A last-in first-out stack data structure implemented in DNA

Annunziata Lopiccolo, Ben Shirt-Ediss, Emanuela Torelli, Abimbola Feyisara Adedeji Olulana, Matteo Castronovo, Harold Fellermann () and Natalio Krasnogor ()
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Annunziata Lopiccolo: Newcastle University
Ben Shirt-Ediss: Newcastle University
Emanuela Torelli: Newcastle University
Abimbola Feyisara Adedeji Olulana: University of Leeds
Matteo Castronovo: University of Leeds
Harold Fellermann: Newcastle University
Natalio Krasnogor: Newcastle University

Nature Communications, 2021, vol. 12, issue 1, 1-10

Abstract: Abstract DNA-based memory systems are being reported with increasing frequency. However, dynamic DNA data structures able to store and recall information in an ordered way, and able to be interfaced with external nucleic acid computing circuits, have so far received little attention. Here we present an in vitro implementation of a stack data structure using DNA polymers. The stack is able to record combinations of two different DNA signals, release the signals into solution in reverse order, and then re-record. We explore the accuracy limits of the stack data structure through a stochastic rule-based model of the underlying polymerisation chemistry. We derive how the performance of the stack increases with the efficiency of washing steps between successive reaction stages, and report how stack performance depends on the history of stack operations under inefficient washing. Finally, we discuss refinements to improve molecular synchronisation and future open problems in implementing an autonomous chemical data structure.

Date: 2021
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DOI: 10.1038/s41467-021-25023-6

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