A DNA superstructure-based replicator without product inhibition

Natural Computing

Volumn 5, Issue 2, 2006, Pages 183-202

  Zhang, David Y ^a   Yurke, Bernard ^b  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^b LUCENT TECHNOLOGIES   (United States)

Author keywords

DNA based polymers; DNA motors; Self replication

Indexed keywords

MONOMER; OLIGONUCLEOTIDE; POLYMER;

ANALYTICAL ERROR; ARTICLE; CHEMICAL STRUCTURE; CONTROLLED STUDY; DNA HYBRIDIZATION; DNA REPLICATION; DNA STRAND; DNA STRUCTURE; DNA SYNTHESIS; NUCLEOTIDE SEQUENCE; POLYMERIZATION; PROTEIN SECONDARY STRUCTURE; SEPARATION TECHNIQUE;

EID: 33745131836     PISSN: 15677818     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11047-005-4465-x     Document Type: Article

References (46)

1. T Achilles G Kiedrowski von 1993 A self-replicating system from three precursors Angewandte Chemie (International ed.) 32 1198-1201
2. P Alberti JL Mergny 2003 DNA duplex-quadruples exchange as the basis for a nanomolecular machine PNAS 100 1569-1573 10.1073/pnas.0335459100
3. B Alberts 2003 DNA replication and recombination Nature 421 431-435 10.1038/nature01407
4. JJ Bull HA Wichman 2001 Applied evolution Annual Review of Ecology and Systematics 32 183-271 10.1146/annurev.ecolsys.32.081501.114020
5. J Chen NC Seeman 1991 The synthesis from DNA of a molecule with the connectivity of a cube Nature 350 631-633 10.1038/350631a0
6. Q Fang TK Park JA Rebek 1992 Crossover reactions between synthetic replicators yield active and inactive recombinants Science 256 1179-1180
7. L Feng SH Park JH Reif H Yan 2003 A two-state DNA lattice switched by DNA nanoactuator Angewandte Chemie (International ed.) 42 4342-4346 10.1002/anie.200351818
8. JI Hong Q Fang V Rotello JA Rebek 1992 Competition, cooperation, and mutation improving a synthetic replicator by light irradiation Science 255 848-850
9. WK Johnston PJ Unrau MS Lawrence ME Glasner DP Bartel 2001 RNA-catalyzed RNA polymerization: Accurate and general RNA-templated primer extension Science 292 1319-1325 10.1126/science.1060786
10. G Kiedrowski von 1986 A self-replicating hexadeoxynucleotide Angewandte Chemie (International ed. in English) 25 932-935 10.1002/anie.198609322
11. G Kiedrowski von B Wlotzka J Helbing M Matzen S Jordan 1991 Parabolic growth of a hexadeoxynucleotide analogue bearing a 3′-5′-phosphoamidate link Angewandte Chemie (International ed. in English) 30 423-426 10.1002/anie.199104231
12. TH LaBean H Yan J Kopatsch F Liu E Winfree JH Reif NC Seeman 2000 Construction, analysis, ligation, and self-assembly of DNA triple crossover complexes Journal of the American Chemical Society 122 1848-1860 10.1021/ja993393e
13. DH Lee JR Granja JA Martinez K Severin MR Ghadiri 1996 A self-replicating peptide Nature 382 525-528 10.1038/382525a0
14. JJ Li W Tan 2002 A single DNA molecular nanomotor Nano Letters 2 315-318 10.1021/nl015713+
15. T Li KC Nicolaou 1994 Chemical self-replication of palindromic duplex DNA Nature 369 21810.1038/369218a0
16. A Luther R Brandsch G Kiedrowski von 1998 Surface-promoted replication and exponential amplification of DNA analogues Nature 396 245-248 10.1038/24343
17. C Mao W Sun NC Seeman 1999a Designed two-dimensional DNA Holiday junction arrays visualized by atomic force microscopy Journal of the American Chemical Society 121 5437-5443 10.1021/ja9900398
18. C Mao W Sun Z Shen NC Seeman 1999b A nanomechanical device based on the B-Z transition of DNA Nature 297 144-146
19. C Mao TH LaBean JH Reif NC Seeman 2000 Logical computation using algorithmic self-assembly of DNA triple-crossover molecules Nature 407 493-496 10.1038/35035038
20. B Martin R Micura S Pitsch A Eschenmoser 1997 Pyranosyl-RNA: Further observations on replication Helvetica Chimica Acta 80 1901-1951 10.1002/ hlca.19970800613
21. LE Orgel 1995 Unnatural selection in chemical systems Accounts of Chemical Research 28 109-118 10.1021/ar00051a004
22. N Paul GF Joyce 2002 A self-replicating ligase ribozyme PNAS 99 12733-12740 10.1073/pnas.202471099
23. LS Penrose 1959 Self-reproducing machines Scientific American 200 6 105-114
24. RJ Pieters I Huc JA Rebek 1994 Reciprocal template effect in a replication cycle Angewandte Chemie (International ed. in English) 106 1579-1581 10.1002/anie.199415791
25. DN Reinhoudt DM Rudkevich F Jong de 1996 Kinetic analysis of the Rebek self-replicating system: Is there a controversy? Journal of the American Chemical Society 118 6880-6889 10.1021/ja960324g
26. A Saghathelian Y Yokobayashi K Soltani MR Ghadiri 2001 A chiroselective peptide replicator Nature 409 797-801 10.1038/35057238
27. H Schoneborn J Bulle G Kiedrowski von 2001 Kinetic monitoring of self-replicating systems through measurement of fluorescence resonance energy transfer Chembiochem: A European Journal of Chemical Biology 2 922-927
28. NC Seeman 1998 Nucleic acid nanostructures and topology Angewandte Chemie (International ed. in English) 37 3220-3238 10.1002/ (SICI)1521-3773(19981217)37:23<3220::AID-ANIE3220>3.0.CO;2-C
29. NC Seeman 2003 DNA in a material world Nature 421 427-431 2052315 10.1038/nature01406
30. KS Severin DH Lee JA Martinez MR Ghadiri 1997 Peptide self-replication via template-directed ligation Chemistry-A European Journal 3 1017-1024
31. KS Severin DH Lee JA Martinez M Vieth MR Ghadiri 1998 Dynamic error correction in autocatalytic peptide networks Angewandte Chemie (International ed. in English) 37 126-128 10.1002/ (SICI)1521-3773(19980202)37:1/2<126::AID-ANIE126>3.0.CO;2-4
32. D Sievers G Kiedrowski von 1994 Self-replication of complementary nucleotide-based oligomers Nature 369 221-224 10.1038/369221a0
33. D Sievers G Kiedrowski von 1998 Self-replication of hexadeoxynucleotide analogues: Autocatalysis versus cross-catalysis Chemistry-A European Journal 4 629-641 10.1002/ (SICI)1521-3765(19980416)4:4<629::AID-CHEM629>3.0.CO;2-0
34. FC Simmel B Yurke 2001 Using DNA to construct and power a nanoactuator Physical Review. E 63 04191310.1103/PhysRevE.63.041913
35. FC Simmel B Yurke 2002 A DNA-based molecular device switchable between three distinct mechanical states Applied Physics Letters 80 883-885 10.1063/1.1447008
36. E Szathmary I Gladkih 1989 Sub-exponential growth and coexistence of non-enzymatically replicating templates Journal of Theoretical Biology 138 55-58
37. A Terfort G Kiedrowski von 1992 Self-replication during condensation of 3-aminobenzamidines with 2-formylphenoxyacetic acids Angewandte Chemie (International ed. in English) 31 654-656 10.1002/anie.199206541
38. T Tjivikua P Ballester JA Rebek 1990 A self-replicating system Journal of the American Chemical Society 112 1249-1250 10.1021/ja00159a057
39. B Wang IO Sutherland 1997 Self-replication in a Diels-Alder reaction Chemical Communications 16 1495-1496 10.1039/a701573i
40. PR Wills SA Kauffman BMR Stadler 1998 Selection dynamics in autocatalytic systems: Templates replicating through binary ligation Bulletin of Mathematical Biology 60 1073-1098 10.1016/ S0092-8240(98)90003-9
41. E Winfree F Liu LA Wenzler NC Seeman 1998 Design and self-assembly of two-dimensional DNA crystals Nature 394 539-544 10.1038/28998
42. EA Wintner MM Conn J Rebek 1994 Studies in molecular replication Accounts of Chemical Research 27 198-203 10.1021/ar00043a003
43. H Yan X Zhang Z Shen NC Seeman 2002 A robust DNA mechanical device controlled by hybridization topology Nature 415 62-65 10.1038/415062a
44. S Yao I Ghosh R Zutshi JA Chmielewski 1998 A self-replicating peptide under ionic control Angewandte Chemie (International ed. in English) 37 478-481 10.1002/ (SICI)1521-3773(19980302)37:4<478::AID-ANIE478>3.0.CO;2-V
45. B Yurke AJ Turberfield AP Mills Jr FC Simmel JL Neumann 2000 A DNA-fuelled molecular machine made of DNA Nature 406 605-608 10.1038/ 35020524
46. WS Zielinski LE Orgel 1987 Autocatalytic synthesis of a tetranucleotide analogue Nature 327 346-347 10.1038/327346a0