Design of an environment-indipendent, tunable 3D DNA-origami plasmonic sensor

DNA origami nanotechnology engineers DNA as the building blocks of newly conceived self-assembled materials and devices. Due to its high degree of customization and its precise spatial addressability, DNA origami provides an unmatched platform for nanoscale structures and devices design. Gold nanoparticles (AuNP) have been largely investigated because of their peculiar optical properties and in particular their localized surface plasmon resonance (LSPR) that modifies significantly the electromagnetic environment in a thin shell around them, and provides a tool with unrivalled potential to tune the local optical properties. The combination of DNA origami frameworks and AuNP into DNA based-plasmonic nanostructures offers a concrete approach for optical properties engineering. It has been successfully applied to design biosensor and to enhance Raman scattering or fluorescence emission. Moreover, it has been exploited to design molecular ruler in which the inter-particle gap is controlled with nanometric precision through the transduction of the conformational changes into univocally detectable optical signals. In this thesis I present my PhD work which aims at the design of an environment-independent AuNP decorated-DNA origami. A tetrahedral DNA shape structure has been selected for its three dimensional robustness and thus a DNA origami prototype has been assembled, characterized with SEM, TEM and AFM to verify the proper folding of the structure. The origami was equipped with an actuator probe which recognizes a specific target oligonucleotide inducing a structural reconfiguration of the tetrahedron. To detect the conformational change triggered by the hybridization event, I functionalized the origami with two gold nanoparticles placed in two opposite facets at a known distance of 10 nm: the change of the interparticle gap is effectively transduced in a LSPR shift. This working principle has been verified with optical extinction measurements and the interparticle distance reduction has been confirmed by SEM imaging and SAXS analysis performed in the SAXS beamline of Elettra Synchrotron, thus confirming that the operation of the device and its transduction mechanism are the same no matter of the external conditions, being them dry, liquid or solid.