SERS molecular-ruler based DNA aptamer single-molecule and its application to multi-level optical storage

Abstract Real-time analysis of DNA aptamer conformational changes is essential to understanding the function of DNA aptamers at the single-molecular level. Herein, we design core-satellite nanostructures as surface-enhanced Raman scattering (SERS) molecular-rulers to monitor the change process of single Hg2+ aptamer under dark-field microscopy (DFM-) correlated Raman spectroscopy. Applying the SERS molecular-ruler, the individual Hg2+ aptamer conformational change events triggered by Hg2+ that leads to the stepwise closing of the satellite to the core is continuously monitored by changes in SERS intensity. Moreover, individual Hg2+ aptamer conformational change events are confirmed by in-situ scanning electron microscopy (SEM) and finite difference time-domain (FDTD) calculation. Furthermore, the SERS molecular-ruler is a valid method for studying aptamer intermediate states, the binding sites in aptamer and the kinetics of Hg2+ aptamer configuration change at the single-molecule level. Such findings are promising for exploring the mechanism of DNA aptamer configuration change and providing the fundamental understanding for designing various DNA aptamer based biological applications. For future applications, SERS molecular-ruler has the potential to realize multi-level optical storage and presents a new practical and effective method for designing multi-level storage system.