Advertisement

Chinese Science Bulletin

, Volume 58, Issue 1, pp 32–38 | Cite as

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

  • Cheng Zhang
  • LiNa Ma
  • YaFei Dong
  • Jing YangEmail author
  • Jin XuEmail author
Open Access
Article Progress of Project Supported by NSFC Computer Science & Technology

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.

Keywords

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

References

  1. 1.
    Adleman L. Molecular computation of solution to combinatorial problems. Science, 1994, 66: 1021–1024CrossRefGoogle Scholar
  2. 2.
    Ouyang Q, Kaplan P D, Liu S, et al. DNA solution of the maximal clique problem. Science, 1997, 278: 446–449CrossRefGoogle Scholar
  3. 3.
    Mao C D, LaBean T H, Reif J H. Logical computation using algorithmic self-assembly of DNA triple-crossover molecules. Nature, 2000, 28: 493–496Google Scholar
  4. 4.
    Qian L L, Winfree E. Scaling up digital circuit computation with DNA strand displacement cascades. Science, 2011, 332: 1196–1201CrossRefGoogle Scholar
  5. 5.
    Qian L L, Winfree E, Bruck J. Neural network computation with DNA strand displacement cascades. Nature, 2011, 475: 368–372CrossRefGoogle Scholar
  6. 6.
    Pei R J, Matamoros E, Liu M H, et al. Training a molecular automaton to play a game. Nat Nanotechnol, 2010, 5: 773–777CrossRefGoogle Scholar
  7. 7.
    Gu H Z, Chao J, Xiao S J, et al. Molecular robots guided by prescriptive landscapes. Nature, 2010, 465: 202–205CrossRefGoogle Scholar
  8. 8.
    Rinaudo K, Bleris L, Maddamsetti R. A universal RNAi-based logic evaluator that operates in mammalian cells. Nat Biotechnol, 2007, 25: 795–801CrossRefGoogle Scholar
  9. 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: 61–66CrossRefGoogle Scholar
  10. 10.
    Morrow T J, Li M W, Kim J, et al. Programmed assembly of DNA-coated nanowire devices. Science, 2009, 323: 352–353CrossRefGoogle Scholar
  11. 11.
    Clelland C T, Risca V, Bancroft C. Hiding messages in DNA microdots. Nature, 1999, 399: 533–534CrossRefGoogle Scholar
  12. 12.
    Seelig G, Soloveichik D, Zhang Y D, et al. Enzyme-free nucleic acid logic circuits. Science, 2006, 314: 1585–1588CrossRefGoogle Scholar
  13. 13.
    Shin J S, Pierce N A. Rewritable memory by controllable nanopatterning of DNA. Nano Lett, 2004, 4: 905–909CrossRefGoogle Scholar
  14. 14.
    Zhang D Y, Turberfield A J, Yurke B, et al. Engineering entropy-driven reactions and networks catalyzed by DNA. Science, 2007, 318: 1121–1125CrossRefGoogle Scholar
  15. 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: 14875–14879CrossRefGoogle Scholar
  16. 16.
    Winfree E. Design and self-assembly of two-dimensional DNA crystals. Nature, 1998, 394: 539–544CrossRefGoogle Scholar
  17. 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: 1848–1860CrossRefGoogle Scholar
  18. 18.
    Carbone A, Seeman N C. Circuits and programmable self-assembling DNA structures. Proc Natl Acad Sci USA, 2002, 99: 12577–12582CrossRefGoogle Scholar
  19. 19.
    Rothemund P W. Folding DNA to create nanoscale shapes and patterns. Nature, 2006, 440: 297–302CrossRefGoogle Scholar
  20. 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: 1661–1665CrossRefGoogle Scholar
  21. 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: 10665–10669CrossRefGoogle Scholar
  22. 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: 349–352CrossRefGoogle Scholar
  23. 23.
    Han D R, Pal S, Nangreave J, et al. DNA origami with complex curvatures in three-dimensional space. Science, 2011, 332: 342–346CrossRefGoogle Scholar
  24. 24.
    Ackermann D, Schmidt T L, Hannam J S, et al. A double-stranded DNA rotaxane. Nat Nanotechnol, 2010, 5: 436–442CrossRefGoogle Scholar
  25. 25.
    Thomas C. DNA as a logic operator. Nature, 2011, 469: 45–46CrossRefGoogle Scholar
  26. 26.
    Liu Q H, Wang L M, Frutos A G, et al. DNA computing on surfaces. Nature, 2000, 403: 175–179CrossRefGoogle Scholar
  27. 27.
    Benenson Y, Elizur T P, Adar R, et al. Programmable and autonomous computing machine made of biomolecules. Nature, 2001, 411: 430–434CrossRefGoogle Scholar
  28. 28.
    Benenson Y, Gil B, Dor U B, et al. An autonomous molecular computer for logical control of gene expression. Nature, 2004, 429: 423–429CrossRefGoogle Scholar

Copyright information

© The Author(s) 2013

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 2.0 International License (https://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Authors and Affiliations

  1. 1.Institute of Software, School of Electronics Engineering and Computer Science, Key Laboratory of High Confidence Software Technologies of Ministry of EducationPeking UniversityBeijingChina
  2. 2.College of Life ScienceShaanxi Normal UniversityXi’anChina
  3. 3.School of Control and Computer EngineeringNorth China Electric Power UniversityBeijingChina

Personalised recommendations