Promoter G-Quadruplex Binding Styryl Benzothiazolium Derivative for Applications in Ligand Affinity Ranking and as Ethidium Bromide Substitute in Gel Staining

Role of Alkali Cations in DNA-Thioflavin T Interaction

This study investigates the role of alkali cations in modulating the interaction between deoxyribonucleic acid (DNA) and Thioflavin T (ThT) in dilute and condensed phases. The emission characteristics of ThT were analyzed in the presence of double-stranded DNA and G-quadruplex structures with a focus on the effects of four cations: sodium, potassium, calcium, and magnesium. The ThT emission in double-stranded DNA was influenced by direct DNA binding and steric hindrance within the hydration shell of DNA, which was modulated by the presence of alkali cations. Lasing spectroscopy experiments further highlighted ThT sensitivity to the spatial arrangement of water molecules in the DNA hydration shell. Lasing was exclusively observed in the presence of Mg2+ in the G-quadruplex structure, suggesting that the parallel propeller configuration of G4 provides an optimal environment for ThT light amplification. This study highlights the critical role of cations in DNA-dye interactions and reaffirms the significance of ThT in biophysical studies.

Designer tryptophan-rich peptide modulates structural dynamics of HIF-1α DNA i-motif DNA

Cytosine-rich DNA sequences can fold into intercalated motifs known as i-motifs, through noncanonical hydrogen bonding interactions. Molecular probes can provide valuable insights into the conformational stability and potential cellular functions of i-motifs. W5K5, a decapeptide composed of alternating tryptophan (W) and lysine (K) units, has been identified as a lead candidate to modulate the structural dynamics of the hypoxia-inducible factor 1-alpha (HIF-1α) DNA i-motif. This finding is expected to facilitate the rational design of peptide-based probes for studying the structure and functional dynamics of i-motifs.

Preferential Binding of a Red Emissive Julolidine Derivative to a Promoter G-Quadruplex

The therapeutic potential of G-quadruplexes has increased significantly with the growing understanding of their functional roles in pathogens apart from human diseases such as cancer. Here, we report the synthesis of three julolidine-based molecules and their binding to nucleic acids. Among the synthesized molecules, compound 1 exhibited red emissive fluorescence with a distinct preference for Pu22 G-quadruplex. The binding of compound 1 to Pu22 G-quadruplex, initially identified through a fluorescence-based screening, was further confirmed by UV-vis, fluorescence spectroscopy, and circular dichroism-based experiments. Thermal denaturation of compound 1 in the presence of Pu22 G-quadruplex revealed a concentration-dependent stabilization (~10.0 °C at 1 : 3 stoichiometry). Fluorescence-based experiments revealed 1 : 1 stoichiometry of the interaction and an association constant (Ka ) of 5.67×106  M-1 . CD experiments displayed that the parallel conformation of the G-quadruplex was retained on compound 1's binding and signs of higher order binding/complex formation were observed at high compound 1 to DNA ratio. Molecular docking studies revealed the dominance of stacking and van der Waals interactions in the molecular recognition which was aided by some close-distance interactions involving the quinolinium nitrogen atom.

Cavity Lasing Characteristics of Thioflavin T and Thioflavin X in Different Solvents and Their Interaction with DNA for the Controlled Reduction of a Light Amplification Threshold in Solid-State Biofilms

The lasing characteristics of Thioflavin T (ThT) and Thioflavin X (ThX) dyes were investigated in solvents with increasing viscosity: water, ethanol, butanol, ethylene glycol, and glycerol and three forms of DNA (double-helix natural, fragmented, and aggregated). The results identified that lasing thresholds and photostability depend on three critical factors: the solvation shell surrounding dye molecules, the organization of their dipole moments, which is driven by the DNA structure, and the molecules diffusion coefficient in the excitation focal spot. The research highlights that dye doped to DNA accumulated in binding sites fosters long-range dye orientation, facilitating a marked reduction of lasing thresholds in the liquid phase as well as amplified spontaneous emission (ASE) thresholds in the solid state. Leveraging insights from lasing characteristics obtained in liquid, ASE in the solid state was optimized in a controlled way by changing the parameters influencing the DNA structure, i.e., magnesium salt addition, heating, and sonication. The modifications led to a large decrease in the ASE thresholds in the dye-doped DNA films. It was shown that the examination of lasing in cavities can be useful for preparing optical materials with improved architectures and functionalities for solid-state lasers.