Methods for Small-Angle Scattering Measurements on Peptiplexes of DNA with Cell-Penetrating Peptides

Peptiplexes are soft biomaterials formed through the noncovalent association between cell-penetrating peptides and nucleic acids. Although internalization often involves electrostatic anchoring followed by endocytosis, the mode of action of these transporters remains elusive in many cases, and proper understanding of mechanisms behind their penetrating capabilities necessarily entails structural data at the nanoscopic scale. In this chapter, we examine the structural landscape of peptiplexes, emphasizing the complex behavior of these polyelectrolyte self-assemblies and how supramolecular order impacts their translocation efficiency. We discuss experimental tools commonly used to investigate the structure of peptiplexes and pay special attention to small-angle X-ray scattering (SAXS) as a suitable method for unveiling their nanoscale organization. A roadmap for standard SAXS measurements in CPP/DNA samples is presented alongside a selection of observations from our own experience dealing with SAXS applied to the investigation of CPPs.