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A simple DNA gate motif for synthesizing large-scale circuits.

Qian L, Winfree E - J R Soc Interface (2011)

Bottom Line: The prospects of programming molecular systems to perform complex autonomous tasks have motivated research into the design of synthetic biochemical circuits.To date, circuits involving at most tens of gates have been demonstrated experimentally.Here, we propose a simple DNA gate architecture that appears suitable for practical synthesis of large-scale circuits involving possibly thousands of gates.

View Article: PubMed Central - PubMed

Affiliation: Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA.

ABSTRACT
The prospects of programming molecular systems to perform complex autonomous tasks have motivated research into the design of synthetic biochemical circuits. Of particular interest to us are cell-free nucleic acid systems that exploit non-covalent hybridization and strand displacement reactions to create cascades that implement digital and analogue circuits. To date, circuits involving at most tens of gates have been demonstrated experimentally. Here, we propose a simple DNA gate architecture that appears suitable for practical synthesis of large-scale circuits involving possibly thousands of gates.

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Related in: MedlinePlus

A 74L85 standard 4-bit magnitude comparator (four layers deep) and its seesaw circuit simulation, with 1x = 50 nM. (a) The digital logic circuit diagram. The corresponding seesaw circuit has roughly 100 seesaw gates. (b) Seesaw circuit simulation with selected input vector of A greater than B. (c) Seesaw circuit simulation with selected input vector of A smaller than B. (d) Seesaw circuit simulation with selected input vector of A equal to B.
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RSIF20100729F5: A 74L85 standard 4-bit magnitude comparator (four layers deep) and its seesaw circuit simulation, with 1x = 50 nM. (a) The digital logic circuit diagram. The corresponding seesaw circuit has roughly 100 seesaw gates. (b) Seesaw circuit simulation with selected input vector of A greater than B. (c) Seesaw circuit simulation with selected input vector of A smaller than B. (d) Seesaw circuit simulation with selected input vector of A equal to B.

Mentions: With realistic rate constants, our simulations suggest that the timescales for seesaw circuits are the order of an hour per layer of digital logic. This being a bit slow, it is worth noting that there are interesting computations that require not too many layers. For example, a standard 74L85 4-bit magnitude comparator, with roughly 30 logic gates, requires only four layers. We compiled this circuit to seesaw gates using the 2-2 scheme, and ODE simulations demonstrated correct behaviour (figureĀ 5).Figure 5.


A simple DNA gate motif for synthesizing large-scale circuits.

Qian L, Winfree E - J R Soc Interface (2011)

A 74L85 standard 4-bit magnitude comparator (four layers deep) and its seesaw circuit simulation, with 1x = 50 nM. (a) The digital logic circuit diagram. The corresponding seesaw circuit has roughly 100 seesaw gates. (b) Seesaw circuit simulation with selected input vector of A greater than B. (c) Seesaw circuit simulation with selected input vector of A smaller than B. (d) Seesaw circuit simulation with selected input vector of A equal to B.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3140723&req=5

RSIF20100729F5: A 74L85 standard 4-bit magnitude comparator (four layers deep) and its seesaw circuit simulation, with 1x = 50 nM. (a) The digital logic circuit diagram. The corresponding seesaw circuit has roughly 100 seesaw gates. (b) Seesaw circuit simulation with selected input vector of A greater than B. (c) Seesaw circuit simulation with selected input vector of A smaller than B. (d) Seesaw circuit simulation with selected input vector of A equal to B.
Mentions: With realistic rate constants, our simulations suggest that the timescales for seesaw circuits are the order of an hour per layer of digital logic. This being a bit slow, it is worth noting that there are interesting computations that require not too many layers. For example, a standard 74L85 4-bit magnitude comparator, with roughly 30 logic gates, requires only four layers. We compiled this circuit to seesaw gates using the 2-2 scheme, and ODE simulations demonstrated correct behaviour (figureĀ 5).Figure 5.

Bottom Line: The prospects of programming molecular systems to perform complex autonomous tasks have motivated research into the design of synthetic biochemical circuits.To date, circuits involving at most tens of gates have been demonstrated experimentally.Here, we propose a simple DNA gate architecture that appears suitable for practical synthesis of large-scale circuits involving possibly thousands of gates.

View Article: PubMed Central - PubMed

Affiliation: Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA.

ABSTRACT
The prospects of programming molecular systems to perform complex autonomous tasks have motivated research into the design of synthetic biochemical circuits. Of particular interest to us are cell-free nucleic acid systems that exploit non-covalent hybridization and strand displacement reactions to create cascades that implement digital and analogue circuits. To date, circuits involving at most tens of gates have been demonstrated experimentally. Here, we propose a simple DNA gate architecture that appears suitable for practical synthesis of large-scale circuits involving possibly thousands of gates.

Show MeSH
Related in: MedlinePlus