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.
Over the last years we deeply investigated DNA stacking and steric interactions with the aim to build realistic but simple coarse-grained models of DNA constructs. Our coarse-grained approach for modelling DNA macromolecules offers the unique possibility of a realistic investigation of their physical properties, such as their phase behavior, while keeping the simulation times at a manageable level. We firmly proved the effectiveness of our approach to provide accurate predictions on these systems and to understand experimental findings. Within this project we want to make a further step forward and design novel models for more complex DNA constructs with the aim to obtain an even richer phase behavior of DNA-based liquid crystals.
Up to few years ago no evidence of a smectic phase in DNA-based liquid crystals was found, hence the territory of DNA-based mesophases is largely unexplored. With this project we want to start investigating these fascinating systems with the aim to gain more control on the phase behavior. The ambitious final outcome of this project would be to acquire the ability of designing DNA macromolecules targeting specific liquid crystal phases under predetermined experimental conditions.
In particular, within this project we will demonstrate that stiff DNA duplexes can self-assemble into different types of a one-dimensional layered smectic phases in aqueous solutions on the basis of hairpin-capped DNA blunt-ends.
We plan to provide conclusive experimental evidence, as well as computer simulations, which will reveal that DNA helices capped on one or both ends with short PolyT loops can form thermodynamically stable bilayer and monolayer smectic-A type of phases, respectively. Our results will also offer a compelling evidence about the role of blunt-end stacking interactions in DNA self assembly, allowing to identify general guidelines for the re-examination of the liquid crystalline phase diagram of short duplex DNA fragments with any length.
About DNA bricks we add to the game more control parameters for the formation of mesophases, such as the number of patches and the biaxiality of the DNA constructs. The presence of more 2 or 4 patches allow the formation of up to 4 bonds per particles, thus enabling the emergence of branched microstructure in the systems. Directed self-assembly of DNA nanobricks offers the exquisite opportunity to build very complex microstructures [21,27] and our study will provide a very convenient way to investigate these assemblies through very efficient computer simulations. It is worth noting that more information can be obtained from computer simulation than experiments. Computer simulations allow a detailed investigation of the microscopic organization of the constituent particles, whose phase behavior is just the macroscopic manifestation.
Finally, our coarse-grained approach is a rather general tool to investigate the physical properties of complex DNA molecules and this project can be also intended as a proof-of-concept of our method.