Fluorogenic chemosensors for double-stranded DNA: Structure-performance relationships and bioanalytical applications

Domahidy, Farkas and Kovács, Ervin (2026) Fluorogenic chemosensors for double-stranded DNA: Structure-performance relationships and bioanalytical applications. TRENDS IN ANALYTICAL CHEMISTRY, 203. No. 119019. ISSN 0165-9936

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Abstract

Fluorogenic DNA chemosensors are indispensable tools in modern bioanalytical chemistry, enabling sensitive nucleic acid detection in molecular diagnostics, fluorescent imaging, PCR monitoring, and emerging point-of-care platforms. Since in most DNA sensor molecules the fluorophore itself is also responsible for molecular recognition, their development requires the simultaneous optimization of binding affinity and selectivity, as well as spectral properties, fluorogenic response, and photostability, alongside further application-specific requirements. This review surveys the various fluorophores used as turn-on sensors for double-stranded DNA, summarizes their photophysical and DNA-binding properties, and lays out their typical applications. Since some of these fluorophores have been extensively optimised to fit the demands of different application areas, we aim to explore the structure-property relationships that govern analytical performance by affecting DNA binding and the excited-state dynamics behind environment-sensitive fluorescence. The review further highlights current trends towards near-infrared-emissive probes, two-photon-active dyes, super-resolution imaging agents, and modular fluorogenic sensors with independently tunable targeting and fluorophore units. Finally, we aim to outline current challenges towards clinically relevant DNA sensing platforms.

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