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A Clocked DNA-Based Replicator

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DNA Computing (DNA 2004)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 3384))

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Abstract

A stepped replicator is described that uses the energy of hybridization to pry the product from the template in order to prevent product inhibition of replication. Toehold-mediated strand displacement is used to reset the system to its initial state after a round of replication. It is argued that the formation of dimers between structures in the process of replicating should not be able to form and, consequently, the system should exhibit exponential growth.

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References

  1. Alberts, B.: DNA replication and recombination. Nature 421, 431–435 (2003)

    Article  Google Scholar 

  2. Wintner, E.A., Conn, M.M., Rebek, J.: Studies in molecular replication. Acc. Chen. Res. 27, 198–203 (1994)

    Article  Google Scholar 

  3. Penrose, L.S.: Self-Reproducing Machines. Scientific American 200(6), 105–114 (1959)

    Article  Google Scholar 

  4. Orgel, L.E.: Unnatural Selection in Chemical Systems. Acc. Chem. Res. 28, 109–118 (1995)

    Article  Google Scholar 

  5. Bull, J.J., Wichman, H.A.: Applied Evolution. Annu. Rev. Ecol. Syst. 32, 183–271 (2001)

    Article  Google Scholar 

  6. Johnston, W.K., Unrau, P.J., Lawrence, M.S., Glasner, M.E., Bartel, D.P.: RNA-Catalyzed RNA Polymerization: Accurate and General RNA-Templated Primer Extension. Science 292, 1319–1325 (2001)

    Article  Google Scholar 

  7. von Kiedrowski, G.: A self-replicating hexadeoxynucleotide. Angew. Chem. Int. Edn Engl. 25, 932–935 (1986)

    Google Scholar 

  8. Zielinski, W.S., Orgel, L.E.: Autocatalytic synthesis of a tetranucleotide analogue. Nature 327, 346–347 (1987)

    Article  Google Scholar 

  9. von Kiedrowski, G., Wlotzka, B., Helbing, J., Matzen, M., Jordan, S.: Parabolic growth of a hexadeoxynucleotide analogue bearing a 3’-5’-phosphoamidate link. Angew. Chem. Int. Edn Engl. 30, 423–426, 892 (1991)

    Article  Google Scholar 

  10. Achilles, T., von Kiedrowski, G.: A self-replicating system from three precursors. Angew. Chem. Int. Edn 32, 1198–1201 (1993)

    Article  Google Scholar 

  11. Sievers, D., von Kiedrowski, G.: Self-replication of complementary nucleotide-based oligomers. Nature 369, 221–224 (1994)

    Article  Google Scholar 

  12. Li, T., Nicolaou, K.C.: Chemical self-replication of palindromic duplex DNA. Nature 369, 218 (1994)

    Article  Google Scholar 

  13. Martin, B., Micura, R., Pitsch, S., Eschenmoser, A.: Pyranosyl-RNA: further observations on replication. Helv. Chim. Acta 80, 1901–1951 (1997)

    Article  Google Scholar 

  14. Sievers, D., von Kiedrowski, G.: Self-replication of hexadeoxynucleotide analogues: autocatalysis versus cross-catalysis. Chem. Eur. J. 4, 629–641 (1998)

    Article  Google Scholar 

  15. Schöneborn, H., Bülle, J., von Kiedrowski, G.: Kinetic monitoring of self-replicating systems through measurement of fluorescence resonance energy transfer. Chembiochem 2, 922–927 (2001)

    Article  Google Scholar 

  16. Lee, D.H., Granja, J.R., Martinez, J.A., Severin, K., Ghadiri, M.R.: A self-replicating peptide. Nature 382, 525–528 (1996)

    Article  Google Scholar 

  17. Severin, K.S., Lee, D.H., Martinez, J.A., Ghadiri, M.R.: Peptide self-replication via template-directed ligation. Chem. Eur. J. 3, 1017–1024 (1997)

    Article  Google Scholar 

  18. Severin, K., Lee, D.H., Martinez, J.A., Vieth, M., Ghadiri, M.R.: Dynamic error correction in autocatalytic peptide networks. Angew, Chem. Int. Edn Engl. 37, 126–128 (1998)

    Article  Google Scholar 

  19. Yao, S., Ghosh, I., Zutshi, R., Chmielewski, J.A.: A self-replicating peptide under ionic control. Angew. Chem. Int. Edn Engl. 37, 478–481 (1998)

    Article  Google Scholar 

  20. Saghathelian, A., Yokobayashi, Y., Soltani, K., Ghadiri, M.R.: A chiroselective peptide replicator. Nature 409, 797–801 (2001)

    Article  Google Scholar 

  21. Tjivikua, T., Ballester, P., Rebek, J.A.: A self-replicating system. J. Am. Chem. Soc. 112, 1249–1250 (1990)

    Article  Google Scholar 

  22. Terfort, A., von Kiedrowski, G.: Self-replication during condensation of 3-aminobenzamidines with 2-formylphenoxyacetic acids. Angew. Chem. Int. Edn Engl. 31, 654–656 (1992)

    Article  Google Scholar 

  23. Hong, J.-I., Fang, Q., Rotello, V., Rebek, J.: Competition, cooperation, and mutation improving a synthetic replicator by light irradiation. Science 255, 848–850 (1992)

    Article  Google Scholar 

  24. Fang, Q., Park, T.K., Rebek, J.: Crossover reactions between synthetic replicators yield active and inactive recombinants. Science 256, 1179–1180 (1992)

    Article  Google Scholar 

  25. Pieters, R.J., Huc, I., Rebek, J.: Reciprocal template effect in a replication cycle. Angew. Chem. Int. Edn Engl. 106, 1579–1581 (1994)

    Article  Google Scholar 

  26. Reinhoudt, D.N., Rudkevich, D.M., de Jong, F.: Kinetic analysis of the Rebek self-replicating system: Is there a controversy? J. Am. Chem. Soc. 118, 6880–6889 (1996)

    Article  Google Scholar 

  27. Wang, B., Sutherland, I.O.: Self-replication in a Diels-Alder reaction. Chem. Commun. 16, 1495–1496 (1997)

    Article  Google Scholar 

  28. Szathmáry, E., Gladkih, I.: Sub-exponential growth and coexistence of non-enzymatically replicating templates. J. Theor. Biol. 138, 55–58 (1989)

    Article  Google Scholar 

  29. Wills, P.R., Kauffman, S.A., Stadler, B.M.R.: Selection dynamics in autocatalytic systems: Templates replicating through binary ligation. Bull. Math. Bio. 60, 1073–1098 (1998)

    Article  MATH  Google Scholar 

  30. Paul, N., Joyce, G.F.: A self-replicating ligase ribozyme. PNAS 99, 12733–12740 (2002)

    Article  Google Scholar 

  31. Luther, A., Brandsch, R., von Kiedrowski, G.: Surface-promoted replication and exponential amplification of DNA analogues. Nature 396, 245–248 (1998)

    Article  Google Scholar 

  32. Chen, J., Seeman, N.C.: The synthesis from DNA of a molecule with the connectivity of a cube. Nature 350, 631–633 (1991)

    Article  Google Scholar 

  33. Seeman, N.C.: Nucleic acid nanostructures and topology. Angew. Chem. Int. Edn Engl. 37, 3220–3238 (1998)

    Article  Google Scholar 

  34. Winfree, E., Liu, F., Wenzler, L.A., Seeman, N.C.: Design and self-assembly of two-dimensional DNA crystals. Nature 394, 539–544 (1998)

    Article  Google Scholar 

  35. Mao, C., Sun, W., Seeman, N.C.: Designed two-dimensional DNA Holiday junction arrays visualized by atomic force microscopy. J. Am. Chem. Soc. 121, 5437–5443 (1999)

    Article  Google Scholar 

  36. LaBean, T.H., Yan, H., Kopatsch, J., Liu, F., Winfree, E., Reif, J.H., Seeman, N.C.: Construction, analysis, ligation, and self-assembly of DNA triple crossover complexes. J. Am. Chem. Soc. 122, 1848–1860 (2000)

    Article  Google Scholar 

  37. Mao, C., LaBean, T.H., Reif, J.H., Seeman, N.C.: Logical computation using algorithmic self-assembly of DNA triple-crossover molecules. Nature 407, 493–496 (2000)

    Article  Google Scholar 

  38. Seeman, N.C.: DNA in a material world. Nature 421, 427–431 (2003)

    Article  MathSciNet  Google Scholar 

  39. Mao, C., Sun, W., Shen, Z., Seeman, N.C.: A nanomechanical device based on the B-Z transition of DNA. Nature 297, 144–146 (1999)

    Google Scholar 

  40. Yurke, B., Turberfield, A.J., Mills Jr., A.P., Simmel, F.C., Neumann, J.L.: A DNA-fuelled molecular machine made of DNA. Nature 406, 605–608 (2000)

    Article  Google Scholar 

  41. Simmel, F.C., Yurke, B.: Using DNA to construct and power a nanoactuator. Phys. Rev. E 63, art. no. 041913 (2001)

    Google Scholar 

  42. Simmel, F.C., Yurke, B.: A DNA-based molecular device switchable between three distinct mechanical states. Appl. Phys. Lett. 80, 883–885 (2002)

    Article  Google Scholar 

  43. Yan, H., Zhang, X., Shen, Z., Seeman, N.C.: A robust DNA mechanical device controlled by hybridization topology. Nature 415, 62–65 (2002)

    Article  Google Scholar 

  44. Li, J.J., Tan, W.: A single DNA molecular nanomotor. Nano Lett. 2, 315–318 (2002)

    Article  Google Scholar 

  45. Alberti, P., Mergny, J.-L.: DNA duplex-quadruples exchange as the basis for a nanomolecular machine. PNAS 100, 1569–1573 (2003)

    Article  Google Scholar 

  46. Feng, L., Park, S.H., Reif, J.H., Yan, H.: A two-state DNA lattice switched by DNA nanoactuator. Angew. Chem. Int. Ed. 42, 4342–4346 (2003)

    Article  Google Scholar 

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Author information

Authors and Affiliations

  1. Bell Laboratories, 600 Mountain Ave., Murray Hill, NJ, 07974, USA

    Bernard Yurke

  2. California Institute of Technology, Pasadena, California, 91125

    Bernard Yurke & David Zhang

Authors
  1. Bernard Yurke
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  2. David Zhang
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Editor information

Editors and Affiliations

  1. Dipartimento di Informatica, Sistemistica e Comunicazione, Università degli Studi di Milano – Bicocca, Via Bicocca degli Arcimboldi 8, 20126, Milano, Italy

    Claudio Ferretti  & Claudio Zandron  & 

  2. Complex Systems and Artificial Intelligence Research Center, University of Milan–Bicocca, Italy

    Giancarlo Mauri

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© 2005 Springer-Verlag Berlin Heidelberg

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Yurke, B., Zhang, D. (2005). A Clocked DNA-Based Replicator. In: Ferretti, C., Mauri, G., Zandron, C. (eds) DNA Computing. DNA 2004. Lecture Notes in Computer Science, vol 3384. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11493785_38

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  • DOI: https://doi.org/10.1007/11493785_38

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-26174-2

  • Online ISBN: 978-3-540-31844-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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