Toehold-mediated DNA strand displacement-driven super-fast tripedal DNA walker for ultrasensitive and label-free electrochemical detection of ochratoxin A

Wang, Yeru; Wang, Yu; Liu, Su; Sun, Wenyu; Zhang, Manru; Jiang, Long; Li, Ming-Han; Yu, Jinghua

doi:10.1016/j.aca.2020.11.013

Cited by 39 publications

(17 citation statements)

References 36 publications

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“…For the sake of improving the signal strength of ECL detection, some nucleic acid amplification technologies, such as rolling circle amplification (RCA), loop-mediated isothermal amplification (LAMP), and strand-displacement amplification (SDA), have been manufactured widely. Nevertheless, as a special species of nanomachines, inspired by the biological protein motors, a DNA walker can amplify the signal by providing energy to drive the walking chain, moving along a specific track, which further improves its operability, accuracy, and flexibility. − In the process of walking, driven by the strand-displacement reaction, the DNA walker can move autonomously along the predetermined orbit through a swing arm probe and track probe, improving the local concentration and achieving the accumulation of signal. , Furthermore, compared with one-dimensional (1D) and two-dimensional (2D) orbital DNA nanomachines, the three-dimensional (3D) orbital DNA walker − exhibits satisfactory achievements in the field of nucleic acid amplification with high-throughput cargo loading capacity, high-density walking steps, and faster target recovery rates. Therefore, through the justifiable design of the orbit, the accurate identification and multicycle amplification , of target miRNA can be realized, and the intensity of ECL signal response can be improved vigorously.…”

Section: Introductionmentioning

confidence: 99%

3D DNA Walker-Assisted CRISPR/Cas12a Trans-Cleavage for Ultrasensitive Electrochemiluminescence Detection of miRNA-141

et al. 2021

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In this study, a CRISPR/Cas12a (LbCpf1)mediated electrochemiluminescence (ECL) paper-based platform on the basis of a three-dimensional (3D) DNA walker was proposed for the ultrasensitive detection of miRNA-141. Initially, 3D-rGO with a tremendous loading space was modified on the paper working electrode (PWE) to construct an excellent conductive substrate and facilitate the growth of AuPd nanoparticles (NPs). Afterward, the AuPd NPs were introduced as the coreaction emitter medium of the 3D-rGO/PWE to provide convenience for the transformation between S 2 O 8 2− and SO 4 2− , amplifying the ECL emission of g-C 3 N 4 nanosheets (NSs). Meanwhile, with the help of Nt.BsmAI nicking endonuclease, a 3D DNA walker signal amplifier was designed to convert and magnify the target miRNA-141 into a particular trigger sequence, which could act as activator DNA to motivate the trans-acting deoxyribonuclease activity of CRISPR/Cas12a to further achieve efficient annihilation of the ECL signal. Furthermore, the proposed multimechanism-driven biosensor exhibited excellent sensitivity and specificity, with a relatively low detection limit at 0.331 fM (S/ N = 3) in the concentration range between 1 fM and 10 nM. Consequently, the designed strategy not only extended the application scope of CRISPR/Cas12a but also devoted a new approach for the clinical diagnosis of modern medicine.

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Section: Introductionmentioning

confidence: 99%

3D DNA Walker-Assisted CRISPR/Cas12a Trans-Cleavage for Ultrasensitive Electrochemiluminescence Detection of miRNA-141

et al. 2021

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“…Therefore, the DNAzymes can quickly explore another adjacent substrate site to attach to. Under the strand displacement driven by branch migration, the three-leg DNAzyme walkers find another SHP to bind to, cleave, and substitute, contributing to the higher efficiency movement of the walkers and the formation of numerous ssDNA on the electrode surface . Hence, MB is unable to insert into the double-stranded sections of the SHP, which leads to generating weak electrochemical signals.…”

Section: Resultsmentioning

confidence: 99%

“…Under the strand displacement driven by branch migration, the three-leg DNAzyme walkers find another SHP to bind to, cleave, and substitute, contributing to the higher efficiency movement of the walkers and the formation of numerous ssDNA on the electrode surface. 29 Hence, MB is unable to insert into the double-stranded sections of the SHP, which leads to generating weak electrochemical signals. Thus, a label-free and sensitive electrochemical biosensor was constructed for miR-155 detection.…”

Section: ■ Results and Discussionmentioning

confidence: 99%

“…With the assistance of metal-ion cofactors, DNAzymes could cleave the substrate by the catalytic domain and the two arms. , In view of their flexibility of design, simplicity of modification, and excellent catalytic ability, the application of DNAzyme-based gene silencing has been explored in a broad range, especially in sensing and biomedical devices. − DNA walkers are DNA machines that can autonomously move along the nucleic acid “track” under the motivation of strand displacement strategies or cleavage site . Huang groups, for example, have designed a electrochemical biosensor for the ultrasensitive detection of ochratoxin A, which utilize the strand displacement-driven super-fast tripedal DNA walker to transduce and amplify the electrochemical signals. Moreover, some previous reports have applied DNAzymes to stimulate DNA walkers by virtue of their excellent cleavage activity toward substrates.…”

mentioning

confidence: 99%

“…25−27 DNA walkers are DNA machines that can autonomously move along the nucleic acid "track" under the motivation of strand displacement strategies or cleavage site. 28 Huang groups, 29 for example, have designed a electrochemical biosensor for the ultrasensitive detection of ochratoxin A, which utilize the strand displacement-driven super-fast tripedal DNA walker to transduce and amplify the electrochemical signals. Moreover, some previous reports have applied DNAzymes to stimulate DNA walkers by virtue of their excellent cleavage activity toward substrates.…”

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Label-Free and Sensitive Electrochemical Biosensor for Amplification Detection of Target Nucleic Acids Based on Transduction Hairpins and Three-Leg DNAzyme Walkers

et al. 2021

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Nucleic acids are regarded as reliable biomarkers for the early diagnosis of various diseases. By ingeniously combining a transduction hairpin (THP) with the toehold-mediated strand displacement reaction (TSDR) to form three-leg DNAzyme walkers, for the first time, we constructed a label-free and sensitive electrochemical sensing system for the amplification detection of target nucleic acids. With microRNA-155 (miR-155) as a model target, the feasibility of the biosensing strategy and the conformational states of DNA in the recognition process were studied in detail on the basis of electrochemical and dual polarization interferometry techniques. With the assistance of THP, miR-155 indirectly triggered the TSDR between three hairpins (H1, H2, and H3), then massive Mg2+-dependent three-leg DNAzyme walkers were formed in aqueous solutions. After the binding/cleaving/moving process of three-leg DNAzyme walkers on the electrode surface modified with substrate hairpins (SHPs), a number of single-stranded DNAs (ssDNAs) were generated. Hence, the interaction of methylene blue (MB) with the duplex section of SHPs was impeded, which brought about a decreased electrochemical signal. Benefiting from the cyclic amplification of the TSDR and the higher cleavage activity of three-leg DNAzyme walkers, the proposed sensing strategy showed remarkable improvement in sensitivity with a low detection limit of 0.27 fM for miR-155. Owing to the precise design of the THP, this method exhibited excellent specificity to distinguish miR-155 from the single-base and triplex-base mismatched sequences. This sensing strategy importing the flexible THP can be utilized to detect various nucleic acid biomarkers by only redesigning the THP without changing the main circuit or reporter constructs, showing the great versatility and potential for the early diagnostics and biological analysis.

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Research progress in the detection of common foodborne hazardous substances based on functional nucleic acids biosensors

Chen,

Liu,

Liu

et al. 2023

Biotech & Bioengineering

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With the further improvement of food safety requirements, the development of fast, highly sensitive, and portable methods for the determination of foodborne hazardous substances has become a new trend in the food industry. In recent years, biosensors and platforms based on functional nucleic acids, along with a range of signal amplification devices and methods, have been established to enable rapid and sensitive determination of specific substances in samples, opening up a new avenue of analysis and detection. In this paper, functional nucleic acid types including aptamers, deoxyribozymes, and G‐quadruplexes which are commonly used in the detection of food source pollutants are introduced. Signal amplification elements include quantum dots, noble metal nanoparticles, magnetic nanoparticles, DNA walkers, and DNA logic gates. Signal amplification technologies including nucleic acid isothermal amplification, hybridization chain reaction, catalytic hairpin assembly, biological barcodes, and microfluidic system are combined with functional nucleic acids sensors and applied to the detection of many foodborne hazardous substances, such as foodborne pathogens, mycotoxins, residual antibiotics, residual pesticides, industrial pollutants, heavy metals, and allergens. Finally, the potential opportunities and broad prospects of functional nucleic acids biosensors in the field of food analysis are discussed.

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Toehold-mediated DNA strand displacement-driven super-fast tripedal DNA walker for ultrasensitive and label-free electrochemical detection of ochratoxin A

Cited by 39 publications

References 36 publications

3D DNA Walker-Assisted CRISPR/Cas12a Trans-Cleavage for Ultrasensitive Electrochemiluminescence Detection of miRNA-141

3D DNA Walker-Assisted CRISPR/Cas12a Trans-Cleavage for Ultrasensitive Electrochemiluminescence Detection of miRNA-141

Label-Free and Sensitive Electrochemical Biosensor for Amplification Detection of Target Nucleic Acids Based on Transduction Hairpins and Three-Leg DNAzyme Walkers

Research progress in the detection of common foodborne hazardous substances based on functional nucleic acids biosensors

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