Engineered Regulon to Enable Autonomous Azide Ion Biosensing, Recombinant Protein Production, and in Vivo Glycoengineering

Detection of azide-tagged biomolecules (e.g., azido sugars) inside living cells using "click" chemistry has been revolutionary to the field of chemical biology. However, we currently still lack suitable synthetic biology tools to autonomously and rapidly detect azide ions. Here, we have developed an engineered synthetic promoter system called cyn regulon, and complementary Escherichia coli engineered strains, to selectively detect azide ions and autonomously induce downstream expression of reporter genes. The engineered cyn azide operon allowed highly tunable reporter green fluorescent protein (GFP) expression over three orders of inducer azide ion concentrations (0.01-5 mM) and rapidly induced GFP expression by over 600-fold compared to the uninduced control. Next, we showcase the superior performance of this engineered cyn-operon over the classical lac-operon for recombinant protein production. Finally, we highlight how this synthetic biology toolkit can enable glycoengineering-based applications by facilitating in vivo activity screening of mutant carbohydrate-active enzymes (CAZymes), called glycosynthases, using azido sugars as donor substrates.

Cu(I)-I-2,4-diaminopyrimidine Coordination Polymers with Optoelectronic Properties as a Proof of Concept for Solar Cells

Two coordination polymers with formulas [CuI(dapym)]_n and [Cu₂I₂(dapym)]_n (dapym = 2,4-diaminopyrimidine) have been synthesized in water at room temperature. According to the stoichiometry used, mono (1D) and the two-dimensional (2D) structures can be obtained. Both are made up of Cu₂I₂ double chains. Their high insolubility in the reaction medium also makes it possible to obtain them on a nanometric scale. Their structural flexibility and short Cu-Cu distances provoke interesting optoelectronic properties and respond to physical stimuli such as pressure and temperature, making them interesting for sensor applications. The experimental and theoretical studies allow us to propose different emission mechanisms with different behaviors despite containing the same organic ligand. These behaviors are attributed to their structural differences. The emission spectra versus pressure and temperature suggest competencies between different transitions, founding critical Cu₂I₂ environments, i.e., symmetric in the 1D compound and asymmetric for the 2D one. The intensity in the 2D compound's emission increases with decreasing temperature, and this behavior can be rationalized with a structural constriction that decreases the Cu-Cu and Cu-I distances. However, compound 1D exhibits a contrary behavior that may be related to a change of the organic ligand's molecular configuration. These changes imply that a more significant Π-Π interaction counteracts the contraction in distances and angles when the temperature decreased. Also, the experimental conductivity measurements and theoretical calculations show a semiconductor behavior. The absorption of the 1D compound in UV, its intense emission at room temperature, and the reduction to nanometric size have allowed us to combine it homogeneously with ethyl vinyl acetate (EVA), creating a new composite material. The external quantum efficiency of this material in a Si photovoltaic mini-module has shown that this compound is an active species with application in solar cells since it can move the photons of the incident radiation (UV region) to longer wavelengths.

A unique benzimidazole-naphthalene hybrid molecule for independent detection of Zn2+ and N3- ions: Experimental and theoretical investigations

Single crystal X-ray structurally characterized benzimidazole-naphthalene hybrid (NABI) functions as a unique dual analyte sensor that can detect Zn²⁺ cation and N₃^- anion independently. The NABI forms chelate with Zn²⁺ to inhibit internal charge transfer (ICT) and CHN isomerisation resulting chelation enhanced fluorescence (CHEF). On the other hand, the sensing of N₃^- is based on formation of supramolecular H-bonded rigid assembly. The association constant of NABI for Zn²⁺ and N₃^- ions are 19 × 10⁴ M^-1 and 11 × 10² M^-1, respectively. Corresponding limit of detections (LOD) are 6.85 × 10^-8 and 1.82 × 10^-7 M, respectively. NABI efficiently detects intracellular Zn²⁺ and N₃^- ions with no cytotoxicity on J774A.1cells under fluorescence microscope. DFT studies unlock underlying spectroscopic properties of free NABI and Zn²⁺/N₃^- bound forms.

Pyrrole- and Naphthobipyrrole-Strapped Calix[4]pyrroles as Azide Anion Receptors

The binding interactions between the azide anion (N₃^-) and the strapped calix[4]pyrroles 2 and 3 bearing auxiliary hydrogen bonding donors on the bridging moieties, as well as of normal calix[4]pyrrole 1, were investigated via ¹H NMR spectroscopic and isothermal titration calorimetry analyses. The resulting data revealed that receptors 2 and 3 have significantly higher affinities for the azide anion in organic media as compared with the unfunctionalized calix[4]pyrrole 1 and other azide receptors reported to date. Single crystal X-ray diffraction analyses and calculations using density functional theory revealed that receptor 2 binds CsN₃ in two distinct structural forms. As judged from the metric parameters, in the resulting complexes one limiting azide anion resonance contributor is favored over the other, with the specifics depending on the binding mode. In contrast to what is seen for 2, receptor 3 forms a CsN₃ complex in 20% CD₃OD in CDCl₃, wherein the azide anion is bound only vertically to the NH protons of the calix[4]pyrrole and the cesium cation is complexed within the cone shaped-calix[4]pyrrole bowl. The bound cesium cation is also in close proximity to a naphthobipyrrole subunit present in a different molecule, forming an apparent cation-π complex.

Modulating the DNA cleavage ability of copper(ii) Schiff bases through ternary complex formation

Copper(ii) Schiff-bases were electrochemically synthesized and characterized. The presence of co-ligands such as 2,2′-bpy or phen in the metal coordination environment increases the DNA cleavage efficiency.

A curcumin derived probe for colorimetric detection of azide ions in water

A curcumin based probe (CUC-P) having an active alkyne moiety has been synthesised for selective detection of azide (N₃⁻) ions in aqueous medium.

A metal-free turn-on fluorescent probe for the fast and sensitive detection of inorganic azides

Sodium azide is toxic and widely used in agricultural, commercial products, and research laboratories. Thus it is of a significant environmental concern and there is a need for the development of a rapid detection method. A fluorogenic dibenzylcyclooctyne derivative (Fl-DIBO) is herein described as a fluorescent probe for the rapid detection of inorganic azide via Strain-Promoted Azide-Alkyne Cycloaddition (SPAAC). Fl-DIBO was found to be highly selective toward NaN3 in comparison to other common anions with good sensitivity and detection limit of 10μM.

Pattern-Based Detection of Anion Pollutants in Water with DNA Polyfluorophores

Many existing irrigation, industrial and chemical storage sites are currently introducing hazardous anions into groundwater, making the monitoring of such sites a high priority. Detecting and quantifying anions in water samples typically requires complex instrumentation, adding cost and delaying analysis. Here we address these challenges by development of an optical molecular method to detect and discriminate a broad range of anionic contaminants with DNA-based fluorescent sensors. A library of 1296 tetrameric-length oligodeoxyfluorosides (ODFs) composed of metal ligand and fluorescence modulating monomers was constructed with a DNA synthesizer on PEG-polystyrene microbeads. These oligomers on beads were incubated with YIII or ZnII ions to provide affinity and responsiveness to anions. Seventeen anions were screened with the library under an epifluorescence microscope, ultimately yielding eight chemosensors that could discriminate 250 μM solutions of all 17 anions in buffered water using their patterns of response. This sensor set was able to identify two unknown anion samples from ten closely-responding anions and could also function quantitatively, determining unknown concentrations of anions such as cyanide (as low as 1 mM) and selenate (as low as 50 μM). Further studies with calibration curves established detection limits of selected anions including thiocyanate (detection limit ~300 μM) and arsenate (~800 μM). The results demonstrate DNA-like fluorescent chemosensors as versatile tools for optically analyzing environmentally hazardous anions in aqueous environments.

Synthesis, characterization, TDDFT calculation and biological activity of tetradentate ligand based square pyramidal Cu(ii) complexes

Fluorescent Cu(ii) compounds have been synthesized, and characterized by structure analyses and DFT/TD-DFT calculations. Compounds show catecholase and anticancer activities.

Effect of metal oxidation state on FRET: a Cu(i) silent but selectively Cu(ii) responsive fluorescent reporter and its bioimaging applications

A new structurally characterized cell permeable rhodamine-cinnamaldehyde hybrid (HL) behaves as a Cu(ii) ions selective chemosensor through FRET process which depends on +2 state of copper ion exclusively.

CB[8] gated photochromism of a diarylethene derivative containing thiazole orange groups

Photochromism in a diarylethene derivative (1O) can be gated by a host–guest interaction where the thiazole orange groups are bound into the hydrophobic cavity of CB[8] in water.

Selective and sensitive turn-on chemosensor for Al(iii) ions applicable in living organisms: nanomolar detection in aqueous medium

A new crystallographically characterized non-cytotoxic CHEF based highly sensitive Al(iii) ion selective chemosensor (L) is useful to detect the Al(iii) ions' distribution in A549 cell lines and also able to sense Al(iii) ions in tea extract.

Two types of nitrito support for μ4-oxido-bridged [Cu4] complexes: synthesis, crystal structures, magnetic properties and DFT analysis

In situ generated NO₂⁻ and externally added NO₂⁻ and AcO⁻ ions have been utilized for the isolation of μ₄-oxido-bridged Cu₄ aggregates showing magnetic coupling which can be rationalized by DFT calculations.

Single molecular multianalyte signaling of sulfide and azide ions by a nitrobenzoxadiazole-based probe

Sulfide- and azide-selective multianalyte optical signaling using nitrobenzoxadiazole-pivalate was realized by regioselective cleavage of the probe under the same conditions.

A dual-responsive “turn-on” bifunctional receptor: a chemosensor for Fe3+ and chemodosimeter for Hg2+

Synthesis and characterization of L1–L3 along with their selective detection toward Fe³⁺ and Hg²⁺ at ppb level, exhibiting bifunctional behaviour have been presented.

A napthelene–pyrazol conjugate: Al(iii) ion-selective blue shifting chemosensor applicable as biomarker in aqueous solution

A new crystallographically characterized napthelene–pyrazol conjugate acts as an Al(III) ion selective chemosensor in 100 mM HEPES buffer (water–DMSO 5 : 1, v/v) at biological pH. It is an efficient biomarker in detecting Al(III) ions in living cells.

A FRET-based ‘off–on’ molecular switch: an effective design strategy for the selective detection of nanomolar Al3+ ions in aqueous media

A FRET-based ratiometric chemosensor (L1) is highly selective for Al³⁺ ions (as low as 6.19 × 10⁻⁹ M) and could be used to acquire images of Al³⁺ ions in living cells.

A quinazoline derivative as quick-response red-shifted reporter for nanomolar Al3+and applicable to living cell staining

A newly designed and structurally characterized non-cytotoxic quinazoline based ratiometric chemosensor (L) selectively detects Al³⁺ions upto 1.48 nM through ICT and CHEF processes in water–DMSO (9 : 1, v/v) and it is also applicable in living cell staining.

Development of a rhodamine–benzimidazol hybrid derivative as a novel FRET based chemosensor selective for trace level water

A newly designed FRET-based rhodamine–benzimidazol hybrid molecule has been developed as a dual channel chemosensor for the detection of trace level water in both protic and aprotic organic solvents.

Twin applications of highly selective Cu2+ fluorescent chemosensor and cytotoxicity of 2-(2-phenylhydrazono)-1H-indene-1,3(2H)-dione and 2-(2-(4-methoxyphenyl)hydrazono)-1H-indene-1,3(2H)-dione: molecular docking and DFT studies

Turn on chemosensor for paramagnetic Cu²⁺ have been developed based on indene 1,3-dione. Their ability to inhibit KB cell, molecular docking and DFT studies also carried out.

A water soluble FRET-based ratiometric chemosensor for Hg(ii) and S2−applicable in living cell staining

A new water soluble rhodamine-based ratiometric dual ‘off–on–off’ probe can selectively detect Hg²⁺ions in ppb level through time dependent FRET process with reversibility in presence of S²⁻anions.

Chromogenic and fluorogenic chemosensors and reagents for anions. A comprehensive review of the years 2010-2011

This review focuses on examples reported in the years 2010-2011 dealing with the design of chromogenic and fluorogenic chemosensors or reagents for anions.

A water soluble Al3+ selective colorimetric and fluorescent turn-on chemosensor and its application in living cell imaging

An efficient water soluble fluorescent Al(3+) receptor, 1-[[(2-furanylmethyl)imino]methyl]-2-naphthol (1-H) was synthesized and characterized by physico-chemical and spectroscopic tools along with single crystal X-ray crystallography. High selectivity and affinity of 1-H towards Al(3+) in HEPES buffer (DMSO/water: 1/100) of pH 7.4 at 25 °C showed it to be suitable for detection of intracellular Al(3+) by fluorescence microscopy. Metal ions, viz. alkali (Na(+), K(+)), alkaline earth (Mg(2+), Ca(2+)), and transition-metal ions (Ni(2+), Zn(2+), Cd(2+), Co(2+), Cu(2+), Fe(3+), Cr(3+/6+), Hg(2+)) and Pb(2+), Ag(+) did not interfere. The lowest detection limit for Al(3+) was calculated to be 6.03 × 10(-7) M in 100 mM HEPES buffer (DMSO/water: 1/100). Theoretical calculations have also been included in support of the configuration of the probe-aluminium complex.

A ratiometric fluorescent chemosensor for iron: discrimination of Fe2+ and Fe3+ and living cell application

A newly designed probe, 6-thiophen-2-yl-5,6-dihydrobenzo[4,5]imidazo-[1,2-c] quinazoline (HL(1)) behaves as a highly selective ratiometric fluorescent sensor for Fe(2+) at pH 4.0-5.0 and Fe(3+) at pH 6.5-8.0 in acetonitrile-HEPES buffer (1/4) (v/v) medium. A decrease in fluorescence at 412 nm and increase in fluorescence at 472 nm with an isoemissive point at 436 nm with the addition of Fe(2+) salt solution is due to the formation of mononuclear Fe(2+) complex [Fe(II)(HL)(ClO(4))(2)(CH(3)CN)(2)] (1) in acetonitrile-HEPES buffer (100 mM, 1/4, v/v) at pH 4.5 and a decrease in fluorescence at 412 nm and increase in fluorescence at 482 nm with an isoemissive point at 445 nm during titration by Fe(3+) salt due to the formation of binary Fe(3+) complex, [Fe(III)(L)(2)(ClO(4))(H(2)O)] (2) with co-solvent at biological pH 7.4 have been established. Binding constants (K(a)) in the solution state were calculated to be 3.88 × 10(5) M(-1) for Fe(2+) and 0.21 × 10(3) M(-1/2) for Fe(3+) and ratiometric detection limits for Fe(2+) and Fe(3+) were found to be 2.0 μM and 3.5 μM, respectively. The probe is a "naked eye" chemosensor for two states of iron. Theoretical calculations were studied to establish the configurations of probe-iron complexes. The sensor is efficient for detecting Fe(3+)in vitro by developing a good image of the biological organelles.