Design of the Model DNA Probe

To create a hybridized double-stranded DNA (dsDNA) model, 1 μL of 100 μM of 6-carboxyfluorescein (FAM)-tagged ssDNA (Table S1, probe 1), 1 μL of 100 μM of biotin-tagged ssDNA (Table S1, probe 2), 10 μL of 10× isothermal amplification buffer I, and 88 μL of DNase/RNase free water were combined in a small PCR tube. The PCR tube was placed in a thermocycler and run on a protocol of 95 °C for 1 min followed by 25 °C for 1 min, for a total of 20 min. The concentration of the probe was determined using a NanoDrop 2000c (50 ng/μL per 1 OD). The hybridized dsDNA probe was stored at −20 °C until use. Single-stranded DNA (ssDNA) tagged with both FAM and biotin (Table S1, probe 3), provided by IDT, was used as the ssDNA model.