Determination of Transcription Nuclear Factor-Kappa B Using an Electrochemical, DNA-Based Nanoswitch

Analytical Letters

Volumn 47, Issue 16, 2014, Pages 2691-2698

  Liang, Zhiqiang ^a   Duan, Aiping ^b   Li, Xiaoxi ^b   Liu, Fengzhen ^c   Liu, Li ^a   Wang, Keming ^c   Liu, Xinjian ^b  

^a First People Hospital of Jining   (China)

^b NANJING UNIVERSITY   (China)

^c THE SECOND AFFILIATED HOSPITAL OF NANJING MEDICAL UNIVERSITY   (China)

Author keywords

Biosensor; DNA nanostructure; Electrochemical; Transcription factor

Indexed keywords

EID: 84907573428     PISSN: 00032719     EISSN: 1532236X     Source Type: Journal    
DOI: 10.1080/00032719.2014.921821     Document Type: Article

References (38)

1. Awwad , Y. , T. Geng , A. S. Baldwin , and C. Lu . 2012 . Observing single cell NF-kappa B dynamics under stimulant concentration gradient . Anal. Chem. 84 (3): 1224 – 1228 .
2. Bonham , A. J. , K. Hsieh , B. S. Ferguson , A. Vallee-Belisle , F. Ricci , H. T. Soh , and K. W. Plaxco . 2012 . Quantification of transcription factor binding in cell extracts using an electrochemical, structure-switching biosensor . J. Am. Chem. Soc. 134 (7): 3346 – 3348 .
3. Cash , K. J., A. J. Heeger, K. W. Plaxco, and Y. Xiao. 2009. Optimization of a reusable, DNA pseudoknot-based electrochemical sensor for sequence-specific DNA detection in blood serum. Anal. Chem.81(2): 656–661.
4. Crawford , R. , K. Lymperopoulos , J. P. Torella , M. Heilemann , L. C. Hwang , S. J. Holden , and A. Kapanidis . 2010 . Single-molecule DNA biosensors for quantitative transcription factor detection . Biophys. J. 98 (3): 611a – 611a .
5. Fan , C. H. , K. W. Plaxco , and A. J. Heeger . 2003 . Electrochemical interrogation of conformational changes as a reagentless method for the sequence-specific detection of DNA . Proc. Natl. Acad. Sci. USA. 100 (16): 9134 – 9137 .
6. Fan , C. H. , K. W. Plaxco , and A. J. Heeger . 2005 . Biosensors based on binding-modulated donor-acceptor distances . Trends. Biotechnol. 23 (4): 186 – 192 .
7. Fried , M. , and D. M. Crothers . 1981 . Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide-gel electrophoresis . Nucleic. Acids. Res. 9 (23): 6505 – 6525 .
8. Galas , D. J. , and A. Schmitz . 1978 . Dnaase footprinting - Simple method for detection of protein-DNA binding specificity . Nucleic. Acids. Res. 5 (9): 3157 – 3170 .
9. Garner , M. M. , and A. Revzin . 1981 . A gel-electrophoresis method for quantifying the binding of proteins to specific DNA regions - Application to components of the escherichia-coli lactose operon regulatory system . Nucleic Acids Res. 9 (13): 3047 – 3060 .
10. Govan , J. M. , M. O. Lively , and A. Deiters . 2011 . Photochemical control of DNA decoy function enables precise regulation of nuclear factor kappa B activity . J. Am. Chem. Soc. 133 (33): 13176 – 13182 .
11. Gupta , S. V. , R. M. McGowen , D. M. Callewaert , T. R. Brown , Y. Li , and F. H. Sarkar . 2005 . Quantitative chemiluminescent immunoassay for NF-kappaB-DNA binding activity . J. Immunoassay. Immunochem. 26 (2): 125 – 143 .
12. Harari , O. A. , and J. K. Liao . 2010 . NF-kappa B and innate immunity in ischemic stroke . Innate. Inflamm. Stroke. 1207 : 32 – 40 .
13. Hayden , M. S. , and S. Ghosh . 2012 . NF-kappa B, the first quarter-century: Remarkable progress and outstanding questions . Genes Develop. 26 (3): 203 – 234 .
14. Hecht , A. H. , G. J. Sommer , R. H. Durland , X. B. Yang , A. K. Singh , and A. V. Hatch . 2010 . Aptamers as affinity reagents in an integrated electrophoretic lab-on-a-chip platform . Anal. Chem. 82 (21): 8813 – 8820 .
15. Huber , F. , M. Hegner , C. Gerber , H. J. Guntherodt , and H. P. Lang . 2006 . Label free analysis of transcription factors using microcantilever arrays . Biosens. Bioelectron. 21 (8): 1599 – 1605 .
16. Jolma , A. , J. Yan , T. Whitington , J. Toivonen , K. R. Nitta , P. Rastas , . 2013 . DNA-binding specificities of human transcription factors . Cell 152 (1–2): 327 – 339 .
17. Kang , D. , R. J. White , F. Xia , X. L. Zuo , A. Vallee-Belisle , and K. W. Plaxco . 2012 . DNA biomolecular-electronic encoder and decoder devices constructed by multiplex biosensors . Npg Asia Mater. 4 .
18. Kang , D. , X. L. Zuo , R. Q. Yang , F. Xia , K. W. Plaxco , and R. J. White . 2009 . Comparing the properties of electrochemical-based DNA sensors employing different redox tags . Anal. Chem. 81 (21): 9109 – 9113 .
19. Li , D. , S. P. Song , and C. H. Fan . 2010 . Target-responsive structural switching for nucleic acid-based sensors . Acc. Chem. Res. 43 (5): 631 – 641 .
20. Liu , G. , Y. Wan , V. Gau , J. Zhang , L. H. Wang , S. P. Song , and C. H. Fan . 2008 . An enzyme-based E-DNA sensor for sequence-specific detection of femtomolar DNA targets . J. Am. Chem. Soc. 130 (21): 6820 – 6825 .
21. Pei , H. , N. Lu , Y. L. Wen , S. P. Song , Y. Liu , H. Yan , and C. H. Fan . 2010 . A DNA nanostructure-based biomolecular probe carrier platform for electrochemical biosensing . Adv. Mater. 22 (42): 4754 .
22. Smith , E. A., M. G. Erickson, A. T. Ulijasz, B. Weisblum, and R. M. Corn. 2003. Surface plasmon resonance imaging of transcription factor proteins: Interactions of bacterial response regulators with DNA arrays on gold films. Langmuir19(5): 1486–1492.
23. Swensen , J. S. , Y. Xiao , B. S. Ferguson , A. A. Lubin , R. Y. Lai , A. J. Heeger , K. W. Plaxco , and H. T. Soh . 2009 . Continuous, real-time monitoring of cocaine in undiluted blood serum via a microfluidic, electrochemical aptamer-based sensor . J. Am. Chem. Soc. 131 (12): 4262 – 4266 .
24. Vallee-Belisle , A. , A. J. Bonham , N. O. Reich , F. Ricci , and K. W. Plaxco . 2011 . Transcription factor beacons for the quantitative detection of DNA binding activity . J. Am. Chem. Soc. 133 (35): 13836 – 13839 .
25. Wen , Y. L. , H. Pei , Y. Shen , J. J. Xi , M. H. Lin , N. Lu , X. Z. Shen , J. Li , and C. H. Fan . 2012 . DNA nanostructure-based interfacial engineering for PCR-free ultrasensitive electrochemical analysis of microRNA . Sci. Rep. 2 .
26. Wen , Y. L. , H. Pei , Y. Wan , Y. Su , Q. Huang , S. P. Song , and C. H. Fan . 2011 . DNA nanostructure-decorated surfaces for enhanced aptamer-target binding and electrochemical cocaine sensors . Anal. Chem. 83 (19): 7418 – 7423 .
27. Xia , F. , R. J. White , X. L. Zuo , A. Patterson , Y. Xiao , D. Kang , X. Gong , K. W. Plaxco , and A. J. Heeger . 2010 . An electrochemical super sandwich assay for sensitive and selective DNA detection in complex matrices . J. Am. Chem. Soc. 132 (41): 14346 – 14348 .
28. Xiao , Y. , A. A. Lubin , B. R. Baker , K. W. Plaxco , and A. J. Heeger . 2006 . Single-step electronic detection of femtomolar DNA by target-induced strand displacement in an electrode-bound duplex . Proc. Natl. Acad. Sci. USA. 103 (45): 16677 – 16680 .
29. Xiao , Y. , A. A. Lubin , A. J. Heeger , and K. W. Plaxco . 2005 . Label-free electronic detection of thrombin in blood serum by using an aptamer-based sensor . Angew. Chem. Int. Ed. 44 (34): 5456 – 5459 .
30. Xiao , Y. , B. D. Piorek , K. W. Plaxco , and A. J. Heeger . 2005 . A reagentless signal-on architecture for electronic, aptamer-based sensors via target-induced strand displacement . J. Am. Chem. Soc. 127 (51): 17990 – 17991 .
31. Xiao , Y. , X. G. Qu , K. W. Plaxco , and A. J. Heeger . 2007 . Label-free electrochemical detection of DNA in blood serum via target-induced resolution of an electrode-bound DNA pseudoknot . J. Am. Chem. Soc. 129 (39): 11896 .
32. Xiao , Y. , A. A. Rowe , K. W. Plaxco , and A. J. Heeger . 2007 . Electrochemical detection of parts per billion lead via an electrode-bound DNAzyme assembly . J. Am. Chem. Soc. 233 : 449 – 449 .
33. Yan , J. , M. Enge , T. Whitington , K. Dave , J. P. Liu , I. Sur , . 2013 . Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites . Cell 154 (4): 801 – 813 .
34. Zhang , J. , S. P. Song , L. Y. Zhang , L. H. Wang , H. P. Wu , D. Pan , and C. H. Fan . 2006 . Sequence-specific detection of femtomolar DNA via a chronocoulometric DNA sensor (CDS): Effects of nanoparticle-mediated amplification and nanoscale control of DNA assembly at electrodes . J. Am. Chem. Soc. 128 (26): 8575 – 8580 .
35. Zhang , S. , V. Metelev , D. Tabatadze , P. C. Zamecnik , and A. Bogdanov . 2008 . Fluorescence resonance energy transfer in near-infrared fluorescent oligonucleoticle probes for detecting protein-DNA interactions . Proc. Natl. Acad. Sci. U. S. A. 105 (11): 4156 – 4161 .
36. Zhang , Y. , J. Hu , and C. Y. Zhang . 2012 . Sensitive detection of transcription factors by isothermal exponential amplification-based colorimetric assay . Anal. Chem. 84 (21): 9544 – 9549 .
37. Zuo , X. L. , S. P. Song , J. Zhang , D. Pan , L. H. Wang , and C. H. Fan . 2007 . A target-responsive electrochemical aptamer switch (TREAS) for reagentless detection of nanomolar ATP . J. Am. Chem. Soc. 129 (5): 1042 – 1043 .
38. Zuo , X. L. , Y. Xiao , and K. W. Plaxco . 2009 . High specificity, electrochemical sandwich assays based on single aptamer sequences and suitable for the direct detection of small-molecule targets in blood and other complex matrices . J. Am. Chem. Soc. 131 (20): 6944 – 6945 .