Thiazole Orange Dimers in DNA: Fluorescent Base Substitutions with Hybridization Readout

Real-time Imaging of Nascent DNA in Live Cells by Monitoring the Fluorescence Lifetime of DNA-Incorporated Thiazole Orange-Modified Nucleotides

A modified 2'-deoxycytidine triphosphate derivative (dCTO TP) bearing a thiazole orange moiety tethered via an oligoethylene glycol linker was designed and synthesized. The nucleotide was incorporated into DNA by DNA polymerases in vitro as well as in live cells. Upon incorporation of dCTO TP into DNA, the thiazole orange moiety exhibited a fluorescence lifetime that differed significantly from the non-incorporated (i.e. free and non-covalently intercalated) forms of dCTO TP. When dCTO TP was delivered into live U-2 OS cells using a synthetic nucleoside triphosphate transporter, it allowed us to distinguish and monitor cells that were actively synthesizing DNA in real time, from the very first moments after the treatment. We anticipate that this probe could be used to study chromatin organization and dynamics.

A novel photoreactive DNA-binding dye for detecting viable Klebsiella pneumoniae in powdered infant formula

In addition to Cronobacter spp., Klebsiella pneumoniae is another opportunistic bacterial pathogen present in powdered infant formula (PIF) that can cause pneumonia, septicemia, and other diseases. In this study, a rapid and specific method based on a fluorescence probe was developed for detecting viable K. pneumoniae in PIF samples via the combination of recombinase-aided amplification (RAA) with thiazole orange monoazide (TOMA) dye (the TOMA-RAA assay hereafter). As a novel photosensitive DNA-intercalating dye, TOMA was used to penetrate bacterial cells, including both dead and viable cells, as verified by confocal laser scanning microscopy and fluorescent emission spectrometry. Importantly, the RAA assay exhibited good performance in detecting K. pneumoniae within 40 min at 39°C. Under optimal conditions, the TOMA-RAA assay can detect as low as 2.6 × 10³ cfu/mL of K. pneumoniae in pure culture and 2.3 × 10⁴ cfu/g of K. pneumoniae in spiked PIF sample. After 3 h of pre-enrichment, 3 × 10⁰ cfu/g of K. pneumoniae can be detected. Furthermore, the TOMA-RAA assay displayed an excellent anti-interference ability to nontarget bacteria. In short, the proposed method has great potential application for the rapid and accurate detection of viable K. pneumoniae in PIF.

Tuning exciton coupling of merocyanine nucleoside dimers by RNA, DNA and GNA double helix conformations

Exciton coupling between two or more chromophores in a specific environment is a key mechanism associated with color tuning and modulation of absorption energies. This concept is well exemplified by natural photosynthetic proteins, and can also be achieved in synthetic nucleic acid nanostructures. Here we report the coupling of barbituric acid merocyanine (BAM) nucleoside analogues and show that exciton coupling can be tuned by the double helix conformation. BAM is a nucleobase mimic that was incorporated in the phosphodiester backbone of RNA, DNA and GNA oligonucleotides. Duplexes with different backbone constitutions and geometries afforded different mutual dye arrangements, leading to distinct optical signatures due to competing modes of chromophore organization via electrostatic, dipolar, π–π‐stacking and hydrogen‐bonding interactions. The realized supramolecular motifs include hydrogen‐bonded BAM–adenine base pairs and antiparallel as well as rotationally stacked BAM dimer aggregates with distinct absorption, CD and fluorescence properties.

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.

Stacked Thiazole Orange Dyes in DNA Capable of Switching Emissive Behavior in Response to Structural Transitions

Functional nucleic acids with the capability of generating fluorescence in response to hybridization events, microenvironment or structural changes are valuable as structural probes and chemical sensors. We now demonstrate the enzyme-assisted preparation of nucleic acids possessing multiple thiazole orange (TO) dyes and their fluorescent behavior, that show a spectral change from the typical monomer emission to the excimer-type red-shifted emission. We found that the fluorescent response and emission wavelength of the TO dyes were dependent on both the state of the DNA structure (single- or double-stranded DNA) and the arrangement of the TO dyes. We showed that the fluorescent behavior of the TO dyes can be applied for the detection of RNA molecules, suggesting that our approach for preparing the fluorescent nucleic acids functionalized with multiple TO dyes could be useful to design a fluorescence bioimaging and detection technique of biomolecules.

Nucleotide-Bearing Benzylidene-Tetrahydroxanthylium Near-IR Fluorophore for Sensing DNA Replication, Secondary Structures and Interactions

Thymidine triphosphate bearing benzylidene‐tetrahydroxanthylium near‐IR fluorophore linked to the 5‐methyl group via triazole was synthesized through the CuAAC reaction and was used for polymerase synthesis of labelled DNA probes. The fluorophore lights up upon incorporation to DNA (up to 348‐times) presumably due to interactions in major groove and the fluorescence further increases in the single‐stranded oligonucleotide. The labelled dsDNA senses binding of small molecules and proteins by a strong decrease of fluorescence. The nucleotide was used as a light‐up building block in real‐time PCR for detection of SARS‐CoV‐2 virus.

Design of thiazole orange oligonucleotide probes for detection of DNA and RNA by fluorescence and duplex melting

We have synthesised a range of thiazole orange (TO) functionalised oligonucleotides for nucleic acid detection in which TO is attached to the nucleobase or sugar of thymidine. The properties of duplexes between TO-probes and their DNA and RNA targets strongly depend on the length of the linker between TO and the oligonucleotide, the position of attachment of TO to the nucleotide (major or minor groove) and the mode of attachment of thiazole orange (via benzothiazole or quinoline moiety). This information can be used to design probes for detection of target nucleic acids by fluorescence or duplex melting. With cellular imaging in mind we show that 2'-OMe RNA probes with TO at the 5-position of uracil or the 2'-position of the ribose sugar are particularly effective, exhibiting up to 44-fold fluorescence enhancement against DNA and RNA, and high duplex stability. Excellent mismatch discrimination is achieved when the mispaired base is located adjacent to the TO-modified nucleotide rather than opposite to it. The simple design, ease of synthesis and favourable properties of these TO probes suggest applications in fluorescent imaging of DNA and RNA in a cellular context.

Modular design for fluorophore homodimer probes using diethylentriamine as a common spacer

Cationic fluorophore homodimer probes 1 and 2 bearing 7-aminocoumarin and naphthalimide dyes, respectively, connected via diethylenetriamine (DETA) spacer, have been developed to demonstrate the validity of our modular probe design on the basis of the triamine-based spacer.

A light-up probe targeting for Bcl-2 2345 G-quadruplex DNA with carbazole TO

As its significant role, the selective recognition of G-quadruplex with specific structures and functions is important in biological and medicinal chemistry. Carbazole derivatives have been reported as a kind of fluorescent probe with many excellent optical properties. In the present study, the fluorescence of the dye (carbazole TO) increased almost 70 fold in the presence of bcl-2 2345 G4 compared to that alone in aqueous buffer condition with almost no fluorescence and 10-30 fold than those in the presence of other DNAs. The binding study results by activity inhibition of G4/Hemin peroxidase experiment, NMR titration and molecular docking simulation showed the high affinity and selectivity to bcl-2 2345 G4 arises from its end-stacking interaction with G-quartet. It is said that a facile approach with excellent sensitive, good selectivity and quick response for bcl-2 2345 G-quadruplex was developed and may be used for antitumor recognition or antitumor agents.

Rationalisation of a mechanism for sensing single point variants in target DNA using anthracene-tagged base discriminating probes

The fluorescence sensing mechanism for identifying single base changes in target DNA strands has been established through detailed biophysical measurements.

Halogen-containing thiazole orange analogues - new fluorogenic DNA stains

Novel asymmetric monomeric monomethine cyanine dyes 5a–d, which are analogues of the commercial dsDNA fluorescence binder thiazole orange (TO), have been synthesized. The synthesis was achieved by using a simple, efficient and environmetally benign synthetic procedure to obtain these cationic dyes in good to excellent yields. Interactions of the new derivatives of TO with dsDNA have been investigated by absorption and fluorescence spectroscopy. The longest wavelength absorption bands in the UV–vis spectra of the target compounds are in the range of 509–519 nm and these are characterized by high molar absorptivities (63000–91480 L·mol⁻¹·cm⁻¹). All investigated dyes from the series are either not fluorescent or their fluorescence is quite low, but they become strongly fluorescent after binding to dsDNA. The influence of the substituents attached to the chromophores was investigated by combination of spectroscopic (UV–vis and fluorescence spectroscopy) and theoretical (DFT and TDDFT calculations) methods.

Photoresponsive Electrodes Modified with DNA Duplexes Possessing a Porphyrin Dimer

This work describes the formation of a porphyrin (Por) dimer using a DNA duplex as a scaffold and photocurrent generation from electrodes modified with a monolayer of Por-DNA conjugates. The solid-phase click reaction between an azide-porphyrin and oligonucleotide labeled with an ethynyl group on CPG support was utilized to conjugate the Por to the DNA. UV/Vis absorption and circular dichroism (CD) spectral studies revealed that the Por dimer can be formed through DNA hybridization and that through-space electronic interactions, characterized from the exciton-coupled absorption and the bisignate CD, can occur between the two Por molecules. Photoelectrochemical experiments were performed for the electrodes functionalized with a monolayer composed of the Por-DNA conjugates. It was found that the Por dimer on the electrode, which was designed to resemble the special pair in natural photosynthesis, shows efficient photocurrent generation in the presence of electron-acceptor reagents compared with the Por monomer. These findings strongly support the idea that the DNA structures could be useful to construct Por arrays, which is essential for the design of photo- and bio-electronic devices.