Simple Molecular Probes Research Articles

Biosynthesis of copper nanoclusters for fluorescence detection of bilirubin in biofluids.

Copper nanoclusters (Cu NCs) have shown significant attention in sensing of molecular and ionic species. In this work, a single-step biosynthetic approach was introduced for the preparation of fluorescent Cu NCs using Holarrhena pubescens (H.pubescens) leaves extract as a template. The synthesized H.pubescens-Cu NCs act as a nanomolecular probe for the detection of bilirubin in biofluids. The synthesized H.pubescens-Cu NCs displayed highest fluorescence intensity at 454 nm, when excited at 330 nm. Importantly, selective detection of bilirubin was obtained by introducing H.pubescens-Cu NCs as a simple molecular probe. The interaction of bilirubin and H.pubescens-Cu NCs resulted in a remarkable decrease in the emission peak intensity. The developed H.pubescens-Cu NCs-based bilirubin molecular probe has a wide linear range of 0.5-20.00 μM with the limit of detection of 30.54 nM for bilirubin. The promising application of H.pubescens-Cu NCs-based molecular probe was assessed by assaying bilirubin in spiked biofluids.

Real-time optical detection of mercury contamination in drinking water using an amphiphilic recognition probe at liquid crystal/aqueous interfaces.

Mercury contamination is a global environmental issue due to its toxicity and persistence in ecosystems. It poses a particular risk in aquatic systems, where it bioaccumulates and biomagnifies, leading to serious health impacts on humans. Therefore, effective detection technologies for mercuric ions in natural water resources are highly desirable. However, most existing detection methods are time-consuming, require complicated sample pre-treatment, and rely on expensive equipment, which hinders their widespread use in real-time detection. Here, we present a convenient, rapid, portable, user-friendly, and cost-effective sensing system for detecting Hg2+ ion contamination in water. This system utilizes a highly selective, amphiphilic, and structurally simple molecular probe, N-dodecylamine-di-thiocarbamate (DDC). DDC molecules align at the interface between the liquid crystal (LC) and water, inducing a homeotropic LC orientation. In water samples contaminated with Hg2+, a bright optical texture is observed, indicating the alignment of the 5CB LC in a planar manner at the LC/aqueous boundary. The minimum detectable concentration (LOD) for Hg2+ ions is 5.0 μM in distilled water, with a broad detection range from 5.0 μM to 2 mM. The sensor selectively detects Hg2+ ions over other common interfering metal ions, including Pb2+, Co2+, Ni2+, Cu2+, Cd2+, Zn2+, Cr2+, Mg2+, Na+, K+, and Ca2+. Boolean logic gates, bar graphs, and truth tables are employed to explain the selectivity of this liquid crystal-based sensor. This work demonstrates the significant potential of the sensor for monitoring mercuric ions in natural water resources, offering a promising strategy for controlling mercury pollution.

A Ratiometric Fluorescent Probe for Hypochlorite and Lipid Droplets to Monitor Oxidative Stress.

Mitochondria are valuable subcellular organelles and play crucial roles in redox signaling in living cells. Substantial evidence proved that mitochondria are one of the critical sources of reactive oxygen species (ROS), and overproduction of ROS accompanies redox imbalance and cell immunity. Among ROS, hydrogen peroxide (H2O2) is the foremost redox regulator, which reacts with chloride ions in the presence of myeloperoxidase (MPO) to generate another biogenic redox molecule, hypochlorous acid (HOCl). These highly reactive ROS are the primary cause of damage to DNA (deoxyribonucleic acid), RNA (ribonucleic acid), and proteins, leading to various neuronal diseases and cell death. Cellular damage, related cell death, and oxidative stress are also associated with lysosomes which act as recycling units in the cytoplasm. Hence, simultaneous monitoring of multiple organelles using simple molecular probes is an exciting area of research that is yet to be explored. Significant evidence also suggests that oxidative stress induces the accumulation of lipid droplets in cells. Hence, monitoring redox biomolecules in mitochondria and lipid droplets in cells may give a new insight into cell damage, leading to cell death and related disease progressions. Herein, we developed simple hemicyanine-based small molecular probes with a boronic acid trigger. A fluorescent probe AB that could efficiently detect mitochondrial ROS, especially HOCl, and viscosity simultaneously. When the AB probe released phenylboronic acid after reacting with ROS, the product AB-OH exhibited ratiometric emissions depending on excitation. This AB-OH nicely translocates to lysosomes and efficiently monitors the lysosomal lipid droplets. Photoluminescence and confocal fluorescence imaging analysis suggest that AB and corresponding AB-OH molecules are potential chemical probes for studying oxidative stress.

Assessing the impact of USER-treatment on hyRAD capture applied to ancient DNA.

Ancient DNA preservation in subfossil specimens provides a unique opportunity to retrieve genetic information from the past. As ancient DNA extracts are generally dominated by molecules originating from environmental microbes, capture techniques are often used to economically retrieve orthologous sequence data at the population scale. Post-mortem DNA damage, especially the deamination of cytosine residues into uracils, also considerably inflates sequence error rates unless ancient DNA extracts are treated with the USER enzymatic mix prior to library construction. While both approaches have recently gained popularity in ancient DNA research, the impact of USER-treatment on capture efficacy still remains untested. In this study, we applied hyRAD capture to eight ancient equine subfossil specimens from France (1st-17th century CE), including horses, donkeys and their first-generation mule hybrids. We found that USER-treatment could reduce capture efficacy and introduce significant experimental bias. It differentially affected the size distribution of on-target templates following capture with two distinct hyRAD probe sets in a manner that was not driven by differences in probe sizes and DNA methylation levels. Finally, we recovered unbalanced proportions of donkey-specific and horse-specific alleles in mule capture sequence data, due to the combined effects of USER-treatment, probe sets and reference bias. Our work demonstrates that while USER-treatment can improve the quality of ancient DNA sequence data, it can also significantly affect hyRAD capture outcomes, introducing bias in the sequence data that is difficult to predict based on simple molecular probe features. Such technical batch effects may prove easier to model and correct for using capture with synthetic probes of controlled sizes and diversity content.

Nitric Oxide Sensing through 1,2,3,4-Oxatriazole Formation from Acylhydrazide: A Kinetic Study.

A simple molecular probe displays highly selective turn-on response toward NO by the unprecedented NO-induced formation of a 1,2,3,4-oxatriazole ring exhibiting no interference from various endogenous biomolecules including DHA, AA, etc. Kinetics of the reactions between NO and the probe provide a mechanistic insight into the formation of 1,2,3,4-oxatriazole which showed that, though initially 1,2,3,4-oxatriazole is formed and extractable in solid form, it exists in equilibrium with the ring opened azide form which ultimately hydrolyzed and converted to carboxylic acid and nitrate. The reaction displays second-order dependence on [NO] and first-order on [Probe]. The probe is water-soluble, cell permeable, and noncytotoxic and appropriates for live cell imaging. This constitutes the first report where there is a direct evidence of NO-induced ring closing reaction of an acyl hydrazide moiety leading to the formation of 1,2,3,4-oxatriazole.

Identifying Interactions that Determine Fragment Binding at Protein Hotspots.

Locating a ligand-binding site is an important first step in structure-guided drug discovery, but current methods do little to suggest which interactions within a pocket are the most important for binding. Here we illustrate a method that samples atomic hotspots with simple molecular probes to produce fragment hotspot maps. These maps specifically highlight fragment-binding sites and their corresponding pharmacophores. For ligand-bound structures, they provide an intuitive visual guide within the binding site, directing medicinal chemists where to grow the molecule and alerting them to suboptimal interactions within the original hit. The fragment hotspot map calculation is validated using experimental binding positions of 21 fragments and subsequent lead molecules. The ligands are found in high scoring areas of the fragment hotspot maps, with fragment atoms having a median percentage rank of 97%. Protein kinase B and pantothenate synthetase are examined in detail. In each case, the fragment hotspot maps are able to rationalize a Free-Wilson analysis of SAR data from a fragment-based drug design project.

A Novel and Simple Molecular Probe Sensing Hg(II) in Living Cells by Chelation‐enhanced Fluorescence

AbstractMercury is currently widely used in industries which leads to various means of Hg(II) waste exposure and its accumulation in organisms will cause neurological damages. Thus, there is a great need for the design of probes or sensors with high sensitivity and selectivity for detecting and monitoring Hg(II) at physiological pH. Thus a novel and simple molecular probe P1 was prepared from 1,1′‐(1,3‐phenylene)‐bis(2,4‐pentanedionato) for sensing Hg(II) via chelation‐enhanced fluorescence (CHEF) mechanism. The probe indicated a selectively fluorescent response to Hg(II) in aqueous media excited by the ultraviolet light of 254 nm. The recognition mechanism was further studied by semi‐empirical AM1 and molecular mechanics MM+ methods in HyperChem 8.0. The calculation indicated a tetrahedron coordination geometry for Hg(II) and a chair‐like configuration for the total molecule. The fluorescent images sensing Hg(II) in living mouse fibroblast cells by the probe were obtained by fluorescence microscope.

Development of new simple molecular probes of DNA bulged structures

NCSi-gb is a neocarzinostatin chromophore (NCS-chrom) metabolite which binds strongly to certain two-base DNA bulges. Compared with previously reported NCSi-gb analogues, a new analogue with a different aminoglycoside position was synthesized, and it showed strong fluorescence and improved binding and sequence selectivity to DNA bulges. The N-dimethylated form of this analogue had a similar binding pattern, and it competitively inhibited bulge-specific cleavage by NCS-chrom.

Infrared spectroscopic study of the interaction of cations in zeolites with simple molecular probes. Part 3.—Adsorption and polarization of methane and ethane on cationic forms of high-silica zeolites

Download options Please wait... Article information DOI https://doi.org/10.1039/FT9938901393 Article type Paper Download Citation J. Chem. Soc., Faraday Trans., 1993,89, 1393-1395 BibTex EndNote MEDLINE ProCite ReferenceManager RefWorks RIS Permissions Request permissions Infrared spectroscopic study of the interaction of cations in zeolites with simple molecular probes. Part 3.—Adsorption and polarization of methane and ethane on cationic forms of high-silica zeolites A. Yu. Khodakov, L. M. Kustov, V. B. Kazansky and C. Williams, J. Chem. Soc., Faraday Trans., 1993, 89, 1393 DOI: 10.1039/FT9938901393 To request permission to reproduce material from this article, please go to the Copyright Clearance Center request page. If you are an author contributing to an RSC publication, you do not need to request permission provided correct acknowledgement is given. If you are the author of this article, you do not need to request permission to reproduce figures and diagrams provided correct acknowledgement is given. If you want to reproduce the whole article in a third-party publication (excluding your thesis/dissertation for which permission is not required) please go to the Copyright Clearance Center request page. Read more about how to correctly acknowledge RSC content. Search articles by author Andrew Yu. Khodakov Leonid M. Kustov Vladimir B. Kazansky Carol Williams

Infrared spectroscopic study of the interactions of cations in zeolites with simple molecular probes. Part 2.—Adsorption and polarization of molecular hydrogen on zeolites containing polyvalent cations

Download options Please wait... Article information DOI https://doi.org/10.1039/FT9928803251 Article type Paper Download Citation J. Chem. Soc., Faraday Trans., 1992,88, 3251-3253 BibTex EndNote MEDLINE ProCite ReferenceManager RefWorks RIS Permissions Request permissions Infrared spectroscopic study of the interactions of cations in zeolites with simple molecular probes. Part 2.—Adsorption and polarization of molecular hydrogen on zeolites containing polyvalent cations A. Yu. Khodakov, L. M. Kustov, V. B. Kazansky and C. Williams, J. Chem. Soc., Faraday Trans., 1992, 88, 3251 DOI: 10.1039/FT9928803251 To request permission to reproduce material from this article, please go to the Copyright Clearance Center request page. If you are an author contributing to an RSC publication, you do not need to request permission provided correct acknowledgement is given. If you are the author of this article, you do not need to request permission to reproduce figures and diagrams provided correct acknowledgement is given. If you want to reproduce the whole article in a third-party publication (excluding your thesis/dissertation for which permission is not required) please go to the Copyright Clearance Center request page. Read more about how to correctly acknowledge RSC content. Search articles by author Andrew Yu. Khodakov Leonid M. Kustov Vladimir B. Kazansky Carol Williams

Infrared spectroscopic study of the interaction of cations in zeolites with simple molecular probes. Part 1.—Adsorption of molecular hydrogen on alkaline forms of zeolites as a test for localization sites

The localization sites for univalent cations in cationic forms of zeolites (A, X, Y, ZSM-5 and mordenite) have been investigated using the low-temperature adsorption of molecular hydrogen as a spectroscopic test. The extent of H—H bond polarization, estimated from the low-frequency shift of the fundamental stretching vibration of perturbed H2 molecules, was found to be strongly dependent on the basicity of the neighbouring oxygen atoms of the framework.

The use of submicroscopic gold particles combined with video contrast enhancement as a simple molecular probe for the living cell.

We describe a new approach to probe the molecular biology of the living cell that uses small colloidal gold particles coupled to specific ligands. They are visualized in cells by bright-field, video enhanced contrast microscopy. We describe the basic aspects of the technique and provide examples of applications to intracellular motility, cell membrane dynamics, receptor translocation, internalization, and intracellular routing. We also provide examples of the use of this approach in immunospecific labelling of cells and tissue sections.