Abstract
DNA splicing in the test tube may generate DNA molecules other than well-formed ones having two blunt ends. We introduce an example splicing system that generates all possible molecular types. We use differential equations to model the system, and Mathematica to simulate its dynamics. We find that most simulation results match our predictions, and acknowledge that a more comprehensive program is needed for further investigations. This is the first model and simulation of which we are aware that specifically treats the fact that several molecular types in addition to well-formed molecules may be present in a splicing system, even at equilibrium.
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References
Culik II, K., Harju, T.: Splicing semigroups of dominoes and DNA. Discrete Applied Mathematics 31, 261–277 (1991)
Freund, R., Csuhaj-Varjú, E., Wachtler, F.: Test tube systems with cutting/recombination operations. In \(\cite{|PSB97}\)
Goode, E., Pixton, D.: Splicing to the limit. In: Jonoska, N., Păun, G., Rozenberg, G. (eds.) Aspects of Molecular Computing. LNCS, vol. 2950, pp. 189–201. Springer, Heidelberg (2003)
Head, T.: Formal language theory and DNA: An analysis of the generative capacity of specific recombinant behaviors. Bulletin of Mathematical Biology 49(6), 737–759 (1987)
Head, T., Păun, G., Pixton, D.: Generative mechanisms suggested by DNA recombination. In \(\cite{|Handbook96}\)
Mauri, G., Bonizzoni, P., DeFelice, C., Zizza, R.: DNA and circular splicing. In: Condon, A., Rozenberg, G. (eds.) DNA 2000. LNCS, vol. 2054, pp. 117–129. Springer, Heidelberg (2001)
Pacific Symposium on Biocomputing (1997), http://WWW-SMI.Stanford.EDU/people/altman/psb97/index.html
Păun, G.: Regular extended H systems are computationally universal. J. Autom. Lang. Comb. 1(1), 27–36 (1996)
Păun, G.: Controlled H systems and the Chomsky Hierarchy. Fundam. Inf. 30(1), 45–57 (1997)
Păun, G. (ed.): Computing with Bio-Molecules: Theory and Experiments. Springer, New York (1998)
Pixton, D.: Linear and circular splicing systems. In: INBS 1995. Proceedings of the First International Symposium on Intelligence in Neural and Biological Systems, p. 181. IEEE Computer Society, Washington (1995)
Pixton, D.: Regularity of splicing languages. Discrete Applied Mathematics 69(1-2), 101–124 (1996)
Pixton, D.: Splicing in abstract families of languages. Theoretical Computer Science 234, 135–166 (2000)
Rozenberg, G., Salomaa, A. (eds.): Handbook of Formal Languages. Springer, New York (1996)
Siromoney, R., Subramanian, K.G., Rajkumar Dare, V.: Circular DNA and splicing systems. In: ICPIA 1992. Proceedings of the Second International Conference on Parallel Image Analysis, pp. 260–273. Springer, London (1992)
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Goode, E., DeLorbe, W. (2008). DNA Splicing Systems. In: Garzon, M.H., Yan, H. (eds) DNA Computing. DNA 2007. Lecture Notes in Computer Science, vol 4848. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-77962-9_25
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DOI: https://doi.org/10.1007/978-3-540-77962-9_25
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-77961-2
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