Since hybrid DNA-Agn clusters and their photophysical properties were discovered, their use in nanotechnology, as potential LED devices, even in medicine as specific biosensors o biological markers, has grown radically. Even though great advances have been made towards the understanding of the processes that govern the photophysics of these systems, their fine structure, still unknown, plays a fundamental role in direction to a rational design for using in other application fields. In this sense, infrared-spectroscopy in He droplets as well as ion-mobility mass-spectrometry, coupled with infrared spectroscopy, are suitable techniques towers this goal.