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.

Implementing digital computing with DNA-based switching circuits

“…3f). This circuit also had the same function of logic gate circuit AND (OR(x,y),z), whereas the computing speed was much faster than the reported two-layer logic gate circuits in solution 22,26 With the abilities to perform basic functions including cascading, fan-in, and fan-out, theoretically the molecular switches can be used to build DSCs with arbitrary topologies. We next explored the circuit design strategy to perform arbitrary Boolean functions.…”

“…Molecular implementation of the switch function is realized by toehold-mediated SDR. A single-stranded DNA acting as a switching signal binds to the double-stranded switch molecule via a 5 nt toehold 26 , displaces the current signal strand, and frees it in an entropy-driven manner. The released current signal is transmitted to a downstream switch to activate the responsive function of the downstream switch (Fig.…”

“…However, limitations associated with logic gate circuits emerges, which hinders the scale-up for practical achievable computational tasks as follows. (i) Typical approaches to increase the scalability involves the combination of basic gates such as AND and OR 5,13,20,21 , which nevertheless increases the use of gates [22][23][24][25][26] . (ii) Using uniform motif and implementing AND and OR gate with different threshold concentrations have shown high modularity and potential for constructing complex computing networks.…”

Utilizing the Organizational Power of DNA Scaffolds for New Nanophotonic Applications

“…These could be achieved on simple DNA wire structures but use of DNA‐triads scaffolds enhanced the interactions of the FRET signals and allowed for far more varied inputs 192a,198. This technology has shown remarkable progress with recent examples from the Reif lab reporting on renewable circuits which provide for multiuse gates as well as including a time‐component to the response . The dynamic modulation aspect is also the key to molecular photonic switches demonstrated on DNA templates.…”

Hamiltonian path problem solution using DNA computing

“…The research of new ways of solving the Hamiltonian path problem and a comparison of their time consumption is both of fundamental interest, since it can provide us with novel principles of building a new computer [Garg et al, 2018;Eshra et al, 2019], and practical ones on their basis: the tasks of building optimal motion patterns, recognizing trajectories, images can be solved using the Hamiltonian path.…”