Skip to main content

Advertisement

SpringerLink
Go to cart
  1. Home
  2. Chinese Science Bulletin
  3. Article
Molecular logic computing model based on DNA self-assembly strand branch migration
Download PDF
Your article has downloaded

Similar articles being viewed by others

Slider with three articles shown per slide. Use the Previous and Next buttons to navigate the slides or the slide controller buttons at the end to navigate through each slide.

Autonomous and Programmable Strand Generator Implemented as DNA and Enzymatic Chemical Reaction Cascade

27 February 2022

Ibuki Kawamata, Shin-ichiro M. Nomura & Satoshi Murata

XOR Gate Design Toward a Practical Complete Set for DNA Computing

21 March 2020

Katsuhiro Nishijima & Takashi Nakakuki

Engineering DNA logic systems with non-canonical DNA-nanostructures: basic principles, recent developments and bio-applications

29 December 2021

Daoqing Fan, Jun Wang, … Shaojun Dong

Programmable Assembly of DNA-protein Hybrid Structures

10 December 2019

Xue Li, Donglei Yang, … Pengfei Wang

Cascaded DNA circuits-programmed self-assembly of spherical nucleic acids for high signal amplification

21 October 2019

Xiang Li, Dongbao Yao, … Haojun Liang

Towards Active Self-Assembly Through DNA Nanotechnology

12 March 2020

Jinyi Dong, Chao Zhou & Qiangbin Wang

High-performance biosensing based on autonomous enzyme-free DNA circuits

03 February 2020

Hong Wang, Huimin Wang, … Fuan Wang

Locked nucleic acids based DNA circuits with ultra-low leakage

17 August 2022

Hao Hu, Liquan Liu, … Xianjin Xiao

Design and Simulation of an Autonomous Molecular Mechanism Using Spatially Localized DNA Computation

10 February 2023

Yue Wang, Luhui Wang, … Yafei Dong

Download PDF
  • Article
  • Open Access
  • Published: 18 January 2013

Molecular logic computing model based on DNA self-assembly strand branch migration

  • Cheng Zhang1,
  • LiNa Ma2,
  • YaFei Dong2,
  • Jing Yang3 &
  • …
  • Jin Xu1 

Chinese Science Bulletin volume 58, pages 32–38 (2013)Cite this article

  • 1026 Accesses

  • 13 Citations

  • Metrics details

Abstract

In this study, the DNA logic computing model is established based on the methods of DNA self-assembly and strand branch migration. By adding the signal strands, the preprogrammed signals are released with the disintegrating of initial assembly structures. Then, the computing results are able to be detected by gel electrophoresis. The whole process is controlled automatically and parallely, even triggered by the mixture of input signals. In addition, the conception of single polar and bipolar is introduced into system designing, which leads to synchronization and modularization. Recognizing the specific signal DNA strands, the computing model gives all correct results by gel experiment.

Download to read the full article text

Working on a manuscript?

Avoid the common mistakes

References

  1. Adleman L. Molecular computation of solution to combinatorial problems. Science, 1994, 66: 1021–1024

    Article  Google Scholar 

  2. Ouyang Q, Kaplan P D, Liu S, et al. DNA solution of the maximal clique problem. Science, 1997, 278: 446–449

    Article  Google Scholar 

  3. Mao C D, LaBean T H, Reif J H. Logical computation using algorithmic self-assembly of DNA triple-crossover molecules. Nature, 2000, 28: 493–496

    Google Scholar 

  4. Qian L L, Winfree E. Scaling up digital circuit computation with DNA strand displacement cascades. Science, 2011, 332: 1196–1201

    Article  Google Scholar 

  5. Qian L L, Winfree E, Bruck J. Neural network computation with DNA strand displacement cascades. Nature, 2011, 475: 368–372

    Article  Google Scholar 

  6. Pei R J, Matamoros E, Liu M H, et al. Training a molecular automaton to play a game. Nat Nanotechnol, 2010, 5: 773–777

    Article  Google Scholar 

  7. Gu H Z, Chao J, Xiao S J, et al. Molecular robots guided by prescriptive landscapes. Nature, 2010, 465: 202–205

    Article  Google Scholar 

  8. Rinaudo K, Bleris L, Maddamsetti R. A universal RNAi-based logic evaluator that operates in mammalian cells. Nat Biotechnol, 2007, 25: 795–801

    Article  Google Scholar 

  9. Maune H T, Han S P, Barish R D, et al. Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates. Nat Nanotechnol, 2010, 5: 61–66

    Article  Google Scholar 

  10. Morrow T J, Li M W, Kim J, et al. Programmed assembly of DNA-coated nanowire devices. Science, 2009, 323: 352–353

    Article  Google Scholar 

  11. Clelland C T, Risca V, Bancroft C. Hiding messages in DNA microdots. Nature, 1999, 399: 533–534

    Article  Google Scholar 

  12. Seelig G, Soloveichik D, Zhang Y D, et al. Enzyme-free nucleic acid logic circuits. Science, 2006, 314: 1585–1588

    Article  Google Scholar 

  13. Shin J S, Pierce N A. Rewritable memory by controllable nanopatterning of DNA. Nano Lett, 2004, 4: 905–909

    Article  Google Scholar 

  14. Zhang D Y, Turberfield A J, Yurke B, et al. Engineering entropy-driven reactions and networks catalyzed by DNA. Science, 2007, 318: 1121–1125

    Article  Google Scholar 

  15. Frezza B M, Cockroft S L, Ghadiri M R. Modular multi-level circuits from immobilized DNA-based logic gates. J Am Chem Soc, 2007, 129: 14875–14879

    Article  Google Scholar 

  16. Winfree E. Design and self-assembly of two-dimensional DNA crystals. Nature, 1998, 394: 539–544

    Article  Google Scholar 

  17. LaBean T H, Reif J H, Seeman N C, et al. Construction, analysis, ligation, and self assembly of DNA triple crossover complexes. J Am Chem Soc, 2000, 122: 1848–1860

    Article  Google Scholar 

  18. Carbone A, Seeman N C. Circuits and programmable self-assembling DNA structures. Proc Natl Acad Sci USA, 2002, 99: 12577–12582

    Article  Google Scholar 

  19. Rothemund P W. Folding DNA to create nanoscale shapes and patterns. Nature, 2006, 440: 297–302

    Article  Google Scholar 

  20. Goodman R P, Schaap I A T, Tardin C F, et al. Rapid chiral assembly of rigid DNA building blocks for molecular nanofabrication. Science, 2005, 310: 1661–1665

    Article  Google Scholar 

  21. Zhang C, Su M, He Y, et al. Conformational flexibility facilitates self-assembly of complex DNA nanostructures. Proc Natl Acad Sci USA, 2008, 105: 10665–10669

    Article  Google Scholar 

  22. Aldaye F A, Lo P K, Karam P, et al. Modular construction of DNA nanotubes of tunable geometry and single- or double-stranded character. Nat Nanotechnol, 2009, 4: 349–352

    Article  Google Scholar 

  23. Han D R, Pal S, Nangreave J, et al. DNA origami with complex curvatures in three-dimensional space. Science, 2011, 332: 342–346

    Article  Google Scholar 

  24. Ackermann D, Schmidt T L, Hannam J S, et al. A double-stranded DNA rotaxane. Nat Nanotechnol, 2010, 5: 436–442

    Article  Google Scholar 

  25. Thomas C. DNA as a logic operator. Nature, 2011, 469: 45–46

    Article  Google Scholar 

  26. Liu Q H, Wang L M, Frutos A G, et al. DNA computing on surfaces. Nature, 2000, 403: 175–179

    Article  Google Scholar 

  27. Benenson Y, Elizur T P, Adar R, et al. Programmable and autonomous computing machine made of biomolecules. Nature, 2001, 411: 430–434

    Article  Google Scholar 

  28. Benenson Y, Gil B, Dor U B, et al. An autonomous molecular computer for logical control of gene expression. Nature, 2004, 429: 423–429

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Institute of Software, School of Electronics Engineering and Computer Science, Key Laboratory of High Confidence Software Technologies of Ministry of Education, Peking University, Beijing, 100871, China

    Cheng Zhang & Jin Xu

  2. College of Life Science, Shaanxi Normal University, Xi’an, 710062, China

    LiNa Ma & YaFei Dong

  3. School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, China

    Jing Yang

Authors
  1. Cheng Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. LiNa Ma
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. YaFei Dong
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jing Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jin Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Jing Yang or Jin Xu.

Additional information

These authors contributed equally to the work.

This article is published with open access at Springerlink.com

Rights and permissions

This article is published under an open access license. Please check the 'Copyright Information' section either on this page or in the PDF for details of this license and what re-use is permitted. If your intended use exceeds what is permitted by the license or if you are unable to locate the licence and re-use information, please contact the Rights and Permissions team.

About this article

Cite this article

Zhang, C., Ma, L., Dong, Y. et al. Molecular logic computing model based on DNA self-assembly strand branch migration. Chin. Sci. Bull. 58, 32–38 (2013). https://doi.org/10.1007/s11434-012-5498-z

Download citation

  • Received: 01 June 2012

  • Accepted: 04 September 2012

  • Published: 18 January 2013

  • Issue Date: January 2013

  • DOI: https://doi.org/10.1007/s11434-012-5498-z

Share this article

Anyone you share the following link with will be able to read this content:

Sorry, a shareable link is not currently available for this article.

Provided by the Springer Nature SharedIt content-sharing initiative

Keywords

  • DNA strand branch migration
  • DNA self-assembly
  • molecular logic computing
  • molecular intelligence
  • modularized design
Download PDF

Working on a manuscript?

Avoid the common mistakes

Advertisement

Over 10 million scientific documents at your fingertips

Switch Edition
  • Academic Edition
  • Corporate Edition
  • Home
  • Impressum
  • Legal information
  • Privacy statement
  • Your US state privacy rights
  • How we use cookies
  • Your privacy choices/Manage cookies
  • Accessibility
  • FAQ
  • Contact us
  • Affiliate program

Not affiliated

Springer Nature

© 2023 Springer Nature Switzerland AG. Part of Springer Nature.