Treffer: Multiplexed and high-bandwidth DNA computing circuits with superresolution DNA origami displays.

Title:
Multiplexed and high-bandwidth DNA computing circuits with superresolution DNA origami displays.
Authors:
Jin Z; State Key Laboratory of Synergistic Chem-Bio Synthesis, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China., Tang Y; State Key Laboratory of Synergistic Chem-Bio Synthesis, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China., Jia S; Zhangjiang Laboratory, Shanghai 201210, China., Dai Z; State Key Laboratory of Synergistic Chem-Bio Synthesis, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China., Zhao Z; State Key Laboratory of Synergistic Chem-Bio Synthesis, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China., Li J; Institute of Materiobiology, College of Sciences, Shanghai University, Shanghai 200444, China., Xia K; Jiaxing Key Laboratory of Biosemiconductors, Xiangfu Laboratory, Jiashan, Zhejiang 314102, China., Liu J; Lenovo Research, Lenovo Group, Beijing 100094, China., Ke K; Lenovo Research, Lenovo Group, Beijing 100094, China., Lv H; Institute of Materiobiology, College of Sciences, Shanghai University, Shanghai 200444, China., Li Q; State Key Laboratory of Synergistic Chem-Bio Synthesis, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China., Wang F; State Key Laboratory of Synergistic Chem-Bio Synthesis, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China., Fan C; State Key Laboratory of Synergistic Chem-Bio Synthesis, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China.
Source:
Proceedings of the National Academy of Sciences of the United States of America [Proc Natl Acad Sci U S A] 2025 Nov 18; Vol. 122 (46), pp. e2517114122. Date of Electronic Publication: 2025 Nov 13.
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: National Academy of Sciences Country of Publication: United States NLM ID: 7505876 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1091-6490 (Electronic) Linking ISSN: 00278424 NLM ISO Abbreviation: Proc Natl Acad Sci U S A Subsets: MEDLINE
Imprint Name(s):
Original Publication: Washington, DC : National Academy of Sciences
MeSH Terms:
DNA*/chemistry , Computers, Molecular*, Biosensing Techniques/methods
Grant Information:
2023YFA0915200 MOST | National Key Research and Development Program of China (NKPs); T2188102 22322704 223B2404 U24A20497 National Natural Science Foundation of China; 21TQ1400222 Shanghai Polit Program for Basic Research - Shanghai Jiao Tong University; XF012022E0100 Xiangfu Lab Research Project; NA New Cornerstone Science Foundation; NA K. C. Wong Education Foundation
Contributed Indexing:
Keywords: DNA computing; DNA origami; DNA-PAINT; high-throughput readout
Substance Nomenclature:
9007-49-2 (DNA)
Entry Date(s):
Date Created: 20251113 Date Completed: 20251113 Latest Revision: 20251127
Update Code:
20251127
PubMed Central ID:
PMC12646223
DOI:
10.1073/pnas.2517114122
PMID:
41231958
Database:
MEDLINE

Weitere Informationen

DNA computing circuits leverage molecular interactions to construct a highly parallel and biologically compatible information processing paradigm. However, their development has been constrained by a critical gap between intrinsic computational parallelism and the limited readout bandwidth. Multibit outputs from complex circuits often require multiple separate tests, limiting the integration and debugging efficiency. Here, we overcome this bottleneck by decoupling computation from readout via a DNA origami display-based interface by integrating strand displacement and unstable binding reactions. We convert multibit molecular outputs from DNA circuits into spatially resolved geometric bits, enabling direct visualization via superresolution microscopy for high-throughput readout. We experimentally demonstrated the direct readout of an 8-bit decoder circuit and simultaneous display of 16 parallel-running logic gates. This high-bandwidth platform unlocks capabilities in circuit debugging and multiplexed execution, paving the way for large-scale DNA computing and high-throughput biosensing.

Competing interests statement:The authors declare no competing interest.