DNA nanotechnology

Overview of modeling activities in DNA nanotechnologyDNA nanotechnology holds great promise for creating mechanically dynamic and functional nanomachines with potential applications in drug delivery, sensing, soft robotics, and manufacturing. We have recently embarked on a new project on the design of DNA-based nanostructures capable of actuated mechanical motion, in collaboration with Dr. Carlos Castro. Our lab is developing software tools that will allow researchers to build 3D atomistic models of DNA-origami structure designs. We are also developing simulation tools to study the molecular-scale dynamics of these DNA nanostructures, which will then be used for optimizing the design parameters. Last but not least, we are developing mesoscopic and statistical-mechanical models to investigate the long-time dynamics of these structures including self-assembly and actuation (Fig. 10).

Equilibrium angles and the size of their fluctuations obtained from modeling versus experimentsOne of our first projects was on investigating the conformational dynamics of mechanically-compliant devices using coarse-grained molecular dynamics simulations. In particular, we studied a set of tunable DNA-origami hinges designed and synthesized by the Carlos lab, whereby the angle subtended by the hinge arms can be tuned by varying the length of the single-stranded DNA connections. Our results showed that oxDNA--a recently developed coarse-grained model of DNA--could accurately reproduce the experimentally measured equilibrium angles between hinge arms, and their fluctuations, for a range of hinge designs (Fig. 11).

A force-balance approach for rapidly predicting hinge equilibrium anglesThe simulations also revealed important insights into various properties of the hinges that are challenging to obtain experimentally, such as the local stability of their hybridized portions, conformations of their single- and double-stranded components, their global or principal motions, and differences in their bending mechanisms with respect to design parameters. We also introduced a novel approach for rapidly predicting the equilibrium angles of the hinges based on individual force-deformation characteristics of their components, namely the single-stranded springs and the double-stranded bare hinge (Fig. 12).