Rational design of DNA-based nanodevices controlled by allosteric mechanisms

DNA Nanotechnology employs nucleic acids (DNA and RNA) as non-biological engineering nanomaterials rather than as the carriers of genetic information in living cells. This use of nucleic acids is enabled by their strict base pairing rules; in fact thanks to the high specificity and predictability of the Watson-Crick interactions is possible to create rationally engineer stimuli-responsive nanodevices or nanomachines that can be employed for different purposes like drug-delivery, sensing, or diagnostics. The first part of this PhD thesis (chapter 2) is focused on the possibility to mimic the cooperativity and the allosteric control employed by hemoglobin into an engineered DNA-nanodevice. Cooperativity is used by nature to finely control the activity of biomolecular receptors in order to obtain a very sensible response to small changes in ligand concentration (i.e. oxygen for hemoglobin). In the second part of my PhD thesis (chapter 3), I demonstrated a novel and elegant approach to control the affinity of a clamp-like DNA-based receptor that recognizes a specific DNA sequence and an ATPbinding aptamer through the use of intrinsically disordered domains. By exploiting the entropic cost associated with disordered domains I have been able to modulate the activity and binding affinity of my DNA-based nanodevices. The results showed in this PhD thesis represent a further step towards the employment of new possible inputs and control mechanisms to regulate the activation of DNA-based nanomachines.