Enzymatic logic gates with noise-reducing sigmoid response

International Journal of Unconventional Computing

Volumn 6, Issue 6, 2010, Pages 451-460

  Pedrosa, Valber ^a,b   Melnikov, Dmitriy ^c   Pita, Marcos ^c,d   Halámek, Jan ^c   Privman, Vladimir ^c   Simonian, Aleksandr ^a   Katz, Evgeny ^c  

^a AUBURN UNIVERSITY   (United States)

^b SÃO PAULO STATE UNIVERSITY UNESP   (Brazil)

^c CLARKSON UNIVERSITY   (United States)

^d INSTITUTO DE CATÁLISIS Y PETROLEOQUÍMICA   (Spain)

Author keywords

Binary logic; Biocomputing; Enzyme logic; Logic gate; Sigmoid response

Indexed keywords

BINARY LOGIC; BIOCOMPUTING; BIOLOGICAL OBJECTS; DIGITAL LOGIC; ENZYME LOGIC; GLUCOSE-6-PHOSPHATE DEHYDROGENASE; KINETIC MODELS; PROCESS INFORMATION; SIGMOID RESPONSE; UNCONVENTIONAL COMPUTING;

BOOLEAN FUNCTIONS; ENZYME ELECTRODES; ENZYMES; GLUCOSE; MOLECULAR BIOLOGY;

LOGIC GATES;

EID: 79951758037     PISSN: 15487199     EISSN: 15487202     Source Type: Journal    
DOI: None     Document Type: Article

References (38)

1. De Silva, A.P., Uchiyama, S., Vance, T.P., Wannalerse, B. (2007). A supramolecular chemistry basis for molecular logic and computation. Coord. Chem. Rev. 251, 1623-1632.
2. Credi, A. (2007). Molecules that make decisions. Angew. Chem. Int. Ed. 46, 5472-5475.
3. Pischel, U. (2007). Chemical approaches to molecular logic elements for addition and subtraction. Angew. Chem. Int. Ed. 46, 4026-4040.
4. Szacilowski, K. (2008). Digital information processing in molecular systems. Chem. Rev. 108, 3481-3548.
5. Pischel, U. (2010). Digital operations with molecules - Advances, challenges, and perspectives. Austral. J. Chem. 63, 148-164.
6. Andreasson, J., Pischel, U. (2010). Smart molecules at work-mimicking advanced logic operations. Chem. Soc. Rev. 39, 174-188.
7. Benenson, Y., Gil, B., Ben-Dor, U., Adar, R., Shapiro, E. (2004). An autonomous molecular computer for logical control of gene expression. Nature 429, 423-429.
8. Shapiro, E., Gil, B. (2007). Biotechnology - Logic goes in vitro. Nature Nanotechnol. 2, 84-85.
9. Benenson, Y. (2009). Biocomputers: from test tubes to live cells. Molecular Biosystems 5, 675-685.
10. Stojanovic, M.N., Stefanovic, D., LaBean, T., Yan, H. (2005). Computing with nucleic acids. In: Willner, I., Katz, E. (Eds.), Bioelectronics: From Theory to Applications, Wiley- VCH, Weinheim, pp. 427-455.
11. Win, M.N., Smolke, C.D. (2008). Higher-order cellular information processing with synthetic RNA devices. Science 322, 456-460.
12. Katz, E., Privman, V. (2010). Enzyme-based logic systems for information processing. Chem. Soc. Rev. 39, 1835-1857.
13. Baron, R., Lioubashevski, O., Katz, E., Niazov, T., Willner, I. (2006). Logic gates and elementary computing by enzymes. J. Phys. Chem. A 110, 8548-8553.
14. Strack, G., Pita, M., Ornatska, M., Katz, E. (2008). Boolean logic gates using enzymes as input signals. ChemBioChem 9, 1260-1266.
15. Zhou, J., Arugula, M.A., Halámek, J., Pita, M., Katz, E. (2009). Enzyme-based universal NAND and NOR logic gates with modular design. J. Phys. Chem. B 113, 16065-16070.
16. Baron, R., Lioubashevski, O., Katz, E., Niazov, T., Willner, I. (2006). Elementary arithmetic operations by enzymes: A model for metabolic pathway based computing. Angew. Chem. Int. Ed. 45, 1572-1576.
17. Niazov, T., Baron, R., Katz, E., Lioubashevski, O., Willner, I. (2006). Concatenated logic gates using four coupled biocatalysts operating in series. Proc. Natl. Acad. Sci. USA 103, 17160-17163.
18. Strack, G., Ornatska, M., Pita, M., Katz, E. (2008). Biocomputing security system: Concatenated enzyme-based logic gates operating as a biomolecular keypad lock. J. Am. Chem. Soc. 130, 4234-4235.
19. Privman, M., Tam, T.K., Pita, M., Katz, E. (2009). Switchable electrode controlled by enzyme logic network system: Approaching physiologically regulated bioelectronics, J. Am. Chem. Soc. 131, 1314-1321.
20. Tam, T.K., Pita, M., Katz, E. (2009). Enzyme logic network analyzing combinations of biochemical inputs and producing fluorescent output signals: Towards multi-signal digital biosensors. Sens. Actuat. B 140, 1-4.
21. Margulies, D., Hamilton, A.D. (2009). Digital analysis of protein properties by an ensemble of DNA quadruplexes. J. Am. Chem. Soc. 131, 9142-9143.
22. Adar, R., Benenson, Y., Linshiz, G., Rosner, A., Tishby, N., Shapiro, E. (2004). Stochastic computing with biomolecular automata. Proc. Natl. Acad. USA 101, 9960-9965.
23. May, E.E., Dolan, P.L., Crozier, P.S., Brozik, S., Manginell, M. (2008). Towards de novo design of deoxyribozyme biosensors for GMO detection. IEEE Sens. J. 8, 1011-1019.
24. Manesh, K.M., Halámek, J., Pita, M., Zhou, J., Tam, T.K., Santhosh, P., Chuang, M.-C., Windmiller, J.R., Abidin, D., Katz, E., Wang, J. (2009). Enzyme logic gates for the digital analysis of physiological level upon injury. Biosens. Bioelectron. 24, 3569-3574.
25. Pita, M., Zhou, J., Manesh, K.M., Halámek, J., Katz, E., Wang, J. (2009). Enzyme logic gates for assessing physiological conditions during an injury: Towards digital sensors and actuators. Sens. Actuat. B 139, 631-636.
26. Halámek, J., Windmiller, J.R., Zhou, J., Chuang, M.-C., Santhosh, P., Strack, G., Arugula, M.A., Chinnapareddy, S., Bocharova, V., Wang, J., Katz, E. (2010). Multiplexing of injury codes for the parallel operation of enzyme logic gates. Analyst 135, 2249-2259.
27. Wang, J., Katz, E. (2010). Digital biosensors with built-in logic for biomedical applications - Biosensors based on biocomputing concept. Anal. Bioanal. Chem. 398, 1591-1603.
28. Windmiller, J.R., Strack, G., Chuan, M.-C., Halámek, J., Santhosh, P., Bocharova, V., Zhou, J., Katz, E., Wang, J. (2010). Boolean-format biocatalytic processing of enzyme biomarkers for the diagnosis of soft tissue injury. Sens. Actuat. B 150, 285-290.
29. Privman, V., Strack, G., Solenov, D., Pita, M., Katz, E. (2008). Optimization of enzymatic biochemical logic for noise reduction and scalability: How many biocomputing gates can be interconnected in a circuit? J. Phys. Chem. B 112, 11777-11784.
30. Privman, V., Arugula, M.A., Halámek, J., Pita, M., Katz, E. (2009). Network analysis of biochemical logic for noise reduction and stability: A system of three coupled enzymatic AND gates. J. Phys. Chem. B 113, 5301-5310.
31. Buchler, N.E., Gerland, U., Hwa, T. (2005). Nonlinear protein degradation and the function of genetic circuits. Proc. Natl. Acad. Sci. USA 102, 9559-9564.
32. Setty, Y., Mayo, A.E., Surette, M.G., Alon, U. (2003). Detailed map of a cis-regulatory input function. Proc. Natl. Acad. Sci. USA 100, 7702-7707.
33. Alon, U. (2007). An Introduction to Systems Biology. Design Principles of Biological Circuits, Boca Raton, Florida: Chapman & Hall/CRC Press.
34. Privman, V., Halámek, J., Arugula, M. A., Melnikov, D., Bocharova, V., Katz, E. (2010). Biochemical filter with sigmoidal response: Increasing the complexity of biomolecular logic. J. Phys. Chem. B 114, 14103-14109.
35. Privman, V., Pedrosa, V., Melnikov, D., Pita, M., Simonian, A., Katz, E. (2009). Enzymatic AND-gate based on electrode-immobilized glucose-6-phosphate dehydrogenase: Towards digital biosensors and biochemical logic systems with low noise. Biosens. Bioelect. 25, 695-701.
36. Researchers from Clarkson University report details of new studies and findings in the area of biosensors and bioelectronics. Electronics Newsweekly (Atlanta, GA), Issue: Jan. 13, 2010, Page: 161 (online version at http://www.verticalnews.com/article.php?articleID=3010969).
37. Willner, I., Katz, E. (2000). Integration of layered redox-proteins and conductive supports for bioelectronic applications. Angew. Chem. Int. Ed. 39, 1180-1218.
38. Rabinowitz, J. D., Hsiao, J. J., Gryncel, K. R., Kantrowitz, E. R., Feng, X.-J. (2008). Dissecting enzyme regulation by multiple allosteric effectors: Nucleotide regulation of aspartate transcarbamoylase. Biochemistry 47, 5881-5888.