Transport Properties of Self-Assembled DNA Systems

University Of Illinois At Urbana-Champaign, Urbana IL

Investigators

Abstract

Nontechnical Summary Practical nanotechnology requires precise and inexpensive placement of nanometer-size components into an operational unit. The DNA nanotechnology achieves exactly that by utilizing the self-assembly property of DNA. This project will explore the use of self-assembled DNA materials for controlling the motion of molecules through fluid environment. Computer simulations will elucidate the mechanism of electrical conductivity of self-assembled DNA structures. Nanoscale objects will be designed to function as analogs of electrical wires, pipes and transistors. Mimicking nature, membrane-spanning DNA systems will be developed to regulate the passage of biomolecules across a cell boundary. These research activities will be closely integrated with education and outreach and will provide the rapidly expanding field of DNA nanotechnology with computational methods and tools for theoretical exploration of self-assembled DNA structures. Technical Summary This project aims to characterize the transport properties of self-assembled DNA nanostructures for possible applications in biosensing, nanofluidics, and biomimetic systems. All-atom molecular dynamics simulations will characterize the ionic conductivity of various DNA origami designs and probe their structural integrity in an external electric field. The simulations will explore the behavior of DNA gridirons and DNA bricks structures, and evaluate their usefulness for nanopore sensing applications. Charged and hollow DNA origami constructs will be designed to serve as conduits for ions and small biomolecules in fluid environment, analogous to macroscopic wires and pipes. The structural response of the DNA origami to electric field will be exploited to design and demonstrate a DNA origami transistor. The physical principles of gated and selective biological ion channels will be implemented in membrane-spanning DNA constructs. The theoretical work will be carried out in close collaboration with experimentalists characterizing the transport through self-assembled DNA structures. This project is expected to provide new insights into the physical mechanisms of charged solutes transport in fluid environment, finding practical application in nanopore detection of biomolecules, unconventional computing and synthetic tissue engineering. This research program will have a direct impact on the development of functional DNA nanotechnology by providing the research community with methods and tools to build, visualize and simulate self-assembled DNA systems. The technological knowledge and expertise acquired through this program will be made available through step-by-step tutorials, modules of the popular computer program VMD and as research and educational tools at nanoHUB. Material generated within this project will be used to prepare a set of lectures and demos for the biophysics undergraduate and graduate courses. The project will develop educational DNA origami puzzles and a DNA LEGO constructor kit and will make them available to everyone by taking advantage of the 3D printing technology.