Anomalous DNA hybridisation kinetics on gold nanorods revealed via a dual single-molecule imaging and optoplasmonic sensing platform

TL;DR

This study introduces a novel dual imaging and sensing platform combining optoplasmonic and DNA-PAINT techniques to analyze DNA hybridisation kinetics on gold nanorods, revealing accumulation of irreversible hybridisation events and new stabilization mechanisms.

Contribution

The paper presents the first integrated setup for simultaneous optoplasmonic and DNA-PAINT detection, enabling direct comparison and new insights into single-molecule hybridisation processes.

Findings

Decreased association rate over time during hybridisation.

Accumulation of irreversible hybridisation events.

Identification of stabilization mechanisms on plasmonic nanoparticles.

Abstract

Observing the hybridisation kinetics of DNA probes immobilised on plasmonic nanoparticles is key in plamon enhanced fluorescence detection from weak emitting species, and refractive index based single-molecule detection on optoplasmonic sensors. The role of the local field in providing plasmonic signal enhancements for single-molecule detection has been studied in great detail. Nevertheless, few studies have compared the experimental results in both techniques for single-molecule studies. Here we developed the first optical setup that integrates optoplasmonic and DNA-PAINT based detection of oligonucleotides to compare these sub-platforms and provide complementary insights into single-molecule processes. We record the fluorescence and optoplasmonic sensor signals for individual, transient hybridisation events. The hybridisation events are observed in the same sample cell and over a prolonged time (i.e. towards high binding site occupancies). A decrease in the association rate over the measurement duration is reported. Our dual optoplasmonic sensing and imaging platform offers insight into the observed phenomenon, revealing that irreversible hybridisation events accumulate over detected step signals in optoplasmonic sensing. Our results point to novel physicochemical mechanisms that result in the stabilisation of DNA hybridisation on optically-excited plasmonic nanoparticles.