DNA-Based Dynamic Reaction Networks

Fu, Ting; Lyu, Yifan; Liu, Hui; Peng, Richard; Zhang, Xiaobing; Ye, Mao; Tan, Weihong

doi:10.1016/j.tibs.2018.04.010

Cited by 78 publications

(61 citation statements)

References 77 publications

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“…[9] Signal amplification strategies that use DNA dynamic reaction networks are widely used for sensing biomolecular activity because they can increase the sensitivity with a limit of detection of biomolecules and shorten the detection time. [10] We tested two detection systems based on hybridization-sensitive fluorescent probes O1 or O2, which have a modified nucleotide unit bearing a different dye homodimer (Figure 1 A). The fluorescence of O1 or O2 is quenched by the exciton coupling effect in the single-stranded state in which dyes arrange in a homodimeric state.…”

Section: Resultsmentioning

confidence: 99%

Live‐Cell Sensing of Telomerase Activity by Using Hybridization‐Sensitive Fluorescent Oligonucleotide Probes

et al. 2019

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Live‐cell sensing of telomerase activity with simple and efficient strategies remains a challenging target. In this work, a strategy for telomerase sensing by using hybridization‐sensitive fluorescent oligonucleotide probes is reported. In the presence of telomerase and dNTPs, the designed supporting strand was extended and generated the hairpin structure that catalyzed the next telomerase extending reaction. The special extension mechanism increased the local concentration of another supporting strand and telomerase, which resulted in enhanced telomerase activity. The hybridization‐sensitive oligonucleotide probes bound to the hairpin catalyst and generated turn‐on fluorescence. This method realized the sensing of telomerase activity in HeLa cell extract with a detection limit below 1.6×10−6 IU μL−1. The real‐time in situ observation of telomerase extension was achieved in living HeLa cells. This strategy has been applied to monitor the efficiency of telomerase‐targeting anticancer drugs in situ.

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Section: Resultsmentioning

confidence: 99%

Live‐Cell Sensing of Telomerase Activity by Using Hybridization‐Sensitive Fluorescent Oligonucleotide Probes

et al. 2019

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“…As a powerful mathematical language to describe and analyze chemical reactions of DNA systems, [ 1,2 ] DNA‐CRNs can display a variety of reaction network behaviors, either in equilibrium state or in a nonequilibrium state. [ 2,3 ] The concept of equilibrium state used in this Review is to describe a closed system, where the concentrations of reactant DNAs and product DNAs no longer change with time. While the nonequilibrium state was used to describe an open system, where the concentrations of reactant DNAs and product DNAs still can be changed with the dynamic change of environment, e.g., pH or temperature.…”

Section: Introductionmentioning

confidence: 99%

DNA‐Based Chemical Reaction Networks for Biosensing Applications

Jiang

Yuan

et al. 2020

Advanced Intelligent Systems

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The nature of biosensing is a biochemical reaction. DNA‐based chemical reaction networks (DNA‐CRNs) as a powerful programming language for describing behaviors of chemical reactions have shown great potential in designs and applications of biosensors. Due to their programmability, modularity, and versatility of the DNA strand, the performance of different detection strategies can be improved mainly by the rational design of DNA‐CRNs. Herein, an overview of the fundamental theory and biosensing processes of DNA‐CRNs is provided. Various detection strategies of DNA‐CRNs are introduced, either in a simple low‐order reaction model or in a complicated high‐order reaction type, in combination with some typical cases for the different detection purposes. In addition, an overview of the recent development of DNA‐CRNs for monitoring the cell microenvironment is presented, which is of significance to uncover some specific cell behaviors and functions. Finally, the roles of DNA‐CRNs in the rational design of high‐performance biosensors are summarized by pointing out the remaining challenges that impede the precise biosensing using DNA‐CRNs in complicated biological environments.

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“…Molecular logic gates can carry out different computations at the molecular level, and the working mechanism or principle is similar to silicon processors [ 1 , 2 , 3 , 4 ]. Molecular logic gates, a type of logic gates system, can use biological materials or biomolecules such as enzymes, DNA, or proteins to establish basic or -simple molecular devices and equipment [ 3 , 4 , 5 , 6 , 7 ]. For example, Liu’s group successfully established 4-input/7-output biomolecular logic gates, and provided a new method to construct complex biomolecular logic gate system based on bio-electrocatalysis of natural DNA [ 8 ].…”

Section: Introductionmentioning

confidence: 99%

Construction of Multiple Switchable Sensors and Logic Gates Based on Carboxylated Multi-Walled Carbon Nanotubes/Poly(N,N-Diethylacrylamide)

Bai

et al. 2018

Sensors

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In this work, binary hydrogel films based on carboxylated multi-walled carbon nanotubes/poly(N,N-diethylacrylamide) (c-MWCNTs/PDEA) were successfully polymerized and assembled on a glassy carbon (GC) electrode surface. The electroactive drug probes matrine and sophoridine in solution showed reversible thermal-, salt-, methanol- and pH-responsive switchable cyclic voltammetric (CV) behaviors at the film electrodes. The control experiments showed that the pH-responsive property of the system could be ascribed to the drug components of the solutions, whereas the thermal-, salt- and methanol-sensitive behaviors were attributed to the PDEA constituent of the films. The CV signals particularly, of matrine and sophoridine were significantly amplified by the electrocatalysis of c-MWCNTs in the films at 1.02 V and 0.91 V, respectively. Moreover, the addition of esterase, urease, ethyl butyrate, and urea to the solution also changed the pH of the system, and produced similar CV peaks as with dilution by HCl or NaOH. Based on these experiments, a 6-input/5-output logic gate system and 2-to-1 encoder were successfully constructed. The present system may lead to the development of novel types of molecular computing systems.

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DNA-Based Dynamic Reaction Networks

Cited by 78 publications

References 77 publications

Live‐Cell Sensing of Telomerase Activity by Using Hybridization‐Sensitive Fluorescent Oligonucleotide Probes

Live‐Cell Sensing of Telomerase Activity by Using Hybridization‐Sensitive Fluorescent Oligonucleotide Probes

DNA‐Based Chemical Reaction Networks for Biosensing Applications

Construction of Multiple Switchable Sensors and Logic Gates Based on Carboxylated Multi-Walled Carbon Nanotubes/Poly(N,N-Diethylacrylamide)

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