Design, Simulation, and Experimental Demonstration of Self-Assembled DNA Nanostructures and DNA Motors

Self-assembly is the spontaneous self-ordering of substructures into superstructures driven by the selective aÆnity of the substructures. DNA provides a molecular scale material for programmable self-assembly, using the selective aÆnity of pairs of DNA strands to form DNA nanostructures. DNA self-assembly is the most advanced and versatile system that has been experimentally demonstrated for programmable construction of patterned systems on the molecular scale. The methodology of DNA self-assembly begins with the synthesis of singlestrand DNA molecules that self-assemble into macromolecular building blocks called DNA tiles. These tiles have sticky ends that match the sticky ends of other DNA tiles, facilitating further assembly into larger structures known as DNA tiling lattices. In principle, DNA tiling assemblies can form any computable two or three-dimensional pattern, however complex, with the appropriate choice of the tiles component DNA. Recent experimental results indicate that this technique is scalable and molecular imaging devices such as atomic force microscopes and transmission electron microscopes allow visualization of self-assembled two-dimensional DNA tiling lattices composed of hundreds of thousands of tiles. These assemblies can be used as sca olding on which to position molecular electronics and robotics components with precision and speci city. This programmability renders the sca olding the patterning required for fabricating complex devices made of these components. We overview the evolution of DNA self-assembly techniques from pure theory, through design and simulation, and then to experimental practice. We will begin with an overview of theoretical models and algorithms for DNA lattice self-assembly. Then we describe our software for the design, simulation and optimization of DNA tiling assemblies and DNA robotics. As an example, we brie y discuss models and algorithms for the key problem of error control in DNA lattice self-assembly, as well as the computer simulation of these methods for error control. We will then brie y discuss our experimental laboratory demonstrations, including those using the designs derived by our software. These experimental demonstrations of DNA self-assemblies include the assembly of patterned objects at the molecular scale, the execution of molecular computations, and freely running autonomous DNA motors.