Probing Local Folding Allows for Robust Metal Sensing based on a Na+-specific DNAzyme.

Fluorescent metal sensors based on DNA often rely on changes in end-to-end distance or local environmental near fluorophore labels. Since metal ions can also non-specifically interact with DNA via various mechanisms such as charge screening, base binding, and increase or decrease duplex stability, robust and specific sensing of metal ions has been quite challenging. In this work, we performed a side-by-side comparison of two signaling strategies on a Na+-specific DNAzyme that contained a Na+ binding aptamer. The duplex regions of the DNAzyme was systematically shortened and its effect was studied using a 2-aminopurine (2AP) labeled substrate strand. Na+ binding affected the local environmental of the 2AP label and increased its fluorescence. We observed a synergistic process of Na+ binding and forming the duplex on the 5´-end of the enzyme strand, and this end is close to the aptamer loop. Effective Na+ binding was achieved with a 5 base pair stem. The effect on the 3´-end is more continuous, and the stem needs to form first before Na+ can bind. With an optimized substrate binding arm, a FRET-based sensor is designed by labeling the two ends of a cis-form of the DNAzyme with two fluorophores. In this case, Na+ failed to show a distinct difference from Li+ or K+ indicating probing local environment change allows more robust sensing of metal ions.