Spectroscopic Characterization of Thiazole Orange-3 DNA Interaction

Cellular Visualization of G-Quadruplex RNA via Fluorescence- Lifetime Imaging Microscopy

Over the past decade, appreciation of the roles of G-quadruplex (G4) structures in cellular regulation and maintenance has rapidly grown, making the establishment of robust methods to visualize G4s increasingly important. Fluorescent probes are commonly used for G4 detection in vitro; however, achieving sufficient selectivity to detect G4s in a dense and structurally diverse cellular environment is challenging. The use of fluorescent probes for G4 detection is further complicated by variations of probe uptake into cells, which may affect fluorescence intensity independently of G4 abundance. In this work, we report an alternative small-molecule approach to visualize G4s that does not rely on fluorescence intensity switch-on and, thus, does not require the use of molecules with exclusive G4 binding selectivity. Specifically, we have developed a novel thiazole orange derivative, TOR-G4, that exhibits a unique fluorescence lifetime when bound to G4s compared to other structures, allowing G4 binding to be sensitively distinguished from non-G4 binding, independent of the local probe concentration. Furthermore, TOR-G4 primarily colocalizes with RNA in the cytoplasm and nucleoli of cells, making it the first lifetime-based probe validated for exploring the emerging roles of RNA G4s in cellulo.

Trimethine cyanine dyes as deep-red fluorescent indicators with high selectivity to the internal loop of the bacterial A-site RNA

We report that TO-PRO-3 functions as a deep-red fluorescent indicator for the internal loop structure of the bacterial (Escherichia coli) A-site, which enables the assessment of A-site binding capability of various test compounds including blue and even-green-emitting compounds.

Novel Naphthalimide Derivatives as Selective G-Quadruplex DNA Binders

A new derivate of 4-bromo-1,8-naphthalic anhydride and its quaternized analogue have been prepared and characterized. The interactions of both derivatives with human telomere quadruplex-DNA and ds-DNA have been comparatively studied by UV-visible (UV-Vis), fluorescent intercalator displacement assays, competition dialysis, circular dichroism (CD), agarose gel electrophoresis, and polyacrylamide gel electrophoresis. The results show that both derivatives can stabilize G-quadruplexes DNA, and they show different binding affinities for G-quadruplexes-DNA and ds-DNA. All spectroscopic studies have shown that the derivatives have a modest selectivity for G-quadruplex versus ds-DNA.

Partial intercalative binding of the food colorant erythrosine to herring sperm DNA

Erythrosine partially inserts into the G–C rich region of hsDNA and induces moderate conformational perturbation of the DNA.

Spectroscopic studies on the interaction between tetrandrine and two serum albumins by chemometrics methods

The binding interactions of tetrandrine (TETD) with bovine serum albumin (BSA) and human serum albumin (HSA) have been investigated by spectroscopic methods. These experimental data were further analyzed using multivariate curve resolution-alternating least squares (MCR-ALS) method, and the concentration profiles and pure spectra for three species (BSA/HSA, TETD and TETD-BSA/HSA) existed in the interaction procedure, as well as, the apparent equilibrium constants Kapp were evaluated. The binding sites number n and the binding constants K were obtained at various temperatures. The binding distance between TETD and BSA/HSA was 1.455/1.451nm. The site markers competitive experiments indicated that TETD primarily bound to the tryptophan residue of BSA/HSA within site I. The thermodynamic parameters (ΔG, ΔH and ΔS) calculated on the basis of different temperatures revealed that the binding of TETD-BSA was mainly depended on the hydrophobic interaction strongly and electrostatic interaction, and yet the binding of TETD-HSA was strongly relied on the hydrophobic interaction. The results of synchronous fluorescence, 3D fluorescence and FT-IR spectra show that the conformation of proteins has altered in the presence of TETD. In addition, the effect of some common ions on the binding constants between TETD and proteins were also discussed.

Probe design for the effective fluorescence imaging of intracellular RNA

Over the past two decades, the spatiotemporal analysis of fluorescently labeled single RNA species has provided a broad insight into the synthesis, localization, degradation, and transport of RNA. To elucidate the dynamic behavior of functional RNAs in living cells, researchers throughout the world have proposed numerous fluorometric strategies for intracellular RNA imaging. Because, like most other biological molecules, RNA is intrinsically nonfluorescent, the development of methods for the labeling of RNAs of interest with fluorescent molecules is essential. Several artificial tag sequences have been attached onto the 3' end of target RNAs and used as scaffolds for interacting with their fluorescent counterparts. In this Personal Account, we focus on the methods that have been developed to show how RNAs expressed in cells can be labeled and visualized by fluorescent proteins, small molecules, or nucleic acids. Each of these methods is designed to increase the sensitivity and specificity for imaging or to decrease the background fluorescence.

ECHO probes: a concept of fluorescence control for practical nucleic acid sensing

An excitonic interaction caused by the H-aggregation of fluorescent dyes is a new type of useful photophysical process for fluorescence-controlled nucleic acid sensing. This critical review points out the recent advances in exciton-controlled hybridization-sensitive fluorescent oligonucleotide (ECHO) probes, which have a fluorescence-labeled nucleotide in which two molecules of thiazole orange or its derivatives are linked covalently. ECHO probes show absorption shift and emission switching depending on hybridization with the target nucleic acid. The hybridization-sensitive fluorescence emission of ECHO probes and the further modification of probes have made possible a variety of practical applications, such as multicolor RNA imaging in living cells and facile detection of gene polymorphism (144 references).

Thiazole orange-induced c-di-GMP quadruplex formation facilitates a simple fluorescent detection of this ubiquitous biofilm regulating molecule

Recently, there has been an explosion of research activities in the cyclic dinucleotides field. Cyclic dinucleotides, such as c-di-GMP and c-di-AMP, have been shown to regulate bacterial virulence and biofilm formation. c-di-GMP can exist in different aggregate forms, and it has been demonstrated that the polymorphism of c-di-GMP is influenced by the nature of cation that is present in solution. In previous work, polymorphism of c-di-GMP could only be demonstrated at hundreds of micromolar concentrations of the dinucleotide, and it has been a matter of debate if polymorphism of c-di-GMP exists under in vivo conditions. In this Article, we demonstrate that c-di-GMP can form G-quadruplexes at low micromolar concentrations when aromatic molecules such as thiazole orange template the quadruplex formation. We then use this property of aromatic molecule-induced G-quadruplex formation of c-di-GMP to design a thiazole orange-based fluorescent detection of this important signaling molecule. We determine, using this thiazole orange assay on a crude bacterial cell lysate, that WspR D70E (a constitutively activated diguanylate cyclase) is functional in vivo when overexpressed in E. Coli . The intracellular concentration of c-di-GMP in an E. Coli cell that is overexpressed with WspR D70E is very high and can reach 2.92 mM.

Interference with spectrophotometric analysis of nucleic acids and proteins by leaching of chemicals from plastic tubes

Absorbance spectroscopy is routinely used to monitor the concentrations of nucleic acids and proteins within solutions and to assess changes in their structure caused by interaction with chemicals or other biomolecules. Biological samples used for such analyses are manipulated and stored in small microcentrifuge tubes (microtubes) composed of polypropylene plus several plastic additives. Here we demonstrate that normal handling of laboratory microtubes causes leaching of light-absorbing chemicals into biological samples that interfere with spectrophotometric measurements. The leached chromophores absorbed UV light strongly at 220 and 260 nm, which are the wavelengths normally used to detect and quantitate proteins and DNA. Some common laboratory techniques, including sonication and PCR, were particularly effective inducers of leaching. The magnitude of the increase in absorbance was dependent upon both exposure time and heat history, with greatest induction after tubes were warmed to temperatures at or above 37 degrees C. Mass spectrometry revealed that aqueous solutions stored in plastic microtubes accumulate a complex mixture of leached chemicals with molecular masses of 200-1400 Da. Leaching was ubiquitous among commercially available brands of microtubes, indicating a persistent source of error in biomolecule detection and concentration measurements.

Photophysical properties of N-alkylated azahelicene derivatives as DNA intercalators: counterion effects

In this work, three compounds having the same organic moiety (N-methyl-5-azahelicenium salts) but different counterions (I-, NO3- and COOCF3-) have been investigated in buffered aqueous solutions and in the presence of DNA to give information on the counterion effects on the binding. In particular, the absorption spectra, fluorescence quantum yields and fluorescence lifetimes in aqueous solution for free organic molecules have been determined by steady-state and time-resolved spectrofluorimetric measurements. The obtained values are compared with those of the chromophores in the presence of increasing concentrations of DNA. The results allow determination of the association constants (K(a)) and the number of base couples per chromophore molecule (n) by means of the McGhee Von Hippel model. The binding parameters are strongly affected by the nature of counterions since the highest K(a) value was determined for the compound having COOCF3-; on the other hand the NO3- derivative is able to interact with the highest number of binding sites. The morphology and structural properties of the DNA-chromophore complexes were investigated by circular dichroism (CD) and atomic force microscopy (AFM). The data revealed that I- and COOCF3- derivatives preferentially form intercalation complexes, while the NO3- salt is able to form intercalation and grove binding complexes at the same time.