Experiments and simulation models of a basic computation element of an autonomous molecular computing system

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 78, Issue 4, 2008, Pages

  Takinoue, Masahiro ^a,c   Kiga, Daisuke ^b   Shohda, Koh Ichiroh ^a   Suyama, Akira ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b Tokyo Institute of Technology ^*  (Japan)

^c KYOTO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER CIRCUITS; COMPUTER SCIENCE; COMPUTER SYSTEMS; DNA; EXPERIMENTS; GENES; MOLECULES; ORGANIC ACIDS; RNA; TRANSCRIPTION;

AND GATES; AUTONOMOUS COMPUTING; AUTONOMOUS DNAS; COMPUTATIONAL ABILITIES; COMPUTATIONAL CIRCUITS; DNA MOLECULES; LIVING CELLS; MATHEMATICAL MODELING; MOLECULAR COMPUTERS; MOLECULAR COMPUTING; MOLECULAR REACTIONS; PROCESS INFORMATIONS; RNA MOLECULES; SIMULATION MODELS;

NUCLEIC ACIDS;

EID: 56149111222     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.78.041921     Document Type: Article

References (21)

1. Y. Benenson, T. Paz-Elizur, R. Adar, E. Keinan, Z. Livneh, and E. Shapiro, Nature (London) 10.1038/35106533 414, 430 (2001).
2. Y. Benenson, R. Adar, T. Paz-Elizur, Z. Livneh, and E. Shapiro, Proc. Natl. Acad. Sci. U.S.A. 10.1073/pnas.0535624100 100, 2191 (2003).
3. Y. Benenson, B. Gil, U. Ben-Dor, R. Adar, and E. Shapiro, Nature (London) 10.1038/nature02551 429, 423 (2004).
4. K. Sakamoto, D. Kiga, K. Komiya, H. Gouzu, S. Yokoyama, S. Ikeda, H. Sugiyama, and M. Hagiya, BioSystems 10.1016/S0303-2647(99)00035-0 52, 81 (1999).
5. K. Komiya, K. Sakamoto, A. Kameda, M. Yamamoto, A. Ohuchi, D. Kiga, S. Yokoyama, and M. Hagiya, BioSystems 10.1016/j.biosystems.2005.07.005 83, 18 (2006).
6. J. A. Rose, R. J. Deaton, M. Hagiya, and A. Suyama, Phys. Rev. E 10.1103/PhysRevE.65.021910 65, 021910 (2002).
7. G. Seelig, D. Soloveichik, D. Y. Zhang, and E. Winfree, Science 10.1126/science.1132493 314, 1585 (2006).
8. D. Y. Zhang, A. J. Turberfield, B. Yurke, and E. Winfree, Science 10.1126/science.1148532 318, 1121 (2007).
9. N. Nitta and A. Suyama, Lect. Notes Comput. Sci. 2943, 203 (2004).
10. H. Yoshida and A. Suyama, DIMACS Series in Discrete Mathematics and Theoretical Computer Science 54, 9 (2000).
11. N. Nishida, T. Tanabe, K. Hashido, K. Hirayasu, M. Takasu, A. Suyama, and K. Tokunaga, Anal. Biochem. 346, 281 (2005). 10.1016/j.ab.2005.08.007
12. T. Kitajima, M. Takinoue, K. Shohda, and A. Suyama, Lect. Notes Comput. Sci. 4848, 119 (2008). 10.1007/978-3-540-77962-9_12
13. M. Majlessi, N. C. Nelson, and M. M. Becker, Nucleic Acids Res. 26, 2224 (1998). 10.1093/nar/26.9.2224
14. A. Tsourkas, M. A. Behlke, and G. Bao, Nucleic Acids Res. 30, 5168 (2002). 10.1093/nar/gkf635
15. V. V. Didenko, BioTechniques 31, 1106 (2001).
16. T. A. Brown, Molecular Biology LABFAX, I: Recombinant DNA, 2nd ed. (Academic Press, New York, 1998), pp. 123-232.
17. J. G. Wetmur, Crit. Rev. Biochem. Mol. Biol. 26, 227 (1991). 10.3109/10409239109114069
18. M. S. Krug and S. L. Berger, Biochemistry 30, 10614 (1991). 10.1021/bi00108a003
19. H. Yu and M. F. Goodman, J. Biol. Chem. 267, 10888 (1992).
20. C. T. Martin and J. E. Coleman, Biochemistry 26, 2690 (1987). 10.1021/bi00384a006
21. N. Hirano, M. Haruki, M. Morikawa, and S. Kanaya, Biochemistry 39, 13285 (2000). 10.1021/bi0015008