Algorithmic self-assembly of DNA Sierpinski triangles.

@article{Rothemund2004, abstract = {Algorithms and information, fundamental to technological and biological organization, are also an essential aspect of many elementary physical phenomena, such as molecular self-assembly. Here we report the molecular realization, using two-dimensional self-assembly of DNA tiles, of a cellular automaton whose update rule computes the binary function XOR and thus fabricates a fractal pattern--a Sierpinski triangle--as it grows. To achieve this, abstract tiles were translated into DNA tiles based on double-crossover motifs. Serving as input for the computation, long single-stranded DNA molecules were used to nucleate growth of tiles into algorithmic crystals. For both of two independent molecular realizations, atomic force microscopy revealed recognizable Sierpinski triangles containing 100-200 correct tiles. Error rates during assembly appear to range from 1\% to 10\%. Although imperfect, the growth of Sierpinski triangles demonstrates all the necessary mechanisms for the molecular implementation of arbitrary cellular automata. This shows that engineered DNA self-assembly can be treated as a Turing-universal biomolecular system, capable of implementing any desired algorithm for computation or construction tasks.}, address = {Computation and Neural Systems, California Institute of Technology, Pasadena, USA.}, author = {Rothemund, P. W. and Papadakis, N. and Winfree, E. }, citeulike-article-id = {176801}, doi = {10.1371/journal.pbio.0020424}, issn = {1545-7885}, journal = {PLoS Biol}, keywords = {origami, origami-alternatives}, month = {December}, number = {12}, posted-at = {2008-05-10 21:07:06}, priority = {2}, title = {Algorithmic self-assembly of DNA Sierpinski triangles.}, url = {http://dx.doi.org/10.1371/journal.pbio.0020424}, volume = {2}, year = {2004} }

TY - JOUR ID - Rothemund2004 L3 - citeulike-article-id:176801 TI - Algorithmic self-assembly of DNA Sierpinski triangles. JF - PLoS Biol VL - 2 IS - 12 AD - Computation and Neural Systems, California Institute of Technology, Pasadena, USA. SN - 1545-7885 N2 - Algorithms and information, fundamental to technological and biological organization, are also an essential aspect of many elementary physical phenomena, such as molecular self-assembly. Here we report the molecular realization, using two-dimensional self-assembly of DNA tiles, of a cellular automaton whose update rule computes the binary function XOR and thus fabricates a fractal pattern--a Sierpinski triangle--as it grows. To achieve this, abstract tiles were translated into DNA tiles based on double-crossover motifs. Serving as input for the computation, long single-stranded DNA molecules were used to nucleate growth of tiles into algorithmic crystals. For both of two independent molecular realizations, atomic force microscopy revealed recognizable Sierpinski triangles containing 100-200 correct tiles. Error rates during assembly appear to range from 1% to 10%. Although imperfect, the growth of Sierpinski triangles demonstrates all the necessary mechanisms for the molecular implementation of arbitrary cellular automata. This shows that engineered DNA self-assembly can be treated as a Turing-universal biomolecular system, capable of implementing any desired algorithm for computation or construction tasks. KW - origami KW - origami-alternatives AU - Rothemund, PW AU - Papadakis, N AU - Winfree, E PY - 2004/12// UR - http://dx.doi.org/10.1371/journal.pbio.0020424 ER -