DNA-encoded signal conversion for sensitive microgravimetric detection of small molecule-protein interaction

Bioconjugate Chemistry

Volumn 22, Issue 12, 2011, Pages 2369-2376

  Fei, Yue Hua ^a   Liu, Dengyou ^b   Wu, Zai Sheng ^a   Shen, Guo Li ^a   Yu, Ru Qin ^a  

^a HUNAN UNIVERSITY   (China)

^b HUNAN AGRICULTURAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEINS;

ABSCISIC ACID; CENTRAL PROBLEMS; ENCODED SIGNALS; INDOLEACETIC ACID; PROOF OF PRINCIPLES; PROTEIN INTERACTION; SIGNAL CONVERSION; SMALL MOLECULES; SMALL ORGANIC MOLECULES; SMALL TARGETS;

DNA;

2,4 DICHLOROPHENOXYACETIC ACID; ABSCISIC ACID; INDOLEACETIC ACID;

ANTIGEN BINDING; ARTICLE; DNA DETERMINATION; DNA PROBE; DNA SEQUENCE; GRAVIMETRY; LIMIT OF DETECTION; NUCLEIC ACID AMPLIFICATION; POLYMERASE CHAIN REACTION; PROTEIN INTERACTION; QUARTZ CRYSTAL MICROBALANCE; SIGNAL TRANSDUCTION;

EID: 84555195096     PISSN: 10431802     EISSN: 15204812     Source Type: Journal    
DOI: 10.1021/bc200086c     Document Type: Article

References (39)

1. Tagliaro, F., Antonioli, C., De Battisti, Z., Ghielmi, S., and Marigo, M. (1994) Reversed-phase high-performance liquid chromatographic determination of cocaine in plasma and human hair with direct fluorimetric detection J. Chromatogr, A. 674 (1-2) 207-215 (Pubitemid 24244776)
2. Trachta, G., Schwarze, B., Saegmuller, B., Brehm, G., and Schneider, S. (2004) Combination of high-performance liquid chromatography and SERS detection applied to the analysis of drugs in human blood and urine. J. Mol. Struct. 693 (1-3) 175-185 (Pubitemid 38510460)
3. Buryakov, I. A. (2004) Express analysis of explosives, chemical warfare agents and drugs with multicapillary column gas chromatography and ion mobility increment spectrometry. J. Chromatogr., B 800 (1-2) 75-82 (Pubitemid 38041009)
4. Strano-Rossi, S., Molaioni, F., Rossi, F., and Botre, F. (2005) Rapid screening of drugs of abuse and their metabolites by gas chromatography/mass spectrometry: application to urinalysis Rapid Commun. Mass Spectrom. 19 (11) 1529-1535 (Pubitemid 40801996)
5. Baker, B. R., Lai, R. Y., Wood, M. S., Doctor, E. H., Heeger, A. J., and Plaxco, K. W. (2006) An electronic, aptamer-based small-molecule sensor for the rapid, label-free detection of cocaine in adulterated samples and biological fluids J. Am. Chem. Soc. 128, 3138-3139
6. Wu, Z., Zhen, Z., Jiang, J.-H., Shen, G.-L., and Yu, R.-Q. (2009) Terminal protection of small-molecule-linked DNA for sensitive electrochemical detection of protein binding via selective carbon nanotube assembly J. Am. Chem. Soc. 131, 12325-12332
7. Huh, Y. S., Lowe, A. J., Strickland, A. D., Batt, C. A., and Erickson, D. (2009) Surface-enhanced raman scattering based ligase detection reaction J. Am. Chem. Soc. 131, 2208-2213
8. Hill, H. D. and Mirkin, C. A. (2006) The bio-barcode assay for the detection of protein and nucleic acid targets using DTT-induced ligand exchange Nat. Protoc. 1, 324-336
9. Huang, Y., Zhang, Y. L., Xu, X. M., Jiang, J. H., Shen, G. L., and Yu, R. Q. (2009) Highly specific and sensitive electrochemical genotyping via gap ligation reaction and surface hybridization detection J. Am. Chem. Soc. 131, 2478-2480
10. Schweitzer, B. and Kingsmore, S. (2001) Combining nucleic acid amplification and detection Curr. Opin. Biotechnol. 12, 21-27 (Pubitemid 32843139)
11. Xu, X. Y., Georganopoulou, D. G., Hill, H. D., and Mirkin, C. A. (2007) Homogeneous detection of nucleic acids based upon the light scattering properties of silver-coated nanoparticle probes Anal. Chem. 79, 6650-6654 (Pubitemid 47395050)
12. Mannocci, L., Zhang, Y., Scheuermann, J., Leimbacher, M., De Bellis, G., Rizzi, E., Dumelin, C., Melkko, S., and Neri, D. (2008) High-throughput sequencing allows the identification of binding molecules isolated from DNA-encoded chemical libraries Proc. Natl. Acad. Sci. U.S.A. 105 (46) 17670-17675
13. Stojanovic, M. N., Prada, P., and Landry, D. W. (2001) Aptamer-based folding fluorescent sensor for cocaine J. Am. Chem. Soc. 123, 4928-4931 (Pubitemid 32905648)
14. Stojanovic, M. N., Prada, P., and Landry, D. W. (2000) Fluorescent sensors based on aptamer self-assembly J. Am. Chem. Soc. 122, 11547-11548
15. He, J. L., Wu, Z. S., Zhou, H., Wang, H. Q., Jiang, J. H., Shen, G. L., and Yu, R. Q. (2010) Fluorescence aptameric sensor for strand displacement amplification detection of cocaine Anal. Chem. 82, 1358-1364
16. Wu, Z. S., Guo, M. M., Zhang, S. B., Chen, C. R., Jiang, J. H., Shen, G. L., and Yu, R. Q. (2007) Reusable electrochemical sensing platform for highly sensitive detection of small molecules based on structure-switching signaling aptamers Anal. Chem. 79, 2933-2939
17. Zuo, X., Xiao, Y., and Plaxco, K. W. (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, 6944-6945
18. Melkko, S., Scheuermann, J., Dumelin, C. E., and Neri, D. (2004) Encoded self-assembling chemical libraries Nat. Biotechnol. 22, 568-574 (Pubitemid 38585909)
19. Zhang, S., Metelev, V., Tabatadze, D., Zamecnik, P. C., and Bogdanov, A., Jr. (2008) Fluorescence resonance energy transfer in near-infrared fluorescent oligonucleotide probes for detecting protein-DNA interactions Proc. Natl. Acad. Sci. U.S.A. 105, 4156-4161 (Pubitemid 351754350)
20. Zhu, C. F., Wen, Y. Q., Li, D., Wang, L. H., Song, S. P., Fan, C. H., and Willner, I. (2009) Inhibition of the in vitro replication of DNA by an aptamer-protein complex in an autonomous DNA machine Chem. - Eur. J. 15, 11898-11903
21. Kobayashi, N., Iwakami, K., Kotoshiba, S., Niwa, T., Kato, Y., Mano, N., and Goto, J. (2006) Immunoenzymometric assay for a small molecule,11- deoxycortisol, with attomole-range sensitivity employing an scFv-enzyme fusion protein and anti-idiotype antibodies Anal. Chem. 78, 2244-2253
22. Jiao, C. X., Niu, C. G., Chen, L. X., Shen, G. L., and Yu, R. Q. (2003) 4-Allyloxy-7-aminocoumarin as a fluorescent carrier for optical sensor preparation and indole-3-acetic acid assay Sens. Actuators, B 94, 176-183
23. Li, J., Xiao, L. T., Zeng, G. M., Huang, G. H., Shen, G. L., and Yu, R. Q. (2003) A renewable amperometric immunosensor for phytohormone β-indole acetic acid assay Anal. Chim. Acta 494, 177-185 (Pubitemid 37203365)
24. González-Techera, A., Vanrell, L., Last, J. A., Hammock, B. D., and González-Sapienza, G. (2007) Phage anti-immune complex assay: general strategy for noncompetitive immunodetection of small molecules Anal. Chem. 79, 7799-7806 (Pubitemid 47622410)
25. Nutiu, R. and Li, Y. (2003) Structure-switching signaling aptamers J. Am. Chem. Soc. 125, 4771-4778 (Pubitemid 36505368)
26. Zuo, X., Song, S., Zhang, J., Pan, D., Wang, L., and Fan, C. (2007) A target-responsive electrochemical aptamer switch (TREAS) for reagentless detection of nanomolar ATP J. Am. Chem. Soc. 129, 1042-1043 (Pubitemid 46208568)
27. Zhang, S. B., Hu, R., Hu, P., Wu, Z. S., Shen, G. L., and Yu, R. Q. (2010) Blank peak current-suppressed electrochemical aptameric sensing platform for highly sensitive signal-on detection of small molecule Nucleic Acids Res. 38, e185
28. Fahlman, R. P. and Sen, D. (2002) DNA conformational switches as sensitive electronic sensors of analytes J. Am. Chem. Soc. 124, 4610-4616 (Pubitemid 34464999)
29. Jin, X. F., Jin, X. Y., Liu, X. P., Chen, L. G., Jiang, J. H., Shen, G. L., and Yu, R. Q. (2009) Biocatalyzed deposition amplification for detection of aflatoxin B1 based on quartz crystal microbalance Anal. Chim. Acta 645, 92-97
30. Sano, T., Smith, C. L., and Cantor, C. R. (1992) Immuno-PCR: very sensitive antigen detection by means of specific antibody-DNA conjugates Science 258, 120-122
31. Ruzicka, V., Marz, W., Russ, A., and Gross, W. (1993) Immuno-PCR with a commercially available avidin system Science 260, 698-699 (Pubitemid 23167597)
32. Javaherian, S., Musheev, M. U., Kanoatov, M., Berezovski, M. V., and Krylov, S. N. (2009) Selection of aptamers for a protein target in cell lysate and their application to protein purification Nucleic Acids Res. 37, e62
33. Gullberg, M., Gú stafsdó ttir, S. M., Schallmeiner, E., Jarvius, J., Bjarnegård, M., Betsholtz, C., Landegren, U., and Fredriksson, S. (2004) Cytokine detection by antibody-based proximity ligation Proc. Natl. Acad. Sci. U.S.A. 101, 8420-8424 (Pubitemid 38736590)
34. Schweitzer, B., Wiltshire, S., Lambert, J., OMalley, S., Kukanskis, K., Zhu, Z., Kingsmore, S. F., Lizardi, P. M., and Ward, D. C. (2000) Immunoassays with rolling circle DNA amplification: a versatile platform for ultrasensitive antigen detection Proc. Natl. Acad. Sci. U.S.A. 97, 10113-10119
35. Schweitzer, B., Roberts, S., Grimwade, B., Shao, W., Wang, M., Fu, Q., Shu, Q., Laroche, I., Zhou, Z., Tchernev, V. T., Christiansen, J., Velleca, M., and Kingsmore, S. F. (2002) Multiplexed protein profiling on microarrays by rolling-circle amplification Nat. Biotechnol. 20, 359-365 (Pubitemid 34288474)
36. Nam, J. M., Thaxton, C. S., and Mirkin, C. A. (2003) Nanoparticle-based bio-bar codes for the ultrasensitive detection of proteins Science 301, 1884-1886 (Pubitemid 37221389)
37. Fredriksson, S., Gullberg, M., Jarvius, J., Olsson, C., Pietras, K., Gú stafsdo ́ ttir, S. M., östman, A., and Landegren, U. (2002) Protein detection using proximity-dependent DNA ligation assays Nat. Biotechnol. 20, 473-477 (Pubitemid 34495933)
38. Di Giusto, D. A., Wlassoff, W. A., Gooding, J. J., Messerle, B. A., and King, G. C. (2005) Proximity extension of circular DNA aptamers with real-time protein detection Nucleic Acids Res. 33, e64
39. Zhou, L., Ou, L. J., Chu, X., Shen, G. L., and Yu, R. Q. (2007) Aptamer-based rolling circle amplification: a platform for electrochemical detection of protein Anal. Chem. 79, 7492-7500 (Pubitemid 47606117)