Metal ions triggered ligase activity for rolling circle amplification and its application in molecular logic gate operations

Supramolecular structures composed of padlock probes and primers were used to perform rolling circle amplification (RCA) which was achieved by metal ion (Hg2+ or Ag+) induced DNA ligase activity. In the presence of Hg2+ (or Ag+), the specific and strong interaction between thymidine–thymidine and Hg2+ (or cytosine–cytosine and Ag+) at the terminal of the padlock probe enabled the circularization of the padlock probe with primer in the aid of DNA ligase. An RCA process was then accomplished by DNA polymerase/dNTPs. The RCA product containing multiple tandem repeats could hybridize with a large number of molecular beacons (reporter), resulting in an enhanced fluorescence signal. This proposed single-input YES gate enabled the sensitive and selective detection of Hg2+ (or Ag+). Additionally, based on the principle of DNA hybridization and displacement, a NOT logic gate was constructed by designing a double-stranded fluorescence probe as reporter. Significantly, this assay was further applied to the construction of a complete set of two-input molecular-scale logic gates and three advanced logic devices.