A Multiplexable Plasmonic Hairpin-DNA Sensor Based On Target-specific Tether Dynamics

The need for measurements of multiple biomarkers simultaneously at subnanomolar concentrations asks for the development of new sensors with high sensitivity, specificity, precision, and accuracy. Currently, multiplexed sensing in single molecule sensors increases the complexity of the system in terms of reagents and sample read-out. In this letter, we propose a novel approach to multiplex hairpin-based single-DNA molecule sensors, which overcomes the limitations of the present approaches for multiplexing. By target-dependent ssDNA hairpin design, we can create DNA tethers that have distinct tether dynamics upon target binding. Our numerical model shows that by changing the stem length of the ssDNA hairpin, significantly different dynamic tether behavior will be observed. By exploiting the distance-dependent coupling of AuNPs to gold films, we can probe this dynamic behavior along the z-axis using a simple laser equipped microscope.