Sensitive Fluorescent Determination of Nucleic Acids by a Cytosine-Rich Loop and Silver Nanoclusters in the Hybridization Chain Reaction (HCR)

Deep understanding of the effect of DNA sequence and structure on the fluorescent properties of DNA-templated silver nanoclusters (DNA-Ag NCs) affords alternative strategies for developing and exploiting DNA biosensors. DNA secondary structures (e.g., DNA loop) are essential for generating highly emissive DNA-Ag NCs. In this study, a cytosine-rich DNA loop was used as a facile template for the formation of silver nanoclusters. The fluorescence of silver nanocluster encapsulated within a cytosine-rich DNA loop was turned on by switching the size of the loop from large to small. Target nucleic acid served as the trigger for the hybridization chain reaction of hairpin probe 1 (H1) containing an inactivated cytosine-rich DNA loop with a large size at the ends and hairpin probe 2 (H2). Long-nicked double helices were obtained coupled with the opening of the large-size cytosine-rich DNA loop in H1 and switching to an activated cytosine-rich DNA loop with a small size. As a result, an increase in the fluorescent signal was observed. A sensitive detection limit of 10 pM and a linear detection range from 10 pM to 400 nM were obtained for nucleic acid determination. This facile assay provides a new approach capable of switching the fluorescence emission of DNA-Ag NCs for nucleic acid biosensing.