Robust self-replication of combinatorial information via crystal growth and scission

Proceedings of the National Academy of Sciences of the United States of America

Volumn 109, Issue 17, 2012, Pages 6405-6410

  Schulman, Rebecca ^a   Yurke, Bernard ^b   Winfree, Erik ^a,c  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^b Boise State University   (United States)

^c California Institute of Technology   (United States)

Author keywords

Algorithmic self assembly; DNA nanotechnology; Self assembly

Indexed keywords

MONOMER;

ARTICLE; CATALYSIS; CHEMICAL ANALYSIS; CHEMICAL PHENOMENA; COVALENT BOND; CRYSTALLIZATION; DNA HYBRIDIZATION; DNA REPLICATION; DNA SEQUENCE; DNA STRAND; PRIORITY JOURNAL; SCISSION;

BIOCATALYSIS; CRYSTALLIZATION; DNA; DNA REPLICATION; EVOLUTION, MOLECULAR;

EID: 84860147587     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1117813109     Document Type: Article

References (46)

1. Paul N, Joyce GF (2004) Minimal self-replicating systems. Curr Opin Chem Biol 8:634-639. (Pubitemid 39535726)
2. Vidonne A, Philp D (2009) Making molecules make themselves: The chemistry of artificial replicators. Eur J Org Chem 2009:593-610.
3. Rubinov B, Wagner N, Rapaport H, Ashkenasy G (2009) Self-replicating amphiphilic β-sheet peptides. Angew Chem Int Ed 48:6683-6686.
4. Lincoln TA, Joyce GF (2009) Self-sustained replication of an RNA enzyme. Science 323:1229-1232.
5. Carnall JMA, et al. (2010) Mechanosensitive self-replication driven by self-organization. Science 327:1502-1506.
6. Rasmussen S, et al. (2004) Transitions from nonliving to living matter. Science 303:963-965. (Pubitemid 38209688)
7. Johnston WK, Unrau PJ, Lawrence MS, Glasner ME, Bartel DP (2001) RNA-catalyzed RNA polymerization: Accurate and general RNA-templated primer extension. Science 292:1319-1325. (Pubitemid 32476210)
8. Wochner A, Attwater J, Coulson A, Holliger P (2011) Ribozyme-catalyzed transcription of an active ribozyme. Science 332:209-212.
9. Deck C, Jauker M, Richert C (2011) Efficient enzyme-free copying of all four nucleobases templated by immobilized RNA. Nat Chem 3:603-608.
10. Schrum JP, Ricardo A, Krishnamurthy M, Blain JC, Szostak JW (2009) Efficient and rapid template-directed nucleic acid copying using 2′-amino-2′,3′-dideoxyribonucleoside-5′- phosphorimidazolide monomers. J Am Chem Soc 131:14560-14570.
11. Kervio E, Hochges A, Steiner UE, Richert C (2010) Templating efficiency of naked DNA. Proc Natl Acad Sci USA 107:12074-12079.
12. Scheel HJ, Fukuda T (2003) Crystal Growth Technology (John Wiley and Sons).
13. Collins SR, Douglass A, Vale RD,Weissman JS (2004) Mechanism of prion propagation: Amyloid growth occurs by monomer addition. PLoS Biol 2:e321.
14. Viedma C (2005) Chiral symmetry breaking during crystallization: Complete chiral purity induced by nonlinear autocatalysis and recycling. Phys Rev Lett 94:065504.
15. Cairns-Smith AG (1966) The origin of life and the nature of the primitive gene. J Theor Biol 10:53-88.
16. Orgel LE, Crick FHC (1993) Anticipating an RNA world. Some past speculations on the origin of life: Where are they today? FASEB J 7:238-239.
17. Bullard T, Freudenthal J, Avagyan S, Kahr B (2007) Test of Cairns-Smith's crystalsas- genes hypothesis. Faraday Discuss 136:231-245.
18. Winfree E, Liu F, Wenzler LA, Seeman NC (1998) Design and self-assembly of twodimensional DNA crystals. Nature 394:539-544. (Pubitemid 28366820)
19. Barish RD, Schulman R, Rothemund PWK, Winfree E (2009) An information-bearing seed for nucleating algorithmic self-assembly. Proc Natl Acad Sci USA 106:6054-6059.
20. Schulman R, Winfree E (2005) Self-replication and evolution of DNA crystals. Advances in Artificial Life, 8th European Conference, (Springer-Verlag, Berlin Heidelberg), Vol. 3630.
21. Mao C, LaBean TH, Reif JH, Seeman NC (2000) Logical computation using algorithmic self-assembly of DNA triple-crossover molecules. Nature 407:493-496.
22. Rothemund PWK, Papadakis N, Winfree E (2004) Algorithmic self-assembly of DNA Sierpinski triangles. PLoS Biology 2:e424-436.
23. Winfree E, Bekbolatov R (2004) Proofreading tile sets: Error-correction for algorithmic self-assembly. DNA Computing 9, eds J Chen and J Reif (Springer-Verlag, Berlin Heidelberg), Vol. LNCS 2943, pp 126-144.
24. Schulman R, Winfree E (2009) Programmable control of nucleation for algorithmic self-assembly. SIAM J Comput 39:1581-1616.
25. Schulman R, Winfree E (2007) Synthesis of crystals with a programmable kinetic barrier to nucleation. Proc Natl Acad Sci USA 104:15236-15241. (Pubitemid 47502902)
26. Rothemund PWK (2006) Folding DNA to create nanoscale shapes and patterns. Nature 440:297-302.
27. Eigen M, McCaskill J, Schuster P (1988) Molecular quasi-species. J Phys Chem 92:6881-6891.
28. Hariadi R, Yurke B (2010) Elongational-flow-induced scission of DNA nanotubes in laminar flow. Phys Rev E 82:046307.
29. Cloitre M, Mongruel A (1999) Dynamics of non-Brownian rodlike particles in a nonuniform elongational flow. Phys Fluids 11:773-777. (Pubitemid 129518633)
30. Schulman R, Winfree E (2008) How crystals that sense and respond to their environments could evolve. Nat Comp 7:219-237. (Pubitemid 351722422)
31. Knowles TPJ, et al. (2009) An analytical solution to the kinetics of breakable filament assembly. Science 326:1533-1537.
32. Seeman NC (2010) Nanomaterials based on DNA. Ann Rev Biochem 79:65-87.
33. Zhang DY, Yurke B (2006) A DNA superstructure-based replicator without product inhibition. Natur Comp 5:183-202. (Pubitemid 43899159)
34. Chandran H, Gopalkrishnan N, Yurke B, Reif J (2012) Meta-DNA: Synthetic biology via DNA nanostructures and hybridization reactions. J R Soc Interface rsif.2011.0819v1-rsif20110819.
35. Wang T, et al. (2011) Self-replication of information-bearing nanoscale patterns. Nature 478:225-228.
36. Fujibayashi K, Hariadi R, Park SH, Winfree E, Murata S (2008) Toward reliable algorithmic self-assembly of DNA tiles: a fixed-width cellular automaton pattern. Nano Lett 8:3554-3560.
37. Schulman R, Winfree E (2010) Simple evolution of complex crystal species. DNA Computing 16, eds Y Sakakibara and M Yongli (Springer-Verlag, Berlin Heidelberg), Vol. 6518.
38. Soloveichik D, Winfree E (2007) Complexity of self-assembled shapes. SIAM J Comput 36:1544-1569.
39. Winfree E (2006) Self-Healing Tile Sets. Nanotechnology: Science and Computation, eds J Chen, N Jonoska, and G Rozenberg (Springer-Verlag, Berlin Heidelberg), pp 55-78.
40. Chen HL, Goel A, Winfree E, Luhrs C (2007) Self-assembling tile systems that heal from small fragments. Preliminary Proceedings of DNA Computing 13, eds M Garzon and H Yan (Springer-Verlag, Berlin Heidelberg), Vol. LNCS 4848, pp 30-46.
41. Smalley RE, et al. (2006) Single wall carbon nanotube amplification: En route to a type-specific growth mechanism. J Am Chem Soc 128:15824-15829. (Pubitemid 44894123)
42. Li H, Carter JD, LaBean TH (2009) Nanofabrication by DNA self-assembly. Mater Today 12:24-32.
43. Wang H, Brandl DW, Nordlander P, Halas NJ (2007) Plasmonic nanostructures: Artificial molecules. Acc Chem Res 40:53-62.
44. Dutta PK, et al. (2011) DNA-directed artificial light-harvesting antenna. J AmChem Soc 133:11985-11993.
45. Huppa JB, Davis MM (2003) T-cell-antigen recognition and the immunological synapse. Nat Rev Immunol 3:973-983. (Pubitemid 37521539)
46. Smith SB, Cui Y, Bustamante C (1996) Overstretching B-DNA: The elastic response of individual double-stranded and single-stranded molecules. Science 271:795-799.