Complex patterns in a trans-cooperatively coupled DNA amplification system

Chemical Engineering Science

Volumn 55, Issue 2, 2000, Pages 245-256

  Kirner, T ^a   Ackermann, J ^a   Steen, D ^a   Ehricht, R ^a   Ellinger, T ^a   Foerster, P ^a   McCaskill, J S ^a  

^a FRITZ LIPMANN INSTITUTE   (Germany)

Author keywords

Cooperation; Evolution; Pattern formation; Reaction diffusion; Self replicating spots

Indexed keywords

BIOREACTORS; COMPUTER SIMULATION; DNA; REACTION KINETICS;

IN VITRO AMPLIFICATION SYSTEM;

BIOCHEMISTRY;

AMPLIFICATION; BIOLOGICAL ENVIRONMENT; REACTION-DIFFUSION EQUATION;

EID: 0345504196     PISSN: 00092509     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0009-2509(99)00320-6     Document Type: Article

References (53)

1. Ackermann J., Kirner T. Parasites and pattern formation. Zeitschrift fuer Naturforschung A. 54a:1999;146-152.
2. Ackermann J., Wlotzka B., McCaskill J.S. In-vitro DNA-based predator-prey system with oscillatory kinetics. Bulletin of Mathematical Biology. 60:1998;329-354.
3. Baras F., Mansour M.M., Pearson J.E. Microscopic simulation of chemical bistability in homogeneous systems. Journal of Chemical Physics. 105(18):1996;8257-8261.
4. Baras F., Pearson J.E., Mansour M.M. Microscopic simulation of chemical oscillations in a homogeneous system. Journal of Chemical Physics. 93(8):1990;5747-5750.
5. Bochmann, A. (1997). Experimentelle Untersuchungen an biochemischen Reaktionssystemen mittels fluriometrischer Methoden und stömungsmechanische Simulation eines Flußreaktors. Diploma thesis, University of Jena, Germany.
6. Böddeker, B. (1995). Physikalische Modelle für Koevolution und Simulation auf einem hardwareprogrammierbaren Prozessor. Diploma thesis, University of Göttingen, Germany.
7. Boerlijst M.C., Hogeweg P. Spiral wave structures in prebiotic evolution. Hypercycles stable against parasites Physica D. 48:1991;17-28.
8. Breaker R.R., Joyce G.F. Emergence of replicating species from in vitro RNA evolution reaction. Proceedings of the National Academy of Sciences USA. 91:1994;6093-6097.
9. Compton J. Nucleic acid sequence-based amplification. Nature. 350:1991;91-92.
10. Cronhjort M.B., Blomberg C. Cluster compartmentalization may provide resistance to parasites for catalytic networks. Physica D. 101:1997;289-298.
11. Dulos E., Davies P., Rudovics B., Kepper P.D. From quasi-2D to 3D Turing patterns in ramped systems. Physica D. 98:1996;53-66.
12. Dyson F.J. A model for the origin of life. Journal of Molecular Evolution. 118:1982;344-350.
13. Ehricht R., Ellinger T., McCaskill J.S. Cooperative amplification of templates by cross hybridization (CATCH). European Journal of Biochemistry. 243:1997;358-364.
14. Ehricht R., Kirner T., Ellinger T., Foerster P., McCaskill J.S. Monitoring the amplification of CATCH, a 3SR based cooperatively coupled isothermal amplification system, by fluorimetric methods. Nucleic Acids Research. 25:1997;4697-4699.
15. Eigen M. The quasispecies model. Naturwissenschaften. 58:1971;465-523.
16. Eigen M., McCaskill J.S., Schuster P. The molecular quasi-species. Advances in Chemical Physics. 75:1989;149-263.
17. Eigen M., Schuster P. The hypercycle. Naturwissenschaften. 11:1977;541-565.
18. Eigen M., Schuster P. The hypercycle. 1979;Springer, Berlin.
19. Ellinger T., Ehricht R., McCaskill J.S. In vitro evolution of molecular cooperation in CATCH, a cooperatively coupled amplification system. Chemistry and Biology. 5:1998;729-741.
20. Fahy E., Kwoh D.Y., Gingeras T.R. Self-sustained sequence replication (3SR). An isothermal transcription-based amplification system alternative to PCR PCR Methods and Applications. 1:1991;25-33.
21. Fang J.Q., Pearson J.E., Mansour M.M. Colored noise induced nonequilibrium transition in a new chemical oscillator. Communications in Theoretical Physics. 17(1):1992;39-48.
22. Gray P., Scott S.K. Sustained oscillations and exotic patterns of behavior in isothermal reactions. Journal of Physical Chemistry. 89:1985;22-32.
23. Guatelli J.C., Whitefield K.M., Deborah K.J.B., Kwoh Y., Richman D.D., Gingeras T.R. Isothermal, in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication. Proceedings of the National Academy of Sciences. 87:1990;1874-1878.
24. Haugland, R. P. (1992). Handbook of fluorescent probes and research chemicals (5th ed.) Molecular Probes Inc., Eugene, U.S.A. (p. 223).
25. Kauffman S.A. The origin of order. Self organization and selection in evolution:1990;Oxford University, Oxford.
26. Kirner, T., Ackermann, J., Ehricht, R., & McCaskill, J. S. (1998). Complex patterns predicted in an in vitro experimental model system for the evolution of molecular cooperation. Biophysical Chemistry, in press.
27. Kuramoto, Y. (1984). Chemical oscillations, waves and turbulence (1st ed.). Berlin: Springer.
28. Kwoh D.Y., Davis G.R., Whitefield K.M., Chappelle H.L., DiMichele L., Gingeras T.R. Transcription-based amplification system and detection of amplified human immunodeficiency virus type 1 with a bead-based sandwich hybridization format. Proceedings of the National Academy of Sciences. 86:1989;1173-1177.
29. Maynard Smith J. Hypercycles and the origin of life. Nature. 280:1979;445-446.
30. McCaskill, J. S. (1995). Ursprünge der Molekularen Kooperation: Theorie und Experiment. In P. Schuster, Antrittsvorlesungen 1994 an der Friedrich-Schiller-Universität Jena (pp. 27-40). Jena, Germany, Institut für Molekulare Biotechnologie e.V.
31. McCaskill J.S. Spatially resolved in vitro molecular ecology. Biophysical Chemistry. 66:1997;145-158.
32. McCaskill J.S., Bauer G.J. Images of evolution. origin of spontaneous RNA replication waves Proceedings of the National Academy of Sciences USA. 90:1993;4191-4195.
33. McCaskill, J. S., Maeke, T., Gemm, U., Schulte, L., & Tangen, U. (1997). NGEN: A massively parallel reconfigurable computer for biological simulation: Towards a self-organisation computer. Lecture Notes in Computer Science, vol. 1259 (pp. 260-276). Berlin: Springer.
34. McCaskill J.S., Tangen U., Ackermann J. VLSE very large scale evolution in hardware. Husband P., Harvey I. Fourth European conference on artificial life (ECAL). 1997;398-406 MIT Press/Bradford Books, Cambridge, MA.
35. Mullis K.B., Faloona F.A. Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods in Enzymology. 155:1987;335-340.
36. Muratov C.B. Self-replication and splitting of domain patterns in reaction-diffusion systems with fast inhibitors. Physical Review E. 54:1996;3369-3376.
37. Muratov C.B., Osipov V.V. Scenarios of domain pattern formation in reaction-diffusion systems. Physical Review E. 54:1996;4860-4879.
38. Pearson J.E. Complex patterns in a simple system. Science. 261:1993;189-192.
39. Reynolds W.N., Pearson J.E., Ponce-Dawson S. Dynamics of self-replicating patterns in reaction-diffusion systems. Physical Review Letters. 72:1994;2797-2800.
40. Romano J.W., Shurtliff R.N., Sarngadharan M.G., Pal R. Detection of HIV-1 infection in vitro using NASBA. an isothermal RNA amplification technique Journal of Virology Methods. 54:1995;109-119.
41. Rössler O.E. Ein systemtheoretisches Modell zur Biogenese. Zeitschrift fuer Naturforschung. 26b:1971;741-746.
42. Rössler O.E. Chemical turbulence. Chaos in a simple reaction-diffusion system Zeitschrift fuer Naturforschung. 31a:1976;1168-1172.
43. Saiki R.K., Scharf S., Faloona F.A., Mullis K.B., Horn C.T., Ehrlich H.A., Arnheim N. Enzymatic amplification of. β -globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia Science. 230:1985;1350-1354.
44. Schmidt, K., Foerster, P., Bochmann, A., & McCaskill, J. S. (1998). A microflow reactor for two dimensional investigations of in vitro amplification systems. In W. Ehrenfeld, Microreaction technology (pp. 234-244). Berlin: Springer. Proceedings of the first international conference on microreaction technology.
45. Schmidt, K., & McCaskill, J. S. (1996). Microstructuring for evolution biotechnology and molecular information processing. imb annual report, Institute for molecular biotechnology, Jena, Germany, 92.
46. Strasser P., Rössler O.E., Baier G. Hyperchaos and chemical turbulence in enzymatic reaction-diffusion systems. Journal of Chemical Physics. 104:1996;9974-9982.
47. Szathmary E. The integration of the earliest genetic information. Trends in Ecology Evolution. 4:1989;200-204.
48. Tyagi S., Kramer F.R. Molecular beacons. Probes that fluoresce upon hybridization Nature Biotechnology. 14:1996;303-308.
49. Voroney J.P., Lawniczak A.T., Kapral R. Turing pattern formation in heterogeneous media. Physica D. 99:1996;303-317.
50. Wilhelm T., Heinrich R. Smallest chemical reaction system with Hopf bifurcation. Journal of Mathematical Chemistry. 17:1995;1-14.
51. Wilhelm T., Heinrich R. Mathematical analysis of the smallest chemical reaction system with Hopf bifurcation. Journal of Mathematical Chemistry. 19:1996;111-130.
52. Witt A.D., Dewel G., Borckmans P. Chaotic Turing-Hopf mixed mode. Physical Review E. 48:1993;R4191.
53. Wlotzka B., McCaskill J.S. A molecular predator and its prey. Coupled isothermal amplification of nucleic acids Chemistry and Biology. 4:1997;25-33.