Ensemble-Based Coarse-Grained Molecular Dynamics Simulations of Multifunctional DNA Nanopores

Transmembrane pores are highly specialised nano-devices, with intrinsic specificity and gate-keeping properties that can be exploited in the field of nanobiotechnology. Recently, DNA-origami inspired transmembrane pores with tailorable surface chemistry and programmable dimensions have been rationally designed in an effort to overcome the limitations of protein-based membrane pores such as their fixed lumen size and limited structural repertoire. Ongoing experimental research into the potential applications of triethylene glycol-cholesterol DNA nanopores (DNPs) has been fruitful, with a particular emphasis on drug delivery and biosensing. In this thesis, I describe an ensemble-based coarse-grained MD protocol devised to probe the interactions between bilayer lipids and DNPs, and to determine the effect of membrane encapsulation and salt concentration on the dynamics, structure and conductance of these nanopores. Furthermore, I aim to elucidate the mechanisms by which DNPs mediate translocation of small molecules across lipid bilayers, and the energetics associated with these mechanisms with constant-velocity steered MD and umbrella sampling simulations. I have found that the DNP has no distinct lumen in bulk solution, where it adopts a bloated, amorphous structure with strained and constricted termini regardless of the salt conditions, with significant kinking and fraying of helices. However, salt conditions have a profound effect on the structure of a DNP as it spans a planar lipid bilayer, where it assumes a barrel-like structure with a defined lumen. Sites of constriction in the lumen of the membrane-spanning DNP present a significant barrier to translocation of fluorophores bearing dense negative charges