DFT study of dye complexes with cucurbit[7]uril and DNA: Structural, energetic, and spectroscopic insights

Fluorescent dyes are a diverse class of compounds that can absorb light at specific wavelengths and emit light at longer wavelengths. They are essential for bioimaging, protein labeling, and industrial tracking, as they enable researchers to visualize structures and processes that would otherwise remain invisible. Fluorescent dyes used for nucleic acid detection generally interact strongly with DNA/RNA via non-covalent binding modes such as intercalation, groove association, and electrostatic attraction to the phosphate backbone. On the other hand, dyes can also participate in interactions with macrocyclic molecules, such as cucurbit[ n ]urils (CB[ n ]s), which may significantly influence their spectroscopic behavior and binding properties. The formation of dye-CB complexes may affect the stability and optical properties of the dyes. In the present study, the interactions of several DNA-binding dyes—Ethidium Bromide, SYBR Green I, SYBR Green II, SYBR Safe, SYBR Gold, and EvaGreen—with DNA fragments and the host molecule cucurbit[7]uril (CB[7]) were investigated using Density Functional Theory (DFT) and time-dependent DFT (TD-DFT) calculations. Both dye–CB[7] complexes and DNA–dye–CB[7] ternary systems were examined. The calculations indicate that the inclusion of the dyes within the CB[7] cavity depends on the structural and electronic characteristics of the dyes. TD-DFT calculations were employed to simulate the UV–Vis absorption spectra of both free and complexed dyes. These findings provide molecular-level insight into the recognition process between fluorescent dyes, CB[7], and DNA, and highlight the ability of macrocyclic hosts to modulate the photophysical behavior of the investigated systems.