Abstract
This paper deals with the problem of designing the secondary structure of a multi-state molecular machine in which the formation of repeated DNA hairpin structures changes sequentially with the aim of implementing more sophisticated DNA nanomachines. Existing methods are insufficient to construct such a huge molecular machine using multiple DNA molecules. The method used in this paper validates the changes in formation exhaustively by dividing the secondary structure into hairpin units. It considers the minimum free energy of the structure, the structure transition paths, and the total frequency of optimal and sub-optimal structures. Hence, it can better design base sequences using the principles of thermodynamics.
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Uejima, H., Hagiya, M. (2004). Secondary Structure Design of Multi-state DNA Machines Based on Sequential Structure Transitions. In: Chen, J., Reif, J. (eds) DNA Computing. DNA 2003. Lecture Notes in Computer Science, vol 2943. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-24628-2_9
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DOI: https://doi.org/10.1007/978-3-540-24628-2_9
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