Abstract
We previously described a tic-tac-toe playing molecular auto- maton, MAYA-II, constructed from a molecular array of deoxyribozyme- based logic gates, that uses oligonucleotides as inputs and outputs. We are now developing an ensemble modeling tool for high-throughput oligonucleotide input and logic gate designs. The modeling tool is based on exhaustive reconstruction of both intended and unintended reactions between MAYA-II gates and inputs, and seeks to correlate empirical observations with computational predictions. We present results from computational analysis of the MAYA-II Yes logic gate and input interactions. Results indicate that in silico modeling correlates with experimental results, creating a predictive value and benchmark. These studies serve purpose towards our goal of constructing a generalized oligonucleotide library for expansion of molecular computation networks beyond hundreds, to millions of potential interactions, conferring greater functionality in terms of both reliability and complexity.
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References
Adleman, L.: Molecular computation of solutions to combinatorial problems. Sci. 266, 1021–1024 (1994)
Andronescu, M., Dees, D., Slaybaugh, L., Zhao, Y., Condon, A., Cohen, B., Skiena, S.: Algorithms for testing that sets of DNA words concatenate without secondary structure. In: Hagiya, M., Ohuchi, A. (eds.) DNA 2002. LNCS, vol. 2568, pp. 182–195. Springer, Heidelberg (2003)
Benenson, Y., Gil, B., Ben-Dor, U., Adar, R., Shapiro, E.: An autonomous molecular computer for logical control of gene expression. Nat. 429, 423–429 (2004)
Cardelli, L.: Strand algebras for DNA computing (2009), http://lucacardelli.name/Papers
Dirks, R., Lin, M., Winfree, E., Pierce, N.: Paradigms for Computational Nucleic Acid Design. Nucl. Acids Res. 32(4), 1392–1403 (2004)
Dirks, R., Bois, J., Schaeffer, J., Winfree, E., Pierce, N.: Thermodynamic Analysis of Interacting Nucleic Acid Strands. SIAM 49(1), 65–88 (2007)
Flamm, C., Hofacker, I.: Beyond energy minimization: approaches to the kinetic folding of RNA. Chem. Mon. 139(4), 447–457 (2008)
Harvey, S., Wang, C., Teletchea, S., Lavery, R.: Motifs in Nucleic Acids: Molecular Mechanics Restraints for Base Pairing and Base Stacking. Jour. Comp. Chem. 24(1), 1–9 (2003)
Heitsch, C., Condon, A., Hoos, H.: From RNA Secondary Structure to Coding Theory: A Combinatorial Approach. In: Hagiya, M., Ohuchi, A. (eds.) DNA 2002. LNCS, vol. 2568, pp. 215–228. Springer, Heidelberg (2003)
Hinsen, K.: The Molecular Modeling Toolkit: A New Approach to Molecular Simulations. Jour. Comp. Chem. 21(2), 79–85 (2000)
Hoops, S., Sahle, S., Gauges, R., Lee, C., Pahle, J., Simus, N., Singhal, M., Xu, L., Mendes, P., Kummer, U.: COPASI - A Complex Pathway SImulator. Bionfrmtcs. 22, 3067–3074 (2006)
Langtangen, H.: Python Scripting for Computational Science. Springer, Heidelberg (2004)
Macdonald, J., Yang, L., Sutovic, M., Lederman, H., Pendri, K., Lu, W., Andrews, B., Stefanovic, D., Stojanovic, M.: Medium Scale Integration of Molecular Logic Gates in an Automaton. Nano. Ltrs. 6(11), 2598–2603 (2006)
Markham, N., Zuker, M.: DINAMelt web server for nucleic acid melting prediction. Nucl. Acids Res. 33, W577–W581 (2005)
Stojanovic, M., Stefanovic, D.: A deoxyribozyme-based molecular automaton. Nat. Biotech. 21(9), 1069–1074
Xayaphoummine, T., Bucher, T., Isambert, H.: Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots. Nucl. Acids Res. 33, 605–610 (2005)
Zuker, M.: Mfold Web Server for Nucleic Acid Folding and Hybridization Prediction. Nucl. Acids Res. 31(13), 3406–3415
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Fanning, M.L., Macdonald, J., Stefanovic, D. (2009). Advancing the Deoxyribozyme-Based Logic Gate Design Process. In: Deaton, R., Suyama, A. (eds) DNA Computing and Molecular Programming. DNA 2009. Lecture Notes in Computer Science, vol 5877. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-10604-0_5
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DOI: https://doi.org/10.1007/978-3-642-10604-0_5
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