Synthetic biology

New Generation Computing

Volumn 26, Issue 4, 2008, Pages 347-364

  Kiga, Daisuke ^a   Yamamura, Masayuki ^a  

^a TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

Author keywords

Autonomous system; Bifurcation analysis; DNA synthesis; Genetic code; Gillespie's method; Michaelis Menten formula; Non linear dynamics; Phase plain analysis; Stochastic physics; Synthetic Biology

Indexed keywords

MOLECULAR BIOLOGY;

AUTONOMOUS SYSTEM; BIFURCATION ANALYSIS; DNA SYNTHESIS; GENETIC CODE; GILLESPIE'S METHOD; MICHAELIS-MENTEN FORMULA; NON-LINEAR DYNAMICS; PHASE PLAIN ANALYSIS; STOCHASTIC PHYSICS; SYNTHETIC BIOLOGY;

BIOLOGY;

EID: 51649096945     PISSN: 02883635     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00354-008-0050-z     Document Type: Article

References (31)

1. Elf, J. and Ehrenberg, M., "Fast evaluation of fluctuations in biochemical networks with the linear noise approximation," Genome Res, 13, 11, pp. 2475-2484, 2003.
2. Becskei, A. and Serrano, L., "Engineering stability in gene networks by autoregulation," Nature, 405, 6786, pp. 590-593, 2000.
3. Gardner, T. S., Cantor, C. R. and Collins, J. J., "Construction of a genetic toggle switch in Escherichia coli," Nature, 403, 6767, pp. 339-342, 2000.
4. Elowitz, M. B. and Leibler, S., "A synthetic oscillatory network of transcriptional regulators," Nature, 403, 6767, pp. 335-338, 2000.
5. http://bbf.openware.org.
6. http://www.pipra.org.
7. http://www.cambia.org.
8. Ayukawa, S., Kobayashi, A., Nakashima, Y., Takagi, H., Hamada, S., Uchiyama, M., Yugi, K., Murata, S., Sakakibara, Y., Hagiya, M., Yamamura, M. and Kiga., D., "SYANAC: SYnthetic biological Automaton for Noughts And Crosses," IET Synthetic Biology, 1, 1-2, pp. 64-67, 2007.
9. Itaya, M., Fujita, K., Kuroki, A. and Tsuge, K., "Bottom-up genome assembly using the Bacillus subtilis genome vector," Nat Methods, 5, 1, pp. 41-43, 2008.
10. Cello, J., Paul, A. V. and Wimmer, E., "Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template," Science, 297, 5583, pp. 1016-1018, 2002.
11. Smith, H. O., Hutchison, C. A., 3rd, Pfannkoch, C. and Venter, J. C., "Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides," Proc. Natl Acad Sci U S A, 100, 26, pp. 15440-15445, 2003.
12. Tian, J., Gong, H., Sheng, N., Zhou, X., Gulari, E., Gao, X. and Church, G., "Accurate multiplex gene synthesis from programmable DNA microchips," Nature, 432, 7020, pp. 1050-1054, 2004.
13. http://www.blueheronbio.com/company/press/mar26-07.html.
14. Gibson, D. G., Benders, G. A., Andrews-Pfannkoch, C., Denisova, E. A., Baden-Tillson, H., Zaveri, J., Stockwell, T. B., Brownley, A., Thomas, D. W., Algire, M. A., Merryman, C., Young, L., Noskov, V. N., Glass, J. I., Venter, J. C., Hutchison, C. A., 3rd and Smith, H. O., "Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome," Science, 319, 5867, pp. 1215-1220, 2008.
15. Yu, W., Sato, K., Wakabayashi, M., Nakaishi, T., Ko-Mitamura, E. P., Shima, Y., Urabe, I. and Yomo, T., "Synthesis of functional protein in liposome," J Biosci Bioeng, 92, 6, pp. 590-593, 2001.
16. Nomura, S. M., Tsumoto, K., Hamada, T., Akiyoshi, K., Nakatani, Y. and Yoshikawa, K., "Gene expression within cell-sized lipid vesicles," Chembiochem, 4, 11, pp. 1172-1175, 2003.
17. Noireaux, V. and Libchaber, A., "A vesicle bioreactor as a step toward an artificial cell assembly," Proc. Natl Acad Sci U S A, 101, 51, pp. 17669-17674, 2004.
18. Shimizu, Y., Inoue, A., Tomari, Y., Suzuki, T., Yokogawa, T., Nishikawa, K. and Ueda, T., "Cell-free translation reconstituted with purified components," Nat Biotechnol, 19, 8, pp. 751-755, 2001.
19. Murakami, H., Ohta, A., Ashigai, H. and Suga, H., "A highly flexible tRNA acylation method for non-natural polypeptide synthesis," Nat Methods, 3, 5, pp. 357-359, 2006.
20. Takinoue, M., Kiga, D., Shoda, K.-I. and Suyama, A., in press.
21. Nitta, N. and Suyama, A., "Autonomous biomolecular computer modeled after retroviral replication," LNCS, 2943, pp. 203-212, 2004.
22. Kiga, D., Mochida, T., Takinoue, M. and Suyama, A., "Realization of RTRAC: Reverse transcription and Transcription-based Autonomous Computer," Preliminary proceedings of DNA 11, pp. 397, 2005.
23. Kiga, D., Shoda, K.-i., Takinoue, M. and Suyama, A., "Autonomous DNA computer in small vesicle," Preliminary proceedings of DNA 12, pp.420, 2006.
24. Lee, Y. H., Shoda, K.-i., Kiga, D. and Suyama, A., "In Vitro Proteosynthesis Molecular Automaton Based on RTRACS," Preliminary proceedings of DNA 14, to be appeared, 2008.
25. Kim, J., White, K. S. and Winfree, E., "Construction of an in vitro bistable circuit from synthetic transcriptional switches," Mol Syst Biol, 2, pp. 68, 2006.
26. Wang, L., Brock, A., Herberich, B. and Schultz, P. G., "Expanding the genetic code of Escherichia coli," Science, 292, 5516, pp. 498-500, 2001.
27. Kiga, D., Sakamoto, K., Kodama, K., Kigawa, T., Matsuda, T., Yabuki, T., Shirouzu, M., Harada, Y., Nakayama, H., Takio, K., Hasegawa, Y., Endo, Y., Hirao, I. and Yokoyama, S., "An engineered Escherichia coli tyrosyl-tRNA synthetase for site-specific incorporation of an unnatural amino acid into proteins in eukaryotic translation and its application in a wheat germ cell-free system," Proc Natl Acad Sci U S A, 99, 15, pp. 9715-9720, 2002.
28. Lo Surdo, P., Walsh, M. A. and Sollazzo, M., "A novel ADP- and zinc-binding fold from function-directed in vitro evolution," Nat Struct Mol Biol, 11, 4, pp. 382-383, 2004.
29. http://hdl.handle.net/1721.1/21168.
30. http://webcast.berkeley.edu/event_details.php?webcastid=15766.
31. http://www.syntheticbiology3.ethz.ch/index.htm.