Error suppression mechanisms for DNA tile self-assembly and their simulation

Natural Computing

Volumn 8, Issue 3, 2009, Pages 589-612

  Fujibayashi, Kenichi ^a   Zhang, David Yu ^b   Winfree, Erik ^b   Murata, Satoshi ^a  

^a TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

^b CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Algorithmic self assembly; Assembly errors; Branch migration; DNA self assembly; Protecting molecules

Indexed keywords

DNA;

ANALYTICAL ERROR; CONFERENCE PAPER; DNA HYBRIDIZATION; GENETIC ALGORITHM; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MOLECULAR DYNAMICS; PREDICTION; SIMULATION; TEMPERATURE; THERMODYNAMICS;

EID: 70349142294     PISSN: 15677818     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11047-008-9093-9     Document Type: Conference Paper

References (35)

1. Adleman L, Cheng Q, Goel A, Huang M-D (2001) Running time and program size for self-assembled squares. In: STOC'01: Proceedings of the 33rd annual ACM symposium on theory of computing. ACM Press, New York, NY, pp 740-748
2. Barish RD, Rothemund PWK, Winfree E (2005) Two computational primitives for algorithmic self-assembly: Copying and counting. Nano Lett 5:2586-2592
3. Baryshnikov Y, Coffman E, Seeman N, Yimwadsana T (2006) Self-correcting self-assembly: Growth models and the Hammersley process. In: Carbone A, Pierce NA (eds) DNA Computing 11, vol. 3892 of LNCS. Springer-Verlag, Berlin, pp 1-11
4. Biswas I, Yamamoto A, Hsieh P (1998) Branch migration through DNA sequence heterology. J Mol Biol 279:795-806
5. Chen H-L, Goel A (2005) Error free self-assembly using error prone tiles. In: Ferretti C, Mauri G, Zandron C (eds) DNA Computing 10, vol 3384 of LNCS. Springer-Verlag, Berlin, pp 1-11
6. Chen H-L, Cheng Q, Goel A, Huang M-D, de Espanes PM (2004) Invadable self-assembly: Combining robustness with efficiency. In: SODA '04: Proceedings of the 15th annual ACM-SIAM symposium on discrete algorithms. SIAM, Philadelphia, PA, pp 890-899
7. Chen H-L, Schulman R, Goel A, Winfree E (2007) Reducing facet nucleation during algorithmic self-assembly. Nano Lett 7:2913-2919
8. Cook M, Rothemund PWK, Winfree E (2004) Self-assembled circuit patterns. In: Chen J, Reif JH (eds) DNA Computing 9, vol 2943 of LNCS. Springer-Verlag, Berlin, pp 91-107
9. Dirks RM, Pierce NA (2004) Triggered amplification by hybridization chain reaction. Proc Natl Acad Sci USA 101:15275-15278
10. Fu T-J, Seeman NC (1993) DNA double-crossover molecules. Biochemistry 32:3211-3220
11. Fujibayashi K, Murata S (2005) A method of error suppression for self-assembling DNA tiles. In: Ferretti C, Mauri G, Zandron C (eds) DNA Computing 10, vol 3384 of LNCS. Springer-Verlag, Berlin, pp 113-127
12. Panyutin IG, Hsieh P (1994) The kinetics of spontaneous DNA branch migration. Proc Natl Acad Sci USA 91:2021-2025
13. Panyutin IG, Biswas I, Hsieh P (1995) A pivotal role for the structure of the Holliday junction in DNA branch migration. EMBO J 14:1819-1826
14. Reif JH (1999) Local parallel biomolecular computation. In: Rubin H, Wood DH (eds) DNA based computers III, vol 48 of DIMACS. AMS Press, Providence, RI, pp 217-254
15. Reif JH, Sahu S, Yin P (2005) Compact error-resilient computational DNA tiling assemblies. In: Ferretti C, Mauri G, Zandron C (eds) DNA Computing 10, vol 3384 of LNCS. Springer-Verlag, Berlin, pp 293-307
16. Reynaldo LP, Vologodskii AV, Neri BP, Lyamichev VI (2000) The kinetics of oligonucleotide replacements. J Mol Biol 297:511-520
17. Rothemund PWK, Winfree E (2000) The program-size complexity of self-assembled squares (extended abstract). In: STOC'00: Proceedings of the thirty-second annual ACM symposium on theory of computing. ACM Press, New York, NY, pp 459-468
18. Rothemund PWK, Papadakis N, Winfree E (2004) Algorithmic self-assembly of DNA Sierpinski triangles. PLoS Biol 2: 2041-2053
19. Sahu S, Reif JH (2006) Capabilities and limits of compact error resilience methods for algorithmic self-assembly in two and three dimensions. In: Mao C, Yokomori T (eds) DNA Computing 12, vol 4287 of LNCS. Springer-Verlag, Berlin, pp 223-238
20. Schulman R, Winfree E (2005) Programmable control of nucleation for algorithmic self-assembly. In: Ferretti C, Mauri G, Zandron C (eds) DNA Computing 10, vol 3384 of LNCS. Springer-Verlag, Berlin, pp 319-328. Extended abstract in DNA Computing 10; preprint of the full paper is cond-mat/0607317 on http://arXiv.org
21. Schulman R, Winfree E (2007) Synthesis of crystals with a programmable kinetic barrier to nucleation. Proc Natl Acad Sci USA 104:15236-15241
22. Seeman NC (2005) The challenge of structural control on the nanoscale: Bottom-up self-assembly of nucleic acids in 3D. Int J Nanotechnol 2:348-370
23. Soloveichik D, Winfree E (2004) Complexity of self-assembled shapes. SIAM J Comput 36:1544-1569, 2007. Extended abstract in LNCS 3384: 344-354 (2004); preprint is cs.CC/0412096 on http://arXiv.org
24. Somei K, Kaneda S, Fujii T, Murata S (2006) A microfluidic device for DNA tile self-assembly. In: Carbone A, Pierce NA (eds) DNA Computing 11, vol 3892 of LNCS. Springer-Verlag, Berlin, pp 325-335
25. Turberfield AJ, Yurke B, Mills AP Jr (2000) DNA hybridization catalysts and molecular tweezers. In: Winfree E, Gifford DK (eds) DNA based computers V, vol 54 of DIMACS. AMS Press, Providence, RI, pp 171-182
26. Wang H (1961) Proving theorems by pattern recognition II. Bell Syst Tech J 40:1-42
27. Wang H (1963) Dominoes and the AEA case of the decision problem. In: Fox J (ed) Proceedings of the symposium on the mathematical theory of automata. Polytechnic Press, Brooklyn, NY, pp 23-55
28. Wetmur JG (1991) DNA probes: Applications of the principles of nucleic acid hybridization. Crit Rev Biochem Mol Biol 26:227-259
29. Whitesides GM, Mathias JP, Seto CT (1991) Molecular self-assembly and nanochemistry: A chemical strategy for the synthesis of nanostructures. Science 254:1312-1319
30. Winfree E (1996) On the computational power of DNA annealing and ligation. In: Lipton RJ, Baum EB (eds) DNA based computers, vol 27 of DIMACS. AMS Press, Providence, RI, pp 199-221
31. Winfree E (1998) Simulations of computing by self-assembly. CaltechCSTR:1998.22. California Institute of Technology
32. Winfree E, Bekbolatov R (2004) Proofreading tile sets: Error correction for algorithmic self-assembly. In: Chen J, Reif JH (eds) DNA Computing 9, vol 2943 of LNCS. Springer-Verlag, Berlin, pp 126-144
33. Winfree E, Liu F, Wenzler LA, Seeman NC (1998) Design and self-assembly of two-dimensional DNA crystals. Nature 394:539-544
34. Yurke B, Mills AP Jr (2003) Using DNA to power nanostructures. Genet Program Evol Machines 4:111-122
35. Yurke B, Turberfield AJ, Mills AP Jr, Simmel FC, Nuemann JL (2000) A DNA-fuelled molecular machine made of DNA. Nature 406:605-608