Ricerc@Sapienza

Blunt-end stacking interactions are weak attractions between the ends of double-stranded DNA helices that terminate with a base-pair. This type of interaction, which is actually a complex interaction that depends on several noncovalent forces, is one of the two most important contributions to the overall DNA double helix thermodynamic stability together with the Watson-Crick base pairing. In fact, the stacking between adjacent base-pairs is the dominant interaction, while the pairing between complementary bases primarily confers specificity to DNA duplex. In the research area of DNA lyotropic liquid crystals, the base stacking and in particular the blunt-end stacking interaction, was hypothesized to be an essential ingredient that governs the unusual bulk phase behaviour in concentrated aqueous solutions of ultrashort double stranded DNA fragments. In addition, the same stacking attraction was suggested as a key mechanism in the formation and stability of a novel smectic liquid crystal phase in concentrated aqueous suspensions of blunt-ended all-DNA chain-stick constructs (gapped DNA duplexes), with the molecules attaining a folded conformation in this layered mesophase. Moreover, more complex DNA based nanostructures can be designed and synthesized by exploiting DNA stacking and pairing. For example, rectangular-shaped DNA nanostructures (also known as DNA tiles or DNA nanobricks) containing several interwinded DNA helices can be easily built. Within this project, inspired by the aforementioned DNA aggregates, we want to design and study, both numerically and experimentally, new DNA based nanostructures, which form novel liquid crystal phases. On one hand, our study will provide new insight into the physical mechanism behind the formation of DNA macromolecules and, on the other hand, the novel DNA-based mesophases will offer many opportunities in nanotechnological applications due to their biocompatibility.