Meta-DNA: A DNA-Based Approach to Synthetic Biology



The goal of synthetic biology is to design and assemble synthetic systems that mimic biological systems. One of the most fundamental challenges in synthetic biology is to synthesize artificial biochemical systems, which we will call meta-biochemical systems, that provide the same functionality as biological nucleic acids-enzyme Enzymesystems, but that use a very limited number of types of molecules. The motivation for developing such synthetic biology systems is to enable a better understanding of the basic processes of natural biology, and also to enable re-engineering and programmability of synthetic versions of biological systems. One of the key aspects of modern nucleic acid biochemistry is its extensive use of protein enzymes that were originally evolved in cells to manipulate nucleic acids, and then later adapted by man for laboratory use. This practice provided powerful tools for manipulating nucleic acids, but also limited the extent of the programmability of the available chemistry for manipulating nucleic acids, since it is very difficult to predictively modify the behavior of protein enzymes. Meta-biochemical systems offer the possible advantage of being far easier to re-engineer and program for desired functionality. The approach taken here is to develop a biochemical system which we call meta-DNA (abbreviated as mDNA),Meta-DNA (mDNA) based entirely on strands of DNA as the only component molecules. Our work leverages prior work on the development of self-assembled DNA nanostructures (see [1, 2, 5, 9, 11, 18, 26] for excellent reviews of the field). Each base of a mDNA Meta-DNA (mDNA)is a DNA nanostructure. Our mDNA bases are paired similar to DNA bases, but have a much larger alphabet of bases, thereby providing increased power of base addressability. Our mDNA bases can be assembled to form flexible linear assemblies (single stranded mDNA) analogous to single stranded DNA, and can be hybridized to form stiff helical structures (duplex mDNA) analogous to double Double strand meta-DNA (dsmDNA) stranded DNA, and also can be denatured back to single stranded mDNA. Our work also leverages the abstract activatable tile model developed by Majumder et al. [12] and prior work on the development of enzyme-free isothermal Isothermalprotocols based on DNA hybridization and sophisticated strand displacement hybridization reactions (see [6, 15, 16, 19, 21, 27, 28]). We describe various isothermal hybridization reactions that manipulate our mDNA in powerful ways analogous to DNA–DNA reactions and the action of various enzymes on DNA. These operations on mDNA include (i) hybridization of single strand mDNA (ssmDNA)Single strand meta-DNA (ssmDNA) into a double strand mDNA (dsmDNA)Double strand meta-DNA (dsmDNA) and heat denaturation of a dsmDNA Double strand meta-DNA (dsmDNA)into its component ssmDNA Single strand meta-DNA (ssmDNA)(analogous to DNA hybridization and denaturation), (ii) strand displacement of one ssmDNA Single strand meta-DNA (ssmDNA)by another (similar to strand displacement in DNA), (iii) restriction cuts on the backbones of ssmDNA Single strand meta-DNA (ssmDNA)and dsmDNA Double strand meta-DNA (dsmDNA)(similar to the action of restriction enzymes on DNA), (iv) polymerization chain reactions that extend ssmDNA Single strand meta-DNA (ssmDNA)on a template to form a complete dsmDNA Double strand meta-DNA (dsmDNA)(similar to the action of polymerase enzyme on DNA), (v) isothermal denaturation of a dsmDNA Double strand meta-DNA (dsmDNA)into its component ssmDNA Single strand meta-DNA (ssmDNA)(like the activity of helicase enzyme on DNA) and (vi) an isothermal replicator reaction which exponentially amplifies ssmDNA Single strand meta-DNA (ssmDNA)strands (similar to the isothermal PCR reaction). We provide a formal model to describe the required properties and operations of our mDNA, and show that our proposed DNA nanostructures and hybridization reactions provide these properties and functionality.


Enzyme DNA Meta-DNA (mDNA) Isothermal Hybridization Strand displacement Single strand meta-DNA (ssmDNA) Double strand meta-DNA (dsmDNA) 



We wish to acknowledge support by NSF grants CCF-0829797, CCF-0829798, CCF-1217457 and CCF-1141847.


  1. 1.
    Amin R, Kim S, Park SH, LaBean T (2009) Artifically designed DNA nanostructures. NANO: Br Rep Rev 4(3):119–139Google Scholar
  2. 2.
    Bath J, Turberfield A (2007) DNA nanomachines. Nature Nanotechnol 2:275–284CrossRefGoogle Scholar
  3. 3.
    Bedau M, McCaskill J, Packard N, Rasmussen S, Adami C, Green D, Ikegami T, Kaneko K, Ray T (2000) Open problems in artificial life. Artif Life 6(4):363–376PubMedCrossRefGoogle Scholar
  4. 4.
    Dadon Z, Wagner N, Ashkenasy G (2008) The road to non-enzymatic molecular networks. Angewandte Chemie Int Ed 47(33):6128–6136CrossRefGoogle Scholar
  5. 5.
    Deng Z, Chen Y, Tian Y, Mao C (2006) A fresh look at DNA nanotechnology. Nanotechnol: Sci Comput, 23–34Google Scholar
  6. 6.
    Dirks R, Pierce N (2004) Triggered amplification by hybridization chain reaction. Proc Natl Acad Sci USA 101(43):15275–15278PubMedCentralPubMedCrossRefGoogle Scholar
  7. 7.
    Hamada S, Murata S (2009) Substrate-assisted assembly of interconnected single-duplex DNA nanostructures. Angewandte Chemie Int Ed 48(37):6820–6823CrossRefGoogle Scholar
  8. 8.
    Koval V, Gnedenko O, Ivanov Y, Fedorova O, Archakov A, Knorre D (1999) Real-time oligonucleotide hybridization kinetics monitored by resonant mirror technique. IUBMB Life 48(3):317–320PubMedCrossRefGoogle Scholar
  9. 9.
    LaBean T, Gothelf K, Reif J (2007) Self-assembling DNA nanostructures for patterned molecular assembly. Nanobiotechnology II 79–97Google Scholar
  10. 10.
    Luisi PL (2006) The emergence of life—from chemical origins to synthetic biology. Cambridge University Press, CambridgeGoogle Scholar
  11. 11.
    Lund K, Williams B, Ke Y, Liu Y, Yan H (2006) DNA nanotechnology: a rapidly evolving field. Curr Nanosci 2:113–122CrossRefGoogle Scholar
  12. 12.
    Majumder U, LaBean T, Reif J (2007) Activatable tiles: compact, robust programmable assembly and other applications. In: DNA ComputingGoogle Scholar
  13. 13.
    Packard N, Bedau M (2003) Artificial Life. Encycl Cogn Sci 1:209–215Google Scholar
  14. 14.
    Park SH, Pistol C, Ahn SJ, Reif J, Lebeck A, LaBean CDT (2006) Finite-size, fully addressable DNA tile lattices formed by hierarchical assembly procedures. Angewandte Chemie Int Ed 45(5):735–739CrossRefGoogle Scholar
  15. 15.
    Reif J, Majumder U (2008) Isothermal reactivating Whiplash PCR for locally programmable molecular computation. DNA Comput 41–56Google Scholar
  16. 16.
    Sakamoto K, Kiga D, Momiya K, Gouzu H, Yokoyama S, Ikeda S, Sugiyama H, Hagiya M (1999) State Transitions by Molecules. Biosystems 81–91Google Scholar
  17. 17.
    Schulman R, Winfree E (2008) How crystals that sense and respond to their environments could evolve. Nat Comput 7(2):219–237CrossRefGoogle Scholar
  18. 18.
    Seeman N (2004) Nanotechnology and the double helix. Sci Am 290(6):64–75PubMedCrossRefGoogle Scholar
  19. 19.
    Sherman W, Seeman N (2004) A precisely controlled DNA biped walking device. Nano Lett 4:1203–1207CrossRefGoogle Scholar
  20. 20.
    Smith A, Turney P, Ewaschuk R (2002) JohnnyVon: self-replicating automata in continuous two-dimensional space. Comput Res RepositoryGoogle Scholar
  21. 21.
    Tian Y, He Y, Mao C (2006) Cascade signal amplification for DNA detection. ChemBioChem 7(12):1862–1864PubMedCrossRefGoogle Scholar
  22. 22.
    Tjivikua T, Ballester P, Rebek J (1990) A self-replicating system. J Am Chem Soc 112(2):1249–1250CrossRefGoogle Scholar
  23. 23.
    Vidonne A, Philp D (2009) Making molecules make themselves—the chemistry of artificial replicators. Eur J Org Chem 5:593–610CrossRefGoogle Scholar
  24. 24.
    von Kiedrowski G (1986) A self-replicating hexadeoxynucleotide. Angewandte Chemie International Edition 25(10):932–935CrossRefGoogle Scholar
  25. 25.
    von Kiedrowski G, Patzke V (2007) Self replicating systems. ARKIVOK 293–310Google Scholar
  26. 26.
    Winfree E (2003) DNA computing by self-assembly. NAE’s Bridge 33:31–38Google Scholar
  27. 27.
    Yin P, Yan H, Daniell X, Turberfield A, Reif J (2004) A unidirectional DNA walker moving autonomously along a linear track. Angewandte Chemie Int Ed 116(37):5014–5019CrossRefGoogle Scholar
  28. 28.
    Zhang D, Turberfield A, Yurke B, Winfree E (2007) Engineering entropy-driven reactions and networks catalyzed by DNA. Science 318:1121–1125PubMedCrossRefGoogle Scholar
  29. 29.
    Zhang DY, Winfree E (2009) Control of DNA strand displacement kinetics using toehold exchange. J Am Chem Soc 131(48):17303–17314PubMedCrossRefGoogle Scholar
  30. 30.
    Zhang DY, Yurke B (2006) A DNA superstructure-based replicator without product inhibition. Nat Comput 5(2):183–202CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  1. 1.Department of Computer ScienceDuke UniversityNCUSA
  2. 2.Department of Materials Science and Engineering and Department of Electrical and Computer EngineeringBoise State UniversityIDUSA
  3. 3.Adjunct Faculty of Computing and Information TechnologyKing Abdulaziz UniversityJeddahSaudi Arabia

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