Robustness and modularity properties of a non-covalent DNA catalytic reaction

Nucleic Acids Research

Volumn 38, Issue 12, 2010, Pages 4182-4197

  Zhang, David Yu ^a   Winfree, Erik ^a  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SINGLE STRANDED DNA; DEOXYRIBOZYME; DNA;

ARTICLE; CATALYSIS; CHEMICAL REACTION; CONTROLLED STUDY; COVALENT BOND; DNA STRAND; GENE MUTATION; GENE SEQUENCE; MOLECULAR MECHANICS; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY; BIOLOGICAL MODEL; CHEMISTRY; ENZYME SPECIFICITY; KINETICS; METABOLISM;

CATALYSIS; DNA; DNA, CATALYTIC; DNA, SINGLE-STRANDED; KINETICS; MODELS, BIOLOGICAL; SUBSTRATE SPECIFICITY;

EID: 77955064536     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq088     Document Type: Article

References (28)

1. Santa Lucia, J. (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl Acad. Sci. USA, 95, 1460-1465.
2. Zhang, D.Y. and Winfree, E. (2009) Control of DNA strand displacement kinetics using toehold exchange. J. Am. Chem. Soc. 131, 17303-17314.
3. Yurke, B. and Mills, A.P. (2003) Using DNA to power nanostructures. Genet. Prog. Evol. Mach., 4, 111-122.
4. Seelig, G., Soloveichik, D., Zhang, D.Y. and Winfree, E. (2006) Enzyme-free nucleic acid logic circuits. Science, 314, 1585-1588.
5. Hagiya, M., Yaegashi, S. and Takahashi, K. (2006) Computing with hairpins and secondary structures of DNA. In Rozenberg, G., Back, Th., Eiben, A.E., Kok, J.N. and Spaink, H.P. (eds), Nanotechnology: Science and Computation. Springer, Berlin, Heidelberg, pp. 293-308.
6. Frezza, B.M., Cockroft, S.L. and Ghadiri, M.R. (2007) Modular multi-level circuits from immobilized DNA-based logic gates. J. Am. Chem. Soc., 129, 14875-14879.
7. Yurke, B., Turberfield, A.J., Mills, A.P., Simmel, F.C. and Neumann, J.L. (2000) A DNA-fuelled molecular machine made of DNA. Nature, 406, 605-608.
8. Lubrich, D., Lin, J. and Yan, J. (2008) A contractile DNA machine. Angew. Chem. Int. Ed., 47, 7026-7028.
9. Zhang, D.Y., Turberfield, A.J., Yurke, B. and Winfree, E. (2007) Engineering entropy-driven reactions and networks catalyzed by DNA. Science, 318, 1121-1125.
10. Dirks, R.M. and Pierce, N.A. (2004) Triggered amplification by hybridization chain reaction. Proc. Natl Acad. Sci. USA, 101, 15275-15278.
11. Yin, P., Choi, H.M.T., Calvert, C.R. and Pierce, N.A. (2008) Programming biomolecular self-assembly pathways. Nature, 451, 318-322.
12. Zhang, D.Y. and Winfree, E. (2008) Dynamic allosteric control of noncovalent DNA catalysis reactions. J. Am. Chem. Soc., 130, 13921-13926.
13. Seelig, G., Yurke, B. and Winfree, E. (2006) Catalyzed relaxation of a metastable DNA fuel. J. Am. Chem. Soc., 128, 12211-12220.
14. Bois, J.S., Venkataraman, S., Choi, H.M.T., Spakowitz, A.J., Wang, Z.G. and Pierce, N.A. (2006) Topological constraints in nucleic acid hybridization kinetics. Nucleic Acids Res., 33, 4090-4095.
15. Turberfield, A.J., Mitchell, J.C., Yurke, B., Mills, A.P., Blakey, M.I. and Simmel, F.C. (2003) DNA fuel for free-running nanomachines. Phys. Rev. Lett., 90, 118102.
16. Gartner, Z.J., Tse, B.N., Grubina, R., Doyon, J.B., Snyder, T.M. and Liu, D.R. (2004) DNA-templated organic synthesis and selection of a library of macrocycles. Science, 305, 1601-1605.
17. Aldaye, F.A., Palmer, A.L. and Sleiman, H.F. (2008) Assembling materials with DNA as the guide. Science, 321, 1795-1799.
18. Clo, E., Snyder, J.W., Voigt, N.V., Ogilby, P.R. and Gothelf, K.V. (2006) DNA-programmed control of photosensitized singlet oxygen production. J. Am. Chem. Soc., 128, 4200-4201.
19. Feldkamp, U., Sacca, B. and Niemeyer, C.M. (2009) Dendritic DNA building blocks for amplified detection assays and biomaterials. Angew. Chem. Int. Ed., 48, 5996-6000.
20. Marras, S.A.E., Kramer, F.R. and Tyagi, S. (2002) Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes. Nucleic Acids Res., 30, e122.
21. Gao, Y., Wolf, L.K. and Georgiadis, R.M. (2006) Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison. Nucleic Acids Res., 34, 3370-3377.
22. Puglisi, J.D. and Tinoco, I. (1989) Absorbance melting curves of RNA. Methods Enzymol., 180, 304-325.
23. Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415.
24. Bloomfield, V.A., Crothers, D.M. and Tinoco, I. (2000) Nucleic Acids: Structures, Properties, and Functions. University Science Books, Sausalito, CA.
25. Temsamani, J., Kubert, M. and Arawal, S. (1995) Sequence identity of the n-1 product of a synthetic oligonucleotide. Nucleic Acids Res., 23, 1841-1844.
26. Qian, L. and Winfree, E. (2009) A simple DNA gate motif for synthesizing large-scale circuits. In Goel, A., Simmel, F.C. and Sosik, P. (eds), DNA Computing: 14th International Meeting on DNA Computing. Springer, Berlin, Heidelberg, pp. 70-89.
27. Dirks, R.M., Bois, J.S., Schaeffer, J.M., Winfree, E. and Pierce, N.A. (2007) Thermodynamic analysis of interacting nucleic acid strands. SIAM Rev., 49, 65-88.
28. Flamm, C., Fontana, W., Hofacker, I.L. and Schuster, P. (2000) RNA folding at elementary step resolution. RNA, 6, 325-338.