Abstract
Template-guided recombination (TGR) is a formal model for the DNA rearrangement which occurs in certain ciliates. In this paper, the equivalence problem for TGR is considered: given two sets of templates, is their action is the same for all operands? This question is motivated by molecular computation, as we view equivalence in TGR as a method for discerning whether modifications to the functioning of a ciliate via the set of templates has any effect on the rearrangement it defines. This motivation is also suggested by recent experiments into the role of RNA in the rearrangement of ciliate DNA. We give a language-theoretic characterization of equivalence which leads to decidability results for common language classes. In particular, we show a positive answer for regular sets of templates. For context-free sets of templates, the answer is negative. The same language-theoretic characterization also applies to intra-molecular TGR. The problem for iterated TGR remains open.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Angeleska A, Jonoska N, Saito M, Landweber L (2007) RNA-guided DNA assembly. J Theor Biol 248:706–720
Cavalcanti A, Landweber L (2006) Insights into a biological computer: detangling scrambled genes in ciliates. In: Chen J, Jonoska N, Rozenberg G (eds) Nanotechnology: science and computation. Springer-Verlag, pp 349–360
Daley M, Domaratzki M, Morris A (2007) Intra-molecular template-guided recombination. Int J Found Comput Sci 18:1177–1186
Daley M, McQuillan I (2005) Template-guided DNA recombination. Theor Comput Sci 330:237–250
Daley M, McQuillan I (2006a) On computational properties of template-guided DNA recombination in ciliates. In: Carbone A, Pierce N (eds) DNA computing. Lecture notes in computer science, vol 3892. Springer-Verlag, pp 27–37
Daley M, McQuillan I (2006b) Useful templates and iterated template-guided DNA recombination in ciliates. Theory Comput Syst 39:619–633
Ehrenfeucht A, Harju T, Petre I, Prescott D, Rozenberg G (2004) Computation in living cells: gene assembly in ciliates. Springer-Verlag
McQuillan I, Salomaa K, Daley M (2006) Iterated TGR languages: membership problem and effective closure properties. In: Chen D, Lee D (eds) Computing and combinatorics. Lecture notes in computer science, vol 4112. Springer-Verlag, pp 94–103
Păun G, Rozenberg G, Salomaa A (1998) DNA computing. Springer-Verlag
Prescott D, Ehrenfeucht A, Rozenberg G (2003) Template-guided recombination for IES elimination and unscrambling of genes in stichotrichous ciliates. J Theor Biol 222:323–330
Rozenberg G, Salomaa A (eds) (1997) Handbook of formal languages. Springer-Verlag
Vijayan V, Nowacki M, Zhou Y, Doak T, Landweber L (2007) Programming a ciliate computer: template-guided in vivo DNA rearrangements in oxytricha. In: Garzon M, Yan H (eds) DNA 13: preliminary proceedings, p 172
Acknowledgments
We thank the referees of DNA 13 for their helpful comments on an early version of this paper, and in particular, the suggested alternative proof of Corollary 8. We also thank the referees of Natural Computing for their many useful and helpful comments.
Author information
Authors and Affiliations
Corresponding author
Additional information
Research supported in part by a grant from NSERC. A preliminary version of this paper appeared at DNA 13 [Domaratzki M (2008) Equivalence in template-guided recombination. In: Garzon M, Yan H (eds) DNA 13. Springer, LNCS 4848, pp 263–272].
Rights and permissions
About this article
Cite this article
Domaratzki, M. Equivalence in template-guided recombination. Nat Comput 7, 439–449 (2008). https://doi.org/10.1007/s11047-008-9071-2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11047-008-9071-2