Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

High-performance biosensing based on autonomous enzyme-free DNA circuits

  • 88 Accesses

Abstract

Nucleic acids are considered not only extraordinary carriers of genetic information but also are perceived as the perfect elemental materials of molecular recognition and signal transduction/amplification for assembling programmable artificial reaction networks or circuits, which are similar to conventional electronic logic devices. Among these sophisticated DNA-based reaction networks, catalytic hairpin assembly (CHA), hybridization chain reaction (HCR), and DNAzyme represent the typical nonenzymatic amplification methods with high robustness and efficiency. Furthermore, their extensive hierarchically cascade integration into multi-layered autonomous DNA circuits establishes novel paradigms for constructing more different catalytic DNA nanostructures and for regenerating or replicating diverse molecular components with specific functions. Various DNA and inorganic nanoscaffolds have been used to realize the surface-confined DNA reaction networks with significant biomolecular sensing and signal-regulating functions in living cells. Especially, the specific aptamers and metal-ion-bridged duplex DNA nanostructures could extend their paradigms for detecting small molecules and proteins in even living entities. Herein, the varied enzyme-free DNA circuits are introduced in general with an extensive explanation of their underlying molecular reaction mechanisms. Challenges and outlook of the autonomous enzyme-free DNA circuits will also be discussed at the end of this chapter.

This is a preview of subscription content, log in to check access.

Fig. 1

Reprinted with permission from Ref. [17]. Copyright 2009 American Chemical Society

Fig. 2

Reprinted with permission from Ref. [14]. Copyright 2008 Nature Publishing Group

Fig. 3

Reprinted with permission from Ref. [30]. Copyright 2012 Elsevier

Fig. 4

Reprinted with permission from Ref. [31]. Copyright 2016 Nature Publishing Group

Fig. 5

Reprinted with permission from Ref. [33]. Copyright 2018 American Chemical Society

Fig. 6
Fig. 7

Reprinted with permission from Ref. [36]. Copyright 2017 Royal Society of Chemistry

Fig. 8

Reprinted with permission from Ref. [39]. Copyright 2015 American Chemical Society

Fig. 9

Reprinted with permission from Ref. [40]. Copyright 2018 American Chemical Society

Fig. 10

Reprinted with permission from Ref. [52]. Copyright 2009 American Chemical Society

Fig. 11

Reprinted with permission from Ref. [54]. Copyright 2016 American Chemical Society

Fig. 12
Fig. 13
Fig. 14

Reprinted with permission from Ref. [65]. Copyright 2018 Royal Society of Chemistry

Fig. 15

Reprinted with permission from Ref. [68]. Copyright 2019 Royal Society of Chemistry

Fig. 16

Reprinted with permission from Ref. [69]. Copyright 2019 Royal Society of Chemistry

Fig. 17

Reprinted with permission from Ref. [72]. Copyright 2018 Royal Society of Chemistry

Fig. 18

Reprinted with permission from Ref. [73]. Copyright 2011 American Chemical Society

Fig. 19

Reprinted with permission from Ref. [75]. Copyright 2019 American Chemical Society

Fig. 20
Fig. 21

Reprinted with permission from Ref. [78]. Copyright 2012 American Chemical Society

References

  1. 1.

    Wang F-A, Lu CH, Willner I (2014) From cascaded catalytic nucleic acids to enzyme-DNA nanostructures: controlling reactivity, sensing, logic operations, and assembly of complex structures. Chem Rev 114:2881–2941

  2. 2.

    Lam B, Das J, Holmes RD, Live L, Sage A, Sargent EH, Kelley SO (2013) Solution-based circuits enable rapid and multiplexed pathogen detection. Nat Commun 4:2001

  3. 3.

    Benenson Y, Gil B, Ben-Dor U, Adar R, Shapiro E (2004) An autonomous molecular computer for logical control of gene expression. Nature 429:423–429

  4. 4.

    Maojo V, Martin-Sanchez F, Kulikowski C, Rodriguez-Paton A, Fritts M (2010) Nanoinformatics and DNA-based computing: catalyzing nanomedicine. Pediatr Res 67:481–489

  5. 5.

    Jo M, Ahn JY, Lee J, Lee S, Hong SW, Yoo JW, Kang J, Dua P, Lee DK, Hong S, Kim S (2011) Development of single-stranded DNA aptamers for specific bisphenol A detection. Oligonucleotides 21:85–91

  6. 6.

    Edwards K, Johnstone C, Thompson C (1991) A simple and rapid method for the preparation of plant genomic DNA for PCR analysis. Nucleic Acids Res 19:1349

  7. 7.

    Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(t)(-delta delta c) method. Methods 25:402–408

  8. 8.

    Tomita N, Mori Y, Kanda H, Notomi T (2008) Loop-mediated isothermal amplification (lamp) of gene sequences and simple visual detection of products. Nat Protoc 3:877–882

  9. 9.

    Wang J, Wang HM, Wang H, He SZ, Li RM, Deng Z, Liu XQ, Wang F-A (2019) Nonviolent self-catabolic DNAzyme nanosponges for smart anticancer drug delivery. ACS Nano 13:5852–5863

  10. 10.

    Zhang LR, Zhu GC, Zhang CY (2014) Homogeneous and label-free detection of microRNAs using bifunctional strand displacement amplification-mediated hyperbranched rolling circle amplification. Anal Chem 86:6703–6709

  11. 11.

    Walker GT, Fraiser MS, Schram JL, Little MC, Nadeau JG, Malinowski DP (1992) Strand displacement amplification—an isothermal, in vitro DNA amplification technique. Nucleic Acids Res 20:1691–1696

  12. 12.

    Zhou WH, Hu L, Ying LM, Zhao Z, Chu PK, Yu XF (2018) A CRISPR-cas9-triggered strand displacement amplification method for ultrasensitive DNA detection. Nat Commun 9:5012

  13. 13.

    Zhao YX, Chen F, Li Q, Wang LH, Fan CH (2015) Isothermal amplification of nucleic acids. Chem Rev 115:12491–12545

  14. 14.

    Yin P, Choi HM, Calvert CR, Pierce NA (2008) Programming biomolecular self-assembly pathways. Nature 451:318–322

  15. 15.

    Dirks RM, Pierce NA (2004) Triggered amplification by hybridization chain reaction. Proc Natl Acad Sci USA 101:15275–15278

  16. 16.

    Lai W, Xiong XW, Wang F, Li Q, Li L, Fan CH, Pei H (2019) Nonlinear regulation of enzyme-free DNA circuitry with ultrasensitive switches. ACS Synth Biol 8:2106–2112

  17. 17.

    Zhang DY, Winfree E (2009) Control of DNA strand displacement kinetics using toehold exchange. J Am Chem Soc 131:17303–17314

  18. 18.

    Xuan F, Hsing IM (2014) Triggering hairpin-free chain-branching growth of fluorescent DNA dendrimers for nonlinear hybridization chain reaction. J Am Chem Soc 136:9810–9813

  19. 19.

    Ying ZM, Wu Z, Tu B, Tan WH, Jiang JH (2017) Genetically encoded fluorescent RNA sensor for ratiometric imaging of microRNA in living tumor cells. J Am Chem Soc 139:9779–9782

  20. 20.

    Zhang KY, Song ST, Huang S, Yang L, Min QH, Wu XC, Lu F, Zhu JJ (2018) Lighting up microRNA in living cells by the disassembly of lock-like DNA-programmed UCNPS-AUNPS through the target cycling amplification strategy. Small 14:1802292–1802302

  21. 21.

    Zhang B, Liu BQ, Tang DP, Niessner R, Chen G, Knopp D (2012) DNA-based hybridization chain reaction for amplified bioelectronic signal and ultrasensitive detection of proteins. Anal Chem 84:5392–5399

  22. 22.

    Zhou YJ, Yang L, Wei J, Ma K, Gong X, Shang JH, Yu SS, Wang F-A (2019) An autonomous nonenzymatic concatenated DNA circuit for amplified imaging of intracellular ATP. Anal Chem 91:15229–15234

  23. 23.

    Liu NN, Hou RZ, Gao PC, Lou XD, Xia F (2016) Sensitive Zn2+ sensor based on biofunctionalized nanopores via combination of DNAzyme and DNA supersandwich structures. Analyst 141:3626–3629

  24. 24.

    Deng Y, Nie J, Zhang XH, Zhao MZ, Zhou YL, Zhang XX (2014) Hybridization chain reaction-based fluorescence immunoassay using DNA intercalating dye for signal readout. Analyst 139:3378–3383

  25. 25.

    Pan M, Liang M, Sun JL, Liu XQ, Wang F-A (2018) Lighting up fluorescent silver clusters via target-catalyzed hairpin assembly for amplified biosensing. Langmuir 34:14851–14857

  26. 26.

    Quan K, Huang J, Yang XH, Yang YJ, Ying L, Wang H, He Y, Wang KM (2015) An enzyme-free and amplified colorimetric detection strategy via target-aptamer binding triggered catalyzed hairpin assembly. Chem Commun 51:937–940

  27. 27.

    Jo EJ, Mun H, Kim SJ, Shim WB, Kim MG (2016) Detection of ochratoxin a (OTA) in coffee using chemiluminescence resonance energy transfer (CRET) aptasensor. Food Chem 194:1102–1107

  28. 28.

    Liang MJ, Pan M, Hu JL, Wang F-A, Liu XQ (2018) Electrochemical biosensor for microRNA detection based on cascade hybridization chain reaction. Chemelectrochem 5:1380–1386

  29. 29.

    Li BL, Ellington AD, Chen X (2011) Rational, modular adaptation of enzyme-free DNA circuits to multiple detection methods. Nucleic Acids Res 39:e110

  30. 30.

    Zheng AX, Wang JR, Li J, Song XR, Chen GN, Yang HH (2012) Enzyme-free fluorescence aptasensor for amplification detection of human thrombin via target-catalyzed hairpin assembly. Biosens Bioeletron 36:217–221

  31. 31.

    Jung C, Allen PB, Ellington AD (2016) A stochastic DNA walker that traverses a microparticle surface. Nat Nanotechnol 11:157–163

  32. 32.

    Wu CC, Cansiz S, Zhang LQ, Teng I, Qiu LP, Li J, Liu Y, Zhou CS, Hu R, Zhang T, Cui C, Cui L, Tan WH (2015) A nonenzymatic hairpin DNA cascade reaction provides high signal gain of mRNA imaging inside live cells. J Am Chem Soc 137:4900–4903

  33. 33.

    He L, Lu DQ, Liang H, Xie S, Zhang XB, Liu QL, Yuan Q, Tan WH (2018) mRNA-initiated, three-dimensional DNA amplifier able to function inside living cells. J Am Chem Soc 140:258–263

  34. 34.

    Huang J, Wu YR, Chen Y, Zhu Z, Yang XH, Yang CY, Wang KM, Tan WH (2011) Pyrene-excimer probes based on the hybridization chain reaction for the detection of nucleic acids in complex biological fluids. Angew Chem Int Ed 50:401–404

  35. 35.

    Shi ZL, Zhang XF, Cheng R, Li BX, Jin Y (2016) Sensitive detection of intracellular RNA of human telomerase by using graphene oxide as a carrier to deliver the assembly element of hybridization chain reaction. Analyst 141:2727–2732

  36. 36.

    Li L, Feng J, Liu HY, Li QL, Tong LL, Tang B (2016) Two-color imaging of microRNA with enzyme-free signal amplification via hybridization chain reactions in living cells. Chem Sci 7:1940–1945

  37. 37.

    Liu P, Yang XH, Sun S, Wang Q, Wang KM, Huang J, Liu JB, He LL (2013) Enzyme-free colorimetric detection of DNA by using gold nanoparticles and hybridization chain reaction amplification. Anal Chem 85:7689–7695

  38. 38.

    Zou L, Li RM, Zhang MJ, Luo YW, Zhou N, Wang J, Ling LS (2017) A colorimetric sensing platform based upon recognizing hybridization chain reaction products with oligonucleotide modified gold nanoparticles through triplex formation. Nanoscale 9:1986–1992

  39. 39.

    Wu Z, Liu GQ, Yang XL, Jiang JH (2015) Electrostatic nucleic acid nanoassembly enables hybridization chain reaction in living cells for ultrasensitive mRNA imaging. J Am Chem Soc 137:6829–6836

  40. 40.

    Ren KW, Xu YF, Liu Y, Yang M, Ju HX (2018) A responsive “nano string light” for highly efficient mRNA imaging in living cells via accelerated DNA cascade reaction. ACS Nano 12:263–271

  41. 41.

    Breaker RR, Joyce GF (1994) A DNA enzyme that cleaves RNA. Chem Bio 1:223–229

  42. 42.

    Carmi N, Balkhi SR, Breaker RR (1998) Cleaving DNA with DNA. Proc Natl Acad Sci USA 95:2233–2237

  43. 43.

    Liu ZJ, Mei SHJ, Brennan JD, Li YF (2003) Assemblage of signaling DNA enzymes with intriguing metal-ion specificities and ph dependences. J Am Chem Soc 125:7539–7545

  44. 44.

    Liu JW, Lu Y (2007) Rational design of “turn-on” allosteric DNAzyme catalytic beacons for aqueous mercury ions with ultrahigh sensitivity and selectivity. Angew Chem Int Ed 46:7587–7590

  45. 45.

    Santoro SW, Joyce GF, Sakthivel K, Gramatikova S, Barbas CF (2000) RNA cleavage by a DNA enzyme with extended chemical functionality. J Am Chem Soc 122:2433–2439

  46. 46.

    Liang G, Man Y, Li A, Jin XX, Liu XH, Pan LG (2017) DNAzyme-based biosensor for detection of lead ion: a review. Microchem J 131:145–153

  47. 47.

    McGhee CE, Loh KY, Lu Y (2017) DNAzyme sensors for detection of metal ions in the environment and imaging them in living cells. Curr Opin In Biotech 45:191–201

  48. 48.

    Zhou WH, Saran R, Liu JW (2017) Metal sensing by DNA. Chem Rev 117:8272–8325

  49. 49.

    Li J, Lu Y (2000) A highly sensitive and selective catalytic DNA biosensor for lead ions. J Am Chem Soc 122:10466–10467

  50. 50.

    Golub E, Freeman R, Willner I (2011) A hemin/g-quadruplex acts as an NADH oxidase and NADH peroxidase mimicking DNAzyme. Angew Chem Int Ed 50:11710–11714

  51. 51.

    Pavlov V, Xiao Y, Gill R, Dishon A, Kotler M, Willner I (2004) Amplified chemiluminescence surface detection of DNA and telomerase activity using catalytic nucleic acid labels. Anal Chem 76:2152–2156

  52. 52.

    Li T, Shi LL, Wang EK, Dong SJ (2009) Silver-ion-mediated DNAzyme switch for the ultrasensitive and selective colorimetric detection of aqueous Ag + and cysteine. Chemistry 15:3347–3350

  53. 53.

    Liu JW, Lu Y (2003) A colorimetric lead biosensor using DNAzyme-directed assembly of gold nanoparticles. J Am Chem Soc 125:6642–6643

  54. 54.

    Yang YJ, Huang J, Yang XH, Quan K, Wang H, Ying L, Xie N, Ou M, Wang KM (2016) Aptazyme-gold nanoparticle sensor for amplified molecular probing in living cells. Anal Chem 88:5981–5987

  55. 55.

    Zhao XH, Kong RM, Zhang XB, Meng HM, Liu WN, Tan WH, Shen GL, Yu RQ (2011) Graphene-DNAzyme based biosensor for amplified fluorescence “turn-on” detection of Pb2+ with a high selectivity. Anal Chem 83:5062–5066

  56. 56.

    Kong RM, Zhang XB, Chen Z, Meng HM, Song ZL, Tan WH, Shen GL, Yu RQ (2011) Unimolecular catalytic DNA biosensor for amplified detection of l-histidine via an enzymatic recycling cleavage strategy. Anal Chem 83:7603–7607

  57. 57.

    Lu LM, Zhang XB, Kong RM, Yang B, Tan Wh (2011) A ligation-triggered DNAzyme cascade for amplified fluorescence detection of biological small molecules with zero-background signal. J Am Chem Soc 133:11686–11691

  58. 58.

    He KY, Li W, Nie Z, Huang Y, Liu ZL, Nie LH, Yao SZ (2012) Enzyme-regulated activation of DNAzyme: a novel strategy for a label-free colorimetric DNA ligase assay and ligase-based biosensing. Chemistry 18:3992–3999

  59. 59.

    Li BL, Jiang Y, Chen X, Ellington AD (2012) Probing spatial organization of DNA strands using enzyme-free hairpin assembly circuits. J Am Chem Soc 134:13918–13921

  60. 60.

    Dai JY, He HF, Duan ZJ, Guo Y, Xiao D (2017) Self-replicating catalyzed hairpin assembly for rapid signal amplification. Anal Chem 89:11971–11975

  61. 61.

    Feng CJ, Zhu J, Sun JW, Jiang W, Wang L (2015) Hairpin assembly circuit-based fluorescence cooperative amplification strategy for enzyme-free and label-free detection of small molecule. Talanta 143:101–106

  62. 62.

    Quan K, Huang J, Yang XH, Yang YJ, Ying L, Wang H, Xie NL, Ou M, Wang KM (2016) Powerful amplification cascades of FRET-based two-layer nonenzymatic nucleic acid circuits. Anal Chem 88:5857–5864

  63. 63.

    Wei YL, Zhou WJ, Li X, Chai YQ, Yuan R, Xiang Y (2016) Coupling hybridization chain reaction with catalytic hairpin assembly enables non-enzymatic and sensitive fluorescent detection of microRNA cancer biomarkers. Biosens Bioelectron 77:416–420

  64. 64.

    Wu XY, Chai YQ, Yuan R, Zhuo Y, Chen Y (2014) Dual signal amplification strategy for enzyme-free electrochemical detection of microRNAs. Sensors Actuators B-Chem 203:296–302

  65. 65.

    Wang HM, Li CX, Liu XQ, Zhou X, Wang F-A (2018) Construction of an enzyme-free concatenated DNA circuit for signal amplification and intracellular imaging. Chem Sci 9:5842–5849

  66. 66.

    Liu SF, Cheng CB, Gong HW, Wang L (2015) Programmable Mg2+-dependent DNAzyme switch by the catalytic hairpin DNA assembly for dual-signal amplification toward homogeneous analysis of protein and DNA. Chem Commun 51:7364–7367

  67. 67.

    Yang L, Wu Q, Chen YQ, Liu XQ, Wang F-A, Zhou X (2019) Amplified microRNA detection and intracellular imaging based on an autonomous and catalytic assembly of DNAzyme. ACS Sens 4:110–117

  68. 68.

    Zou LN, Wu Q, Zhou YJ, Gong X, Liu XQ, Wang F-A (2019) A DNAzyme-powered cross-catalytic circuit for amplified intracellular imaging. Chem Commun 55:6519–6522

  69. 69.

    Wang H, Wang HM, Wu Q, Liang MJ, Liu XQ, Wang F-A (2019) A DNAzyme-amplified DNA circuit for highly accurate microRNA detection and intracellular imaging. Chem Sci 10:9597–9604

  70. 70.

    Yue SZ, Zhao TT, Qi HJ, Yan YC, Bi S (2017) Cross-catalytic hairpin assembly-based exponential signal amplification for CRET assay with low background noise. Biosens Bioelectron 94:671–676

  71. 71.

    Bi S, Chen M, Jia XQ, Dong Y, Wang ZH (2015) Hyperbranched hybridization chain reaction for triggered signal amplification and concatenated logic circuits. Angew Chem Int Ed 54:8144–8148

  72. 72.

    Wei J, Gong X, Wang Q, Pan M, Liu XQ, Liu J, Xia F, Wang F-A (2018) Construction of an autonomously concatenated hybridization chain reaction for signal amplification and intracellular imaging. Chem Sci 9:52–61

  73. 73.

    Wang F-A, Elbaz J, Orbach R, Magen N, Willner I (2011) Amplified analysis of DNA by the autonomous assembly of polymers consisting of DNAzyme wires. J Am Chem Soc 133:17149–17151

  74. 74.

    He DG, Hai L, Wang HZ, Wu R, Li HW (2018) Enzyme-free quantification of exosomal microRNA by the target-triggered assembly of the polymer DNAzyme nanostructure. Analyst 143:813–816

  75. 75.

    Wu Q, Wang H, Gong KK, Shang JH, Liu XQ, Wang F-A (2019) Construction of an autonomous nonlinear hybridization chain reaction for extracellular vesicles-associated microRNAs discrimination. Anal Chem 91:10172–10179

  76. 76.

    Elbaz J, Shlyahovsky B, Willner I (2008) A DNAzyme cascade for the amplified detection of pb(2 +) ions or L-histidine. Chem Commun 13:1569–1571

  77. 77.

    Wang F-A, Elbaz J, Teller C, Willner I (2011) Amplified detection of DNA through an autocatalytic and catabolic DNAzyme-mediated process. Angew Chem Int Ed 50:295–299

  78. 78.

    Wang F-A, Elbaz J, Willner I (2012) Enzyme-free amplified detection of DNA by an autonomous ligation DNAzyme machinery. J Am Chem Soc 134:5504–5507

  79. 79.

    Zhang ZX, Sharon E, Freeman R, Liu XQ, Willner I (2012) Fluorescence detection of DNA, adenosine-5 ‘-triphosphate (ATP), and telomerase activity by zinc(ii)-protoporphyrin ix/g-quadruplex labels. Anal Chem 84:4789–4797

  80. 80.

    Li CX, Wang HM, Shang JH, Liu XQ, Yuan B, Wang F-A (2018) Highly sensitive assay of methyltransferase activity based on an autonomous concatenated DNA circuit. ACS Sens 3:2359–2366

  81. 81.

    Wang Q, Pan M, Wei J, Liu XQ, Wang F-A (2017) Evaluation of DNA methyltransferase activity and inhibition via isothermal enzyme-free concatenated hybridization chain reaction. ACS Sens 2:932–939

  82. 82.

    Wang J, Pan M, Wei J, Liu XQ, Wang F-A (2017) A C-HCR assembly of branched DNA nanostructures for amplified uracil-DNA glycosylase assays. Chem Commun 53:12878–12881

  83. 83.

    Liu L, Li Q, Tang LJ, Yu RQ, Jiang JH (2016) Silver nanocluster-lightened hybridization chain reaction. RSC Adv 6:57502–57506

  84. 84.

    Chen PP, Wu P, Zhang YX, Chen JB, Jiang XM, Zheng CB, Hou XD (2016) Strand displacement-induced enzyme-free amplification for label-free and separation-free ultrasensitive atomic fluorescence spectrometric detection of nucleic acids and proteins. Anal Chem 88:12386–12392

  85. 85.

    Gong X, Wei J, Liu J, Li RM, Liu XQ, Wang F-A (2019) Programmable intracellular DNA biocomputing circuits for reliable cell recognitions. Chem Sci 10:2989–2997

  86. 86.

    Orbach R, Willner B, Willner I (2015) Catalytic nucleic acids (DNAzymes) as functional units for logic gates and computing circuits: from basic principles to practical applications. Chem Commun 51:4144–4160

  87. 87.

    Hong C, Kim DM, Baek A, Chung H, Jung W, Kim DE (2015) Fluorescence-based detection of single-nucleotide changes in RNA using graphene oxide and DNAzyme. Chem Commun 51:5641–5644

  88. 88.

    Chen XP, Wang L, Sheng SC, Wang T, Yang J, Xie GM, Feng WL (2015) Coupling a universal DNA circuit with graphene sheets/polyaniline/AUNPS nanocomposites for the detection of BCR/ABL fusion gene. Anal Chim Acta 889:90–97

  89. 89.

    Huang J, Wang H, Yang XH, Quan K, Yang YJ, Ying L, Xie NL, Ou M, Wang KM (2016) Fluorescence resonance energy transfer-based hybridization chain reaction for in situ visualization of tumor-related mRNA. Chem Sci 7:3829–3835

  90. 90.

    Wang SF, Ding JS, Zhou WH (2019) An aptamer-tethered, DNAzyme-embedded molecular beacon for simultaneous detection and regulation of tumor-related genes in living cells. Analyst. 144:5098–5107

  91. 91.

    Bi S, Ye JY, Dong Y, Li HT, Cao W (2016) Target-triggered cascade recycling amplification for label-free detection of microRNA and molecular logic operations. Chem Commun 52:402–405

  92. 92.

    Deng RJ, Zhang KX, Li JH (2017) Isothermal amplification for microRNA detection: from the test tube to the cell. Accounts Chem Res 50:1059–1068

  93. 93.

    Wu H, Liu YL, Wang HY, Wu J, Zhu FF, Zou P (2016) Label-free and enzyme-free colorimetric detection of microRNA by catalyzed hairpin assembly coupled with hybridization chain reaction. Biosens Bioeletron 81:303–308

  94. 94.

    Yang L, Liu CH, Ren W, Li ZP (2012) Graphene surface-anchored fluorescence sensor for sensitive detection of microRNA coupled with enzyme-free signal amplification of hybridization chain reaction. ACS Appl Mater Interfaces 4:6450–6453

  95. 95.

    Chang X, Zhang C, Lv C, Sun Y, Zhang MZ, Zhao YM, Yang LL, Han D, Tan WH (2019) Construction of a multiple-aptamer-based DNA logic device on live cell membranes via associative toehold activation for accurate cancer cell identification. J Am Chem Soc 141:12738–12743

  96. 96.

    Yuan BY, Chen YY, Sun YQ, Guo QP, Huang J, Liu JB, Meng XX, Yang XH, Wen XH, Li ZH, Li L, Wang KM (2018) Enhanced imaging of specific cell-surface glycosylation based on multi-FRET. Anal Chem 90:6131–6137

  97. 97.

    Wu PW, Hwang KV, Lan T, Lu Y (2013) A DNAzyme-gold nanoparticle probe for uranyl ion in living cells. J Am Chem Soc 135:5254–5257

  98. 98.

    Feng J, Xu Z, Liu F, Zhao Y, Yu WQ, Pan M, Wang F-A, Liu XQ (2018) Versatile catalytic deoxyribozyme vehicles for multimodal imaging-guided efficient gene regulation and photothermal therapy. ACS Nano 12:12888–12901

  99. 99.

    Brummelkamp TR, Bernards R, Agami R (2002) A system for stable expression of short interfering RNAs in mammalian cells. Science 296:550–553

Download references

Acknowledgements

This work is supported by National Natural Science Foundation of China (no. 21874103), National Basic Research Program of China (973 Program, 2015CB932601), and Fundamental Research Funds for the Central Universities (nos. 2042018kf0210 and 2042019kf0206).

Author information

Correspondence to Fuan Wang.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

This article is part of the Topical Collection “DNA Nanotechnology: From Structure to Functionality”; edited by Chunhai Fan, Yonggang Ke.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Wang, H., Wang, H., Willner, I. et al. High-performance biosensing based on autonomous enzyme-free DNA circuits. Top Curr Chem (Z) 378, 20 (2020). https://doi.org/10.1007/s41061-020-0284-x

Download citation

Keywords

  • Catalytic hairpin assembly
  • Hybridization chain reaction
  • DNAzyme
  • DNA circuit
  • Imaging
  • Biosensor