Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades

@article{Qian2011ScalingUD,
  title={Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades},
  author={Lulu Qian and Erik Winfree},
  journal={Science},
  year={2011},
  volume={332},
  pages={1196 - 1201}
}
Scalability and noise control are demonstrated in a molecular computer built from DNA. To construct sophisticated biochemical circuits from scratch, one needs to understand how simple the building blocks can be and how robustly such circuits can scale up. Using a simple DNA reaction mechanism based on a reversible strand displacement process, we experimentally demonstrated several digital logic circuits, culminating in a four-bit square-root circuit that comprises 130 DNA strands. These… 

Analog Computation by DNA Strand Displacement Circuits.

This work proposes an architecture for the systematic construction of DNA circuits for analog computation based on DNA strand displacement, and describes how DNA circuits to compute polynomial functions of inputs can be built.

Fast and compact DNA logic circuits based on single-stranded gates using strand-displacing polymerase

A new DNA logic circuits architecture based on single-stranded logic gates and strand-displacing DNA polymerase requires less computation time and fewer DNA strands.

Scaling Up Multi-bit DNA Full Adder Circuits with Minimal Strand Displacement Reactions.

This work develops a compact-yet-efficient architecture using cooperative strand displacement reactions (cSDRs) to construct DNA full adder, providing the potential for application-specific circuit customization for scalable digital computing with minimal reactions.

Functional Analysis of Large-Scale DNA Strand Displacement Circuits

This work implements this method as an extension to the Visual DSD tool, and uses it to formalize the behavior of a 4-bit square root circuit, together with the components used for its construction.

A Universal Platform for Building DNA Logic Circuits

Two DNA-based logic circuits that behave as half-subtract and half-adder were implemented relying on strand displacement and fluorescence labeling technique by simply modifying the sequences of the input strands, while retaining the same DNA logical structure as a universal platform.

Abstractions for DNA circuit design

A programming language for designing DNA strand displacement devices is presented, which allows device designs to be programmed using a common syntax and then analysed at varying levels of detail, with or without interference, without needing to modify the program.

Simultaneous G-Quadruplex DNA Logic.

Three G- quadruplex-based logic gates that operate simultaneously in a single reaction vessel are reported that respond to unique Boolean DNA inputs by undergoing topological conversion from duplex to G-quadruplex states that were resolved using a thioflavin T dye and gel electrophoresis.

Design and Analysis of Compact DNA Strand Displacement Circuits for Analog Computation Using Autocatalytic Amplifiers.

A novel architecture to build compact DNA strand displacement circuits to compute a broad scope of functions in an analog fashion is proposed, inspired by Napier's use of logarithm transforms to compute square roots on a slide rule.

Compiler-aided systematic construction of large-scale DNA strand displacement circuits using unpurified components

A systematic procedure for overcoming the challenges involved in using unpurified DNA strands is developed and a model that takes synthesis errors into consideration and semi-quantitatively reproduces the experimental data is developed.

Pattern Transformation with DNA Circuits

This work design and implement non-enzymatic DNA circuits capable of performing pattern transformation algorithms such as edge detection that will provide programmable platforms for prototyping CRNs, for discovering bottom-up construction principles, and for generating patterns in materials.
...

References

SHOWING 1-10 OF 77 REFERENCES

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.

A programming language for composable DNA circuits

A programming language for designing and simulating DNA circuits in which strand displacement is the main computational mechanism and includes basic elements of sequence domains, toeholds and branch migration, and assumes that strands do not possess any secondary structure is presented.

Time-Complexity of Multilayered DNA Strand Displacement Circuits

This work uses mass action kinetics to model DNA strand displacement-based circuits and shows that depending on circuit architecture, the time-complexity does not necessarily scale linearly with the depth as is assumed in the usual study of circuit complexity.

A simple DNA gate motif for synthesizing large-scale circuits

A simple DNA gate architecture that appears suitable for practical synthesis of large-scale circuits involving possibly thousands of gates is proposed.

Scalable, Time-Responsive, Digital, Energy-Efficient Molecular Circuits Using DNA Strand Displacement

A novel theoretical biomolecular design to implement any Boolean circuit using the mechanism of DNA strand displacement, which is scalable, energy-efficient, and digital, which can achieve a digital abstraction of the analog values of concentrations.

DNA as a universal substrate for chemical kinetics

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.

Efficient Turing-Universal Computation with DNA Polymers

This work proposes a chemical implementation of stack machines -- a Turing-universal model of computation similar to Turing machines -- using DNA strand displacement cascades as the underlying chemical primitive, controlled by strand displacement logic.

DNA computing circuits using libraries of DNAzyme subunits.

The construction of a DNA-based computational platform that uses a library of catalytic nucleic acids, and their substrates, for the input-guided dynamic assembly of a universal set of logic gates and a half-adder/half-subtractor system is reported.

Renewable, Time-Responsive DNA Logic Gates for Scalable Digital Circuits

A construction for a set of one and two-input logic gates based on enzymatic restriction of DNA strands is presented and it is argued that this construction can be generalized to implement any Boolean operation.

Engineering Entropy-Driven Reactions and Networks Catalyzed by DNA

A design strategy is introduced that allows a specified input oligonucleotide to catalyze the release of a specified output oligon nucleotide, which in turn can serve as a catalyst for other reactions, which provides an amplifying circuit element that is simple, fast, modular, composable, and robust.
...