Abstract
We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous work has extended results from coding theory to obtain bounds on code size for new biologically motivated constraints and has applied heuristic local search and genetic algorithm techniques for code design. This paper proposes a natural optimization formulation of the DNA code design problem in which the goal is to design n strings that satisfy a given set of constraints while minimizing the length of the strings. For multiple sets of constraints, we provide high-probability algorithms that run in time polynomial in n and any given constraint parameters, and output strings of length within a constant factor of the optimal. To the best of our knowledge, this work is the first to consider this type of optimization problem in the context of DNA code design.
Supported in part by NSF Grant EIA-0112934.
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References
Adleman, L.M.: Molecular Computation of Solutions to Combinatorial Problems. Science 266, 1021–1024 (1994)
Aggarwal, G., Goldwasser, M.H., Kao, M.-Y., Schweller, R.T.: Complexities for Generalized Models of Self-Assembly. In: Proceedings of the 15th Annual ACM-SIAM Symposium on Discrete Algorithms, pp. 880–889 (2004)
Ben-Dor, A., Karp, R., Schiwkowski, B., Yakhini, Z.: Universal DNA Tag Systems: A Combinatorial Design Scheme. In: Proceedings of the 4th Annual International Conference on Computational Molecular Biology, pp. 65–75 (2000)
Brenner, S.: Methods for Sorting Polynucleotides using Oligonucleotide Tags. US Patent Number 5,604,097 (February 1997)
Brenner, S., Lerner, R.A.: Encoded Combinatorial Chemistry. Proceedings of Natianal Academy of Science 89, 5381–5383 (1992)
Brennerman, A., Condon, A.E.: Strand Design for Bio-Molecular Computation. Theoretical Computer Science 287, 39–58 (2001)
Breslauer, K.J., Frank, R., Blocker, H., Marky, L.A.: Predicting DNA Duplex Stability from the Base Sequence . In: Proceedings of the National Academy of Sciences, vol. 83, pp. 3746–3750 (1986)
Cormen, T.H., Leiserson, C.L., Rivest, R.L., Stein, C.: Introduction to Algorithms, 2nd edn. MIT Press, Cambridge (2001)
Deaton, R., Garzon, M., Murphy, R., Franceschetti, D., Stevens, S.: Genetic Search of Reliable Encodings for DNA Based Computation. In: Proceedings of the 1st Annual Conference on Genetic Programming, pp. 9–15 (1996)
Frutos, A.G., Liu, Q., Thiel, A.J., Sanner, A.M.W., Condon, A.E., Smith, L.M., Corn, R.M.: Demonstration of a Word Design Strategy for DNA Computing on Surfaces. Nucleic Acids Research 25, 4748–4757 (1997)
Garzon, M., Deaton, R., Neathery, P., Franceschetti, D., Murphy, R.: A New Metric for DNA Computing. In: Proceedings of the 2nd Genetic Programming Conference, pp. 472–478 (1997)
Marathe, A., Condon, A., Corn, R.M.: On Combinatorial DNA Word Design. Journal of Computational Biology 8, 201–219 (2001)
Shoemaker, D.D., Lashkari, D.A., Morris, D., Mittmann, M., Davis, R.W.: Quantitative Phenotypic Analysis of Yeast Deletion Mutants Using a Highly Parallel Molecular Bar-coding Strategy. Nature 16, 450–456 (1996)
Tsaftaris, S.A.: DNA Computing from a Signal Processing Viewpoint. IEEE Signal Processing Magazine 21, 100–106 (2004)
Tulpan, D.C., Hoos, H.H.: Hybrid Randomised Neighbourhoods Improve Stochastic Local Search for DNA Code Design. In: Xiang, Y., Chaib-draa, B. (eds.) Canadian AI 2003. LNCS (LNAI), vol. 2671, pp. 418–433. Springer, Heidelberg (2003)
Tulpan, D.C., Hoos, H.H., Condon, A.: Stochastic Local Search Algorithms for DNA Word Design. In: Hagiya, M., Ohuchi, A. (eds.) DNA 2002. LNCS, vol. 2568, pp. 229–241. Springer, Heidelberg (2003)
Winfree, E., Liu, F., Wenzler, L., Seeman, N.: Design and Self-Assembly of Two-Dimensional DNA Crystals. Nature 394, 539–544 (1998)
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Kao, MY., Sanghi, M., Schweller, R. (2005). Randomized Fast Design of Short DNA Words. In: Caires, L., Italiano, G.F., Monteiro, L., Palamidessi, C., Yung, M. (eds) Automata, Languages and Programming. ICALP 2005. Lecture Notes in Computer Science, vol 3580. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11523468_103
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DOI: https://doi.org/10.1007/11523468_103
Publisher Name: Springer, Berlin, Heidelberg
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