Design, Simulation, and Experimental Demonstration of Selfassembled DNA Nanostructures and.pdf

Design, Simulation, and Experimental Demonstration of Self-assembled DNA Nanostructures and Motors John H. Reif, Thomas H. LaBean, Sudheer Sahu, Hao Yan, and Peng Yin Department of Computer Science, Duke University, Box 90129, Durham, NC 27708-0129, USA {reif, thl, sudheer, hy1, py}@cs.duke.edu Abstract. Self-assembly is the spontaneous self-ordering of substructures into superstructures, driven by the selective affinity of the substructures. Comple- mentarity of DNA bases renders DNA an ideal material for programmable self- assembly of nanostructures. DNA self-assembly is the most advanced and ver- satile system that has been experimentally demonstrated for programmable con- struction of patterned systems on the molecular scale. The methodology of DNA self-assembly begins with the synthesis of single strand DNA molecules that self-assemble into macromolecular building blocks called DNA tiles. These tiles have single strand “sticky ends” that complement 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. Two-dimensional DNA tiling lattices composed of hun- dreds of thousands of tiles have been demonstrated experimentally. These assem- blies can be used as programmable scaffolding to position molecular electronics and robotics components with precision and specificity, facilitating fabrication of complex nanoscale devices. We overview the evolution of DNA self-assembly te