Concentration Imbalance-Driven Nucleotide Circuit for Tick-Borne Encephalitis Virus Detection via Hybridization-Responsive DNA-Templated Silver Nanoclusters

Tick-borne encephalitis virus (TBEV) is a severe neurotropic <i>Flavivirus</i> that requires early and sensitive detection. We developed a concentration imbalance-driven nucleotide circuit (CIDNC) combined with DNA-templated silver nanoclusters (DNA-AgNCs) for enzyme-free and direct RNA detection. The system converts trace TBEV cDNA or RNA into fluorescence signals via strand displacement under isothermal conditions. It achieved detection limits of 0.023 nM for cDNA and 0.035 nM for RNA, with single-base mismatch discrimination. The assay successfully detected viral RNA from plasma and lysed virions. With rapid response (25 min), high recovery (97-98%), and no enzyme requirement, this portable and programmable CIDNC system offers a promising, low-cost diagnostic strategy for TBEV and other RNA viruses, especially in resource-limited settings.