Plasmon rulers as a probe for real-time microsecond conformational dynamics of single molecules

Biopolymers such as DNA, RNA, and proteins exploit conformational changes to modulate their function. Although state-of-the-art single-molecule approaches enable identification of conformational states, the transition path and metastable intermediates often remain elusive because they occur on microsecond time scales. Here we introduce a method to probe conformational dynamics with microsecond integration times based on a heterodimer of plasmonic particles. By combining Brownian dynamics and electromagnetic simulations, we find that integration times of 1 μs can be routinely achieved, providing the capability to identify short-lived intermediates and transition paths at the single-molecule level in real-time. Importantly, plasmon rulers require no specialized equipment but can be probed on existing fluorescence microscopes equipped with a fast camera. The approach combines the advantages of fluorescent probes (zero-force, parallelization) and mechanical probes such as optical tweezers (continuous microsecond integration times). They offer a unique opportunity to study conformational dynamics and compare measurements to full-atom simulations, where computational demands limit the simulation time.