Sequence programmed DNA three-way junctions for templated assembly of fluorescent silver nanoclusters

Abstract

Fluorescent silver nanoclusters (AgNCs) templated by DNA are promising label free fluorophores with excellent photostability and tunable optical properties. Most of the reported DNA-nanocluster fluorescent tags comprise of programmed strands for the cluster formation either on the edges as overhangs or as loops on the duplex strands. Herein, we report a design strategy for sequence programmed, DNA three-way junctions (DNA-3WJ), comprising of unhybridized cytosine nucleobases in the 3WJ-center, capable of binding to silver ions and stabilizing the AgNCs. The formation of AgNCs in these DNA-3WJs were confirmed by various spectroscopic and microscopic techniques. 3WJ20-C12 comprising of 12 cytosine bases in the center of the DNA-3WJ, form fluorescent nanoclusters with an emission maximum around 630 nm and 12% fluorescence quantum yield. Control DNA-3WJs with six cytosine bases in the center (3WJ20-C6) and ones without cytosine bases (3WJ20) failed to form fluorescent AgNCs confirming the requirement of central, unhybridized cytosine bases for the stabilization of the nanoclusters. Further, the duplex arms of DNA-3WJs were shown to influence the fluorescent properties of AgNCs by varying the size and stability of the cytosine-loop structure of DNA-3WJs. Metal ion interaction studies shows the selectivity of the 3WJ20-C12/AgNCs towards Hg2+ with sensitivity in the nanomolar range.