DNA Nanobiosensors: An Outlook on Signal Readout Strategies

Figure 2

Readout strategies for DNA nanostructure-based biosensors. (a) Fluorescence-based readout: the example shown demonstrates the detection of proteins resulting in stem-loop reconfiguration leading to a fluorescent signal [24]. (b) FRET-based readout: The example shows a DNA nanodevice containing a FRET pair on opposite ends of a nicked duplex. The C-rich single-stranded extensions on either end of the duplex can form an i-motif at low pH resulting in a FRET signal [18]. (c) NP-based color change: nanoparticles aggregated via DNA strands and a DNAzyme are blue; presence or addition of Pb²⁺ ions causes cleavage of the DNAzyme resulting in nanoparticle disaggregation and a change in color to red [25]. (d) Electrochemical readout: DNA tetrahedra with single-stranded pendants can bind partially to target DNA. The remainder of the target DNA strand can bind a reporter strand that produces a HRP-based electrochemical readout [26]. (e) Gel electrophoresis: a DNA nanoswitch containing two single-stranded overhangs that are partially complementary to target DNA. Binding of target DNA to the two detectors causes the linear “off” state to change into a looped “on” state. The two states of the nanoswitch migrate differently on a gel, thus providing a digital on-off signal [27]. (f) AFM-based readout: DNA origami levers that contain C-rich single-stranded extensions can act as pH sensors. In acidic pH, the single-stranded extensions on each half of the lever can form an intermolecular i-motif causing a conformational change that can be visualized on an AFM [28]. (g) SERS-based readout: an ATP-binding aptamer is bound to a single-stranded probe on a gold surface. The presence of ATP triggers conformational change of the aptamer causing it to dissociate from the probe, resulting in a loss of the SERS signal [29].

(a)

(b)

(c)

(d)

(e)

(f)

(g)