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Abstract Chemical systems have the potential to direct the next generation of dynamic materials if they can be integrated with a material while acting as the material’s own regulatory network. Chemical networks that use DNA and RNA strand displacement coupled with RNA synthesis and degradation, such as genelets, are promising chemical systems for this role. Genelets can produce a range of dynamic behaviors that respond to unique sets of environmental inputs. While a number of networks that generate specific types of outputs which vary in both time and amplitude have been developed, there are fewer examples of networks that recognize specific types of inputs in time and amplitude. Advanced chemical circuits in biology are capable of reading a given substrate concentration with relatively high accuracy to direct downstream function, demonstrating that such a chemical circuit is possible. Taking inspiration from this, we designed a genelet circuit which responds to a range of inputs by delivering a binary output based on the input concentration, and tested the network’s performance using an in silico model of circuit behavior. By modifying the concentrations of two circuit elements, we demonstrated that such a network topography could yield various target input concentration profiles to which a given circuit is sensitive. The number of unique elements in the final network topography as well as the individual circuit element concentrations are commensurate with properties of circuits that have been demonstrated experimentally. These factors suggest that such a network could be built and characterized in the laboratory.
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Renewable Time‐Responsive DNA Circuits
Abstract DNA devices have been shown to be capable of evaluating Boolean logic. Several robust designs for DNA circuits have been demonstrated. Some prior DNA‐based circuits are use‐once circuits since the gate motifs of the DNA circuits get permanently destroyed as a side effect of the computation, and hence cannot respond correctly to subsequent changes in inputs. Other DNA‐based circuits use a large reservoir of buffered gates to replace the working gates of the circuit and can be used to drive a finite number of computation cycles. In many applications of DNA circuits, the inputs are inherently asynchronous, and this necessitates that the DNA circuits be asynchronous: the output must always be correct regardless of differences in the arrival time of inputs. This paper demonstrates: 1) renewable DNA circuits, which can be manually reverted to their original state by addition of DNA strands, and 2) time‐responsive DNA circuits, where if the inputs change over time, the DNA circuit can recompute the output correctly based on the new inputs, that are manually added after the system has been reset. The properties of renewable, asynchronous, and time‐responsiveness appear to be central to molecular‐scale systems; for example, self‐regulation in cellular organisms.
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- PAR ID:
- 10064888
- Publisher / Repository:
- Wiley Blackwell (John Wiley & Sons)
- Date Published:
- Journal Name:
- Small
- Volume:
- 14
- Issue:
- 33
- ISSN:
- 1613-6810
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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