A Versatile AIE Fluorogen with Selective Reactivity to Primary Amines for Monitoring Amination, Protein Labeling and Mitochondrial Staining

Specific bioconjugation for native primary amines is highly valuable for both chemistry and biomedical research. Despite all the efforts, scientists lack a proper strategy to achieve high selectivity for primary amines, not to mention the requirement of fast response for real applications. Herein, in this work, we report a chromone-based aggregation-induced emission (AIE) fluorogen called CMVMN as a self-reporting bioconjugation reagent for selective primary amine identification, and its applications for monitoring bioprocesses of amination and protein labeling. CMVMN is AIE-active and is capable of solid-state sensing. Thus, its electrospun films are manufactured for visualization of amine diffusion and leakage process. CMVMN also shows good biocompatibility and potential mitochondria-staining ability, which provides new insight for organelle-staining probe design. Combined with its facile synthesis and good reversibility, CMVMN not only shows wide potential applications in biology, but also offers new possibilities for molecular engineering.

A Genetically Encoded Picolyl Azide for Improved Live Cell Copper Click Labeling

Bioorthogonal chemistry allows rapid and highly selective reactivity in biological environments. The copper-catalyzed azide–alkyne cycloaddition (CuAAC) is a classic bioorthogonal reaction routinely used to modify azides or alkynes that have been introduced into biomolecules. Amber suppression is an efficient method for incorporating such chemical handles into proteins on the ribosome, in which noncanonical amino acids (ncAAs) are site specifically introduced into the polypeptide in response to an amber (UAG) stop codon. A variety of ncAA structures containing azides or alkynes have been proven useful for performing CuAAC chemistry on proteins. To improve CuAAC efficiency, biologically incorporated alkyne groups can be reacted with azide substrates that contain copper-chelating groups. However, the direct incorporation of copper-chelating azides into proteins has not been explored. To remedy this, we prepared the ncAA paz-lysine (PazK), which contains a picolyl azide motif. We show that PazK is efficiently incorporated into proteins by amber suppression in mammalian cells. Furthermore, PazK-labeled proteins show improved reactivity with alkyne reagents in CuAAC.

Dialkynyldiboranes(4) and the selectable reactivity of their C–H, CC and B–B bonds

The second, third and fourth examples of dialkynyldiboranes(4) are prepared and the selective reactivity of their B–B and alkynyl C–H and CC bonds is presented.

A Ligand-Directed Approach to Activity-Based Sensing: Developing Palladacycle Fluorescent Probes that Enable Endogenous Carbon Monoxide Detection

Carbon monoxide (CO) is an emerging gasotransmitter and reactive carbon species with broad anti-inflammatory, cytoprotective, and neurotransmitter functions along with therapeutic potential for the treatment of cardiovascular diseases. The study of CO chemistry in biology and medicine relative to other prominent gasotransmitters such as NO and H2S remains challenging, in large part due to limitations in available tools for the direct visualization of this transient and freely diffusing small molecule in complex living systems. Here we report a ligand-directed activity-based sensing (ABS) approach to CO detection through palladium-mediated carbonylation chemistry. Specifically, the design and synthesis of a series of ABS probes with systematic alterations in the palladium-ligand environment (e.g., sp3-S, sp3-N, sp2-N) establish structureactivity relationships for palladacycles to confer selective reactivity with CO under physiological conditions. These fundamental studies led to the development of an optimized probe, termed Carbon Monoxide Probe-3 Ester Pyridine (COP3E-Py), which enables imaging of CO release in live cell and brain settings, including monitoring of endogenous CO production that triggers presynaptic dopamine release in fly brains. This work provides a unique tool for studying CO in living systems and establishes the utility of a synthetic methods approach to activity-based sensing using principles of organometallic chemistry

A Ligand-Directed Approach to Activity-Based Sensing: Developing Palladacycle Fluorescent Probes that Enable Endogenous Carbon Monoxide Detection

Carbon monoxide (CO) is an emerging gasotransmitter and reactive carbon species with broad anti-inflammatory, cytoprotective, and neurotransmitter functions along with therapeutic potential for the treatment of cardiovascular diseases. The study of CO chemistry in biology and medicine relative to other prominent gasotransmitters such as NO and H2S remains challenging, in large part due to limitations in available tools for the direct visualization of this transient and freely diffusing small molecule in complex living systems. Here we report a ligand-directed activity-based sensing (ABS) approach to CO detection through palladium-mediated carbonylation chemistry. Specifically, the design and synthesis of a series of ABS probes with systematic alterations in the palladium-ligand environment (e.g., sp3-S, sp3-N, sp2-N) establish structureactivity relationships for palladacycles to confer selective reactivity with CO under physiological conditions. These fundamental studies led to the development of an optimized probe, termed Carbon Monoxide Probe-3 Ester Pyridine (COP3E-Py), which enables imaging of CO release in live cell and brain settings, including monitoring of endogenous CO production that triggers presynaptic dopamine release in fly brains. This work provides a unique tool for studying CO in living systems and establishes the utility of a synthetic methods approach to activity-based sensing using principles of organometallic chemistry

Chemical probe-based Nanopore Sequencing to Selectively Assess the RNA modifications

ABSTRACTRNA modifications contribute to RNA and protein diversity in eukaryotes and lead to amino acid substitutions, deletions, and changes in gene expression levels. Several methods have developed to profile RNA modifications, however, a less laborious identification of inosine and pseudouridine modifications in the whole transcriptome is still not available. Herein, we address the first step of the above question by sequencing synthetic RNA constructs with inosine and pseudouridine modification using Oxford Nanopore Technology, which is a direct RNA sequencing platform for rapid detection of RNA modification in a relatively less labor-intensive manner. Our analysis of multiple nanopore parameters reveals mismatch error majorly distinguish unmodified versus modified nucleobase. Moreover, we have shown that acrylonitrile selective reactivity with inosine and pseudouridine generates a differential profile between the modified and treated construct. Our results offer a new methodology to harness selectively reactive chemical probe-based modification along with existing direct RNA sequencing methods to profile multiple RNA modifications on a single RNA.

Selective Reactivity of Anti-Japanese Encephalitis Virus NS4B Antibody Towards Different Flaviviruses

Studies investigating West Nile virus (WNV) NS4B protein function are hindered by the lack of an antibody recognizing WNV NS4B protein. Few laboratories have produced WNV NS4B antibodies, and none have been shown to work consistently. In this report, we describe a NS4B antibody against Japanese encephalitis virus (JEV) NS4B protein that cross-reacts with the NS4B protein of WNV but not of dengue virus (DENV). This JEV NS4B antibody not only recognizes WNV NS4B in infected cells, but also recognizes the NS4B protein expressed using transfection. It is evident from this data that the JEV NS4B antibody is specific to NS4B of WNV but not to NS4B of the four DENV serotypes. The specificity of this antibody may be due to the notable differences that exist between the amino acid sequence identity and antigenic relationships within the NS4B protein of the WNV, DENV, and JEV.

Advances in Nanocatalysts Mediated Biodiesel Production: A Critical Appraisal

The excessive consumption of petroleum resources leads to global warming, fast depletion of petroleum reserves, as well as price instability of gasoline. Thus, there is a strong need for alternative renewable fuels to replace petroleum-derived fuels. The striking features of an alternative fuel include the low carbon footprints, renewability and affordability at manageable prices. Biodiesel, made from waste oils, animal fats, vegetal oils, is a totally renewable and non-toxic liquid fuel which has gained significant attraction in the world. Due to technological advancements in catalytic chemistry, biodiesel can be produced from a variety of feedstock employing a variety of catalysts and recovery technologies. Recently, several ground-breaking advancements have been made in nano-catalyst technology which showed the symmetrical correlation with cost competitive biodiesel production. Nanocatalysts have unique properties such as their selective reactivity, high activation energy and controlled rate of reaction, easy recovery and recyclability. Here, we present an overview of various feedstock used for biodiesel production, their composition and characteristics. The major focus of this review is to appraise the characterization of nanocatalysts, their effect on biodiesel production and methodologies of biodiesel production.