Abstract
Predicting the behavior of DNA molecules in vitro is one of the most fundamental issues on DNA computing, but is also known to be quite difficult. Shiozaki et al. proposed a probabilistic model that can simulate many features of biochemical experiments in terms of the reaction rate [7], although there are several differences between the biochemical experiments and the computational simulations on the model.
In this paper, we extend the model to support base pairs construction among k DNA sequences, which plays an essential role in realizing branch migrations. The simulation results have much more similarities to the biochemical experiments results than ones on the previous model, which implies that the analysis of the model may give some insight about the reaction rate. Through the analysis, we conclude this paper by giving a guideline for designing DNA sequences that can quickly react.
This research partly received financial support from Scientific research fund of Ministry of Education, Culture, Sports, Science and Technology.
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References
Flamm, C.: Kinetic Folding of RNA, Dissertation (1998)
Flamm, C., Fontana, W., Hofacker, I.L., Schuster, P.: RNA Folding at Elementary Step Resolution, Santa Fe Institute 12-078 (1999)
Hofacker, I.L.: The Vienna RNA Secondary Structure Server. Nucleic. Acids Res. 31, 3429–3431 (2003)
Hofacker, I.L., Fontana, W., Stadler, P.F., Bonhoeffer, L.S., Tacker, M., Schuster, P.: Fast Folding and comparison of RNA Secondary Structures. Monatsh. Chem. 125, 167–188 (2003)
Hartemink, A.J., Fifford, D.K.: Thermodynamic Simulation of Deoxyligonucleotide Hybridization for DNA Computation. DIMACS Series in Discrete Mathematics and Theoretical Computer Science
Kobayashi, S.: Strand Design for Molecular Computation, Sciences (2003)
Shiozaki, M., Ono, H., Sadakane, K., Yamashita, M.: Modeling DNA Conformation Change and Theoretical Analysis on the Reaction Rate. In: Preproceedings of the 11th International Meeting on DNA Computing (DNA11), vol. 408 (2005)
Tacker, M., Fontana, W., Stadler, P.F., Schuster, P.: Statistics of RNA Melting Kinetics. Eur. Biophys. J. 23, 29–38 (1993)
Uejima, H., Hagiya, M.: Analyzing Secondary Structure Transition Paths of DNA/RNA molecules. In: PreProceedings of the 9th International Meeting on DNA Computing (DNA9), pp. 4731–4741 (2004)
Wolfinger, M.T., Svrcek-Seiler, W.A., Flamm, C., Hofacker, I.L., Stadler, P.F.: Efficient Computation of RNA Folding Dynamics. J. Phys. A: Math. Gen. 37, 4731–4741 (2004)
Zucker, M.: The Equilibrium Partition Function (2003), http://www.bioinfo.rpi.edu/~zukerm/lectures/RNAfold-html/node3.html
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Shiozaki, M., Ono, H., Sadakane, K., Yamashita, M. (2006). A Probabilistic Model of the DNA Conformational Change. In: Mao, C., Yokomori, T. (eds) DNA Computing. DNA 2006. Lecture Notes in Computer Science, vol 4287. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11925903_21
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DOI: https://doi.org/10.1007/11925903_21
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-49024-1
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