A Molecular Circuit Regenerator to Implement Iterative Strand Displacement Operations

DelRosso, Nicole; Hews, Sarah; Spector, Lee; Derr, Nathan D.

doi:10.1002/ange.201610890

Cited by 6 publications

(3 citation statements)

References 19 publications

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“…Song et al designed autocatalytic amplifiers to compute logarithmic and exponential formulas [26]. DelRosso et al designed a DNA molecular Regenerator and used it for regeneration and multiple cycles of computing [27]. Song et al introduced an architecture method to program DSD reaction networks on cell membranes [28].…”

Section: Introductionmentioning

confidence: 99%

DNA Logic Multiplexing Using Toehold-Mediated Strand Displacement

et al. 2020

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Since the discovery of the DNA Strand Displacement mechanism, researchers have implemented a lot of applications, such as DNA computing, DNA Circuits, Logic gates, and Chemical Reaction network. To achieve those functions, a well-designed system is essential, among which the toehold domains and migration domains play a vital role. In this paper, we designed three basic logic gates based on the toehold mediates DNA strand displacement mechanism, and utilized them to struct a three-layer multiplexer DNA logic circuit. However, the traditional INHIBIT gate annihilated all the inputs strands which obscure the multiplexer in further applications. Therefore, we improved the INHIBIT gate, so the desired input strand can be selected, and the corresponding output strand can be identified. Lastly, we adjusted the multiplexer and realized a cyclic DNA circuit. The simulation results verified the efficiency and reliability of our multiplexer DNA logic circuits. Our method has the ability in architecting complex DNA integrated circuits.INDEX TERMS DNA strand displacement, logic circuits, INHIBIT gate, demultiplexer.

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Section: Introductionmentioning

confidence: 99%

DNA Logic Multiplexing Using Toehold-Mediated Strand Displacement

et al. 2020

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“…The use of nucleic acids as a material to perform computation has been increasingly explored over the last decade . DNA‐based circuits that implement the Boolean logic such as AND, OR, and NOT gates, were first demonstrated to have signal restoration, feedback, and cascading .…”

Section: Introductionmentioning

confidence: 99%

“…Goel et al design is time responsive but suffers from two potential disadvantages: fuel is continuously used up even at steady state, and enzymes with distributed recognition sites are not readily available. A more recent construction by DelRosso et al is more promising, where they implement a regenerator circuit, which can regenerate a threshold gate after it was used up by the input strands. Buffered gates present in the solution help to replace the used‐up threshold gate, which in turn is used to perform Boolean logic computation.…”

Section: Introductionmentioning

confidence: 99%

Renewable Time‐Responsive DNA Circuits

Garg

Shah

Bui

et al. 2018

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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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Dissipative Control over the Toehold‐Mediated DNA Strand Displacement Reaction

et al. 2022

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Here we show a general approach to achieve dissipative control over toehold‐mediated strand‐displacement, the most widely employed reaction in the field of DNA nanotechnology. The approach relies on rationally re‐engineering the classic strand displacement reaction such that the high‐energy invader strand (fuel) is converted into a low‐energy waste product through an energy‐dissipating reaction allowing the spontaneous return to the original state over time. We show that such dissipative control over the toehold‐mediated strand displacement process is reversible (up to 10 cycles), highly controllable and enables unique temporal activation of DNA systems. We show here two possible applications of this strategy: the transient labelling of DNA structures and the additional temporal control of cascade reactions.

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A Molecular Circuit Regenerator to Implement Iterative Strand Displacement Operations

Cited by 6 publications

References 19 publications

DNA Logic Multiplexing Using Toehold-Mediated Strand Displacement

DNA Logic Multiplexing Using Toehold-Mediated Strand Displacement

Renewable Time‐Responsive DNA Circuits

Dissipative Control over the Toehold‐Mediated DNA Strand Displacement Reaction

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