Comparing transient oligonucleotide hybridization kinetics using DNA-PAINT and optoplasmonic single-molecule sensing on gold nanorods

Abstract

We report a comparison of two photonic techniques for single-molecule sensing: fluorescence nanoscopy and optoplasmonic sensing. As the test system, oligonucleotides with and without fluorescent labels are transiently hybridized to complementary “docking” strands attached to gold nanorods. Comparing the measured single-molecule kinetics helps to examine the influence of the fluorescent labels as well as factors arising from different sensing geometries. Our results demonstrate that DNA dissociation is not significantly altered by the fluorescent labels and that DNA association is affected by geometric factors in the two techniques. These findings open the door to exploiting plasmonic sensing and fluorescence nanoscopy in a complementary fashion, which will aid in building more powerful sensors and uncovering the intricate effects that influence the behavior of single molecules.