Gap site-specific rapid formation of fluorescent silver nanoclusters for label-free DNA nucleobase recognition

Silver nanoclusters (Ag NCs) templated with DNAs have attracted much attention as novel fluorophores because of their convenient emission tunability by the sequence and length of the template DNAs. However, the precise production of Ag NCs in a site-specific manner still remains a challenge to attain highly selective and label-free DNA recognition. Here we exploited the availability of a gap site in DNA duplexes as a new scaffold for the synthesis of Ag NCs. Compared to the commonly used DNA templates for the creation of Ag NCs, the gap site in DNA duplexes was found to facilitate the rapid formation of the fluorescent Ag NCs without sacrifice of their bright emission and excellent stability. We found that fluorescent Ag NCs were highly selectively formed when cytosine faced toward the gap site in DNA duplexes, and they were in situ utilized as readout by signal-on manner for the DNA mutation assays. This base-selective growth of the fluorescent Ag NCs at the gap site would find promising applications in practical detection of single nucleotide polymorphism (SNP) and construction of DNA-based functional sensors with label-free and cost-effective merits.

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► A gap site in DNA duplex is exploited as a new scaffold for the rapid synthesis of Ag NCs.
► Fluorescent Ag NCs are highly selectively formed when cytosine faced toward the gap site in DNA duplexes, and they could be utilized as readout with signal-on signaling for DNA single nucleotide polymorphism.
► This base-selective growth of the fluorescent Ag NCs at the gap site would find promising applications in label-free and cost-effective designs of DNA-based functional sensors.