Towards biosensing strategies based on biochemical logic systems

4th International Conference on Quantum, Nano and Micro Technologies, ICQNM 2010

Volumn , Issue , 2010, Pages 1-9

  Katz, Evgeny ^a   Privman, Vladimir ^a   Wang, Joseph ^b  

^a CLARKSON UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Biocomputing; Biosensor; Enzyme; Logic gate; Logic network; Signal processing; Signal transduction

Indexed keywords

BIOCHEMICAL SIGNAL; BIOCOMPUTING; BIOMOLECULAR REACTIONS; BIOSENSING; BOOLEAN LOGIC; ENZYMATIC REACTION; ENZYME LOGIC; HIGH FIDELITY; INFORMATION PROCESSING; LOGIC NETWORK; LOGIC NETWORKS; LOGIC SYSTEMS; OUTPUT SIGNAL; RESEARCH RESULTS; SENSING DEVICES;

BACTERIOPHAGES; BIOSENSORS; DATA PROCESSING; ENZYMES; INDUSTRIAL RESEARCH; LOGIC GATES; SIGNAL PROCESSING;

SIGNAL TRANSDUCTION;

EID: 77952372480     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ICQNM.2010.8     Document Type: Conference Paper

References (56)

1. De Silva, A.P.; Uchiyama, S.; Vance, T.P.; Wannalerse, B. A supramolecular chemistry basis for molecular logic and computation, Coord. Chem. Rev. 2007, 251, 1623-1632.
2. De Silva, A.P.; Uchiyama, S. Molecular Logic and Computing, Nature Nanotechnology 2007, 2, 399-410.
3. Szacilowski, K. Digital information processing in molecular systems, Chem. Rev. 2008, 108, 3481-3548.
4. Credi, A. Molecules that make decisions, Angew. Chem. Int. Ed. 2007, 46, 5472-5475.
5. Shao, X.G.; Jiang, H.Y.; Cai, W.S. Advances in biomolecular computing, Prog. Chem. 2002, 14, 37-46.
6. Saghatelian, A.; Volcker, N.H.; Guckian, K.M.; Lin, V.S.Y.; Ghadiri, M.R. DNA-based photonic logic gates: AND, NAND, and INHIBIT, J. Am. Chem. Soc. 2003, 125, 346-347.
7. Ashkenasy, G.; Ghadiri, M.R. Boolean logic functions of a synthetic peptide network, J. Am. Chem. Soc. 2004, 126, 11140-11141.
8. Sivan, S.; Lotan, N. A biochemical logic gate using an enzyme and its inhibitor. Part I: The inhibitor as switching element, Biotechnol. Prog. 1999, 15, 964-970.
9. Sivan, S.; Tuchman, S.; Lotan, N. A biochemical logic gate using an enzyme and its inhibitor. Part II: The logic gate, Biosystems 2003, 70, 21-33.
10. Deonarine, A.S.; Clark, S.M.; Konermann, L. Implementation of a multifunctional logic gate based on folding/unfolding transitions of a protein, Future Generation Computer Systems 2003, 19, 87-97.
11. Ashkenazi, G.; Ripoll, D.R.; Lotan, N.; Scheraga, H.A. A molecular switch for biochemical logic gates: Conformational studies, Biosens. Bioelectron. 1997, 12, 85-95.
12. Unger, R.; Moult, J. Towards computing with proteins, Proteins 2006, 63, 53-64.
13. Stojanovic, M.N.; Stefanovic, D.; LaBean, T.; Yan, H. Computing with nucleic acids, in: Bioelectronics: From Theory to Applications, In: Bioelectronics: From Theory to Applications, Willner, I.; Katz, E. (Eds.), Wiley-VCH, Weinheim, 2005, pp. 427-455.
14. Saghatelian, A.; Volcker, N.H.; Guckian, K.M.; Lin, V.S.Y.; Ghadiri, M.R. DNA-based photonic logic gates: AND, NAND, and INHIBIT, J. Am. Chem. Soc. 2003, 125, 346-347.
15. Xu, J.; Tan, G.J. A review on DNA computing, J. Comput. Theor. Nanoscience 2007, 4, 1219-1230.
16. Win, M.N.; Smolke, C.D. Higher-order cellular information processing with synthetic RNA devices, Science 2008, 322, 456-460.
17. Simpson, M.L.; Sayler, G.S.; Fleming, J.T.; Applegate, B. Whole-cell biocomputing, Trends Biotechnol. 2001, 19, 317-323.
18. Strack, G.; Pita, M.; Ornatska, M.; Katz, E. Boolean logic gates using enzymes as input signals, ChemBioChem 2008, 9, 1260-1266.
19. Baron, R.; Lioubashevski, O.; Katz, E.; Niazov, T.; Willner, I. Logic gates and elementary computing by enzymes, J. Phys. Chem. A 2006, 110, 8548-8553.
20. Baron, R.; Lioubashevski, O.; Katz, E.; Niazov, T.; Willner, I. Elementary arithmetic operations by enzymes: A model for metabolic pathway based computing, Angew. Chem. Int. Ed. 2006, 45, 1572-1576.
21. Privman, M.; Tam, T.K.; Pita, M.; Katz, E. Switchable electrode controlled by enzyme logic network system: Approaching physiologically regulated bioelectronics, J. Am. Chem. Soc. 2009, 131, 1314-1321.
22. Niazov, T.; Baron, R.; Katz, E.; Lioubashevski, O.; Willner, I. Concatenated logic gates using four coupled biocatalysts operating in series, Proc. Natl. Acad. USA. 2006, 103, 17160-17163.
23. Strack, G.; Ornatska, M.; Pita, M.; Katz, E. Biocomputing security system: Concatenated enzyme-based logic gates operating as a biomolecular keypad lock, J. Am. Chem. Soc. 2008, 130, 4234-4235.
24. Zhou, J.; Arugula, M.A.; Halámek, J.; Pita, M.; Katz, E. Enzyme-based universal NAND and NOR logic gates with modular design, 2009, Submitted for publication.
25. Pita, M.; Zhou, J.; Manesh, K.M.; Halámek, J.; Katz, E.; Wang, J. Enzyme logic gates for assessing physiological conditions during an injury: Towards digital sensors and actuators, Sens. Actuat. B 2009, 139, 631-636.
26. 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. Enzyme logic gates for the digital analysis of physiological level upon injury, Biosensors and Bioelectronics 2009, 24, 3569-3574.
27. Pita, M.; Minko, S.; Katz, E. Enzyme-based logic systems and their applications for novel multi-signal-responsive materials, Journal of Materials Science: Materials in Medicine 2009, 20, 457-462.
28. Tokarev, I.; Gopishetty, V.; Zhou, J.; Pita, M.; Motornov, M.; Katz, E.; Minko, S. Stimuli-responsive hydrogel membranes coupled with biocatalytic processes, ACS Appl. Mater. Interfaces 2009, 1, 532-536.
29. Motornov, M.; Zhou, J.; Pita, M.; Tokarev, I.; Gopishetty, V.; Katz, E.; Minko, S. Integrated multifunctional nanosystem from command nanoparticles and enzymes, Small 2009, 5, 817-820.
30. Pita, M.; Krämer, M.; Zhou, J.; Poghossian, A.; Schöning, M.J.; Fernández, V.M.; Katz, E. Optoelectronic properties of nanostructured ensembles controlled by biomolecular logic systems, ACS Nano 2008, 2, 2160-2166.
31. Motornov, M.; Zhou, J.; Pita, M.; Gopishetty, V.; Tokarev, I.; Katz, E.; Minko, S. "Chemical transformers" from nanoparticle ensembles operated with logic, Nano Lett. 2008, 8, 2993-2997.
32. Tam, T.K.; Zhou, J.; Pita, M.; Ornatska, M.; Minko, S.; Katz, S. Biochemically controlled bioelectrocatalytic interface, J. Am. Chem. Soc. 2008, 130, 10888-10889.
33. Zhou, J.; Tam, T.K.; Pita, M.; Ornatska, M.; Minko, S.; Katz, E. Bioelectrocatylic system coupled with enzyme-based biocomputing ensembles performing Boolean logic operations: Approaching "smart" physiologically controlled biointerfaces, ACS Appl. Mater. Interfaces 2009, 1, 144-149.
34. Wang, X.; Zhou, J.; Tam, T.K.; Katz, E.; Pita, M. Switchable electrode controlled by Boolean logic gates using enzymes as input signals, Bioelectrochemistry 2009, 77, 69-73.
35. Pita, M.; Tam, T.K.; Minko, S.; Katz, E. Dual magneto-biochemical logic control of electrochemical processes based on local interfacial pH changes, ACS Appl. Mater. Interfaces 2009, 1, 1166-1168.
36. Privman, V.; Strack, G.; Solenov, D.; Pita, M.; Katz, E. Optimization of enzymatic biochemical logic for noise reduction and scalability: How many biocomputing gates can be interconnected in a circuit? J. Phys. Chem. B 2008, 112, 11777-11784.
37. Privman, V.; Arugula, M.A.; Halámek, J.; Pita, M.; Katz, E. Network analysis of biochemical logic for noise reduction and stability: A system of three coupled enzymatic AND gates, J. Phys. Chem. B 2009, 113, 5301-5310.
38. Fedichkin, L.; Katz, E.; Privman, V. Error Correction and Digitalization Concepts in Biochemical Computing, J. Comp. Theor. Nanosci. 2008, 5, 36-43.
39. Melnikov, D.; Strack, G.; Pita, M.; Privman, V.; Katz, E. Analog noise reduction in enzymatic logic gates, J. Phys. Chem. B 2009, 113, 10472-10479.
40. Privman, V.; Pedrosa, V.; Melnikov, D.; Pita, M.; Simonian, A.; Katz, E. Enzymatic AND-gate based on electrode-immobilized glucose-6-phosphate dehydrogenase: Towards digital biosensors and biochemical logic systems with low noise, Biosens. Bioelectron. 2009, 25, 695-701.
41. Arugula, M.A.; Halámek, J.; Katz, E.; Melnikov, D.; Pita, M.; Privman, V.; Strack, G. Optimization of enzymatic logic gates and networks for noise reduction and stability, IEEE Comp. Soc. Publ. (Los Alamitos, California) 2009, In press.
42. Wang, J. Real-time electrochemical monitoring: Toward green analytical chemistry, Acct. Chem. Research, 2002, 35, 811-816.
43. Wang, J. Electrochemical biosensors: Towards point-of-care cancer diagnostics, Biosensors Bioelectronics 2006, 21, 1887-1892.
44. Wang, J. Nanomaterial-based amplified transduction of biomolecular interactions Small, 2005, 1, 1036-1043.
45. Wang, J.; Pamidi, P.; Cepria, G.; Basak, S.; K. Rajeshwar, K. Overoxidized poly{pyrrole-co-[3-(pyrrol-1-yl)propanesulfunate]} coated platinum electrodes for selective detection of catecholamine neurotransmitters. Analyst, 1997, 122, 981-984.
46. Wang, J.; Liu, J.; Cepra, G. Remarkable thermal stabilization of enzymes immobilized within carbon paste electrodes. Anal. Chem., 1997, 69, 3124-3128.
47. Wang, J.; Musameh, M.; Mo, J.W. Acid stability of carbon paste enzyme electrodes, Anal. Chem., 2006, 78, 7044-7047.
48. Wang, J.; Wu, H. Permselective lipid/PPD coatings for amperometric biosensing of glucose, Anal. Chim. Acta, 1993, 283, 683-687.
49. Wang, J.; Wu, H. Highly Selective Biosensing of glucose utilizing biocatalytic electrocatalytic permselctive surface microstructure, J. Electroanal. Chem. 1995, 395, 287-291.
50. Wang, J.; Lu, F. Oxygen-rich carbon paste Enzyme electrodes for Operation in oxygen-deficient solutions, J. Am. Chem. Soc., 1998, 120, 1048-1050.
51. Wang, J.; Lu, F.; Angnes, L.; Liu, J.; Sakslund, H.; Hammerich, O. Remarkably selective metalized carbon amperometric biosensors, Anal. Chim. Acta, 1995, 305, 3-8.
52. Musameh, M.; Wang, J.; Merkoci, A. Low-potential stable NADH detection at carbon-nanotube-modified glassy carbon electrodes, Electrochem. Commun. 2002, 4, 743-746.
53. Kagie, A.; Bishop, D.; La Belle, J.; Felder, R.; Dymond, R.; Wang, J. Flexible rolled thick-film miniaturized flow-cell for minimally invasive amperometric sensing, Electroanalysis 2008, 20, 1610-1615.
54. Cai, J.; Cizek, K.; Long, B.; Wang, J. Flexible thick-film electrochemical sensors: Impact of mechanical bending and stress on the electrochemical behavior, Sensors Actuators B Chemical, 2009, 137, 379-385.
55. Wang, J. In vivo glucose monitoring: Towards 'Sense and Act' feedback-loop individualized medical systems, Talanta 2008, 75, 636-641.
56. Nebling, E.; Grunwald, T.; Albers, J.; Schafer, P.; Hintsche, R. Electrical detection of viral DNA using ultramicroelectrode arrays, Anal. Chem. 2004, 76, 689-96.