Optimization of enzymatic biochemical logic for noise reduction and scalability: How many biocomputing gates can be interconnected in a circuit?

Journal of Physical Chemistry B

Volumn 112, Issue 37, 2008, Pages 11777-11784

  Privman, Vladimir ^a   Strack, Guinevere ^a   Solenov, Dmitry ^a   Pita, Marcos ^a   Katz, Evgeny ^a  

^a CLARKSON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

OPTIMIZATION; SCALABILITY;

AND GATES; BOOLEAN LOGIC; EXPERIMENTAL EVALUATIONS; FUTURE CHALLENGES; INPUT-OUTPUT; NOISE AMPLIFICATION; NOISE REDUCTIONS; OPTIMIZED CONDITIONS; PROCESS PARAMETERS; RATE EQUATIONS;

AMPLIFICATION;

EID: 53049092595     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp802673q     Document Type: Article

References (108)

1. (a) Adamatzky, A.; De Lacy Costello, B.; Asai, T. Reaction-Diffusion Computers; Elsevier Science: Amsterdam, The Netherlands, 2005.
2. (b) Teuscher, C., Adamatzky, A., Eds. Unconventional Computing 2005: From Cellular Automata to Wetware; C. Luniver Press: Beckington, U.K., 2005.
3. (c) Dittrich, P. Lect. Notes Comput. Sci. 2005, 3566, 19-32.
4. (d) Hjelmfelt, A.; Ross, J. Physica D 1995, 84, 180-193.
5. (e) Najmabadi, P.; La Clair, J. J.; Burkart, M. D. Org. Biomol. Chem. 2007, 5, 2140-222.
6. (f) Adamatzky, A.; De Lacy Costello, B. Phys. Lett. A 2003, 309, 397-406.
7. (a) De Silva, A. P.; Uchiyama, S. Nat. Nanotechnol. 2007, 2, 399-410.
8. (b) Magri, D. C.; Brown, G. J.; McClean, G. D.; De Silva, A. P. J. Am. Chem. Soc. 2006, 128, 4950-4951.
9. (c) Straight, S. D.; Andreasson, J.; Kodis, G.; Bandyopadhyay, S.; Mitchell, R. H.; Moore, T. A.; Moore, A. L.; Gust, D. J. Am. Chem. Soc. 2005, 127, 9403-9409.
10. (a) Feringa, B. L. Molecular Switches; Wiley-VCH: Weinheim, Germany, 2001.
11. (b) Katz, E.; Shipway, A. N.; Willner, I. In Photoreactive Organic Thin Films; Sekkat, S., Knoll, W., Eds.; Academic Press: New York, 2002; Chapter II-7, pp 219-268.
12. (c) Zhao, L. Y.; Hou, Q. F.; Sui, D.; Wang, Y.; Jiang, S. M. Spectrochim. Acta, Part A 2007, 67, 1120-1125.
13. (d) Giordani, S.; Cejas, M. A.; Raymo, F. M. Tetrahedron 2004, 60, 10973-10981.
14. (e) Raymo, F. M.; Giordani, S.; White, A. J. P.; Williams, D. J. J. Org. Chem. 2003, 68, 4158-4169.
15. (f) Raymo, F. M.; Giordani, S. Proc. Natl. Acad. Sci. USA. 2002, 99, 4941-4944.
16. (g) Katz, E.; Willner, I. Angew. Chem., Int. Ed. 2005, 44, 4791-4794.
17. (h) Gill, R.; Patolsky, F.; Katz, E.; Willner, I. Angew. Chem., Im. Ed. 2005, 44, 4554-4557.
18. (a) Shipway, A. N.; Katz, E.; Willner, I. In Structure and Bonding; Sauvage, J.-P., Ed.; Springer-Verlag: Berlin, 2001; Vol. 99, pp 237-281.
19. (b) Tomizaki, K. Y.; Mihara, H. J. Am. Chem. Soc. 2007, 129, 8345-8352.
20. (c) Guo, Z. Q.; Zhu, W. H.; Shen, L. J.; Tian, H. Angew. Chem., Int. Ed. 2007, 46, 5549-5553.
21. (d) Tsivgoulis, G. M.; Lehn, J.-M. Angew. Chem., Int. Ed. 1995, 34, 1119-1122.
22. (a) Katz, E.; Willner, I. Chem. Commun. 2005, 5641-5643.
23. (b) Pina, F.; Roque, A.; Melo, M. J.; Maestri, I.; Belladelli, L.; Balzani, V. Chem. Eur. J. 1998, 4, 1184-1191.
24. (c) Areephong, J.; Browne, W. R.; Katsonis, N.; Feringa, B. L. Chem. Commun. 2006, 3930-3932.
25. (d) Pina, F.; Lima, J. C.; Parola, A. J.; Afonso, C. A. M. Angew. Chem., Int. Ed. 2004, 43, 1525-1527.
26. (a) Baron, R.; Onopriyenko, A.; Katz, E.; Lioubashevski, O.; Willner, I.; Wang, S.; Tian, H. Chem. Commun. 2006, 2147-2149.
27. (b) Kim, W.; Hardcastle, K. I.; Conticello, V. P. Angew. Chem., Int. Ed. 2006, 45, 8141-8145.
28. (a) Pina, F.; Melo, M. J.; Maestri, M.; Passaniti, P.; Balzani, V. J. Am. Chem. Soc. 2000, 122, 4496-4498.
29. (b) Credi, A.; Balzani, V.; Langford, S. J.; Stoddart, J. F. J. Am. Chem. Soc. 1997, 119, 2679-2681.
30. (c) Zong, G. Q.; Xian, L.; Lu, G. X. Tetrahedron Lett. 2007, 48, 3891-3894.
31. (d) Straight, S. D.; Liddell, P. A.; Terazono, Y.; Moore, T. A.; Moore, A. L.; Gust, D. Adv. Funct. Mater. 2007, 17, 777-785.
32. (a) Li, L.; Yu, M. X.; Li, F. Y.; Yi, T.; Huang, C. H. Colloids Surf., A 2007, 304, 49-53.
33. (b) Wen, G. Y.; Yan, J.; Zhou, Y. C.; Zhang, D. Q.; Mao, L. Q.; Zhu, D. B. Chem. Commun. 2006, 3016-3018.
34. (c) Li, F. Y.; Shi, M.; Huang, C. H.; Jin, L. P. J. Mater. Chem. 2005, 15, 3015-3020.
35. (a) Raitman, O. A.; Katz, E.; Willner, I.; Chegel, V. I.; Popova, G. V. Angew. Chem., Int. Ed. 2001, 40, 3649-3652.
36. (b) Gunnlaugsson, T.; Mac Donail, D. A.; Parker, D. Chem. Commun. 2000, 93-94.
37. (a) Zhou, W. D.; Li, J. B.; He, X. R.; Li, C. H.; Lv, J.; Li, Y. L.; Wang, S.; Liu, H. B.; Zhu, D. B. Chem Eur. J. 2008, 14, 754-763.
38. (b) De Silva, A. P.; Uchiyama, S.; Vance, T. P.; Wannalerse, B. Coord. Chem. Rev. 2007, 251, 1623-1632.
39. (c) Flood, A. H.; Ramirez, R. J. A.; Deng, W. Q.; Muller, R. P.; Goddard, W. A.; Stoddart, J. F. Aust. J. Chem. 2004, 57, 301-322.
40. (d) Katz, E.; Lioubashevsky, O.; Willner, I. J. Am. Chem. Soc. 2004, 126, 15520-15532.
41. (e) Willner, I.; Pardo-Yissar, V.; Kate, E.; Ranjit, K. T. J. Electroanal. Chem. 2001, 497, 172-177.
42. (a) Perez-Inestrosa, E.; Montenegro, J. M.; Collado, D.; Suau, R.; Casado, J. J. Phys. Chem. C 2007, 111, 6904-6909.
43. (b) Fang, C. J.; Zhu, Z.; Sun, W.; Xu, C. H.; Yan, C. H. New J. Chem 2007, 31, 580-586.
44. (c) Sadhu, K. K.; Bag, B.; Bharadwaj, P. K. J. Photochem. Photobiol., A 2007, 185, 231-238.
45. (d) Szacilowski, K.; Macyk, W.; Stochel, G. J. Am. Chem. Soc. 2006, 128, 4550-4551.
46. (e) Biancardo, M.; Bignozzi, C.; Hugh, D. C.; Redmond, G. Chem. Commun. 2005, 3918-3920.
47. (f) Kume, S.; Nishihara, H. Struct. Bonding (Berlin) 2007, 123, 79-112.
48. (a) Zhou, Y. C.; Wu, H.; Qu, L.; Zhang, D. Q.; Zhu, D. B. J. Phys. Chem B 2006, 110, 15676-15679.
49. (b) Mendes, P. M.; Flood, A. H.; Stoddart, J. F. Appl. Phys. A 2005, 80, 1197-1209.
50. (c) Hiratsuka, M.; Ikeda, S.; Aoki, T.; Higuchi, T. IEICE Trans. Electron. 2004, E87C, 1804-1808.
51. (d) Pease, A. R.; Jeppesen, J. O.; Stoddart, J. F.; Luo, Y.; Collier, C. P.; Heath, J. R. Acc Chem. Res. 2001, 34, 433-444.
52. Vasilyev, S.; Pita, M.; Kate, E. Electroanalysis 2008, 20, 22-29.
53. (a) Credi, A.; Balzani, V.; Langford, S. J.; Stoddart, J. F. J. Am. Chem Soc 1997, 119, 2679-2681.
54. (b) Wang, Z. X.; Zheng, G. R.; Lu, P. Org. Lett. 2005, 7, 3669-3672.
55. (c) Nishimura, C.; Maehara, H.; Shiraishi, Y.; Hirai, T. Chem. Eur. J. 2008, 14, 259-271.
56. (a) Pischel, U. Angew. Chem., Int. Ed. 2007, 46, 4026-4040.
57. (b) Andreasson, J.; Straight, S. D.; Kodis, G.; Park, C.-D.; Hambourger, M.; Gervaldo, M.; Albinsson, B.; Moore, T. A.; Moore, A. L.; Gust, D. J. Am. Chem. Soc. 2006, 128, 16259-16265.
58. (c) Liu, Y.; Jiang, W.; Zhang, H.-Y.; Li, C.-J. J. Phys. Chem. B 2006, 110, 14231-14235.
59. (d) Sun, W.; Zheng, Y.-R.; Xu, C.-H.; Fang, C.-J.; Yan, C.-H. J. Phys. Chem. C 2007, 111, 11706-11711.
60. (e) Suresh, M.; Ghosh, A.; Das, A. Tetrahedron Lett. 2007, 48, 8205-8208.
61. (f) Qu, D. H.; Wang, Q. C.; Tian, H. Angew. Chem., Int. Ed. 2005, 44, 5296-5299.
62. (a) Kuznetz, O.; Salman, H.; Shakkour, N.; Eichen, Y.; Speiser, S. Chem. Phys. Lett. 2008, 457, 63-67.
63. (b) Margulies, D.; Melman, G.; Shanzer, A. J. Am. Chem. Soc. 2006, 128, 4865-4871.
64. Andreasson, J.; Straight, S. D.; Bandyopadhyay, S.; Mitchell, R. H.; Moore, T. A.; Moore, A. L.; Gust, D. J. Phys. Chem. C 2007, 111, 14274-14278.
65. Margulies, D.; Felder, C. E.; Melman, G.; Shanzer, A. J. Am. Chem. Soc. 2007, 129, 347-354.
66. (a) Ashkenasy, G.; Ghadiri, M. R. J. Am. Chem. Soc. 2004, 126, 11140-11141.
67. (b) Szacilowski, K. Chem. Eur. J. 2004, 10, 2520-2528.
68. (a) Stadler, R.; Ami, S.; Joachim, C.; Forshaw, M. Nanotechnology 2004, 15, S115-S121.
69. (b) Raymo, F. M.; Giordani, S. J. Am. Chem. Soc. 2001, 123, 4651-4652.
70. (c) Liu, Y.; Jiang, W.; Zhang, H. Y.; Li, C. J. J. Phys. Chem. B 2006, 110, 14231-14235.
71. De Silva, A. P.; Leydet, Y.; Lincheneau, C.; McClenaghan, N. D. J. Phys. 2006, 18, S1847-S1872.
72. Bell, G. ; Gray, J. N. In Beyond Calculation: The Next Fifty Years of Computing; Denning, P. J., Metcalfe, R. M., Eds.; Copernicus/Springer: New York, 1997; Chapter 1, p 30.
73. Shao, X. G.; Jiang, H. Y.; Cai, W. S. Prog. Chem. 2002, 14, 37-46.
74. (a) Stojanovic, M. N.; Stefanovic, D.; LaBean, T.; Yan, H. In Bioelectronics: From Theory to Applications; Willner, I., Katz, E., Eds.; Wiley-VCH: Weinheim, Germany, 2005; pp 427-455.
75. (b) Frezza, B. M.; Cockroft, S. L.; Ghadiri, M. R. J. Am. Chem. Soc. 2007, 129, 14875-14879.
76. (c) Ogasawara, S.; Kyoi, Y.; Fujimoto, K. ChemBioChem 2007, 8, 1520-1525.
77. (d) Yoshida, W.; Yokobayashi, Y. Chem. Commun. 2007, 195-197.
78. (e) Seelig, G.; Soloveichik, D.; Zhang, D. Y.; Winfree, E. Science 2006, 314, 1585-1588.
79. (f) Stojanovic, M. N.; Mitchell, T. E.; Stefanovic, D. J. Am Chem. Soc. 2002, 124, 3555-3561.
80. (g) Ezziane, Z. Nanotechnology 2006, 17, R27-R39.
81. (h) Macdonald, J.; Li, Y.; Sutovic, M.; Lederman, H.; Pendri, K.; Lu, W.; Andrews, B. L.; Stefanovic, D.; Stojanovic, M. N. Nano Lett. 2006, 6, 2598-2603.
82. (a) Unger, R.; Moult, J. Proteins 2006, 63, 53-64.
83. (b) Tomizaki, K. Y.; Mihara, H. J. Am. Chem. Soc. 2007, 129, 8345-8352.
84. (c) Gianneschi, N. C.; Ghadiri, M. R. Angew. Chem., Int. Ed. 2007, 46, 3955-3958.
85. (d) Muramatsu, S.; Kinbara, K.; Taguchi, H.; Ishii, N.; Aida, T. J. Am. Chem. Soc 2006, 128, 3764-3769.
86. (a) Simpson, M. L.; Sayler, G. S.; Fleming, J. T.; Applegate, B. Trends Biotechnol. 2001, 19, 317-323.
87. (b) Rinaudo, K.; Bleris, L.; Maddamsetti, R.; Subramanian, S.; Weiss, R.; Benenson, Y. Nat. Biotechnol. 2007, 25, 795-801.
88. (a) Baron, R.; Lioubashevski, O.; Katz, E.; Niazov, T.; Willner, I. Org. Biomol. Chem. 2006, 4, 989-991.
89. (b) Baron, R.; Lioubashevski, O.; Katz, E.; Niazov, T.; Willner, I. Angew. Chem., Int. Ed. 2006, 45, 1572-1576.
90. (c) Pita, M.; Katz, E. J. Am. Chem. Soc. 2008, 130, 36-37.
91. Baron, R.; Lioubashevski, O.; Katz, E.; Niazov, T.; Willner, I. J. Phys. Chem. A 2006, 110, 8548-8553.
92. Niazov, T.; Baron, R.; Katz, E.; Lioubashevski, O.; Willner, I. Proc. Natl. Acad. USA. 2006, 103, 17160-17163.
93. Strack, G.; Ornatska, M.; Pita, M.; Katz, E. J. Am. Chem. Soc. 2008, 130, 4234-4325.
94. Fedichkin, L.; Katz, E.; Privman, V. J. Comput. Theory Nanosci. 2008, 5, 36-43.
95. (a) Pretzel, O. Error-Correcting Codes and Finite Fields; Oxford University Press: Oxford, 1992.
96. (b) Wakerly, J. F. Digital Design. Principles and Practices, 4th ed.; Pearson Prentice Hall: London, 2005.
97. (a) Bergmeyer, H. U., Ed.; Methods of Enzymatic Analysis, 3rd ed.; Verlug Chemie: Deerfield Beach, FL, 1983; Vol. 3, pp 286-293.
98. (b) Solís-Oba, M.; Ugalde-Saldívar, V. M.; González, I.; Viniegra-González, G. J. Electroanal. Chem 2005, 579, 59-66.
99. (c) Childs, R. E.; Bardsley, W. G. Biochem J. 1975, 745, 93-103.
100. Adams, P. A. In Peroxidases in Chemistry and Biology; Everse, J., Everse, K. E., Grisham, M. B., Eds.; CRC Press: Boca Raton, FL 1991; Vol. 2, Chapter 7, pp 171-200.
101. Setty, Y.; Mayo, A. E.; Surette, M. G.; Alon, U. Proc. Natl. Acad. USA. 2003, 100, 7702-7707.
102. Alon, U. An Introduction to Systems Biology. Design Principles of Biological Circuits; Chapman & Hall/CRC Press: Boca Raton, FL, 2007.
103. Truesdale, G. A.; Downing, A. L. Nature 1954, 173, 1236-1237.
104. (a) Lee, M. Water Res. 2002, 36, 2140-2146.
105. (b) Schladow, S. G.; Lee, M.; Hiirzeler, B. E.; Kelly, P. B. Limnol. Oceanogr. 2002, 47, 1394-1404.
106. Mölder, E.; Mashirin, A.; Tenno, T. Environ Sci. Pollut. Res. 2005, 12, 66-70.
107. Schulz, A. R. Enzyme Kinetics. From Diastase to Multi-Enzyme Systems; Cambridge University Press: Cambridge, 1994.
108. Buchler, N. E.; Gerland, U.; Hwa, T. Proc. Natl. Acad. U.S.A. 2005, 102, 9559-9564.