Colorimetric detection of gene transcript by target-induced three-way junction formation

Talanta

Volumn 158, Issue , 2016, Pages 1-5

  Wang, Xuchu ^a   Liu, Weiwei ^a   Yin, Binbin ^a   Yu, Pan ^a   Duan, Xiuzhi ^a   Liao, Zhaoping ^a   Liu, Chunhua ^a   Sang, Yiwen ^a   Zhang, Gong ^a   Chen, Yuhua ^a   Tao, Zhihua ^a  

^a ZHEJIANG UNIVERSITY SCHOOL OF MEDICINE   (China)

Author keywords

Colorimetric detection; Gene transcript; Three way junction formation

Indexed keywords

COLOR; COLORIMETRY; DIAGNOSIS; MOLECULAR BIOLOGY; PROBES;

ALTERNATIVE SPLICING; COLORIMETRIC ASSAYS; COLORIMETRIC DETECTION; FORMING SEQUENCES; GENE TRANSCRIPTS; JUNCTION FORMATION; MOLECULAR DIAGNOSIS; TARGETED TRANSCRIPTS;

GENE EXPRESSION;

COMPLEMENTARY DNA; GUANINE QUADRUPLEX; PROSTATE CANCER ANTIGEN 3, HUMAN; TUMOR ANTIGEN;

ALTERNATIVE RNA SPLICING; COLORIMETRY; GENETIC TRANSCRIPTION; GENETICS; HUMAN;

ALTERNATIVE SPLICING; ANTIGENS, NEOPLASM; COLORIMETRY; DNA, COMPLEMENTARY; G-QUADRUPLEXES; HUMANS; TRANSCRIPTION, GENETIC;

EID: 84970021799     PISSN: 00399140     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.talanta.2016.05.039     Document Type: Article

References (37)

1. D.L. Black Mechanisms of alternative pre-messenger RNA splicing Annu. Rev. Biochem. 1 2003 291
2. R.I. Skotheim, and M. Nees Alternative splicing in cancer: noise, functional, or systematic? Int. J. Biochem. Cell Biol. 7-8 2007 1432
3. J.D. Fackenthal, and L.A. Godley Aberrant RNA splicing and its functional consequences in cancer cells Dis. Model Mech. 1 2008 37
4. Y.M. Wu, S.S. Kung, and W.Y. Chow Determination of relative abundance of splicing variants of Oreochromis glutamate receptors by quantitative reverse-transcriptase PCR FEBS Lett. 2 1996 157
5. M. Karaglani, I. Toumpoulis, N. Goutas, N. Poumpouridou, D. Vlachodimitropoulos, S. Vasilaros, I. Rizos, and C. Kroupis Development of novel real-time PCR methodology for quantification of COL11A1 mRNA variants and evaluation in breast cancer tissue specimens BMC Cancer 1 2015
6. Y. Xing, P. Stoilov, K. Kapur, A. Han, H. Jiang, S. Shen, D.L. Black, and W.H. Wong MADS: a new and improved method for analysis of differential alternative splicing by exon-tiling microarrays RNA 8 2008 1470
7. K. Lee, Y. Cui, L.P. Lee, and J. Irudayaraj Quantitative imaging of single mRNA splice variants in living cells Nat. Nanotechnol. 6 2014 474
8. C.S. Huertas, L.G. Carrascosa, S. Bonnal, J. Valcárcel, and L.M. Lechuga Quantitative evaluation of alternatively spliced mRNA isoforms by label-free real-time plasmonic sensing Biosens. Bioelectron. 2016 118
9. M. Krawczak, J. Reiss, and D.N. Cooper The mutational spectrum of single base-pair substitutions in mRNA splice junctions of human genes: causes and consequences Hum. Genet. 1-2 1992 41
10. Y. von Kodolitsch, C.A. Nienaber, M. Fliegner, and P.K. Rogan Splice site mutations and atherosclerosis: mechanisms and prediction models Z. Kardiol. 2 2001 87
11. Q. Zhang, F. Chen, F. Xu, Y. Zhao, and C. Fan Target-triggered three-way junction structure and polymerase/nicking enzyme synergetic isothermal quadratic dna machine for highly specific, one-step, and rapid microRNA detection at attomolar level Anal. Chem. 16 2014 8098
12. Y. Zhao, L. Qi, F. Chen, Y. Zhao, and C. Fan Highly sensitive detection of telomerase activity in tumor cells by cascade isothermal signal amplification based on three-way junction and base-stacking hybridization Biosens. Bioelectron. 2013 764
13. S. Tang, P. Tong, H. Li, F. Gu, and L. Zhang The three-way junction DNAzyme based probe for label-free colorimetric detection of DNA Biosens. Bioelectron. 2013 397
14. R. Yuan, S. Ding, Y. Yan, Y. Zhang, Y. Zhang, and W. Cheng A facile and pragmatic electrochemical biosensing strategy for ultrasensitive detection of DNA in real sample based on defective T junction induced transcription amplification Biosens. Bioelectron. 2016 19
15. M. Labib, S.M. Ghobadloo, N. Khan, D.M. Kolpashchikov, and M.V. Berezovski Four-way junction formation promoting ultrasensitive electrochemical detection of microRNA Anal. Chem. 20 2013 9422
16. X. Zhang, J. Zhang, D. Wu, Z. Liu, S. Cai, M. Chen, Y. Zhao, C. Li, H. Yang, and J. Chen Ultraselective electrochemiluminescence biosensor based on locked nucleic acid modified toehold-mediated strand displacement reaction and junction-probe Analyst 23 2014 6109
17. D.M. Kolpashchikov Binary probes for nucleic acid analysis Chem. Rev. 8 2010 4709
18. P. Travascio, Y. Li, and D. Sen DNA-enhanced peroxidase activity of a DNA-aptamer-hemin complex Chem. Biol. 9 1998 505
19. Y. Xiao, V. Pavlov, T. Niazov, A. Dishon, M. Kotler, and I. Willner Catalytic beacons for the detection of DNA and telomerase activity J. Am. Chem. Soc. 24 2004 7430
20. R. Freeman, X. Liu, and I. Willner Chemiluminescent and chemiluminescence resonance energy transfer (CRET) detection of DNA, metal ions, and aptamer-substrate complexes using hemin/G-quadruplexes and CdSe/ZnS quantum dots J. Am. Chem. Soc. 30 2011 11597
21. G. Pelossof, R. Tel-Vered, J. Elbaz, and I. Willner Amplified biosensing using the horseradish peroxidase-mimicking DNAzyme as an electrocatalyst Anal. Chem. 11 2010 4396
22. Z. Cheglakov, Y. Weizmann, B. Basnar, and I. Willner Diagnosing viruses by the rolling circle amplified synthesis of DNAzymes Org. Biomol. Chem. 2 2007 223
23. J. Chen, J. Zhang, Y. Guo, J. Li, F. Fu, H.H. Yang, and G. Chen An ultrasensitive electrochemical biosensor for detection of DNA species related to oral cancer based on nuclease-assisted target recycling and amplification of DNAzyme Chem. Commun. (Camb.) 28 2011 8004
24. J. Dong, X. Cui, Y. Deng, and Z. Tang Amplified detection of nucleic acid by G-quadruplex based hybridization chain reaction Biosens. Bioelectron. 1 2012 258
25. D.M. Kolpashchikov Split DNA enzyme for visual single nucleotide polymorphism typing J. Am. Chem. Soc. 10 2008 2934
26. H.Z. He, D.S. Chan, C.H. Leung, and D.L. Ma A highly selective G-quadruplex-based luminescent switch-on probe for the detection of gene deletion Chem. Commun. (Camb.) 76 2012 9462
27. L. Zhang, J. Zhu, T. Li, and E. Wang Bifunctional colorimetric oligonucleotide probe based on a G-Quadruplex DNAzyme molecular beacon Anal. Chem. 23 2011 8871
28. M. Deng, D. Zhang, Y. Zhou, and X. Zhou Highly effective colorimetric and visual detection of nucleic acids using an asymmetrically split peroxidase DNAzyme J. Am. Chem. Soc. 39 2008 13095
29. Y. Xiao, V. Pavlov, R. Gill, T. Bourenko, and I. Willner Lighting up biochemiluminescence by the surface self-assembly of DNA-Hemin complexes Chem. Biochem. 3 2004 374
30. M.J. Bussemakers, A. van Bokhoven, G.W. Verhaegh, F.P. Smit, H.F. Karthaus, J.A. Schalken, F.M. Debruyne, N. Ru, and W.B. Isaacs DD3: a new prostate-specific gene, highly overexpressed in prostate cancer Cancer Res. 23 1999 5975
31. Z. Tao, M. Shen, Y. Zheng, X. Mao, Z. Chen, Y. Yin, K. Yu, Z. Weng, H. Xie, C. Li, X. Wu, Y. Hu, X. Zhang, O. Wang, Q. Song, and Z. Yu PCA3 gene expression in prostate cancer tissue in a Chinese population: quantification by real-time FQ-RT-PCR based on exon 3 of PCA3 Exp. Mol. Pathol. 1 2010 58
32. R.D. Gray, J. Li, and J.B. Chaires Energetics and kinetics of a conformational switch in G-quadruplex DNA J. Phys. Chem. B 9 2009 2676
33. E.E. Merkina, and K.R. Fox Kinetic stability of intermolecular DNA quadruplexes Biophys. J. 1 2005 365
34. J. Kosman, and B. Juskowiak Peroxidase-mimicking DNAzymes for biosensing applications: a review Anal. Chim. Acta 1-2 2011 7
35. K. Nakatsuka, H. Shigeto, A. Kuroda, and H. Funabashi A split G-quadruplex-based DNA nano-tweezers structure as a signal-transducing molecule for the homogeneous detection of specific nucleic acids Biosens. Bioelectron. 2015 222
36. F. Mitelman, B. Johansson, and F. Mertens The impact of translocations and gene fusions on cancer causation Nat. Rev. Cancer 4 2007 233
37. P.A. Edwards Fusion genes and chromosome translocations in the common epithelial cancers J. Pathol. 2009 (n/a-n/a)