Abstract
We present the design of a novel, irreversible memory element for use in artificial DNA-based computing systems and provide ‘wet-ware’ demonstrations of the validity of key assumptions of our design. The mechanism makes use of a DNA switch with a rotatable mid-section that contains a bacterial promoter and non-rotatable end sections, each of which contains a gene encoding a different fluorescent protein. The state (orientation) of the rotatable mid-section is therefore reported by the fluorescent colour produced when the plasmid is in a system that permits transcription and translation. Rotation of the mid-section from the ‘unset’ to the ‘set’ state is achieved by digestion of specific sites on the switch by the asymmetric restriction enzyme, Bpu10I, followed by ligation. Once set, the rotatable section cannot be cut again by the enzyme, so that state is held irreversibly even when exposed again to the switching signal. This mechanism has potential applications for permanently recording, in DNA, the occurrence of transient events.
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Acknowledgements
We would like to thank Darren Logan and Jane Armstrong for discussions and Jean Pierre Lavergne, Kendra White and Matthias Ehrmann for supplying a discontinued plasmid.
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Blenkiron, M., Arvind, D.K. & Davies, J.A. Design of an irreversible DNA memory element. Nat Comput 6, 403–411 (2007). https://doi.org/10.1007/s11047-007-9051-y
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DOI: https://doi.org/10.1007/s11047-007-9051-y