Programmable DNA biocomputing circuits for rapid and intelligent screening of SARS-CoV-2 variants

Deng, Fang; Pan, Jiafeng; Li, Zhi; Zeng, Lingwen; Chen, Junhua

doi:10.1016/j.bios.2022.115025

Cited by 12 publications

(7 citation statements)

References 42 publications

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“…In silicon-based electronic logic units, the cascade or concatenation of basic logic gates is a crucial strategy to execute sophisticated logical functions and meet high-order or multilevel computing requirements. − The reliability and ultrafast response of the above universal system inspired us to explore the possibility of fabricating concatenated logic circuits. First, a three-input (OR-AND)/INH circuit (Figure A) was constructed by taking the mixture of Cu 2+ , AA, and SG I as the new platform (minor difference from the above CDLNs), and the three inputs were strand P, A30-P, and T30-cP, Figure B.…”

Section: Results and Discussionmentioning

confidence: 99%

Toward Minute-Level DNA Computing: An Ultrafast, Cost-Effective, and Universal System for Lighting Up Various Concurrent DNA Logic Nanodevices (CDLNs) and Concatenated Circuits

Han,

Lv,

Zhang

et al. 2023

Anal. Chem.

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DNA logic nanodevices are powerful tools for both molecular computing tasks and smart bioanalytical applications. Nevertheless, the hour-level operation time and high cost caused by the frequent redesign/reconstruction of gates, tedious strand-displacement reaction, and expensive labeled probes (or tool enzymes) in previous works are ineluctable drawbacks. Herein, we report an ultrafast and costeffective system for engineering concurrent DNA logic nanodevices (CDLNs) by combining polythymine CuNCs with SYBR Green I (SG I) as universal dual-output producers. Particularly, benefiting from the concomitant minute-level quick response of both unlabeled illuminators and the exquisite strand-displacement-free design, all CDLNs including contrary logic pairs (YES ∧ NOT, OR ∧ NOR, and Even ∧ Odd number classifier), noncontrary ones (IDE ∧ IMP, OR ∧ NAND), and concatenated circuits are implemented in just 10 min via a "one-stone-two-birds" method, resulting in only 1/12 the operation time and 1/4 the cost needed in previous works, respectively. Moreover, all of them share the same threshold value, and the dual output can be easily visualized by the naked eye under a portable UV lamp, indicating the universality and practicality of this system. Furthermore, by exploiting the "positive/negative cross-verification" advantages of concurrent contrary logic, the smart in vitro analysis of the polyadenine strand and its polymerase is realized, providing novel molecular tools for the early diagnosis of cancer-related diseases.

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Section: Results and Discussionmentioning

confidence: 99%

Toward Minute-Level DNA Computing: An Ultrafast, Cost-Effective, and Universal System for Lighting Up Various Concurrent DNA Logic Nanodevices (CDLNs) and Concatenated Circuits

Han,

Lv,

Zhang

et al. 2023

Anal. Chem.

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“…Based on the progress we have made, we further wanted to explore whether CLB-based circuits were compatible with binary operation circuits simulated by DNA. We chose half-adder and half-subtractor for the exploration because they have been generally simulated by various principles of DNA circuits 26,41,[48][49][50] .…”

Section: Construction Of Clb-based Half-adder and Half-subtractormentioning

confidence: 99%

Erasable and Field Programmable DNA Circuits Based on Configurable Logic Blocks

Xiao

Liu

Zhai

et al. 2023

Preprint

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DNA is commonly employed as a substrate for the building of artificial logic networks due to its excellent biocompatibility and programmability. Till now, DNA logic circuits have been rapidly evolving to accomplish advanced operations. Nonetheless, the process of creating DNA logic circuits according to personal needs (logical truth table) requires extensive knowledge on digital circuits. Moreover, even after the researchers endeavor to build a DNA circuit, it lacks field programmability and thereby being disposable and inconvenient. Herein, inspired by the Configurable Logic Block (CLB) paradigm in silicon digital circuits, we present the CLB-based field-programmable DNA circuit that uses clip strands as its operation-controlling signals. It substantially simplifies the construction of desired circuits by establishing the relationship between circuits and operation-controlling strands. Additionally, the field programmability enables users to realize diverse functions with limited hardware. We firstly constructed CLB-based basic logic gates (OR and AND), and effectively demonstrate their eras ability and field programmability. Furthermore, by simply adding the appropriate operation-controlling strands, we achieved multiple rounds of switch among 5 different logic operations on a single two-layer circuit. In addition, we successfully built a circuit to implement two fundamental binary calculators: half-adder and half-subtractor, proving that our design could imitate silicon-based binary circuits. Finally, we built a comprehensive CLB-based circuit that enabled multiple rounds of switch among 7 different logic operations including half-adding and half-subtracting. Overall, the CLB-based field-programmable circuit greatly streamlines the process to build DNA circuits and immensely enhances their practicability. We believe our design could be widely used in DNA logic networks due to its efficiency and convenience.

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“…In another example, an orthogonal fluorescent reporter gene was incorporated into the sensing mechanism, achieving multiplex detection of genomic DNA from various species in complex samples. 68 Meanwhile, the development of self-assembling DNA nanodecoys capable of recognizing multiple short RNA targets provided a way to detect and diagnose various respiratory viruses simultaneously. 69 This innovative approach facilitated the identification of viral nucleic acid targets from multiple respiratory viruses, thereby addressing the challenge posed by the indistinguishable nature of these viruses.…”

Section: Dna Logic Programming For Precise Gene Analysis and Regulationmentioning

confidence: 99%

DNA logic programming: From concept to construction

Zhang,

Hu,

et al. 2023

VIEW

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DNA programming, which is based on the principle of base complementary pairing and Boolean operations, exhibits organizational structures and algorithms similar to those observed in machine language. Consequently, the practical implementation of DNA logic programming can be achieved through the utilization of programming techniques, enabling the discrimination and output generation. In recent years, DNA programming has witnessed a convergence with disciplines, such as life sciences, medicine, and other interdisciplinary areas, thereby giving rise to an advanced research system that yields valuable insights. This development has paved the way for multidisciplinary cutting‐edge research. Furthermore, the successful transition from conceptualization to the practical implementation of DNA programming has been accomplished. This review summarizes the recent advances in DNA logic programming within the biomedical fields, specifically emphasizing the conceptualization and execution of DNA logic programming constructs. The benefits and obstacles associated with the adoption of DNA programming in cutting‐edge research areas are also highlighted.

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Programmable DNA biocomputing circuits for rapid and intelligent screening of SARS-CoV-2 variants

Cited by 12 publications

References 42 publications

Toward Minute-Level DNA Computing: An Ultrafast, Cost-Effective, and Universal System for Lighting Up Various Concurrent DNA Logic Nanodevices (CDLNs) and Concatenated Circuits

Toward Minute-Level DNA Computing: An Ultrafast, Cost-Effective, and Universal System for Lighting Up Various Concurrent DNA Logic Nanodevices (CDLNs) and Concatenated Circuits

Erasable and Field Programmable DNA Circuits Based on Configurable Logic Blocks

DNA logic programming: From concept to construction

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