Algorithmic Self-Assembly of DNA
- E. Winfree
- Materials Science
- 9 May 2006
Summary form only given. Nucleic acids have proven to be remarkably versatile as an engineering material for chemical tasks including the storage of information, catalyzing reactions creating and…
The program-size complexity of self-assembled squares (extended abstract)
A formal model of pseudocrystalline self-assembly, called the Tile Assembly Model, in which a tile may be added to the growing object when the total interaction strength with its neighbors exceeds a parameter Τ is studied, which finds a dramatic decrease in complexity.
DNA as a universal substrate for chemical kinetics
- D. Soloveichik, G. Seelig, E. Winfree
- ChemistryProceedings of the National Academy of Sciences
- 6 October 2009
It is shown that systems of DNA molecules can be constructed that closely approximate the dynamic behavior of arbitrary systems of coupled chemical reactions, by using strand displacement reactions as a primitive, and systems implementing feedback digital logic and algorithmic behavior are illustrated.
Design and self-assembly of two-dimensional DNA crystals
The design and observation of two-dimensional crystalline forms of DNA that self-assemble from synthetic DNA double-crossover molecules that create specific periodic patterns on the nanometre scale are reported.
Control of DNA strand displacement kinetics using toehold exchange.
This work improves the understanding of the kinetics of nucleic acid reactions and will be useful in the rational design of dynamic DNA and RNA circuits and nanodevices.
Complexity of Self-Assembled Shapes
It is shown that under the notion of a shape that is independent of scale this is indeed so: in the Tile Assembly Model, the minimal number of distinct tile types necessary to self-assemble an arbitrarily scaled shape can be bounded both above and below in terms of the shape's Kolmogorov complexity.
Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades
This work experimentally demonstrated several digital logic circuits, culminating in a four-bit square-root circuit that comprises 130 DNA strands, which enables fast and reliable function in large circuits with roughly constant switching time and linear signal propagation delays.
Proofreading Tile Sets: Error Correction for Algorithmic Self-Assembly
It is shown that an improved construction can in principle exploit the cooperativity of tile assembly reactions to dramatically improve the scaling behavior to r ≈ βe and better, suggesting that existing DNA-based molecular tile approaches may be improved to produce macroscopic algorithmic crystals with few errors.
Algorithmic Self-Assembly of DNA Sierpinski Triangles
This work reports 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.
Enzyme-Free Nucleic Acid Logic Circuits
The design and experimental implementation of DNA-based digital logic circuits using single-stranded nucleic acids as inputs and outputs are reported, suggesting applications in biotechnology and bioengineering.