We extend the scope of nanometer distance measurements based on coupled pairs of gold nanoparticles, or plasmon rulers, to individual RNA molecules. These sensors were used to monitor the influence of spermidine on the cleavage kinetics of RNA by ribonuclease A. Time-resolved cleavage experiments of individual RNA plasmon rulers reveal transiently stabilized RNA sub-populations at increased spermidine concentrations that indicate spermidine-induced stabilization of weak secondary and tertiary structural elements.