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

TL;DR

This study compares DNA hybridization kinetics using fluorescence nanoscopy and optoplasmonic sensing on gold nanorods, revealing how labels and geometry influence single-molecule interactions to improve sensing strategies.

Contribution

It provides a direct comparison of two single-molecule sensing techniques, highlighting the effects of fluorescent labels and geometry on hybridization kinetics.

Findings

DNA dissociation unaffected by fluorescent labels

DNA association influenced by sensing geometry

Potential for combined use of plasmonic and fluorescence sensing

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 fluorescent labels as well as factors arising from different sensing geometries. Our results demonstrate that DNA dissociation is not significantly altered by the fluorescent label, while 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.