Helical aggregates of bis(styryl) dyes formed by DNA templating

Dual-signal, one-step simultaneous monitoring of genetic mutation in multiple gene regions using Fe3O4@Au and MOF

Genetic testing plays a crucial role in guiding individualized medication, however, detecting fine structural mutations in genes continues to present significant challenges. This study introduces a dual-signal fluorescence system, termed Fe3O4@Au@PEG@P1+MOF@P2, that integrates magnetic separation of Fe3O4@Au with NH2-MIL-88 (MOF) catalysis. Initially, the specimen (T1/T2) facilitated the formation of a specific complex (Fe3O4@Au@PEG@P1+T1/T2) with Fe3O4@Au@PEG@P1. The subsequent addition of Hoechst-33258 produced a robust fluorescence signal at 460 nm, enabling the identification of mutations in the first gene regions. Following this, MOF@P2 was introduced to activate the catalyst through P2 pairing with T2. The complex Fe3O4@Au@PEG@P1+T1/T2+P2+Hoechst-33258 was subsequently isolated using an external magnetic field. Upon adding OPD, fluorescent DAP was detected at 560 nm, allowing for the identification of mutations in the second gene regions. The research demonstrated that the variation in fluorescence signals increased with a higher number of base substitutions and deletion mutations, with deletion mutations resulting in a notably greater alteration rate compared to substitution mutations. Interestingly, triple base substitution mutations, characterized by lower clustering of non-continuous mutations, produced a more pronounced change in fluorescence signal than did a higher clustering of continuous mutations (codon mutations). This single-step methodology effectively differentiates among the number and types of mutations across multiple gene regions while assessing the degree of mutation clustering. Overall, this technology significantly enhances the current capabilities for detecting fine structural mutations in genes. Furthermore, the approach exhibits high sensitivity in detecting concentrations of T1 and T2 ranging from 10-15 M to 10-9 M, with detection limits of 0.19 fM and 0.24 fM, even in 5 % serum samples.

Nucleic Acid-Templated Synthesis of Cationic Styryl Dyes in Vitro and in Living Cells

A novel method for synthesizing cationic styryl dyes through a nucleic acid-templated reaction has been developed. This approach overcomes issues associated with traditional synthesis methods, such as harsh conditions, low throughput, and wasteful chemicals. The presence of a nucleic acid template accelerated the styryl dye formation from quaternized heteroaromatic and cationic aldehyde substrates. These styryl dyes show remarkable optical properties change when bound to nucleic acids, hence the success of the synthesis could be readily monitored in situ by UV-Vis and fluorescence spectroscopy and the optical properties data were also observable at the same time. This method provides the desired products from a broad range of coupling partners. By employing different substrates and templates, it is possible to identify new dyes that can bind to a specific type of nucleic acid such as a G-quadruplex. The templated dye synthesis is also successfully demonstrated in live HeLa cells. This approach is a powerful tool for the rapid synthesis and screening of dyes specific for diverse types of nucleic acids or cellular organelles, facilitating new biological discoveries.

A multipurpose mitochondrial NIR probe for imaging ferroptosis and mitophagy

This paper explores the use of a di-cationic fluorophore for visualizing mitochondria in live cells independent of membrane potential. Through the synthesized di-cationic fluorophore, we investigate the monitoring of viscosity, ferroptosis, stress-induced mitophagy, and lysosomal uptake of damaged mitochondria. The designed fluorophore is based on DQAsomes, cationic vesicles responsible for transporting drugs and DNA to mitochondria. The symmetric fluorophores possess two charge centres separated by an alkyl chain and are distinguished by a pyridinium group for mitochondrial selectivity, the C-12 alkyl substitution for membrane affinity, and an electron donor-π-acceptor fluorescent scaffold for intramolecular charge transfer. The synthesized fluorophores, PP and NP, emit wavelengths exceeding 600 nm, with a significant Stokes shift (130-211 nm), and NP demonstrates near-infrared emission (∼690 nm). Our study underscores the potential of these fluorophores for live-cell imaging, examining physiological responses such as viscosity and ferroptosis, and highlights their utility in investigating mitophagy damage and lysosomal uptake.

DNA-based assemblies with bischromophoric styryl dye-chromene conjugates and cucurbit[7]uril

Novel conjugates consist of 4-styrylpyridinium dye and 2,2-diphenyl-2H-chromene moiety were obtained, and their affinity to double stranded DNA and cucurbit[7]uril was investigated. With a combination of absorption, fluorescence and circular dichroism spectroscopies as well as MALDI-TOF mass spectrometry, we demonstrate that these compounds can interact with macromolecules to form of the supramolecular assemblies due to two suitable binding sites. The ternary complex is formed as a result of the intercalation of a positively charged styryl part between DNA base pairs, while cucurbit[7]uril is located on the alkyl chain between two moieties of conjugate. All these findings provide valuable information into controlling the interaction between organic molecules, DNA and cucurbit[7]uril.

Cationic styryl dyes for DNA labelling and selectivity toward cancer cells and Gram-negative bacteria

Fluorescence-based methods are important tools for the analysis of nucleic acids in vitro and in cells. In this study, two cationic cyanine-styryl derivatives were produced using a two-step synthesis. Their optical properties were evaluated in different solvents, and frontier molecular orbital theory was utilized to interpret the findings. The DNA binding of these molecules was investigated to show fluorescence intensification. The molecular docking of both dyes in DNA illustrated the relevance of the electrostatic interaction between the quaternary ammonium of both dyes and the phosphate of the DNA backbone. Last but not least, applications of the synthesized styryl dyes were demonstrated to be selective towards cancer cells and particular kinds of bacteria.

Fluorescence turn-on probes for intracellular DNA/RNA distribution based on asymmetric bis(styryl) dyes

Two bis(styryl) dyes, varying in type of spacer between two mono(styryl) units, were tested for interactions with ct-DNA or cl-RNA. Both compounds showed strong affinity toward ds-DNA/ss-RNA, the binding mode of the interaction is shifting between DNA groove binding to RNA intercalation. Consequently, interaction with DNA shows a stronger flare-up of fluorescence (151 times for dye 1 and 118 times for dye 2) than when binding with RNA (23 times and 36 times correspondingly). The presence of energy transfer in the bis(styryl) system increases the Stokes shift of the dye, so when irradiating the system in the region of 370-380 nm, fluorescence is detected at 610-620 nm. The biological experiments showed that the efficient intracellular fluorescence quench was observed in the DNase digest test suggested that dyes can be applied by recognition of DNA in the presence of RNA molecules.