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Nucleic Acids Res. 2018 Sep 19;46(16):8532-8541. doi: 10.1093/nar/gky663.

Entropy-driven DNA logic circuits regulated by DNAzyme.

Author information

1
School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China.
2
College of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China.
3
Key Laboratory of Image Information Processing and Intelligent Control, School of Automation, Huazhong University of Science and Technology, Wuhan 430074, China.
4
The State Key Laboratory of Bioelectronics, Southeast University, Nanjing 211189, China.
5
Institute of Software, School of Electronics Engineering and Computer Science, Peking University, Beijing 100871, China.

Abstract

The catalytic DNA circuits play a critical role in engineered biological systems and molecular information processing. Actually, some of the natural or synthetic DNA circuits were triggered by covalent modifications, where conformational changes were induced to facilitate complex DNA engineering functions and signal transmissions. However, most of the reported artificial catalytic DNA circuits were regulated by the toehold-mediated reaction. Therefore, it is significant to propose a strategy to regulate the catalytic DNA circuit not only by the toehold-mediated mechanism, but also by involving the conformational changes induced by the covalent modification. In this study, we developed the catalytic DNA logic circuits regulated by DNAzyme. Here, a regulation strategy based on the covalent modification was proposed to control the DNA circuit, combing two reaction mechanisms: DNAzyme digestion and entropy-driven strand displacement. The DNAzyme and DNA catalyst can participate into the reactions alternatively, thus realizing the cascading catalytic circuits. Using the DNAzyme regulation, a series of logic gates (YES, OR and AND) were constructed. In addition, a two-layer cascading circuit and a feedback self-catalysis circuit were also established. The proposed DNAzyme-regulated strategy shows great potentials as a reliable and feasible method for constructing more complex catalytic DNA circuits.

PMID:
30053158
PMCID:
PMC6144864
DOI:
10.1093/nar/gky663
[Indexed for MEDLINE]
Free PMC Article

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