We study the dynamics of single bonds through the surface enhanced Raman scattering (SERS) from single SERS-marker molecules containing a distinctive single alkyl bond. Assembly of the nanogaps and positioning of single molecules inside the electromagnetic hotspot is precisely controlled using DNA origami constructs. The observed SERS intensities, their spectral wandering, together with electromagnetic simulations, all confirm the role of picocavities in this nanogap geometry in allowing observation of SERS signatures from individual vibrating bonds. The strong electromagnetic field around each picocavity and the transient binding of the SERS-marker molecule reveals significant modifications to bond vibrations and selection rules over time.