A biochemical logic gate using an enzyme and its inhibitor. Part II: The logic gate

BioSystems

Volumn 70, Issue 1, 2003, Pages 21-33

  Sivan, Sarit ^a   Tuchman, Samuel ^a   Lotan, Noah ^a  

^a TECHNION ISRAEL INSTITUTE OF TECHNOLOGY   (Israel)

Author keywords

Biochemical logic gates; Chemical and biochemical computation; ENLOGs; Molecular electronics; Molecular switch

Indexed keywords

4 PHENYLAZOBENZOYL ALPHA CHYMOTRYPSIN; ACRIDINE; CHYMOTRYPSIN A; PROFLAVINE; UNCLASSIFIED DRUG;

BIOCHEMISTRY; ENZYME;

ARTICLE; BIOMOLECULAR ELECTRONICS; ENZYME ACTIVITY; INFORMATION PROCESSING;

EID: 0038330458     PISSN: 03032647     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0303-2647(03)00039-X     Document Type: Article

References (39)

1. Arkin A., Ross J. Computational functions in biochemical reaction networks. Biophys. J. 67:1994;560-578.
2. Ashkenazi, G., 1992. Biochemical molecular logic systems: structure and function. M.Sc. Thesis, Technion - Israel Institute of Technology, Haifa, Israel.
3. Ashkenazi G., Ripoll D.R., Lotan N., Scheraga H.A. A molecular switch for biochemical logic gates: conformational studies. Biosens. Bioelectron. 12:1997;85-95.
4. Aviram, A., Ratner, M. (Eds.), 1988. Molecular electronics: science and technology. Ann. N.Y. Acad. Sci. 852.
5. Berezin I.V., Varfolomeyev S.D., Klibanov A.M., Martinek K. Light and ultrasonic regulation of alpha-chymotrypsin activity: proflavine as a light and sound-sensitive competitive inhibitor. FEBS Lett. 39:1974;329-331.
6. Berezin, I.V., Kazanskaya, N.F., Martinek, K., 1978. Application of immobilized enzymes in non-silver photography. In: Wingard, L.B. (Ed.), Enzyme Engineering. Plenum Press, New York.
7. Carter, F.L., 1982. Conformational switching at the molecular level. In: Carter, F.L. (Ed.), Molecular Electronic Devices. Dekker, New York, pp. 51-71.
8. Carter, F.L., 1987. Soliton switching and its implication for molecular electronics. In: Carter, F.L. (Ed.), Molecular Electronics Devices II. Dekker, New York, pp. 149-182.
9. Chiabrera A., Zitti E.Di., Costa F., Bisio G.M. Physical limits of integration and information processing in molecular systems. J. Phys. D: Appl. Phys. 22:1989;1571-1579.
10. Chiabrera A., Zitti E.Di., Costa F., Bisio G.M. Molecular information processing and physical constraints on computation. CHEMTRONICS. 5:1991;17-22.
11. de Silva A.P., Samankumara S.K.R.A. Fluorescence "off-on" signaling upon linear recognition and binding of α,ω-alkanediyldiammonium ions by 9,10-bis{(1-aza-4,7,10,13,16-pentaoxacycloocatadecyl)methyl}anthracene. Angew. Chem. Int. Ed. Engl. 29:1990;1173-1175.
12. de Silva A.P., Gunaratne H.Q.N., McCoy C.P. A molecular photoionic AND gate based on fluorescent signaling. Nature. 364:1993;42-44.
13. Eisenmesser E.Z., Bosco D.A., Akke M., Kern D. Enzyme dynamics during catalysis. Science. 295:2002;1520-1523.
14. Hjelmfelt A., Ross J. Chemical implementation and thermodynamics of collective neural networks. Proc. Natl. Acad. Sci. U.S.A. 89:1992;388-391.
15. Hjelmfelt A., Ross J. Mass coupled chemical systems with computational properties. J. Phys. Chem. 97:1993;7988-7992.
16. Hjelmfelt A., Ross J. Pattern recognition, chaos, and multiplicity in neural networks of excitable systems. Proc. Natl. Acad. Sci. U.S.A. 91(1):1994;63-67.
17. Hjelmfelt A., Weinberger E.D., Ross J. Chemical implementation of neural networks and Turing machines. Proc. Natl. Acad. Sci. U.S.A. 88:1991;10983-10987.
18. Hjelmfelt A., Weinberger E.D., Ross J. Chemical implementation of finite state machines. Proc. Natl. Acad. Sci. U.S.A. 89:1992;383-387.
19. Hjelmfelt A., Schneider F.W., Ross J. Pattern recognition in coupled chemical kinetic systems. Science. 260:1993;335-337.
20. Hush N.L., Reimers J.R., Hall L.E., Johnston L.A., Crossley M.J. Optimization and chemical control of porphyrin-based molecular wires and switches. Ann. N.Y. Acad. Sci. 852:1998;1-21.
21. Kompa K.L., Levine R.D. A molecular logic gate. Proc. Natl. Acad. Sci. U.S.A. 98(2):2001;410-414.
22. Martinek K., Dorovksa V.N., Varfolomeyev S.D., Berezin I.V. The role of entropy and enthalpy factors in kinetic specificity of alpha-chymotrypsin: temperature dependence study of acyl-alpha-chymotrypsin deacylation. Biochim. Biophys. Acta. 271:1972;80-86.
23. McConn J., Ku E., Himoe A., Grandt K.G., Hess G.P. Investigation of the chymotrypsin-catalyzed hydrolysis of specific substrates. J. Biol. Chem. 246(9):1971;2918-2925.
24. Lotan N., Ashkenazi G., Tuchman S., Nehamkin S. Molecular bio-electronics biomaterials. Mol. Cryst. Liq. Cryst. 236:1993;95-104.
25. Poplawski J., Anders J., Byrne H.G., Roth S. Time-resolved fluorescence and solvatochromism in donor substituted bianthrones. Synth. Metals. 55-57:1993;307-312.
26. Rambidi N.G. Towards a biomolecular computer: 2 - information processing and computing devices based on biochemical non-linear dynamic systems. J. Mol. Elec. 7:1991;115-125.
27. Rambidi N.G. Non discrete biomolecular computing: an approach to computational complexity. BioSystems. 31:1993a;3-13.
28. Rambidi N.G. Towards a biomolecular computer. BioSystems. 27:1993b;219-222.
29. Rambidi N.G. Roots and promises of chemical-based computing. BioSystems. 64(1-3):2002;169-178.
30. Rambidi N.G., Chernavskii D.S., Sandler Yu.M. Towards a biomolecular computer: 1 - ways, means, objectives. J. Mol. Elec. 7:1991;105-114.
31. Rinaldi R., Branca E., Cingolani R., DiFelice R., Calzolari A., Molinari E., Masiero S., Spada G., Gottarelli G., Garbesi A. Biomolecular electronic devices based on self-organized deoxyguanosine nanocrystals. Ann. N.Y. Acad. Sci. 960:2002;184-192.
32. Rosen R. Two factor models, neural nets and biochemical automata. J. Theor. Biol. 15:1967;282-297.
33. Rosen R. Recent developments in the theory of control and regulation of cellular processes. Int. Rev. Cytol. 23:1968;25-88.
34. Sivan, S., 1995. Biochemical-logic systems in molecular electronics: enzyme-based systems. M.Sc. Thesis, Technion - Israel Institute of Technology, Haifa, Israel.
35. Sivan S., Lotan N. A biochemical logic gate using an enzyme and its inhibitor. Part I: the inhibitor as switching element. Biotechnol. Prog. 15:1999;964-970.
36. Stadler R., Ami S., Forshaw M., Joachim C. A tight-binding study of logic circuits for adding numbers inside a molecule. Nanotechnology. 13:2002;424-428.
37. Tuchman, S., 1994. Biochemical systems for molecular logic elements. D.Sc. Thesis, Technion - Israel Institute of Technology, Haifa, Israel.
38. Tuchman, S., Sideman, S., Kenig, S., Lotan, N., 1994. Enzyme-based logic gates controlled by outside signals: principles and design. In: Sienicki, K. (Ed.), Molecular Electronics and Molecular Electronic Devices, vol. III. CRC Press, Boca Raton, pp. 223-238.
39. Zauner K.P., Conrad M. Enzymatic computing. Biotechnol. Prog. 17:2001;553-559.