Cited by 240DNA and Biological ComputingAdvanced biosensing and bioanalysis techniquesNanopore and Nanochannel Transport Studies

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

Song, Tianqi, Eshra, Abeer, Shah, Shalin, Bui, Hieu, Fu, Daniel, Yang, Ming, Mokhtar, Reem, Reif, John·2019·Nature Nanotechnology

DOI 10.1038/s41565-019-0544-5

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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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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
ORCID: Song, Tianqi
Eshra, Abeer
Shah, Shalin
Bui, Hieu
Fu, Daniel
Yang, Ming
Reif, John
Venue: Nature Nanotechnology
Publisher: Springer Science and Business Media LLC
Published: 2019-09-23
Volume: 14
Issue: 11
Pages: 1075-1081
ISSN: 1748-3387 (ISSN-L)
1748-3395
DOI: 10.1038/s41565-019-0544-5
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
Licence: www.springer.com/tdm (tdm)
www.springer.com/tdm (vor)
Locations: Nature Nanotechnology (publishedVersion)
PubMed (publishedVersion)
Funders: National Science Foundation (CCF-1320360, CCF-1217457, CCF-1617791, CCF-1813805)
Topics: Physical Sciences › Mathematics › Theoretical Computer Science › 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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Fast and compact DNA logic circuits based on single-stranded gates using strand-displacing polymerase

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