Fast and compact DNA logic circuits based on single-stranded gates using strand-displacing polymerase
Abstract
DNA is a reliable biomolecule with which to build molecular computation systems. In particular, DNA logic circuits (diffusion-based) have shown good performance regarding scalability and correctness of computation. However, previous architectures of DNA logic circuits have two limitations. First, the speed of computation is slow, often requiring hours to compute a simple function. Second, the circuits are of high complexity regarding the number of DNA strands. Here, we introduce an architecture of DNA logic circuits based on single-stranded logic gates using strand-displacing DNA polymerase. The logic gates consist of only single DNA strands, which largely reduces leakage reactions and signal restoration steps such that the circuits are improved in regard to both speed of computation and the number of DNA strands needed. Large-scale logic circuits can be constructed from the gates by simple cascading strategies. In particular, we have demonstrated a fast and compact logic circuit that computes the square-root function of four-bit input numbers.
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The dynamic nature of DNA nanostructure assemblies can be exploited to perform data operations, allowing DNA data storage to integrate directly into DNA computation.
“Moreover, the dynamic nature of these assemblies can be exploited to perform data operations,13,27 which allows DNA data storage to integrate directly into the field of DNA computation.”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [27]
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- Authors
- Song, T., Eshra, A., Shah, S., Bui, H., Fu, D., Yang, M., Mokhtar, R., & Reif, J.
- Affiliations
- Duke University (US)
- Menoufia University (EG)
- National Academies of Sciences, Engineering, and Medicine (US)
- Corresponding author
- Reif, John
- Venue
- Nature Nanotechnology
- Published
- 2019-09-23
- Volume
- 14
- Issue
- 11
- Pages
- 1075-1081
- ISSN
- 1748-3387 (ISSN-L)
- 1748-3395
- OpenAlex
- W2976321815
- Cited by
- 240
- References
- 22
- Citations by year
- 2026: 18 · 2025: 37 · 2024: 44 · 2023: 54 · 2022: 34 · 2021: 31 · 2020: 19 · 2019: 2
- FWCI
- 7.11
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Nature Nanotechnology (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Science Foundation (CCF-1320360, CCF-1217457, CCF-1617791, CCF-1813805)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Biological Computing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced biosensing and bioanalysis techniques
- Physical Sciences › Engineering › Biomedical Engineering › Nanopore and Nanochannel Transport Studies
- Keywords
- DNA logic circuits, molecular computing, computational speed, signal reconstruction, square root computation
- MeSH terms
- Algorithms, DNA-Directed DNA Polymerase, DNA, Single-Stranded, Nucleic Acid Conformation, Computers, Molecular
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