Toehold-mediated nonenzymatic amplification circuit on graphene oxide fluorescence switching platform for sensitive and homogeneous microRNA detection

Analytica Chimica Acta

Volumn 888, Issue , 2015, Pages 162-172

  Huang, Ru ^a   Liao, Yuhui ^a   Zhou, Xiaoming ^a   Xing, Da ^a  

^a SOUTH CHINA NORMAL UNIVERSITY   (China)

Author keywords

Fluorescence switch; Graphene oxide; Hairpin probe; MicroRNA detection; Nonenzymatic amplification

Indexed keywords

ATOMIC FORCE MICROSCOPY; BIOSENSORS; FLUORESCENCE; GENE ENCODING; GRAPHENE; GRAPHENE OXIDE; RNA; TIMING CIRCUITS;

AMPLIFICATION EFFICIENCIES; FLUORESCENCE SWITCH; FLUORESCENCE SWITCHING; INTERACTION MECHANISMS; MICRORNA DETECTIONS; NON-ENZYMATIC; NONENZYMATIC REACTION; SIGNAL AMPLIFICATIONS;

AMPLIFICATION;

DOUBLE STRANDED DNA; GRAPHENE OXIDE; MICRORNA; MICRORNA 21; FLUORESCENT DYE; GRAPHITE; MIRN21 MICRORNA, HUMAN; OXIDE;

ABSORPTION; ARTICLE; ATOMIC FORCE MICROSCOPY; BIOSENSOR; CONTROLLED STUDY; DNA PROBE; DNA STRUCTURE; FEMALE; FLUORESCENCE ANALYSIS; HUMAN; HUMAN CELL; LIMIT OF DETECTION; MOLECULAR INTERACTION; NUCLEIC ACID AMPLIFICATION; PRIORITY JOURNAL; PROCESS DEVELOPMENT; REACTION OPTIMIZATION; RNA ANALYSIS; TOEHOLD MEDIATED NONENZYMATIC AMPLIFICATION; ZETA POTENTIAL; CHEMISTRY; FLUORESCENCE; HELA CELL LINE; PROCEDURES; SPECTROFLUOROMETRY; SURFACE PROPERTY;

FLUORESCENCE; FLUORESCENT DYES; GRAPHITE; HELA CELLS; HUMANS; LIMIT OF DETECTION; MICRORNAS; OXIDES; SPECTROMETRY, FLUORESCENCE; SURFACE PROPERTIES;

EID: 84946726235     PISSN: 00032670     EISSN: 18734324     Source Type: Journal    
DOI: 10.1016/j.aca.2015.07.041     Document Type: Article

References (54)

1. K. Saha, S.S. Agasti, C. Kim, X. Li, V.M. Rotello, Gold nanoparticles in chemical and biological sensing, Chem. Rev. 112 (2012) 2739-2779.
2. M.F. Frasco, N. Chaniotakis, Semiconductor quantum dots in chemical sensors and biosensors, Sensors 9 (2009) 7266-7286.
3. E. Morales-Narváez, A. Merkoçi, Graphene oxide as an optical biosensing platform, Adv. Mater. 24 (2012) 3298-3308.
4. M. Wu, R. Kempaiah, P.-J.J. Huang, V. Maheshwari, J. Liu, Adsorption and desorption of DNA on graphene oxide studied by fluorescently labeled oligonucleotides, Langmuir 27 (2011) 2731-2738.
5. A.K. Yetisen, I. Naydenova, F. da Cruz Vasconcellos, J. Blyth, C.R. Lowe, Holographic sensors: three-dimensional analyte-sensitive nanostructures and their applications, Chem. Rev. 114 (2014) 10654-10696.
6. A.K. Yetisen, M.M. Qasim, S. Nosheen, T.D. Wilkinson, C.R. Lowe, Pulsed laser writing of holographic nanosensors, J. Mater. Chem. C 2 (2014) 3569-3576.
7. A.K. Yetisen, Y. Montelongo, F. da Cruz Vasconcellos, J.L. Martinez-Hurtado, S. Neupane, H. Butt, M.M. Qasim, J. Blyth, K. Burling, J.B. Carmody, M. Evans, T.D. Wilkinson, L.T. Kubota, M.J. Monteiro, C.R. Lowe, Reusable, robust, and accurate laser-generated photonic nanosensor, Nano Lett. 14 (2014) 3587-3593.
8. A.K. Yetisen, Y. Montelongo, M.M. Qasim, H. Butt, T.D. Wilkinson, M.J. Monteiro, S.H. Yun, Photonic nanosensor for colorimetric detection of metal ions, Anal. Chem. (2015), http://dx.doi.org/10.1021/ac504274q.
9. A.K. Yetisen, H. Butt, F. da Cruz Vasconcellos, Y. Montelongo, C.A.B. Davidson, J. Blyth, L. Chan, J.B. Carmody, S. Vignolini, U. Steiner, J.J. Baumberg, T.D. Wilkinson, C.R. Lowe, Light-directed writing of chemically tunable narrow-band holographic sensors, Adv. Opt. Mater. 2 (2014) 250-254.
10. Z. Lu, L. Zhang, Y. Deng, S. Li, N. He, Graphene oxide for rapid microRNA detection, Nanoscale 4 (2012) 5840-5842.
11. Z. Zhou, C. Zhu, J. Ren, S. Dong, A graphene-based real-time fluorescent assay of deoxyribonuclease I activity and inhibition, Anal. Chim. Acta 740 (2012) 88-92.
12. Y. Wen, F. Xing, S. He, S. Song, L. Wang, Y. Long, D. Li, C.A. Fan, Graphene-based fluorescent nanoprobe for silver (I) ions detection by using graphene oxide and a silver-specific oligonucleotide, Chem. Commun. 46 (2010) 2596-2598.
13. L.M. Lu, X.B. Zhang, R.M. Kong, B. Yang, W. Tan, A Ligation-triggered DNAzyme cascade for amplified fluorescence detection of biological small molecules with zero-background signal, J. Am. Chem. Soc. 133 (2011) 11686e11691.
14. Z. Li, W. Zhu, J. Zhang, J. Jiang, G. Shen, R. Yu, A label-free amplified fluorescence DNA detection based on isothermal circular strand-displacement polymerization reaction and graphene oxide, Analyst 138 (2013) 3616-3620.
15. H. Dong, J. Zhang, H. Ju, H. Lu, S. Wang, S. Jin, K. Hao, H. Du, X. Zhang, Highly sensitive multiple microRNA detection based on fluorescence quenching of graphene oxide and isothermal strand-displacement polymerase reaction, Anal. Chem. 84 (2012) 4587-4593.
16. C. Jamesá Yang, Graphene oxide-protected DNA probes for multiplex micro- RNA analysis in complex biological samples based on a cyclic enzymatic amplification method, Chem. Commun. 48 (2012) 194e196.
17. C.H. Lu, J. Li, M.H. Lin, Y.W. Wang, H.H. Yang, X. Chen, G.N. Chen, Amplified aptamer-based assay through catalytic recycling of the analyte, Angew. Chem. Int. Ed. 122 (2010) 8632-8635.
18. X. Zhu, X. Zhou, D. Xing, Label-free detection of microRNA: two-step signal enhancement with a hairpin-probe-based graphene fluorescence switch and isothermal amplification, Chem. Eur. J. 19 (2013) 5487-5494.
19. X.-H. Zhao, Q.-J. Ma, X.-X. Wu, X. Zhu, Graphene oxide-based biosensor for sensitive fluorescence detection of DNA based on exonuclease III-aided signal amplification, Anal. Chim. Acta 727 (2012) 67-70.
20. X. Tan, T. Chen, X. Xiong, Y. Mao, G. Zhu, E. Yasun, C. Li, Z. Zhu, W. Tan, Semiquantification of ATP in live cells using nonspecific desorption of DNA from graphene oxide as the internal reference, Anal. Chem. 84 (2012) 8622-8627.
21. P.J.J. Huang, J. Liu, Molecular beacon lighting up on graphene oxide, Anal. Chem. 84 (2012) 4192-4198.
22. G. Seelig, D. Soloveichik, D.Y. Zhang, E. Winfree, Enzyme-free nucleic acid logic circuits, Science 314 (2006) 1585-1588.
23. B. Li, A.D. Ellington, X. Chen, Rational, modular adaptation of enzyme-free DNA circuits to multiple detection methods, Nucl. Acids Res. 39 (2011) e110.
24. X. Chen, N. Briggs, J.R. McLain, A.D. Ellington, Stacking nonenzymatic circuits for high signal gain, Proc. Nat. Acad. Sci. U. S. A. 110 (2013) 5386-5391.
25. Y.S. Jiang, B. Li, J. Milligan, S. Bhadra, A.D. Ellington, Real-time detection of isothermal amplification reactions with thermostable catalytic hairpin assembly, J. Am. Chem. Soc. 135 (2013) 7430-7433.
26. J. Hu, Y. Yu, J.C. Brooks, L.A. Godwin, S. Somasundaram, F. Torabinejad, J. Kim, C. Shannon, C.J. Easley, A reusable electrochemical proximity assay for highly selective, real-time protein quantitation in biological matrices, J. Am. Chem. Soc. 136 (2014) 8467-8474.
27. J. Hu, T. Wang, J. Kim, C. Shannon, C.J. Easley, Quantitation of femtomolar protein levels via direct readout with the electrochemical proximity assay, J. Am. Chem. Soc. 134 (2012) 7066-7072.
28. D.P. Bartel, MicroRNAs: target recognition and regulatory functions, Cell 136 (2009) 215-233.
29. X. Chen, Y. Ba, L. Ma, X. Cai, Y. Yin, K. Wang, J. Guo, Y. Zhang, J. Chen, X. Guo, Q. Li, X. Li, W. Wang, Y. Zhang, J. Wang, X. Jiang, Y. Xiang, C. Xu, P. Zheng, J. Zhang, R. Li, H. Zhang, X. Shang, T. Gong, G. Ning, J. Wang, K. Zen, J. Zhang, C.- Y. Zhang, Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases, Cell Res. 18 (2008) 997e1006.
30. P.S. Mitchell, R.K. Parkin, E.M. Kroh, B.R. Fritz, S.K. Wyman, E.L. Pogosova- Agadjanyan, A. Peterson, J. Noteboom, K.C. O'Briant, A. Allen, D.W. Lin, N. Urban, C.W. Drescher, B.S. Knudsen, D.L. Stirewalt, R. Gentleman, R.L. Vessella, P.S. Nelson, D.B. Martin, M. Tewari, Circulating microRNAs as stable blood-based markers for cancer detection, Proc. Nat. Acad. Sci. U. S. A. (2008) 10513-10518.
31. H. Dong, J. Lei, L. Ding, Y. Wen, H. Ju, X. Zhang, MicroRNA: function, detection, and bioanalysis, Chem. Rev. 113 (2013) 6207-6233.
32. C. Chen, D.A. Ridzon, A.J. Broomer, Z. Zhou, D.H. Lee, J.T. Nguyen, M. Barbisin, N.L. Xu, V.R. Mahuvakar, M.R. Andersen, K.Q. Lao, K.J. Livak, K.J. Guegler, Realtime quantification of microRNAs by stem-loop RT-PCR, Nucl. Acids Res. 33 (2005) e179.
33. A. Válóczi, C. Hornyik, N. Varga, J. Burgyán, S. Kauppinen, Z. Havelda, Sensitive and specific detection of microRNAs by northern blot analysis using LNAmodified oligonucleotide probes, Nucl. Acids Res. 32 (2004) e175.
34. M.B. Baker, G. Bao, C.D. Searles, In vitro quantification of specific microRNA using molecular beacons, Nucl. Acids Res. 40 (2012) e13.
35. J.M. Lee, H. Cho, Y. Jung, Fabrication of a structure-specific RNA binder for array detection of label-free microRNA, Angew. Chem. Int. Ed. 49 (2010) 8662-8665.
36. G. Lautner, R.E. Gyurcsányi, Electrochemical detection of miRNAs, Electroanalysis 26 (2014) 1224-1235.
37. Y. Liao, R. Huang, Z. Ma, Y. Wu, X. Zhou, D. Xing, Target-triggered enzyme-free amplification strategy for sensitive detection of microRNA in tumor cells and tissues, Anal. Chem. 86 (2014) 4596-4604.
38. H. Ŝípová, S. Zhang, A.M. Dudley, D. Galas, K. Wang, J. Homola, Surface plasmon resonance biosensor for rapid label-free detection of microribonucleic acid at subfemtomole level, Anal. Chem. 82 (2010) 10110-10115.
39. W. Shen, H. Deng, Y. Ren, Z. Gao, A real-time colorimetric assay for label-free detection of microRNAs down to sub-femetomolar levels, Chem. Commun. 49 (2013) 4959-4961.
40. B. Juskowiak, Nucleic acid-based fluorescent probes and their analytical potential, Anal. Bioanal. Chem. 399 (2011) 3157-3176.
41. F. Li, Y. Huang, Q. Yang, Z. Zhong, D. Li, L. Wang, S. Song, C. Fan, A grapheneenhanced molecular beacon for homogeneous DNA detection, Nanoscale 2 (2010) 1021-1026.
42. P.-J.J. Huang, J. Liu, DNA-length-dependent fluorescence signaling on graphene oxide surface, Small 8 (2012) 977e983.
43. S. Zhu, H. Wu, F. Wu, D. Nie, S. Sheng, Y.Y. Mo, MicroRNA-21 targets tumor suppressor genes in invasion and metastasis, Cell Res. 18 (2008) 350-359.
44. J.A. Chan, A.M. Krichevsky, K.S. Kosik, MicroRNA-21 is an antiapoptotic factor in human glioblastoma cells, Cancer Res. 65 (2005) 6029-6033.
45. H. Zhang, X. Wei, Y. Zang, J. Cao, S. Liu, X. He, Q. Chen, Y. Long, J. Li, G. Chen, K. Chen, Fluorogenic probing of specific recognitions between sugar ligands and glycoprotein receptors on cancer cells by an economic graphene nanocomposite, Adv. Mater. 25 (2013) 4097-4101.
46. D. Zhu, L. Zhang, W. Ma, S. Lu, X. Xing, Detection of microRNA in clinical tumor samples by isothermal enzyme-free amplification and label-free graphene oxide-based SYBR Green I fluorescence platform, Biosens. Bioelectron. 65 (2015) 152e158.
47. X. He, Q. Deng, L. Cai, C. Wang, Y. Zang, J. Li, G. Chen, H. Tian, Fluorogenic resveratrol-confined graphene oxide for economic and rapid detection of Alzheimer's disease, ACS Appl. Mater. Interfaces 6 (2014) 5379-5382.
48. J. Huang, X. Yang, X. He, K. Wang, Y. He, K. Quan, A new strategy for designing a graphene oxide-based DNA hairpin probe: fluorescence upon switching the orientation of the sticky end, Chem. Commun. 49 (2013) 9827-9829.
49. C.G. Baumann, S.B. Smith, V.A. Bloomfield, C. Bustamante, Ionic effects on the elasticity of single DNA molecules, Proc. Natl. Acad. Sci. U. S. A. 94 (1997) 6185-6190.
50. K.J. McConnell, D.L. Beveridge, DNA structure: what's in charge? J. Mol. Biol. (2000) 803-820.
51. R. Chinnappan, A. Dube, J.F. Lemay, D.A. Lafontaine, Fluorescence monitoring of riboswitch transcription regulation using a dual molecular beacon assay, Nucl. Acids Res. 41 (2013) e106.
52. Y.W. Lin, H.T. Ho, C.C. Huang, H.T. Chang, Fluorescence detection of single nucleotide polymorphisms using a universal molecular beacon, Nucl. Acids Res. 36 (2008) e123.
53. P.J. Santangelo, B. Nix, A. Tsourkas, G. Bao, Dual FRET molecular beacons for mRNA detection in living cells, Nucl. Acids Res. 32 (2004) e57.
54. L. Yang, C. Liu, W. Ren, Z. Li, Graphene surface-anchored fluorescence sensor for sensitivedetectionofmicroRNAcoupledwithenzyme-free signalamplificationof hybridization chain reaction, ACS Appl.Mater. Interfaces 4 (2012) 6450-6453.