![]() In Computer Science, a data structure is an object that not only stores information but also organises that information in a way that facilitates the efficient querying, searching, modification, and removal of the data with respect to a particular application context 16. Existing DNA in vitro implementations have been based on hybridisation and amplification 14 and more recently on a strand displacement network that emulates a 4-input Hopfield network 15.Ī fourth potential class of memory platform exists, but has been little explored in DNA: that of a data structure. Finally, associative memory platforms indicate whether a new or incompletely presented pattern is close to a previously remembered pattern. In a second paradigm, archival memory platforms use chemically synthesised DNA as a high density long-term data storage medium information (e.g., images or text) is encoded into a base sequence, to be later read out via sequencing or PCR (reviewed in refs. Writing and erasure of bits has been achieved via the use of temperature changes 8, isothermal strand displacement 9, 10, and electric fields to co-localise strands 11. Conversely, non-volatile DNA memory has been constructed in the test tube by utilising the hybridisation of complementary DNA strands as the basis of addressable memory bits. In vitro, a volatile single bit toggle-on/-toggle-off memory has been demonstrated, based on an away-from-equilibrium chemical reaction network of DNA templates and three enzymes 7. Devices such as logic gates that remember past inputs 4 or sequential logic sensitive to the order of input signals 5, 6 demonstrate that in vivo bit editing approaches can additionally intertwine memory with basic computation. Such in vivo bit editing is billed as a future technology for the in situ recording of intracellular events, persistent across cell generations. More recently, non-volatile in vivo approaches have also been realised that edit single DNA nucleotides (or longer sections of bases) on cellular genomes or plasmids via recombinase or CRISPR techniques 3. In vivo, DNA bit memories have traditionally been engineered as volatile multistable genetic networks 1, 2. To date, three broad classes of DNA-based memory platforms can be identified: bit memory, archival memory, and associative memory.īit memory platforms perform the setting (and sometimes resetting) of individual bits of information when signals are transiently present. Similar content being viewed by othersĭNA is being used to engineer an increasing array of biochemical memory devices, both in vitro and in vivo 1. Finally, we discuss refinements to improve molecular synchronisation and future open problems in implementing an autonomous chemical data structure. 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. ![]() We explore the accuracy limits of the stack data structure through a stochastic rule-based model of the underlying polymerisation chemistry. ![]() The stack is able to record combinations of two different DNA signals, release the signals into solution in reverse order, and then re-record. Here we present an in vitro implementation of a stack data structure using DNA polymers. 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. DNA-based memory systems are being reported with increasing frequency.
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