Biosensing with DNAzymes

Abstract

This article provides a comprehensive review of biosensing with DNAzymes, providing an overview of different sensing applications while highlighting major progress and seminal contributions to the field of portable biosensor devices and point-of-care diagnostics. Specifically, the field of functional nucleic acids is introduced, with a specific focus on DNAzymes. The incorporation of DNAzymes into bioassays is then described, followed by a detailed overview of recent advances in the development of in vivo sensing platforms and portable sensors incorporating DNAzymes for molecular recognition. Finally, a critical perspective on the field, and a summary of where DNAzyme-based devices may make the biggest impact are provided.

Fig. 1

Timeline summary of important events in the development of DNAzyme based biosensors.

Fig. 2

The RNA-cleaving DNAzyme (RCD) system. (A) Chemical transformation of RNA cleavage. Nearly all RCDs whose cleavage mechanism has been elucidated use the 2′-hydroxyl group (blue OH) next to the scissile phosphodiester bond to attack the phosphodiester bond, producing a 5′-cleavage fragment with 2′,3′-cyclic phosphate and 3′ fragment with 5′-OH. RNA-cleaving DNAzymes known as 8–17 (B), 10–23 (C), 17E/17S (D), GR-5 (E), 39E/39S (F) and NaA43 (G). Y and R in panel C: pyrimidine and purine, respectively. Both the 10–23 and 8–17 DNAzymes were originally isolated to cleave an all-RNA substrate; these two DNAzymes cleave the phosphodiester bond following the red ribonucleotide. 17E, GR-5, 39E and NaA43 were isolated to cleave an adenine ribonucleotide (rA) embedded in an otherwise all-DNA sequence.

Fig. 3

Two common strategies for selecting RNA-cleaving DNAzymes. (A) Column or bead-based selection strategy. (B) Gel based strategy.

Fig. 4

Histidine-dependent DNAzymes HD1, HD2 and HD3. Reprinted (adapted) with permission from A. Roth and R. R. Breaker, An amino acid as a cofactor for a catalytic polynucleotide, Proc. Natl. Acad. Sci. U. S. A., 1998, 95, 6027–6031. Copyright (2007) National Academy of Science.

Fig. 5

In vitro selection of RCDs for recognizing an unknown bacterial target using double selection strategy: counter selection (or negative selection) with the cellular mixture from a control bacterium (bacterium B) and positive selection with the cellular mixture from the intended bacterium (bacterium A). Reprinted (adapted) from M. Liu, D. Chang, and Y. Li, Discovery and Biosensing Applications of Diverse RNA-Cleaving DNAzymes, Acc. Chem. Res., 2017, 50, 2273–2283. Copyright 2017 American Chemical Society.

Fig. 6

Representative allosteric DNAzymes and aptazymes using an ATP binding DNA aptamer. (A) An allosteric ligase DNAzyme. Reprinted (adapted) from M. Levy and A. D. Ellington, ATP-Dependent Allosteric DNA Enzymes, Chem. Biol., 2002, 9, 417–426, with permission from Elsevier. (B) Allosteric EtNa (an RCD) activated by AMP in 50% ethanol. rA: adenine ribonucleotide. Reprinted (adapted) with permission from T. Yu, W. Zhou and J. Liu, Ultrasensitive DNAzyme-Based Ca²⁺ Detection Boosted by Ethanol and a Solvent-Compatible Scaffold for Aptazyme Design, ChemBioChem, 2018, 19, 31–36. Copyright 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim. (C) An aptazyme built with pH6DZ1 (an RCD). (D) An aptazyme built with MgZ (an RCD). For panels (C and D): Red A is adenine ribonucleotide; F: fluorescein-dT; Q: DABCYL-dT. Panels (C and D) are reprinted (adapted) from M. Liu, D. Chang, and Y. Li, Discovery and Biosensing Applications of Diverse RNA-Cleaving DNAzymes, Acc. Chem. Res., 2017, 50, 2273–2283. Copyright 2017 American Chemical Society.

Fig. 7

Representative DNAzyme sensors for metal-ion detection. (A) Florescence-based sensors for metal ions using a pair of fluorophore and quencher. Reprinted (adapted) with permission from J. Liu, A. K. Brown, X. Meng, D. M. Cropek, J. D. Istok, D. B. Watson and Y. Lu, A catalytic beacon sensor for uranium with parts-per-trillion sensitivity and millionfold selectivity, Proc. Natl. Acad. Sci. U. S. A., 2007, 104, 2056–2061. (B) Colorimetric sensor based on gold nanoparticle aggregation and cleavage promoted disassembly. Reprinted (adapted) with permission from J. Liu and Y. Lu, A Colorimetric Lead Biosensor Using DNAzyme-Directed Assembly of Gold Nanoparticles, J. Am. Chem. Soc., 2003, 125, 6642–6643. Copyright 2003 American Chemical Society. (C) A multiplex DNAzyme sensor assay involving five DNAzymes. Reprinted (adapted) with permission from P. J. J. Huang, M. Vazin, J. J. Lin, R. Pautler and J. Liu, Distinction of Individual Lanthanide Ions with a DNAzyme Beacon Array, ACS Sens., 2016, 1, 732–738. Copyright 2016 American Chemical Society. (D) Use of a DNAzyme, fluorescent dyes and gold nanoparticles for the detection of Pb(II), Hg(II) and Ag(I) in a one-pot reaction. Reprinted (adapted) with permission from Y. Deng, Y. Chen and X. Zhou, Simultaneous sensitive detection of lead(II), mercury(II) and silver ions using a new nucleic acid-based fluorescence sensor, Acta Chim. Slov., 2018, 65, 271–277. Copyright 2018 Yuan Deng, Yinran Chen, Xiaodong Zhou.

Fig. 8

Timeline of the major milestones of DNAzyme sensors for cellular and in vivo sensing. Major sensor types and sensing target(s) are listed.^,,–

Fig. 9

DNAzyme sensors for metal-ion imaging in living cells. (A) The first intracellular DNAzyme based sensor for uranyl ion detection in living cells using 39E immobilized onto gold nanoparticles. Reprinted (adapted) with permission from P. Wu, K. Hwang, T. Lan and Y. Lu, A DNAzyme-Gold Nanoparticle Probe for Uranyl Ion in Living Cells, J. Am. Chem. Soc., 2013, 135, 5254–5257. Copyright 2013 American Chemical Society. (B) A DNAzyme sensor for metal-ion imaging in living cells with blockage of the 2′-OH of the scissile ribonucleotide with a light-sensitive nitrobenzyl group. Reprinted (adapted) with permission from K. Hwang, P. Wu, T. Kim, L. Lei, S. Tian, Y. Wang and Y. Lu, Photocaged DNAzymes as a General Method for Sensing Metal Ions in Living Cells, Angew. Chem., Int. Ed., 2014, 53, 13798–13802. Copyright 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. (C) Zn²⁺ sensing in vivo using photocaged Zn²⁺-selective DNAzyme conjugated on lanthanide-doped upconversion nanoparticles (UCNPs). Reprinted (adapted) with permission from Z. Yang, K. Y. Loh, Y.-T. Chu, R. Feng, N. S. R. Satyavolu, M. Xiong, S. M. Nakamata Huynh, K. Hwang, L. Li, H. Xing, X. Zhang, Y. R. Chemla, M. Gruebele and Y. Lu, Optical Control of Metal Ion Probes in Cells and Zebrafish Using Highly Selective DNAzymes Conjugated to Upconversion Nanoparticles, J. Am. Chem. Soc., 2018, 140, 17656–17665. Copyright 2018 American Chemical Society.

Fig. 10

DNAzyme sensors for protein and small-molecule detection. (A) A DNAzyme sensor for PSA detection which incorporates an aptamer, an RCD and GO. Reprinted (adapted) from Y. Yan, C. Ma, Z. Tang, M. Chen and H. Zhao, A novel fluorescent assay based on DNAzyme-assisted detection of prostate specific antigen for signal amplification, Anal. Chim. Acta, 2020, 1104, 172–179, with permission from Elsevier. (B) A DNAzyme sensor for in situ monitoring of histidine. Reprinted (adapted) with permission from H.-M. Meng, X. Zhang, Y. Lv, Z. Zhao, N.-N. Wang, T. Fu, H. Fan, H. Liang, L. Qiu, G. Zhu and W. Tan, DNA Dendrimer: An Efficient Nanocarrier of Functional Nucleic Acids for Intracellular Molecular Sensing, ACS Nano, 2014, 8, 6171–6181. Further permissions related to the material excerpted should be directed to the American Chemical Society.

Fig. 11

Aptazyme-based E. coli detection without amplification. (A) Integrated Comprehensive Droplet Digital Detection (IC 3D). Reprinted (adapted) with permission from D. K. Kang, M. M. Ali, K. Zhang, S. S. Huang, E. Peterson, M. A. Digman, E. Gratton and W. Zhao, Rapid detection of single bacteria in unprocessed blood using Integrated Comprehensive Droplet Digital Detection, Nat. Commun., 2014, 5, 1–10. Copyright 2014 Kang et al. (B) Bacterial litmus test. Reprinted (adapted) with permission from K. Tram, P. Kanda, B. J. Salena, S. Huan and Y. Li, Translating Bacterial Detection by DNAzymes into a Litmus Test, Angew. Chem., Int. Ed., 2014, 53, 12799–12802. Copyright 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fig. 12

Aptazyme-based E. coli detection incorporating RCA. (A) Enabling RCA via releasing topological constraint of DNA[2] catenane (D2C) by EC1. Reprinted (adapted) with permission from M. Liu, Q. Zhang, Z. Li, J. Gu, J. D. Brennan and Y. Li, Programming a topologically constrained DNA nanostructure into a sensor, Nat. Commun., 2016, 7, 12074. Copyright 2016 Liu et al. (B) Cross-amplification by RCA and substrate cleavage by RCD produced by RCA. Reprinted (adapted) with permission from M. Liu, Q. Zhang, D. Chang, J. Gu, J. D. Brennan and Y. Li, A DNAzyme Feedback Amplification Strategy for Biosensing, Angew. Chem., Int. Ed., 2017, 56, 6142–6146. Copyright 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fig. 13

Detection of E. coli using RFD-EC1 as part of (A) hairpin chain reaction (HCR) and (B) catalytic hairpin assembly (CHA). Panel A is reprinted (adapted) from F. Yu, Y. Li, M. Li, L. Tang and J. J. He, DNAzyme-integrated plasmonic nanosensor for bacterial sample-to-answer detection, Biosens. Bioelectron., 2017, 89, 880–885, with permission from Elsevier. Panel B is Reprinted (adapted) with permission from Z. Zhou, J. D. Brennan and Y. Li, A Multi-component All-DNA Biosensing System Controlled by a DNAzyme, Angew. Chem., Int. Ed., 2020, 59, 10401–10405. Copyright 2020 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fig. 14

Detection of l-histidine using DNAzymes that do not bind l-histidine directly. Reprinted (adapted) from P. Gu, G. Zhang, Z. Deng, Z. Tang, H. Zhang, F. Y. Khusbu, K. Wu, M. Chen and C. Ma, A novel label-free colorimetric detection of l-histidine using Cu²⁺-modulated G-quadruplex-based DNAzymes, Spectrochim. Acta, Part A, 2018, 203, 195–200, with permission from Elsevier.

Fig. 15

Protein detection using an RCD modified with an affinity probe. (A) Antibody detection. Reprinted (adapted) from C. Li, J. Ma, H. Shi, X. Hu, Y. Xiang, Y. Li and G. Li, Design of a stretchable DNAzyme for sensitive and multiplexed detection of antibodies, Anal. Chim. Acta, 2018, 1041, 102–107, with permission from Elsevier. (B) Protein detection using an RCD walker, AuNP and a pair of DNA aptamers that bind the same target. Reprinted (adapted) with permission from J. Chen, A. Zuehlke, B. Deng, H. Peng, X. Hou and H. Zhang, A Target-Triggered DNAzyme Motor Enabling Homogeneous, Amplified Detection of Proteins, Anal. Chem., 2017, 89, 12888–12895. Further permissions related to the material excerpted should be directed to the American Chemical Society.

Fig. 16

DNA detection using RCDs. (A) Hybridization-triggered DNAzyme cascade (HTDC) assay. Reprinted (adapted) from H. Wang, D. He, R. Wu, H. Cheng, W. Ma, J. Huang, H. Bu, X. He and K. Wang, A hybridization-triggered DNAzyme cascade assay for enzyme-free amplified fluorescence detection of nucleic acids, Analyst, 2019, 144, 143–147, with permission from The Royal Society of Chemistry. (B) Catalytic hairpin assembly-mediated double-end DNAzyme feedback amplification. Reprinted (adapted) from X. Liu, X. Zhou, X. Xia and H. Xiang, Catalytic hairpin assembly-based double-end DNAzyme cascade-feedback amplification for sensitive fluorescence detection of HIV-1 DNA, Anal. Chim. Acta, 2020, 1096, 159–165, with permission from Elsevier.

Fig. 17

Intracellular microRNA detection involving RCDs. (A) An RCD walker on AuNPs. Reprinted (adapted) with permission from H. Peng, X. F. Li, H. Zhang and X. C. Le, A microRNA-initiated DNAzyme motor operating in living cells, Nat. Commun., 2017, 8, 1–13. Copyright 2017, Peng et al. (B) A DNAzyme-containing biocircuit constructed with a honeycomb MnO₂ nanosponge (hMNS). Reprinted (adapted) with permission J. Wei, H. Wang, Q. Wu, X. Gong, K. Ma, X. Liu and F. Wang, A Smart, Autocatalytic, DNAzyme Biocircuit for in vivo, Amplified, MicroRNA Imaging, Angew. Chem., Int. Ed., 2020, 59, 5965–5971. Copyright 2020 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fig. 18

Portable DNAzyme devices for the detection of Pb²⁺ based on visual reading of capillary flow. (A) A portable hydrogel capillary sensor. Reprinted (adapted) from C. Jiang, Y. Li, H. Wang, D. Chen and Y. Wen, A portable visual capillary sensor based on functional DNA crosslinked hydrogel for point-of-care detection of lead ion, Sens. Actuators, B, 2020, 307, 127625, with permission from Elsevier. (B) A portable sensor with a microfluidic particle dam. Reprinted (adapted) with permission from G. Wang, L. T. Chu, H. Hartanto, W. B. Utomo, R. A. Pravasta and T.-H. Chen, Microfluidic Particle Dam for Visual and Quantitative Detection of Lead Ions, ACS Sens., 2020, 5, 19–23. Copyright 2020, American Chemical Society.

Fig. 19

Portable colorimetric devices for the detection of mercury. (A) Schematic representation of the sensing strategy for a 3D-printed rolling circle amplification chip for on-site colorimetric detection of mercury. Reprinted (adapted) from J. W. Lim, T.-Y. Kim, S.-W. Choi and M.-A. Woo, 3D-printed rolling circle amplification chip for on-site colorimetric detection of inorganic mercury in drinking water, Food Chem., 2019, 300, 125177, with permission from Elsevier. (B) Naked-eye colorimetric detection of Hg²⁺ using a AuNP assay. Reprinted (adapted) from J. Chen, J. Pan and S. Chen, A naked-eye colorimetric sensor for Hg²⁺ monitoring with cascade signal amplification based on target-induced conjunction of split DNAzyme fragments, Chem. Commun., 2017, 53, 10224–10227, with permission from The Royal Society of Chemistry.

Fig. 20

Schematic representation of the detection of uranyl ion using a microfluidic SERS device. Reprinted (adapted) from X. He, X. Zhou, Y. Liu and X. Wang, Ultrasensitive, recyclable and portable microfluidic surface-enhanced Raman scattering (SERS) biosensor for uranyl ions detection, Sens. Actuators, B, 2020, 311, 127676, with permission from Elsevier.

Fig. 21

(A) Detection of target analyte using a smart thermometer. Reprinted (adapted) with permission from J. Zhang, H. Xing and Y. Lu, Translating molecular detections into a simple temperature test using a target-responsive smart thermometer, Chem. Sci., 2018, 9, 3906–3910. Copyright 2018, The Royal Society of Chemistry. (B) ANDalyze Portable Fluorescence Reader and disposable sensors. Copyright permission granted by ANDalyze.

Fig. 22

DNAzyme based devices using a PGM for the detection of metal ions. (A) Schematic of method using a PGM to detect UO₂²⁺. Figure reproduced with permission from the corresponding author of Xiang, Y. & Lu, Y. Using personal glucose meters and functional DNA sensors to quantify a variety of analytical targets. Nat. Chem. 3, 697–703 (2011), as per the Nature policy for self-archiving and licence to publish. (B) Schematic representation of the detection of Pb²⁺ and UO₂²⁺ using a PGM. Reprinted (adapted) with permission from Y. Xiang, and Y. Lu, An invasive DNA approach toward a general method for portable quantification of metal ions using a personal glucose meter, Chem. Commun. 2013, 49, 585–587. Copyright 2013, The Royal Society of Chemistry. (C) Schematic illustration of low-cost and highly efficient DNA biosensor for Pb²⁺ detection using 8–17 DNAzyme-modified microplate and PGM. Reprinted (adapted) from J. Zhang, Y. Tang, L. M. Teng, M. H. Lu, and D. P. Tang. Low-cost and highly efficient DNA biosensor for heavy metal ion using specific DNAzyme-modified microplate and portable glucometer-based detection mode. Biosens. Bioelectron. 2015, 68, 232–238, with permission from Elsevier. (D) Nicotinamide adenine dinucleotide (NADH)/PGM system for target detection using NADH-dependent enzymes and a “YES” logic gate for Na⁺ detection based on the Na⁺–DNAzyme-invertase conjugate on magnetic beads through biotinylated using glucose as the signal output. Figures reprinted (adapted) with permission from J. Zhang, Y. Xiang, M. Wang, A. Basu, and Y. Lu, Dose-Dependent Response of Personal Glucose Meters to Nicotinamide Coenzymes: Applications to Point-of-Care Diagnostics of Many Non-Glucose Targets in a Single Step, Angew. Chem., Int. Ed. 2016, 55, 732–736. Copyright 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim. and from J. J. Zhang, and Y. Lu, Biocomputing for Portable, Resettable, and Quantitative Point-of-Care Diagnostics: Making the Glucose Meter a Logic-Gate Responsive Device for Measuring Many Clinically Relevant Targets, Angew. Chem., Int. Ed. 2018, 57, 9702–9706. Copyright 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fig. 23

DNAzyme based devices for the detection of non-metal targets. (A) A PGM-sensor for the detection of aflatoxin B1. Reprinted (adapted) from X. Yang, D. Shi, S. Zhu, B. Wang, X. Zhang and G. Wang, Portable Aptasensor of Aflatoxin B1 in Bread Based on a Personal Glucose Meter and DNA Walking Machine, ACS Sens., 2018, 3, 1368–1375. Copyright 2018, American Chemical Society. (B) Detection of microRNAs by PGM and oligonucleotide cross-linked hydrogel. Reprinted (adapted) from Y. Si, L. Li, N. Wang, J. Zheng, R. Yang and J. Li, Oligonucleotide Cross-Linked Hydrogel for Recognition and Quantitation of MicroRNAs Based on a Portable Glucometer Readout, ACS Appl. Mater. Interfaces, 2019, 11, 7792–7799. Copyright 2019, American Chemical Society.

Fig. 24

DNAzyme based lateral flow devices (LFDs). (A) An LFD for the detection of Pb²⁺ using 8–17 DNAzyme. Reprinted (adapted) from D. Mazumdar, J. Liu, G. Lu, J. Zhou, Y. Lu, Easy-to-use dipstick tests for detection of lead in paints using non-cross-linked gold nanoparticle–DNAzyme conjugates, Chem. Commun., 2010, 46, 1416–1418, with permission from The Royal Society of Chemistry. (B) LFD-based Detection of Cu²⁺ using Cu–DNAzyme. Reprinted (adapted) from Z. Fang, J. Huang, P. Lie, Z. Xiao, C. Ouyang, Q. Wu, G. Liu, L. Zeng, Lateral flow nucleic acid biosensor for Cu²⁺ detection in aqueous solution with high sensitivity and selectivity. Chem. Commun., 2010, 46, 9043–9045, with permission from The Royal Society of Chemistry. (C) A biosensor for Pb²⁺ detection using 8–17 DNAzyme and catalytic hairpin assembly. Reprinted (adapted) from J. Chen, X. Zhou, L. Zeng, Enzyme-free strip biosensor for amplified detection of Pb²⁺ based on a catalytic DNA circuit, Chem. Commun., 2013, 49, 984–986, with permission from The Royal Society of Chemistry.

Fig. 25

DNAzyme based devices for the detection of Pb²⁺. (A) Distance-based visualized analysis (panel A) and ratiometric electrochemiluminescence assay (panel B) with a dual-mode lab-on-paper device. Reprinted (adapted) with permission from Y. Zhang, J. Xu, S. Zhou, L. Zhu, X. Lv, J. Zhang, L. Zhang, P. Zhu and J. Yu, DNAzyme-Triggered Visual and Ratiometric Electrochemiluminescence Dual-Readout Assay for Pb(ii) Based on an Assembled Paper Device, Anal. Chem., 2020, 92, 3874–3881. Copyright 2020 American Chemical Society. (B) Dual-mode colorimetric and electrochemiluminescence analysis using an integrated lab-on-paper device. Reprinted (adapted) with permission J. Xu, Y. Zhang, L. Li, Q. Kong, L. Zhang, S. Ge and J. Yu, Colorimetric and Electrochemiluminescence Dual-Mode Sensing of Lead Ion Based on Integrated Lab-on-Paper Device, ACS Appl. Mater. Interfaces, 2018, 10, 3431–3440. Copyright 2018, American Chemical Society.

Fig. 26

An electrochemiluminescence paper device for the detection of Hg²⁺ and Ni²⁺. Reprinted (adapted) with permission from Y. Huang, L. Li, Y. Zhang, L. Zhang, S. Ge and J. Yu, Auto-cleaning paper-based electrochemiluminescence biosensor coupled with binary catalysis of cubic Cu₂ O–Au and polyethyleneimine for quantification of Ni²⁺ and Hg²⁺, Biosens. Bioelectron., 2019, 126, 339–345. Copyright 2018 Elsevier B.V.

Fig. 27

A paper device for microRNA detection. The recognition of miR-21 is shown on the left and electrochemical response to the released DNAzymes is shown on the right, with CNTs-WE before and after adsorption of Fc-SDNA (upper right). Reprinted (adapted) with permission from X. Liu, X. Li, X. Gao, L. Ge, X. Sun and F. Li, A Universal Paper-Based Electrochemical Sensor for Zero-Background Assay of Diverse Biomarkers, ACS Appl. Mater. Interfaces, 2019, 11, 15381–15388. Copyright 2019 American Chemical Society.

Fig. 28

DNAzyme based paper sensors for bacterial detection. (A) Paper plate sensor for bacterial detection. Reprinted (adapted) with permission from M. M. Ali, C. L. Brown, S. Jahanshahi-Anbuhi, B. Kannan, Y. Li, C. D. M. Filipe and J. D. Brennan, A Printed Multicomponent Paper Sensor for Bacterial Detection, Sci. Rep., 2017, 7, 12335. Copyright 2017 Ali et al. (B) A colorimetric paper-based sensor using the HP DNAzyme and a modified version of the urease-based litmus test for the detection of H. pylori. HP: H. pylori; others are control bacteria. Reprinted (adapted) with permission from M. M. Ali, M. Wolfe, K. Tram, J. Gu, C. D. M. M. Filipe, Y. Li and J. D. Brennan, A DNAzyme-Based Colorimetric Paper Sensor for Helicobacter pylori, Angew. Chem., Int. Ed., 2019, 1, 9907–9911. Copyright 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fig. 29

Paper sensors incorporating DNAzymes and RCA. (A) Printed paper device capable of performing RCA on paper. (B) Detection of RCA products by binding of fluorophore or AuNP labelled DNA, or by producing a PMD in the RCA product. A and B reprinted (adapted) with permission from M. Liu, C. Y. Hui, Q. Zhang, J. Gu, B. Kannan, S. Jahanshahi-Anbuhi, C. D. M. Filipe, J. D. Brennan and Y. Li, Target-Induced and Equipment-Free DNA Amplification with a Simple Paper Device, Angew. Chem., Int. Ed., 2016, 55, 2709–2713. 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. (C) Printed paper sensor using DNAzyme containing 3D DNA created from RCA. (D) 3D DNA-coated nitrocellulose paper strips before and after liquid flow. Reprinted (adapted) with permission from M. Liu, Q. Zhang, B. Kannan, G. A. Botton, J. Yang, L. Soleymani, J. D. Brennan and Y. Li, Self-Assembled Functional DNA Superstructures as High-Density and Versatile Recognition Elements for Printed Paper Sensors, Angew. Chem., Int. Ed., 2018, 57, 12440–12443. Copyright 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim. (E) Foldable 3D DNA paper sensor for E. coli detection. Reprinted (adapted) with permission from Y. Sun, Y. Chang, Q. Zhang and M. Liu, An Origami Paper-Based Device Printed with DNAzyme-Containing DNA Superstructures for Escherichia coli Detection, Micromachines, 2019, 10, 531. Copyright 2019 Sun et al.

Fig. 30

(A) Surface-to-surface product enrichment assay. EC1-SAB: DNAzyme EC1 immobilized on streptavidin-containing agarose beads; P^CDNA: paper strip with a capture DNA sequence (named CDS1); FDNA: the fluorescent cleavage fragment of EC1. Reprinted (adapted) with permission from S. E. Samani, D. Chang, E. M. McConnell, M. Rothen-broker, C. D. M. Filipe and Y. Li, Highly Sensitive RNA-Cleaving DNAzyme Sensors from Surface-to-Surface Product Enrichment, ChemBioChem, 2020, 21, 632–637. Copyright 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim. (B) A foodwrap sensor DNAzyme sensor capable of E. coli. Amine-terminated RFD-EC1 is covalently attached to thin, flexible, and transparent epoxy films. The cleavage of the fluorogenic substrate by the DNAzyme in the presence of the target produced by live E. coli cells produces a detectable signal. Reprinted (adapted) with permission from H. Yousefi, M. M. Ali, H. M. Su, C. D. M. Filipe and T. F. Didar, Sentinel Wraps: Real-Time Monitoring of Food Contamination by Printing DNAzyme Probes on Food Packaging, ACS Nano, 2018, 12, 3287–3294. Copyright 2018 American Chemical Society.