Design, simulation, and experimental demonstration of self-assembled DNA nanostructures and motors

John H. Reif, Thomas H. LaBean, Sudheer Sahu, Hao Yan, Peng Yin

Research output: Chapter in Book/Report/Conference proceedingConference contribution

12 Scopus citations

Abstract

Self-assembly is the spontaneous self-ordering of substructures into superstructures, driven by the selective affinity of the substructures. Complementarity of DNA bases renders DNA an ideal material for programmable self-assembly of 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 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 hundreds of thousands of tiles have been demonstrated experimentally. These assemblies 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 techniques from pure theory, through simulation and design, and then to experimental practice. In particular, we begin with an overview of theoretical models and algorithms for DNA lattice self-assembly. Then we describe our software for the simulation and design of DNA tiling assemblies and DNA nano-mechanical devices. As an example, we discuss models, algorithms, and computer simulations for the key problem of error control in DNA lattice self-assembly. We then briefly discuss our laboratory demonstrations of DNA lattices and motors, including those using the designs aided 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 the autonomous DNA walking and computing devices.

Original languageEnglish (US)
Title of host publicationLecture Notes in Computer Science
EditorsJ.-P. Banatre, P. Fradet, J.-L. Giavitto, O. Michel
Pages173-187
Number of pages15
Volume3566
StatePublished - 2005
Externally publishedYes
EventInternational Workshop on Unconventional Programming Paradigms, UPP 2004 - Le Mont Saint Michel, France
Duration: Sep 15 2004Sep 17 2004

Other

OtherInternational Workshop on Unconventional Programming Paradigms, UPP 2004
CountryFrance
CityLe Mont Saint Michel
Period9/15/049/17/04

ASJC Scopus subject areas

  • Computer Science (miscellaneous)

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  • Cite this

    Reif, J. H., LaBean, T. H., Sahu, S., Yan, H., & Yin, P. (2005). Design, simulation, and experimental demonstration of self-assembled DNA nanostructures and motors. In J-P. Banatre, P. Fradet, J-L. Giavitto, & O. Michel (Eds.), Lecture Notes in Computer Science (Vol. 3566, pp. 173-187)