Abstract
The input data for DNA computing must be encoded into the form of single or double DNA strands. As complementary parts of single strands can bind together forming a double-stranded DNA sequence, one has to impose restrictions on these sets of DNA words (=languages) to prevent them from interacting in undesirable ways. We recall a list of known properties of DNA languages which are free of certain types of undesirable bonds. Then we introduce a general framework in which we can characterize each of these properties by a solution of a uniform formal language inequation. This characterization allows us among others to construct (i) a uniform algorithm deciding in polynomial time whether a given DNA language possesses any of the studied properties, and (ii) in many cases also an algorithm deciding whether a given DNA language is maximal with respect to the desired property.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Arita, M., Kobayashi, S.: DNA sequence design using templates. New Generation Computing 20, 263–277 (2002)
Domaratzki, M.: Deletion Along Trajectories. Tech. Report 464-2003, School of Computing, Queen’s University (2003) (submitted for publication)
Head, T.: Relativised code concepts and multi-tube DNA dictionaries. In: Calude, C.S., Păun, G. (eds.) Finite Versus Infinite: Contributions to an Eternal Dilemma, pp. 175–186. Springer, London (2000)
Hussini, S., Kari, L., Konstantinidis, S.: Coding properties of DNA languages. theoretical Computer Science 290/3, 1557–1579 (2002)
Jonoska, N., Kephart, D., Mahalingam, K.: Generating DNA code words. Congressus Numerantium 156, 99–110 (2002)
Jonoska, N., Mahalingam, K.: Languages of DNA based code words. In: Chen, J., Reif, J.H. (eds.) DNA 2003. LNCS, vol. 2943, pp. 58–68. Springer, Heidelberg (2004)
Kari, L.: On insertion and deletion in formal languages, PhD thesis, University of Turku, Finland (1991)
Kari, L., Kitto, R., Thierrin, G.: Codes, involutions and DNA encoding. In: Brauer, W., Ehrig, H., Karhumäki, J., Salomaa, A. (eds.) Formal and Natural Computing. LNCS, vol. 2300, pp. 376–393. Springer, Heidelberg (2002)
Kari, L., Konstantinidis, S.: Language equations, maximality and error detection (submitted for publication)
Kari, L., Konstantinidis, S., Losseva, E., Wozniak, G.: Sticky-free and overhang-free DNA languages. Acta Informatica 40, 119–157 (2003)
Kari, L., Konstantinidis, S., Sosík, P.: On Properties of Bond-Free DNA Languages. Dept. of Computer Science Tech. Report No. 609, Univ. of Western Ontario (2003) (submitted for publication)
Kari, L., Sosík, P.: Language deletion on trajectories. Dept. of Computer Science Technical Report No. 606, University of Western Ontario, London (2003)
Marathe, A., Condon, A.E., Corn, R.M.: On combinatorial DNA words design. J. Computational Biology 8(3) (2001)
Mauri, G., Ferretti, C.: Word Design for Molecular Computing: A Survey. In: Chen, J., Reif, J.H. (eds.) DNA 2003. LNCS, vol. 2943, pp. 37–46. Springer, Heidelberg (2004)
Mateescu, A., Rozenberg, G., Salomaa, A.: Shuffle on trajectories: syntactic constraints, TUCS technical report No. 41, Turku Centre for Computer Science, 1996, and Theoretical Computer Science 197, 1–56 (1998)
Păun, G., Rozenberg, G., Salomaa, A.: DNA Computing. New Computing Paradigms. Springer, Berlin (1998)
Rozenberg, G., Salomaa, A. (eds.): Handbook of Formal Languages. Springer, Berlin (1997)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Kari, L., Konstantinidis, S., Sosík, P. (2005). Preventing Undesirable Bonds Between DNA Codewords. In: Ferretti, C., Mauri, G., Zandron, C. (eds) DNA Computing. DNA 2004. Lecture Notes in Computer Science, vol 3384. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11493785_16
Download citation
DOI: https://doi.org/10.1007/11493785_16
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-26174-2
Online ISBN: 978-3-540-31844-6
eBook Packages: Computer ScienceComputer Science (R0)