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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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
Publisher Name: Springer, Berlin, Heidelberg
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