Probabilistic switching circuits in DNA

Wilhelm, Daniel; Bruck, Jehoshua; Qian, Lulu

doi:10.1073/pnas.1715926115

Cited by 42 publications

(24 citation statements)

References 34 publications

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“…generate output signals with programmed concentration ratios (42). A catalytic molecular amplifier can be engineered if the output signal produced by the translator cascade is the same as the input signal.…”

Section: Leakless Designmentioning

confidence: 99%

Effective design principles for leakless strand displacement systems

Wang

Thachuk

Ellington

et al. 2018

Proc. Natl. Acad. Sci. U.S.A.

110

151

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Artificially designed molecular systems with programmable behaviors have become a valuable tool in chemistry, biology, material science, and medicine. Although information processing in biological regulatory pathways is remarkably robust to error, it remains a challenge to design molecular systems that are similarly robust. With functionality determined entirely by secondary structure of DNA, strand displacement has emerged as a uniquely versatile building block for cell-free biochemical networks. Here, we experimentally investigate a design principle to reduce undesired triggering in the absence of input (leak), a side reaction that critically reduces sensitivity and disrupts the behavior of strand displacement cascades. Inspired by error correction methods exploiting redundancy in electrical engineering, we ensure a higher-energy penalty to leak via logical redundancy. Our design strategy is, in principle, capable of reducing leak to arbitrarily low levels, and we experimentally test two levels of leak reduction for a core “translator” component that converts a signal of one sequence into that of another. We show that the leak was not measurable in the high-redundancy scheme, even for concentrations that are up to 100 times larger than typical. Beyond a single translator, we constructed a fast and low-leak translator cascade of nine strand displacement steps and a logic OR gate circuit consisting of 10 translators, showing that our design principle can be used to effectively reduce leak in more complex chemical systems.

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Section: Leakless Designmentioning

confidence: 99%

Effective design principles for leakless strand displacement systems

Wang

Thachuk

Ellington

et al. 2018

Proc. Natl. Acad. Sci. U.S.A.

110

151

View full text Add to dashboard Cite

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“…The predictable hybridization between complementary base pairs that underlies the self‐assembly of DNA lays the chemical foundation for engineering highly structured materials, dynamic nanodevices and complex reaction networks for molecular computation . Functional DNA nanotechnology has greatly benefited from the extensive use of programmable strand displacement reactions upholding the design of stimuli‐responsive DNA switches, enzyme‐free catalytic systems, or molecular computers . In addition, DNA‐based dynamic networks have been designed to process information following cell‐inspired paths that mimic more complex molecular mechanisms …”

Section: Introductionmentioning

confidence: 99%

Programming DNA‐Based Systems through Effective Molarity Enforced by Biomolecular Confinement

Rossetti

Bertucci

Patiño

et al. 2020

Chemistry A European J

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The fundamental concept of effective molarity is observed in av ariety of biological processes, such as protein compartmentalization within organelles, membrane localization and signaling paths. To controlm olecular encountering and promotee ffective interactions, nature places biomolecules in specific sites inside the cell in order to generate a high, localized concentration different from the bulk concentration. Inspired by this mechanism, scientists have artificially recreated in the lab the same strategy to actuate and control artificial DNA-based functional systems. Here, it is discussed how harnessing effective molarity has led to the development of an umber of proximity-induced strategies, with applications ranging from DNA-templated organic chemistry and catalysis, to biosensing and protein-supported DNA assembly.

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“…Compare with the traditional complex logic circuit [29], this design presents four kinds output results in the form of computing mode. The design of four-input in multi-layer logic circuit makes the calculations more efficient and accurate [30].…”

Section: Introductionmentioning

confidence: 99%

Four-Input Multi-Layer Majority Logic Circuit Based on DNA Strand Displacement Computing

2020

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Biomolecules have the advantage of high performance parallel computing and large information capacity. The use of biochemical circuits to solve computational problems has been studied by many researchers. In this paper, we use DNA strand displacement technology to construct complex molecular circuits as logic gates. The experimental process is demonstrated by a series of strand displacement reactions, and the feasibility of the design is verified by the strand displacement simulation platform Visual DSD. The key feature of this logic gate design is that when two inputs of the same signal are controlled, the remaining two different input signals implement AND and OR function to determine the output. Based on this feature, a four-input multi-layer logic circuit is designed and implemented. The calculation mode of the other three inputs AND and OR combinations is implemented by controlling each logic gate input. INDEX TERMS DNA strand displacement computing, logic gate, visual DSD.

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Probabilistic switching circuits in DNA

Cited by 42 publications

References 34 publications

Effective design principles for leakless strand displacement systems

Effective design principles for leakless strand displacement systems

Programming DNA‐Based Systems through Effective Molarity Enforced by Biomolecular Confinement

Four-Input Multi-Layer Majority Logic Circuit Based on DNA Strand Displacement Computing

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