Chapter

DNA Computing

Volume 2943 of the series Lecture Notes in Computer Science pp 108-125

One Dimensional Boundaries for DNA Tile Self-Assembly

  • Rebecca SchulmanAffiliated withComputer Science and Computation & Neural Systems, California Institute of Technology
  • , Shaun LeeAffiliated withComputer Science and Computation & Neural Systems, California Institute of Technology
  • , Nick PapadakisAffiliated withComputer Science and Computation & Neural Systems, California Institute of Technology
  • , Erik WinfreeAffiliated withComputer Science and Computation & Neural Systems, California Institute of Technology

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Abstract

In this paper we report the design and synthesis of DNA molecules (referred to as DNA tiles) with specific binding interactions that guide self-assembly to make one-dimensional assemblies shaped as lines, V’s and X’s. These DNA tile assemblies have been visualized by atomic force microscopy. The highly-variable distribution of shapes – e.g., the length of the arms of X-shaped assemblies – gives us insight into how the assembly process is occurring. Using stochastic models that simulate addition and dissociation of each type of DNA tile, as well as simplified models that more cleanly examine the generic phenomena, we dissect the contribution of accretion vs aggregation, reversible vs irreversible and seeded vs unseeded assumptions for describing the growth processes. The results suggest strategies for controlling self-assembly to make more uniformly-shaped assemblies.