93.03 to 107.04, 86.97 to 109.68 and 86.18 to 105.85%, respectively, at these levels. The method is rugged and fast with a total run time of 2 min. The method was successfully applied for a bioequivalence study in 24 human subject samples after oral administration of 60 mg extended release (ER) formulations.     

Exploring bioanalytical applications of assisted protein reassembly

Reassembly of protein from its peptide fragments is a technique that can have many applications in the bioanalytical field. Typically, a reporter protein fragmented into its two peptides is employed as a label in this study. This fragments of peptide can reassemble yielding an active functional reporter. This reassembly of the protein can be assisted by non-covalently interacting peptides or proteins, which are attached to the fragmented reporter. This technique has been employed in several applications including study of protein–protein interactions, antibody screening, immunoassays, and high-throughput screening. This review focuses on different reporters employed in the study of reassembly of proteins and applications of this strategy in bioanalysis.     

Molecular dynamics study of carbon dioxide hydrate dissociation

We present results from a molecular dynamics study of the dissociation behavior of carbon dioxide (CO(2)) hydrates. We explore the effects of hydrate occupancy and temperature on the rate of hydrate dissociation. We quantify the rate of dissociation by tracking CO(2) release into the liquid water phase as well as the velocity of the hydrate-liquid water interface. Our results show that the rate of dissociation is dependent on the fractional occupancy of each cage type and cannot be described simply in terms of overall hydrate occupancy. Specifically, we find that hydrates with similar overall occupancy differ in their dissociation behavior depending on whether the small or large cages are empty. In addition, individual cages behave differently depending on their surrounding environment. For the same overall occupancy, filled small and large cages dissociate faster in the presence of empty large cages than when empty small cages are present. Therefore, hydrate dissociation is a collective phenomenon that cannot be described by focusing solely on individual cage behavior.