ArticleJournal of the Royal Society, Interface2012
Abstractions for DNA circuit design.
Article in Journal of the Royal Society, Interface, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- DNA-Based Boolean Logic Gates for Molecular Computation and Biosensing: A Critical Review.Molecular biotechnology · 2026Review
- Article
- A Localized Scalable DNA Logic Circuit System Based on the DNA Origami Surface.International journal of molecular sciences · 2025Article
- A geometric framework for reaction enumeration in computational nucleic acid devices.Journal of the Royal Society, Interface · 2023Article
- A reaction network scheme for hidden Markov model parameter learning.Journal of the Royal Society, Interface · 2023Article
- Design and Simulation of an Autonomous Molecular Mechanism Using Spatially Localized DNA Computation.Interdisciplinary sciences, computational life sciences · 2023Article
- Massively Parallel DNA Computing Based on Domino DNA Strand Displacement Logic Gates.ACS synthetic biology · 2022Article
- Programming Molecular Systems To Emulate a Learning Spiking Neuron.ACS synthetic biology · 2022Article
- Renewable DNA Proportional-Integral Controller with Photoresponsive Molecules.Micromachines · 2022Article
- Robust finite automata in stochastic chemical reaction networks.Royal Society open science · 2021Article
- Molecular communication relays for dynamic cross-regulation of self-sorting fibrillar self-assemblies.Science advances · 2021Article
- A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures.Journal of the Royal Society, Interface · 2020Article
- Thiol-free oligonucleotide surface modification of gold nanoparticles for nanostructure assembly.Nanoscale advances · 2019Article
- Individually addressable and dynamic DNA gates for multiplexed cell sorting.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Computing with biological switches and clocks.Natural computing · 2018Article
- The importance of thermodynamics for molecular systems, and the importance of molecular systems for thermodynamics.Natural computing · 2018Article
- A strand graph semantics for DNA-based computation.Theoretical computer science · 2016Article
- Modular verification of chemical reaction network encodings via serializability analysis.Theoretical computer science · 2016Article
- Plasmid-derived DNA Strand Displacement Gates for Implementing Chemical Reaction Networks.Journal of visualized experiments : JoVE · 2015Article
- DyNAMiC Workbench: an integrated development environment for dynamic DNA nanotechnology.Journal of the Royal Society, Interface · 2015Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA strand displacement techniques have been used to implement a broad range of information processing devices, from logic gates, to chemical reaction networks, to architectures for universal computation. Strand displacement techniques enable computational devices to be implemented in DNA without the need for additional components, allowing computation to be programmed solely in terms of nucleotide sequences. A major challenge in the design of strand displacement devices has been to enable rapid analysis of high-level designs while also supporting detailed simulations that include known forms of interference. Another challenge has been to design devices capable of sustaining precise reaction kinetics over long periods, without relying on complex experimental equipment to continually replenish depleted species over time. In this paper, we present a programming language for designing DNA strand displacement devices, which supports progressively increasing levels of molecular detail. The language 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. This allows a trade-off to be made between the level of molecular detail and the computational cost of analysis. We use the language to design a buffered architecture for DNA devices, capable of maintaining precise reaction kinetics for a potentially unbounded period. We test the effectiveness of buffered gates to support long-running computation by designing a DNA strand displacement system capable of sustained oscillations.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.