Figure 3.

Because the E-DNA clamp-switch mechanism is based on the possibility of the probe to fold-back and form a triplex structure, its signal is strongly dependent on the probe surface density. We demonstrate this by fabricating E-DNA clamp-switch sensors of different probe densities by varying the concentration of the DNA clamp-switch probe employed during sensor fabrication and interrogating these sensors with a saturating amount of a complementary target (13-mer, 300 nM). At high probe densities, the triplex formation is so unfavored that we only observe a signal decrease (consistent with formation of the sole duplex DNA). As the probe surface density decreases below a critical value of 10^–11 mol/cm², the spacing between the probes increases enough to allow them to fold-back and form the triplex structure (signal-on behavior).