Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades

  title={Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades},
  author={Lulu Qian and Erik Winfree},
  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.

Connecting localized DNA strand displacement reactions.

Appropriate design of the system, including protection and asymmetry between input and fuel strands, leads to a reproducible behaviour, at least one order of magnitude faster than the one observed under bulk conditions.



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

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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.

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.

An autonomous molecular computer for logical control of gene expression

An autonomous biomolecular computer is described that, at least in vitro, logically analyses the levels of messenger RNA species, and in response produces a molecule capable of affecting levels of gene expression.

Beyond allostery: Catalytic regulation of a deoxyribozyme through an entropy-driven DNA amplifier

It is shown that allosteric regulation of nucleic acid enzymes can be coupled to signal amplification in an entropy-driven DNA circuit and provides a new paradigm for the design of enzyme-free biosensors for point-of-care diagnostics.

A Proximity-Based Programmable DNA Nanoscale Assembly Line

It is demonstrated that a nanoscale assembly line can be realized by the judicious combination of three known DNA-based modules: a DNA origami tile that provides a framework and track for the assembly process, cassettes containing three independently controlled two-state DNA machines that serve as programmable cargo-donating devices and a DNA walker that can move on the track from device to device and collect cargo.