The DOI matches its Crossref record; 21 of the 22 references it cites were found in a registry or an index.
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.
Overview
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“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]
Citations
Cites
Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid
WATSON, J. D., & CRICK, F. H. C. (1953) · Nature · doi:10.1038/171737a0 · Cited by 13,584
Enzyme-Free Nucleic Acid Logic Circuits
Seelig, G., Soloveichik, D., Zhang, D. Y., & Winfree, E. (2006) · Science · doi:10.1126/science.1132493 · Cited by 1,545
Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades
Qian, L., & Winfree, E. (2011) · Science · doi:10.1126/science.1200520 · Cited by 1,469
Neural network computation with DNA strand displacement cascades
Qian, L., Winfree, E., & Bruck, J. (2011) · Nature · doi:10.1038/nature10262 · Cited by 1,082
Scaling up molecular pattern recognition with DNA-based winner-take-all neural networks
Cherry, K. M., & Qian, L. (2018) · Nature · doi:10.1038/s41586-018-0289-6 · Cited by 497
Enzyme-free nucleic acid dynamical systems
Srinivas, N., Parkin, J. M., Seelig, G., Winfree, E., & Soloveichik, D. (2017) · Science · doi:10.1126/science.aal2052 · Cited by 364
A spatially localized architecture for fast and modular DNA computing
Chatterjee, G., Dalchau, N., Muscat, R. A., Phillips, A., & Seelig, G. (2017) · Nature Nanotechnology · doi:10.1038/nnano.2017.127 · Cited by 355
Programmable autonomous synthesis of single-stranded DNA
Kishi, J. Y., Schaus, T. E., Gopalkrishnan, N., Xuan, F., & Yin, P. (2017) · Nature Chemistry · doi:10.1038/nchem.2872 · Cited by 324
Programming an in vitro DNA oscillator using a molecular networking strategy
Montagne, K., Plasson, R., Sakai, Y., Fujii, T., & Rondelez, Y. (2011) · Molecular Systems Biology · doi:10.1038/msb.2010.120 · Cited by 285
On the computational power of DNA
Boneh, D., Dunworth, C., Lipton, R. J., & Sgall, J. (1996) · Discrete Applied Mathematics · doi:10.1016/s0166-218x(96)00058-3 · Cited by 188
Cited by
Sorted by citations
Items 201–240 of 240
Seeded growth of adaptive tiles on DNA origami
Liu, Y., Cheng, J. Q., Wang, Y., Ji, B., Tang, L., Zou, K., Xie, Y., Cui, D., Ke, Y., & Song, J. (2022) · Cell Reports Physical Science · doi:10.1016/j.xcrp.2022.101040 · Cited by 1
Sequence‐Independent Logical Regulation of the Assembly and Disassembly of DNA Polyhedra
Mei, Z., Wan, L., Wei, M., & Li, Y. (2023) · ChemBioChem · doi:10.1002/cbic.202300240 · Cited by 1
Yang, M., Wu, J., Hu, M., Li, J., Zhang, Z., Yan, B., & Wu, T. (2025) · Sensors and Actuators B Chemical · doi:10.1016/j.snb.2025.138680 · Cited by 1
Self-citationImplementing parallel arithmetic via acetylation and its application to chemical image processing
Dombroski, A., Oakley, K., Arcadia, C. E., Nouraei, F., Chen, S. L., Rose, C., Rubenstein, B. M., Rosenstein, J. K., Reda, S., & Kim, E. (2021) · Proceedings of the Royal Society A Mathematical Physical and Engineering Sciences · doi:10.1098/rspa.2020.0899 · Cited by 1
Sensitive Logic Nanodevices with Strong Response for Weak Inputs
Lv, W. Y., Li, C. H., Yang, F. F., Li, Y. F., Zhen, S. J., & Huang, C. Z. (2022) · Angewandte Chemie · doi:10.1002/ange.202115561 · Cited by 1
Construction of Complex Logic Circuit Based on DNA Logic Gate AND and OR
Hu, M., Wang, L., Xi, S., Liu, R., & Dong, Y. (2022) · Communications in computer and information science · doi:10.1007/978-981-19-1256-6_29 · Cited by 1
Fuzzy DNA Strand Displacement: A Strategy to Decrease the Complexity of DNA Network Design
Wang, Z., Hu, Y., & Pan, L. (2020) · Angewandte Chemie · doi:10.1002/ange.202005193 · Cited by 1
Digital DNA Strand Displacement for Molecular ComputingPreprint
Zhang, L., Yang, H., Kang, X., Yan, Y., Huang, J., Zhao, H., Yang, J., & Su, X. (2023) · ChemRxiv · doi:10.26434/chemrxiv-2023-smkqb · Cited by 1
Microfluidic Enrichment of Intact Viral Particles by Stoichiometric Balanced DNA ComputationPreprint
Huang, Y., Wu, Q., Zhang, J., Zhang, Y., Cen, S., Yang, C. J., & Song, Y. (2023) · ChemRxiv · doi:10.26434/chemrxiv-2023-vd0b0-v2 · Cited by 1
DNA sequential logic circuits for counters and bioinformatics repositoriesPreprint
Wu, T., Xie, T., Li, C., Hu, M., Zhong, X., Xiao, J., Zhang, Z., & Wang, Z. (2024) · Research Square · doi:10.21203/rs.3.rs-5097045/v1 · Cited by 1
A Thermodynamically Favoured Molecular Computer: Robust, Fast, Renewable, ScalablePreprint
Stérin, T., Eshra, A., Adio, J., Evans, C. G., & Woods, D. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.07.16.664196 · Cited by 1
Self-citationMokhtar, R., Song, T., Fu, D., Shah, S., Song, X., Yang, M., & Reif, J. H. (2021) · Wiley eBooks · doi:10.1002/9783527825424.ch16
Self-citationMicrofluidic Enrichment of Intact Viral Particles by Stoichiometric Balanced DNA ComputationPreprint
Huang, Y., Wu, Q., Zhang, J., Zhang, Y., Cen, S., Yang, C. J., & Song, Y. (2023) · ChemRxiv · doi:10.26434/chemrxiv-2023-vd0b0
Design Guidelines Inspired by Nature for Stimuli‐Responsive Supramolecular Materials
Zha, R. H. (2023) · Wiley eBooks · doi:10.1002/9783527834044.ch37
Erasable and Field Programmable DNA Circuits Based on Configurable Logic BlocksPreprint
Xiao, X., Liu, Y., Zhai, Y., Hu, H., Liao, Y., Liu, H. L., Liu, X., He, J., Wang, L., Wang, H., et al. (2023) · Research Square · doi:10.21203/rs.3.rs-2873793/v1
The Evolution of DNA-Based Molecular Computing
Wang, F., Li, Q., & Fan, C. (2023) · Natural computing series · doi:10.1007/978-981-19-9891-1_3
Computational Design of Nucleic Acid Circuits: Past, Present, and Future
Lakin, M. R., Spaccasassi, C., & Phillips, A. (2023) · Natural computing series · doi:10.1007/978-981-19-9891-1_18
Simple and rewireable biomolecular building blocks for DNA machine-learning algorithmsPreprint
Lee, R. C., Corsano, A., Tseng, C., & Chou, L. Y. T. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.07.20.549967
Polymerase Chain Reaction-based Biomolecular Logic Gate for NAND and NOR Operations
Nojima, T. (2023) · Chemistry Letters · doi:10.1246/cl.230222
The Construction of DNA Coding Sets by an Intelligent Optimization Algorithm: TMOL-TSO
Yan, Y., Wang, W., Fu, Z., & Tian, J. (2023) · Communications in computer and information science · doi:10.1007/978-981-99-8138-0_36
General-purpose DNA computation
Liu, J., & Han, D. (2023) · Science China Chemistry · doi:10.1007/s11426-023-1906-y
Yao, J., Lv, H., & Xiao, Y. (2023) · IEEE Smart World Congress (SWC) · doi:10.1109/swc57546.2023.10449223
Sorrentino, D., Ranallo, S., Ricci, F., & Franco, E. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.03.14.585044
Zheng, Y., Yang, J., Zhang, T., & Jiang, T. (2024) · Communications in computer and information science · doi:10.1007/978-981-97-2272-3_29
Engineering Nucleic Acid Structures for Programmable Intracellular Biocomputation
Wu, N., Hao, P., Fan, C., & Zhao, Y. (2024) · doi:10.1002/9783527840816.ch18
STWM: Sliding Time Window Method Driven by Enzymes for Image Information Access
Shi, Y., Cui, S., Liu, X., Zhang, B., Zhou, H., Zhou, S., Wang, B., & Zhang, Q. (2025) · ACS Applied Materials & Interfaces · doi:10.1021/acsami.5c16558
Additional file 1 of Controllable and reusable seesaw circuit based on nicking endonucleases
Liao, Y., Liu, Y., Liu, H., Liu, X., Li, L., & Xiao, X. (2024) · Figshare · doi:10.6084/m9.figshare.25522659
Electrochemical biosensor based on programmable DNA biocomputing circuits for miRNA detection
Liu, Z., Xie, B., He, H., Li, S., Gao, H., Zhang, J., Fu, H., & Liao, Y. (2025) · Microchemical Journal · doi:10.1016/j.microc.2025.115482
Enzyme-driven triplex structure-based DNA logic circuits
Liu, X., Zhang, J., Zhang, X., Chen, Z., Zhang, S., Wang, X., Liu, J., Wang, Z., Xie, L., Ming, Z., et al. (2025) · Journal of Nanobiotechnology · doi:10.1186/s12951-025-03853-6
Pérez, T. D., Tafoya, A. N., Peabody, D. S., Anastasio, C., Shreve, A. P., Lakin, M. R., Carroll, N. J., & López, G. P. (2026) · ACS Synthetic Biology · doi:10.1021/acssynbio.5c00511
DNA Crystals as a Template for Patterned Functional Materials
Swett, A. A., Kim, Y. H., Park, S., Kesama, M. R., Siraj, N., Mao, C., & Choi, J. H. (2026) · Small Structures · doi:10.1002/sstr.202500693
Application of Self-Assembled DNA Nanomaterials in Tumor Diagnosis and Treatment
Sun, S. J. (2026) · Springer eBooks · doi:10.1007/978-981-96-9478-5_1
Programmable DNA Strand-Displacement Circuits for Emulating Digital Sequential Logic Devices
Gao, R., Dong, W., Xie, A., & Wei, X.-S. (2026) · ACS Applied Materials & Interfaces · doi:10.1021/acsami.6c00972
High-fidelity molecular decoding through tile-guided in situ self-assembly
Hu, X., Guo, X., Xie, J., Wang, L., Yu, Z., Li, H., Qiu, X., Bernardini, S., Gu, W., Luo, Y., et al. (2026) · Science Advances · doi:10.1126/sciadv.aed7719
Programmable one-pot polymerase-mediated DNA synthesis via temperature control
Kim, J., Choi, J. H., Kim, W., Cho, N., Jung, Y., Park, S., Choi, E., Lee, C., Kim, Y., Ryu, T., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-74890-4 · Cited by 1
An autocatalytic DNA circuit via polymerase mediated strand displacement
Lv, S., Wang, G. A., & Li, F. (2026) · Chemical Communications · doi:10.1039/d6cc03616c
A thermodynamically favoured molecular computer
Stérin, T., Eshra, A., Evans, C. G., Adio, J., & Woods, D. (2026) · Nature · doi:10.1038/s41586-026-10996-5 · Cited by 4
Self-citationEnzyme-free DNA Logic Computing for Cancer Diagnosis and Molecular Decision-Making
Yu, J.-Y., Qi, L.-J., Li, X., Du, Y., & Li, Y. (2026) · Journal of Analysis and Testing · doi:10.1007/s41664-026-00509-8
Zhu, M., Wu, X., Zhang, Y., Zhu, Y., Xu, M., Li, F., & Yu, Y. (2026) · Analytical Methods · doi:10.1039/d6ay01745b
He, S., Zhao, L., Liu, Y., Lyu, Y., & Tan, W. (2026) · Journal of the American Chemical Society · doi:10.1021/jacs.6c15525
Metadata
- 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
- 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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review