Tuning the Reactivity of a Substrate for SNAP-Tag Expands Its Application for Recognition-Driven DNA-Protein Conjugation

Recognition-driven modification has been emerging as a novel approach to modifying biomolecular targets of interest site-specifically and efficiently. To this end, protein modular adaptors (MAs) are the ideal reaction model for recognition-driven modification of DNA as they consist of both a sequence-specific DNA-binding domain (DBD) and a self-ligating protein-tag. Coupling DNA recognition by DBD and the chemoselective reaction of the protein tag could provide a highly efficient sequence-specific reaction. However, combining an MA consisting of a reactive protein-tag and its substrate, for example, SNAP-tag and benzyl guanine (BG), revealed rather nonselective reaction with DNA. Therefore new substrates of SNAP-tag have been designed to realize sequence-selective rapid crosslinking reactions of MAs with SNAP-tag. The reactions of substrates with SNAP-tag were verified by kinetic analyses to enable the sequence-selective crosslinking reaction of MA. The new substrate enables the distinctive orthogonality of SNAP-tag against CLIP-tag to achieve orthogonal DNA-protein crosslinking by six unique MAs.     

FTIR SPECTRAL STUDIES OF THE BINARY SOLUTIONS OF ACETONE WITH XYLENE ISOMERS

Journal of Structural Chemistry - FTIR spectra of neat acetone (ACT), xylene isomers (o-xylene (OXY), m-xylene (MXY), and p-xylene (PXY)) and their binary solutions at various ACT molar...     

Synthesis,Structural Characterization,and Theoretical Studies of Silver(I) Complexes of Dihydrobis(2‐mercapto‐benzothiazolyl) Borate

The complexes [Ag{κ³‐S,S′,H‐H₂B(mbz)₂}(PR₃)]_x, ( 1 : x = 2, R = Ph; 2 : x = 1, R = Cy) (mbz = 2‐mercaptobenzothiazolyl) and amidine based dihydro(2‐mercaptobenzo‐thiazolyl) borates, [HN=C(Ph)–NH(R)–H₂B(mbz)] ( 3 : R = 2,6‐diisopropylphenyl and 4 : R = Ph) were synthesized and characterized by various spectroscopic methods and single‐crystal X‐ray crystallography. Complex [Ag{κ³‐S,S′,H‐H₂B(mbz)₂}(PPh₃)]₂ ( 1 ) has a dimeric structure in its crystalline state, in which central silver(I) atoms adopt a distorted trigonal bipyramid arrangement. In contrast, complex [Ag{κ³‐S,S′,H‐H₂B(mbz)₂}(PCy₃)] ( 2 ) has a monomeric structure in its crystalline state, in which the central silver(I) atoms adopt a distorted trigonal planar arrangement. Infrared spectroscopy was utilized as a tool for investigating the presence of M ··· H–B interactions. In addition, density functional theory (DFT) calculations were used to analyse the B–H ··· [M] bonding interaction in the metal borate complexes.     

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.     

Structural and optical properties of ZnSe thin films stacked with PbSe submonolayers

Structural and optical properties of Zinc Selenide (ZnSe) thin films stacked with multiple Lead Selenide (PbSe) submonolayers (ML) were studied. Thermal evaporation was preferred to produce ZnSe–PbSe thin films with the PbSe ML thickness ranges from 2.5 to 10 nm. Polycrystalline nature of the ZnSe was revealed through high resolution X-ray diffractometer measurement. The development of micro strain at the interfaces with increasing PbSe ML thickness was observed. A cross-sectional TEM image shows well-ordered periodicity and reproducibility of the layer thickness. The enhancement of optical absorption of ZnSe was identified upon stacking of PbSe ML. The evidence for quantum confinement in PbSe ML was revealed by the obtained red shift in band gap (2.5–1.8 eV) values as well as photoluminescence emission at 1,071 nm. The presence of tensile strain in the ZnSe layers upon staking of PbSe ML was discussed by the shift in LO phonon modes in Raman spectra.     

Fuzzy inspired image classification algorithm for hyperspectral data using three-dimensional log-Gabor features

In hyperspectral image classification problems, the discriminative efficiency of the classifier depends on the features. To classify the heterogeneous classes present in hyperspectral imagery, biologically inspired models such as log-Gabor features are useful as they exhibit joint spatial-spectral characteristics of each pixel. Log-Gabor features occupy the state-of-the-art hyperspectral research domain for extracting the features at different scales and orientations. In this proposed work, three-dimensional log-Gabor wavelets with different scales and orientations are designed to obtain the complete spatial, spectral and joint spatial-spectral characteristics of individual pixels in the hyperspectral data. Aiming to improve the accuracy, a simple fuzzy inspired algorithm is also proposed. The performance of the proposed algorithm is evaluated and is compared with other existing methods and supremacy is observed. The proposed methods are experimented on airborne visible infrared imaging sensor (AVIRIS) data of Indian Pine Site. The results witness the accuracy of 92.13% even while only 5% of the samples in each class were used for training for 3D log-Gabor features. Fuzzy inspired 3D log-Gabor features produce the accuracy of 93.11% for 5% training samples.     

Preparation and Characterization of Silver Selenide Thin Film

Silver selenide, a phase-changing chalcogenide material, is prepared using electro deposition method for various molarities. X-ray diffraction studies show the cubic lattice of the material. The micro-structural properties such as grain size, strain, dislocation density, and texture coefficient are examined. The lattice constant is calculated using Nelson-Relay function. Morphological studies are done and uniform distributions of grains are observed. High purities of thin films are confirmed by energy dispersive X-ray analysis. The band gap is calculated using UV-vis spectroscopy and photoluminescence technique, and hence, the Stokes’s effect is observed in silver selenide thin films. It is the first time that the lattice constant and the Urbach energy for various molarities in the case of silver selenide thin films are reported.     

Direct and Single‐Molecule Visualization of the Solution‐State Structures of G‐Hairpin and G‐Triplex Intermediates

We present the direct and single‐molecule visualization of the in‐pathway intermediates of the G‐quadruplex folding that have been inaccessible by any experimental method employed to date. Using DNA origami as a novel tool for the structural control and high‐speed atomic force microscopy (HS‐AFM) for direct visualization, we captured images of the unprecedented solution‐state structures of a tetramolecular antiparallel and (3+1)‐type G‐quadruplex intermediates, such as G‐hairpin and G‐triplex, with nanometer precision. No such structural information was reported previously with any direct or indirect technique, solution or solid‐state, single‐molecule or bulk studies, and at any resolution. Based on our results, we proposed a folding mechanism of these G‐quadruplexes.