UC Riverside

The structures of nucleic acids play crucial roles in biological functions but are challenging to rapidly identify and classify. Our study demonstrates the effectiveness of an arrayed suite of synthetic hosts and dyes in detecting and distinguishing various DNA secondary structures. By utilizing multivariate analysis of fluorescence profiles which were generated from cationic dyes with affinities for both DNA and synthetic hosts, discrimination between G-quadruplex structures of identical length and similar topological types, i.e., parallel, antiparallel, and hybrid, is achieved. The host:guest sensor array enables the classification of diverse noncanonical DNA structures, including G-quadruplexes, Hoogsteen triplexes, hairpins, and i-motifs with high selectivity, as well as differentiation between native G-quadruplexes and those with a vacancy or bulge. Machine learning algorithms applied to the sensing data allow for accurate prediction of unknown DNA folding states. Furthermore, the sensor array can detect single oxidation or methylation modifications in one guanine base of G-quadruplexes, even in diluted serum, which provides a powerful tool for identifying structural changes caused by DNA damage. In addition, the host:guest complexes can function for “turn-on” or “turn-off” indicator displacement sensing of neurotransmitter analogs in cellular environments. The dyes selectively accumulate in nucleotide-rich regions of the cell nucleus and cytoplasm. The hosts bind the dyes and promote their relocation to the outer cell membrane. Incubating the cells with structurally similar biomarkers illustrates the selective recognition—choline and butyrylcholine can be bound by the hosts, but minimal binding is seen with betaine or cholamine. Overall, our study highlights the capability of supramolecular host:guest systems for the recognition of nucleic acid secondary structures and offers promising applications in cellular sensing.