Circuits and programmable self-assembling DNA structures

Self-assembly is beginning to be seen as a practical vehicle for computation. We investigate how basic ideas on tiling can be applied to the assembly and evaluation of circuits. We suggest that these procedures can be realized on the molecular scale through the medium of self-assembled DNA tiles. One layer of self-assembled DNA tiles will be used as the program or circuit that leads to the computation of a particular Boolean expression. This layer templates the assembly of tiles, and their associations then lead to the actual evaluation involving the input data. We describe DNA motifs that can be used for this purpose; we show how the template layer can be programmed, in much the way that a general-purpose computer can run programs for a variety of applications. The molecular system that we describe is fundamentally a pair of two-dimensional layers, but it seems possible to extend this system to multiple layers.

[1]  Michael Sipser,et al.  Introduction to the Theory of Computation , 1996, SIGA.

[2]  N. Seeman,et al.  A robust DNA mechanical device controlled by hybridization topology , 2002, Nature.

[3]  C. T. Leondes.  Proceedings of the symposium on mathematical theory of Automata , 1964 .

[4]  N. Seeman,et al.  Design and self-assembly of two-dimensional DNA crystals , 1998, Nature.

[5]  J. Reif,et al.  Logical computation using algorithmic self-assembly of DNA triple-crossover molecules , 2000, Nature.

[6]  David Harlan Wood,et al.  DNA Based Computers III , 1999 .

[7]  N. Seeman,et al.  Modifying the Surface Features of Two-Dimensional DNA Crystals , 1999 .

[8]  N C Seeman,et al.  Atomic force microscopy of parallel DNA branched junction arrays. , 2000, Chemistry & biology.

[9]  Eitan M. Gurari,et al.  Introduction to the theory of computation , 1989 .

[10]  P W Rothemund,et al.  Using lateral capillary forces to compute by self-assembly , 2000, Proc. Natl. Acad. Sci. USA.

[11]  A. Turberfield,et al.  A DNA-fuelled molecular machine made of DNA , 2022 .

[12]  Michael J. Heller,et al.  Photoelectrophoretic Transport and Hybridization of DNA Oligonucleotides on Unpatterned Silicon Substrates , 2000 .

[13]  M. Wigler,et al.  Complex synthetic chemical libraries indexed with molecular tags. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[14]  J. Reif,et al.  Construction, analysis, ligation, and self-assembly of DNA triple crossover complexes , 2000 .

[15]  N. Seeman.  Nucleic acid junctions and lattices. , 1982, Journal of theoretical biology.

[16]  N. Seeman,et al.  Designed Two-Dimensional DNA Holliday Junction Arrays Visualized by Atomic Force Microscopy , 1999 .