A new selective ‘turn-on’ small fluorescent cationic probe for recognition of RNA in cells

Fluorescent imaging probes have revolutionised cell biology by monitoring cellular objects. However, the lack of fluorescent probes with high selectivity for RNA has been a drawback. Thus, selective RNA binding for fluorescent sensors is essential. Here, we report the selective fluorescence enhancement upon addition of RNA. By exploiting a selective recognition of small tetra-cationic probe 1 for RNA, we also explain the possible binding mode for RNA. As a membrane-permeant fluorescence probe, 1 provides selective imaging of RNA not only in human neuroblastoma tumour SH-SY5Y cell line used for Parkinson's disease but also in the unicellular green alga cells. Further exploitation could open new opportunities in neurotoxin and cancer biology.     

Carbazole-based Schiff base: A sensitive fluorescent ‘turn-on’ chemosensor for recognition of Al(III) ions in aqueous-alcohol media

Carbazole-based Schiff base chemosensor was synthesized in one-pot synthesis using 2-hydroxy-1-naphtaldehyde for fluorescent sensing of Al³⁺ ions. Characterization of the ligand (L) was revealed through spectroscopic and physicochemical techniques. The fluorescence emission responses of L to various metal ions and anions were investigated. The chelation was studied by UV–vis, ¹H NMR, LC-MS/MS, fluorescence titration and Job’s plot analysis. Bathochromic shift resulted from charge transfer from L to electrophilic Al³⁺ ion was observed in the chelation of L with Al³⁺. The potentiality of L to be a distinguished probe to detect Al³⁺ ions was due to a chelation enhanced fluorescence (CHEF) effect, concomitant with noticeable fluorescent enhancement. A significant fluorescence enhancement at 533 nm was observed in ethanol–water (1:1, v/v) solution upon addition of Al³⁺ along with a distinct color change from yellow to white. Non-fluorescent ligand exposed highly sensitive turn-on fluorescent sensor behavior for selectively sensing Al³⁺ ions via 1:1 (ligand:metal) stoichiometry. The ligand’s specificity in the existence of other tested metal ions and anions indicated no observation in color change. The ligand-Al³⁺ complex formation was reversible upon addition of chelating agent EDTA. The ligand interacted with Al³⁺ ions with an association constant of K_a = 5 × 10⁴ M^?1. The limit of detection (LOD) was found to be 2.59 × 10^-7 M. The synthesized Schiff base could efficiently detect Al³⁺ ions as a fluorescent sensor.     

Dansyl-Modified γ-Cyclodextrin as a fluorescent sensor for molecular recognition

Dansyl-Modified -Cyclodextrin (1) has been prepared as a sensor for detecting organic compounds.1 shows pure monomer fluorescence whose intensity is decreased or enhanced upon addition of guest species. The value I/I ⁰, whereI andI ⁰ are fluorescence intensities in the presence and absence of a guest and I isI ⁰–I, was used as a parameter of sensitivity.1 exhibits highly sensitive and selective molecular recognition ability, particularly, for ursodeoxycholic acid, chenodeoxycholic acid, and lithocholic acid.     

Dansyl-Modified γ-Cyclodextrin as a fluorescent sensor for molecular recognition

The crystal structure of thiamine iodide sesquihydrate has been determined by X-ray diffraction methods as a host-guest model for coenzyme-substrate interactions. The asymmetric unit contains two chemical units. Both the thiamine molecules A and B, which are crystallographically independent, assume the usualF conformation and have a disordered hydroxyethyl side chain. An iodide anion (or a water molecule) bridges the pyrimidine and thiazolium rings of molecule A (or B) by forming a hydrogen bond with the amino group and an electrostatic contact with the thiazolium ring to stabilize the molecular conformation. In the crystal the thiamine molecules self-associate to form a pipe-like polymeric structure, in which four thiamine hosts surround an iodide guest and hold it through C(2)-H...I hydrogen bonds and thiazolium...I electrostatic interactions. Crystal data: C₁₂H₁₇N₄OS⁺·I^– · 1.5 H₂O, monoclinic,P2₁/c, a=12.585(2), b=25.303(5), c=12.030(2) Å, =115.15(1)°,V=3468(1) ų,Z=8,D _c=1.606 g cm^–3,R=0.045 for 3328 observed reflections. Supplementary Data relating to this article are deposited with the British Library as Supplementary Publication No. SUP. 82156 (13 pages).     

‘Pourbaix sensors’: fluorescent molecular logic gates for pE and pH

Abstract

From the cross-fertilisation of fluorescent pH indicators and fluorescent redox switches, our group has established a new class of molecular sensor that operates as two-input molecular logic gates. These molecular sensors, known as ‘Pourbaix sensors’, are named in honour of Marcel Pourbaix, who developed the pH–potential diagrams for the various states of metal ion species in aqueous solution. This review highlights the evolution of ‘Pourbaix sensors’ based on anthracene and naphthalimide fluorophores. Potential applications of this class of molecule in fields such as corrosion science, cell biology and biomedical diagnostics are highlighted.     

Spectroscopic studies on a ‘turn-on’ fluorescent sensor for transition metals with selective ‘turn-off’ for mercury(II) ions

Spectroscopic studies on a dansyl-based fluorescent sensor N-(4-aminophenyl)-5-(dimethylamino)naphthalene-1-sulphonamide (1) and its interactions with transition metals are reported. The sensor's absorption and emission spectra exhibited different profiles at different polarities and pH values. Enhanced fluorescence was observed in the presence of chromium(III) ions in methanol, while the emission was quenched significantly in the presence of mercury(II) ions both in methanol and aqueous solution. The binding constants of 1 to chromium(III) in methanol and to mercury(II) ions in methanol and aqueous solution were calculated.     

Rh-catalyzed desymmetrization of α-quaternary centers by isomerization-hydroacylation

We describe a Rh-catalyzed desymmetrization of all-carbon quaternary centers from α,α-bis(allyl)aldehydes by a cascade featuring isomerization and hydroacylation. This desymmetrization competes with two other novel olefin functionalizations that are triggered by C–H bond activation, including carboacylation and bisacylation. A BIPHEP ligand promotes enantioselective formation of α-vinylcyclopentanones. Mechanistic studies support irreversible and enantioselective olefin-isomerization followed by olefin-hydroacylation.     

Remote stereoselective deconjugation of α,β-unsaturated esters by simple amidation reactions

The thermodynamically disfavored isomerization of α,β-unsaturated esters to deconjugated β,γ-unsaturated analogues occurs readily when coupled to an amidation. Within the framework of macrocyclic derivatives, it is shown that 15, 16, and 18 membered macrocycles react with tBuOK and anilines to generate, in one-pot, β,γ-unsaturated amides (yields up to 88%). Importantly, single (chiral) diastereomers are isolated (d.r. > 49 : 1, ¹H NMR) irrespective of the size and nature of the rings, showing an effective transmission of remote stereochemistry during the isomerization process. CSP-chromatographic resolution and absolute configuration determination by VCD are achieved.     

Unveiling the nature of supramolecular crown ether–C60 interactions

A series of exTTF-(crown ether)₂ receptors, designed to host C₆₀, has been prepared. The size of the crown ether and the nature of the heteroatoms have been systematically changed to fine tune the association constants. Electrochemical measurements and transient absorption spectroscopy assisted in corroborating charge transfer in the ground state and in the excited state, leading to the formation of radical ion pairs featuring lifetimes in the range from 12 to 21 ps. To rationalize the nature of the exTTF-(crown ether)₂·C₆₀ stabilizing interactions, theoretical calculations have been carried out, suggesting a synergetic interplay of donor–acceptor, π–π, n–π and CH···π interactions, which is the basis for the affinity of our novel receptors towards C₆₀.     

A carbon–carbon hybrid – immobilizing carbon nanodots onto carbon nanotubes

The thrust of this work is to integrate small and uniformly sized carbon nanodots (CNDs) with single-walled carbon nanotubes (SWCNT) of different diameters as electron donors and electron acceptors, respectively, and to test their synergetic interactions in terms of optoelectronic devices. CNDs (denoted pCNDs, where p indicates pressure) were prepared by pressure-controlled microwave decomposition of citric acid and urea. pCNDs were immobilized on single-walled carbon nanotubes by wrapping the latter with poly(4-vinylbenzyl trimethylamine) (PVBTA), which features positively charged ammonium groups in the backbone. Negatively charged surface groups on the CNDs lead to attractive electrostatic interactions. Ground state interactions between the CNDs and SWCNTs were confirmed by a full-fledged photophysical investigation based on steady-state and time-resolved techniques. As a complement, charge injection into the SWCNTs upon photoexcitation was investigated by ultra-short time-resolved spectroscopy.     

Intermolecular carbene S–H insertion catalysed by engineered myoglobin-based catalysts

The first example of a biocatalytic strategy for the synthesis of thioethers via an intermolecular carbene S–H insertion reaction is reported. Engineered variants of sperm whale myoglobin were found to efficiently catalyze this C–S bond forming transformation across a diverse set of aryl and alkyl mercaptan substrates and α-diazoester carbene donors, providing high conversions (60–99%) and high numbers of catalytic turnovers (1100–5400). Furthermore, the enantioselectivity of these biocatalysts could be tuned through mutation of amino acid residues within the distal pocket of the hemoprotein, leading to myoglobin variants capable of supporting asymmetric S–H insertions with up to 49% ee. Rearrangement experiments support a mechanism involving the formation of a sulfonium ylide generated upon attack of the thiol substrate to a heme-bound carbene intermediate.     

Copper-catalyzed intermolecular C(sp3)–H bond functionalization towards the synthesis of tertiary carbamates

We describe the development of an intermolecular unactivated C(sp³)–H bond functionalization towards the direct synthesis of tertiary carbamates. The transformation proceeded using a readily available, abundant first-row transition metal catalyst (copper), and isocyanates as the source of the amide moiety. This is a novel strategy for direct transformation of a variety of unactivated hydrocarbon feedstocks to N-alkyl-N-aryl and N,N-dialkyl carbamates without pre-functionalization or installation of a directing group. The reaction had a broad substrate scope with 3° > 2° > 1° site selectivity. The reaction proceeded even on a gram scale, and a corresponding free amine was directly obtained when the reaction was performed at high temperature. Kinetic studies suggested that radical-mediated C(sp³)–H bond cleavage was the rate-determining step.     

In vitro reconstitution of α-pyrone ring formation in myxopyronin biosynthesis

Myxopyronins are α-pyrone antibiotics produced by the terrestrial bacterium Myxococcus fulvus Mx f50 and possess antibacterial activity against Gram-positive and Gram-negative pathogens. They target the bacterial RNA polymerase (RNAP) “switch region” as non-competitive inhibitors and display no cross-resistance to the established RNAP inhibitor rifampicin. Recent analysis of the myxopyronin biosynthetic pathway led to the hypothesis that this secondary metabolite is produced from two separate polyketide parts, which are condensed by the stand-alone ketosynthase MxnB. Using in vitro assays we show that MxnB catalyzes a unique condensation reaction forming the α-pyrone ring of myxopyronins from two activated acyl chains in form of their β-keto intermediates. MxnB is able to accept thioester substrates coupled to either N-acetylcysteamine (NAC) or a specific carrier protein (CP). The turnover rate of MxnB for substrates bound to CP was 12-fold higher than for NAC substrates, demonstrating the importance of protein–protein interactions in polyketide synthase (PKS) systems. The crystal structure of MxnB reveals the enzyme to be an unusual member of the ketosynthase group capable of binding and condensing two long alkyl chains bound to carrier proteins. The geometry of the two binding tunnels supports the biochemical data and allows us to propose an order of reaction, which is supported by the identification of novel myxopyronin congeners in the extract of the producer strain. Insights into the mechanism of this unique condensation reaction do not only expand our knowledge regarding the thiolase enzyme family but also opens up opportunities for PKS bioengineering to achieve directed structural modifications.     

Pd-η 3-C6H9 complexes of the Trost modular ligand: high nuclearity columnar aggregation controlled by concentration,solvent and counterion

Under optimised conditions, the Trost modular ligand (TML) series induces high levels of asymmetric induction in an extraordinarily wide range of reactions involving palladium π-allyl intermediates. Prior mechanistic investigations into reactions involving Pd-η ³-C₆H₉ intermediates have focussed on the monomeric 13-membered ring formed via P,P-chelation of the ligand to Pd. However, it is also recognised that ring-opening oligomerisation provides a pool of high nuclearity Pd-η ³-C₆H₉ species that, by affording a low level, or even the opposite sense, of asymmetric induction relative to the mononuclear species, are responsible for a reduction in selectivity under non-optimised conditions. Herein we describe an investigation by NMR spectroscopy, molecular mechanics, molecular dynamics, and small-angle neutron scattering (SANS), of a Pd-η ³-C₆H₉ cation bearing the 1,2-diaminocyclohexane TML ligand (2). Using both nondeuterated and perdeuterated (D₄₇) isotopologues of the resulting complexes ([1]⁺), we show that a two-stage oligomerisation-aggregation process forms self assembled cylindrical aggregates of very high nuclearity (up to 56 Pd centres). We also investigate how concentration, solvent and counter-anion all modulate the extent of oligomerisation.     

Mechanical and optical properties of ultralarge flakes of a metal–organic framework with molecular thickness

The isolation of 2D-materials is already a success for graphene, graphene oxide, boron nitride and a few clays or metal chalcogenides, however despite the fact that some of them show very interesting physical properties, they lack useful functionalities. Metal–Organic Frameworks (MOFs) are multifunctional materials showing a wide range of physical and chemical properties that can be structurally designed by suitable selection of their building-blocks. This strategy may allow the production of layers with a variety of useful electronic and molecular recognition functionalities. Herein we isolate 2D-MOF flakes with areas of hundreds of square microns and an excellent control of the molecular thickness (from single up to ca. 50 layers). The samples exhibit such good photoluminescence and mechanical properties as to allow free-standing characterization of few layers’ flakes.     

Catalytic arylsulfonyl radical-triggered 1,5-enyne-bicyclizations and hydrosulfonylation of α,β-conjugates

A catalytic bicyclization reaction of 1,5-enynes anchored by α,β-conjugates with arylsulfonyl radicals generated in situ from sulfonyl hydrazides has been established using TBAI (20 mol%) and Cu(OAc)₂ (5 mol%) as co-catalysts under convenient conditions. In addition, the use of benzoyl peroxide (BPO) as the oxidant and pivalic acid (PivOH) as an additive was proven to be necessary for this reaction. The reactions occurred through 5-exo-dig/6-endo-trig bicyclizations and homolytic aromatic substitution (HAS) cascade mechanisms to give benzo[b]fluorens regioselectively. A similar catalytic process was developed for the synthesis of γ-ketosulfones. These reactions feature readily accessible starting materials and simple one-pot operation.     

Profluorescent verdazyl radicals – synthesis and characterization

The synthesis and characterization of various 6-oxo-verdazyl radicals and their diamagnetic styryl radical trapping products are presented. It is shown that styryl radical trapping products derived from N-phenyl verdazyls show fluorescence whereas the N-methyl congeners are non-fluorescent. In the parent N-phenyl verdazyls fluorescence is fully quenched which renders these compounds highly valuable profluorescent radical probes.     

“Self-repairing” nanoshell for cell protection

Self-repair is nature''s way of protecting living organisms. However, most single cells are inherently less capable of self-repairing, which greatly limits their wide applications. Here, we present a self-assembly approach to create a nanoshell around the cell surface using nanoporous biohybrid aggregates. The biohybrid shells present self-repairing behaviour, resulting in high activity and extended viability of the encapsulated cells (eukaryotic and prokaryotic cells) in harsh micro-environments, such as under UV radiation, natural toxin invasion, high-light radiation and abrupt pH-value changes. Furthermore, an interaction mechanism is proposed and studied, which is successful to guide design and synthesis of self-repairing biohybrid shells using different bioactive molecules.     

Cooperative molecular recognition of dyes by two bis(β-cyclodextrin)s with aromatic,sulfur-containing,diamine tethers

The molecular binding behavior of two bis(β-cyclodextrin (CD))s, that is, 4,4′-diaminodiphenylsulfone-bridged bis(β-CD) 2 and 4,4′-diaminodiphenyldisulfide-bridged bis(β-CD) 3 with some representative organic dyes, i.e., acridine red (AR), neutral red (NR), ammonium 8-anilino-1-naphthalenesulfonate (ANS), sodium 2-(p-toluidinyl)naphthalenesulfonate (TNS), rhodamine B (RhB), and brilliant green (BG), has been investigated at 25 °C in phosphate buffer (pH 7.20) by ultraviolet, fluorescence and 2D NMR spectroscopy. The fluorescence of ANS, TNS, AR, and NR are enhanced, whereas that of RhB is quenched, by inclusion complexation with both host compounds. The results obtained show bridged bis(β-CD)s 2 and 3 with dye guests give higher complex stability constants (K _S) than those of the native β-CD 1, through cooperative binding of two hydrophobic CD cavities with one guest. In addition, the K _S values of all guests with host 3 are much larger than those with 2 except for NR as guest. The 2D ¹H NOESY spectrum of host 3 and RhB was acquired to confirm the cooperative binding mode. The molecular binding ability of dyes by hosts 1–3 are discussed from the viewpoint of the size and shape-fitting relationship between host and guest.