Halogen-containing thiazole orange analogues - new fluorogenic DNA stains

Rational Design of Hydroxylated Thiazole Orange Photocages for Green Light-Triggered DNA Recombination

The precise control of DNA recombination enables the cell- or time-dependent regulation of gene expression in studies of gene function. Caged estrogen receptor ligands combined with a Cre-ERT2/loxP system are useful tools for light-triggered DNA recombination. However, the photolysis of most caged compounds requires ultraviolet or blue light, which is toxic and displays low tissue penetration. Although a cyanine-based photo-responsive protecting group (PPG) can release estrogen receptor ligands with longer-wavelength light, its low photolytic efficiency requires long illumination times. We developed a caged estrogen receptor ligand with improved green light-responsive PPGs. The rational modification of Hydroxylated Thiazole Orange (HTO) photocages using electron-donating groups (EDGs), such as dimethoxy (DiMeO)-substituted HTO, resulted in high photolytic efficiency (up to ϵΦ ≈320 M-1  cm-1 ). Theoretical calculations demonstrated that the enhanced photolytic efficiencies were derived from the increased intramolecular charge transfer by EDGs upon excitation. The efficient uncaging of estrogen receptor ligands enabled the control of gene recombination in a ligand-dependent Cre-ERT2/loxP system in live cells.

Asymmetric Monomethine Cyanine Dyes with Hydrophobic Functionalities for Fluorescent Intercalator Displacement Assay

A new green procedure has been applied for the synthesis and purification of asymmetric monomethine cyanine dyes. The photophysical properties of the newly synthesized compounds have been examined by combined application of spectroscopic and theoretical methods. The structural characteristics of the molecules and dimer formation were characterized by quantum chemical computation and juxtaposed to the aggregachromism in UV/Vis spectra. The applicability of the dyes as fluorogenic nucleic acid probes has been proven by fluorescence titration, and their binding constants have been calculated. The mode of ligand-dsDNA/RNA interaction was rationalized by means of CD spectroscopy, molecular docking analysis, and fluorescent intercalator displacement experiments.

Functional Cyanine-Based PVA:PVP Polymers as Antimicrobial Tools toward Food and Health-Care Bacterial Infections

The rising of multidrug-resistant bacteria and their associated proliferation as harmful microorganisms boosts the creation of new antibacterial surfaces and biomaterials with applications ranging from health to food packing. Herein, low-cost antibacterial PVA:PVP copolymers containing cyanine derivatives (1, 2, and 3) and their respective Cu²⁺ complexes are successfully obtained and tested against Gram-negative and Gram-positive bacteria. The possible application in food packing is addressed by covering the surface of typical paper mockups with the doped polymers. All dye-doped polymers present a broad-spectrum antibacterial effect against Gram-positive bacteria, especially for Bacillus cereus (B. cereus), Staphylococcus aureus (S. aureus), and methicillin-resistant S. aureus (MRSA) strains, with PVA:PVP@3 and PVA:PVP@3-Cu being the most effective. Moreover, polymers containing cyanine derivatives present interesting inhibition effects against Pseudomonas aeruginosa (P. aeruginosa), where the production of its characteristic blue/green virulent pigment is not observed. Of the coated paper mockups, PVA:PVP:paper@2 and PVA:PVP:paper@2-Cu are most effective against B. cereus and S. aureus, while PVA:PVP:paper@3 and PVA:PVP:paper@3-Cu are most effective against the MRSA strain. In these formulations, direct contact inhibition mechanisms appear to be more significant than diffusional mechanisms, due to cyanine release hindrance, making them very interesting and versatile platforms for medical and food applications.

Styryl Hemicyanine Dye (E)-3-Methyl-2-(4-thiomorpholinostyryl)benzo[d]thiazol-3-ium Iodide for Nucleic Acids and Cell Nucleoli Visualization

(E)-3-Methyl-2-(4-thiomorpholinostyryl)benzo[d]thiazol-3-ium iodide 1 was prepared by a convenient and reliable reaction procedure. The slight molar excess of the starting benzaldehyde and the mixture of ethanol: ethyl acetate in the ratio 3:1 as a solvent afforded a pure reaction product. The photophysical properties of the dye in a TE buffer in the absence and presence of double-stranded DNA (dsDNA) were elucidated. The low intrinsic fluorescence of 1 in TE buffer is followed by an increase in the fluorescence after dsDNA binding. The dye is nontoxic for stem cells from apical papilla and the most concentrated fluorescence is detected in the cell nucleoli.

Photophysics of thiazole orange in deep eutectic solvents

Photophysics and torsional dynamics of thiazole orange (TO) as a function of temperature have been studied in two deep eutectic solvents (DESs) using spectroscopic techniques. Two DESs are used as a solvent namely DES-I (choline chloride + urea, mole ratio 1: 2) and DES-II (N,N diethyl ethanol ammonium chloride + urea, mole ratio 1: 2). We explore the influence of DESs on the photophysical properties of TO. The fluorescence quantum yield and fluorescence lifetime of TO decreases with increasing temperature due to thermal deactivation. At higher temperature, fluorescence quantum yield of TO decreases in DESs may be due to the molecular rotor nature of TO, with the benzothiazole and quinoline ring of this dye being able to be rotated relative to each other in the excited state. In these solvents, the free volume idea was found to provide a truthful report of the solvent viscosity-temperature behavior, and the probe torsional dynamics. Fluorescence lifetime imaging microscopy (FLIM) was used to insight and observed the distribution of lifetime of TO in the surface of both DESs. The contact angle was determined to show the hygroscopic nature of the DESs.

Beyond amyloid proteins: Thioflavin T in nucleic acid recognition

Thioflavin T (ThT) is a commercially available fluorescent dye that is commonly used in biomedical research for over five decades. It was first reported as an extrinsic fluorescent probe for the detection of amyloid fibrils and related processes and it has also been used extensively for assessing protein binding in fluorescence-based assays. Although the nucleic acid binding of ThT was reported half of a century ago in the 1970s, it was not widely explored until the start of this decade. In recent years, Thioflavin T has become a major tool in the recognition of many types of non-canonical nucleic acid conformations including duplexes, triplexes, and G-quadruplexes. The propensity of ThT binding is more towards base aberrations, bulges, and mismatches highlighting its importance in serving as a diagnostic tool in a variety of ailments/disease conditions. In this review, we cover major advancements in nucleic acid detection/binding by ThT to a variety of nucleic acid structures.

Cyanine Dyes Containing Quinoline Moieties: History, Synthesis, Optical Properties, and Applications

Cyanine dyes carrying quinoline moieties are an important class of organic molecules that are of great interest for applications in many fields like medicine, pharmacology, and engineering. Despite their exceptional properties, such as stability, high molar extinction coefficients, and high pH-sensitivity, this class of dyes has been less analyzed and reviewed in the last few decades. Therefore, this review article focuses on discussing the history of quinoline compounds, various synthetic routes to prepare quinolinium salts and symmetrical and asymmetrical mono-, di-, tri-, penta- and heptamethine cyanine dyes, containing quinoline moieties, together with their optical properties and applications as photosensitizers in photodynamic therapy, probes in biomolecules for labeling of nucleic acids, as well as imaging agents.