Allosteric aptamers controlling a signal amplification cascade allow visual detection of molecules at picomolar concentrations

Biochemistry

Volumn 45, Issue 7, 2006, Pages 2461-2466

  Chelyapov, Nickolas ^a,b  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b California Institute of Molecular Medicine   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ASSAYS; CATALYSTS; PHASE TRANSITIONS; POLYSTYRENES; RATE CONSTANTS; REACTION KINETICS; RNA;

MICROSPHERES (MS); RUSSELL'S VIPER VENOM FACTOR X ACTIVATOR (RVV-X); SIGNAL AMPLIFIER; VASCULAR ENDOTHELIAL GROWTH FACTOR (VEGF);

BIOCHEMISTRY;

APTAMER; FIBRIN; MICROSPHERE; POLYSTYRENE; PROTEIN TYROSINE PHOSPHATASE; RNA; RUSSELL VIPER VENOM FACTOR X ACTIVATOR; UNCLASSIFIED DRUG; VASCULOTROPIN; VIPER VENOM;

ALLOSTERISM; ARTICLE; BLOOD CLOTTING; CONCENTRATION (PARAMETERS); ENZYME ACTIVITY; ENZYME INHIBITION; EYE; FIBRIN CLOT; INFORMATION PROCESSING; INSTRUMENTATION; MOLECULE; PHASE TRANSITION; PRECIPITATION; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; VISIBILITY;

ALLOSTERIC REGULATION; APTAMERS, NUCLEOTIDE; BASE SEQUENCE; BLOOD COAGULATION; HUMANS; KINETICS; METALLOENDOPEPTIDASES; MICROSPHERES; MOLECULAR SEQUENCE DATA; NANOTECHNOLOGY; SIGNAL TRANSDUCTION; VASCULAR ENDOTHELIAL GROWTH FACTOR A;

VIPERINAE;

EID: 33144485619     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi052106i     Document Type: Article

References (30)

1. Osborne, S. E., Matsumura, I., and Ellington, A. D. (1997) Aptamers as therapeutic and diagnostic reagents: problems and prospects, Curr. Opin. Chem. Biol. 1, 5-9.
2. Jayasena, S. D. (1999) Aptamers: an emerging class of molecules that rival antibodies in diagnostics, Clin. Chem. 45, 1628-1650.
3. Brody, E. N., and Gold, L. (2000) Aptamers as therapeutic and diagnostic agents, Mol. Biotechnol. 74, 5-13.
4. Jhaveri, S. D., Kirby, R., Conrad, R., Maglott, E. J., Bowser, M., Kennedy, R. T., Glick, G., and Ellington, A. D. (2000) Designed signaling aptamers that transduce molecular recognition to changes in fluorescent intensity, J. Am. Chem. Soc. 122, 2469-2473.
5. Jhaveri, S., Rajendran, M., and Ellington, A. D. (2000) In vitro selection of signaling aptamers, Nat. Biotechnol. 18, 1293-1297.
6. Hamaguchi, N., Ellington, A., and Stanton, M. (2001) Aptamer beacons for direct detection of proteins, Anal. Biochem. 294, 126-131.
7. Silverman, S. K. (2003) Rube Goldberg goes (ribo)nuclear? Molecular switches and sensors made of RNA, RNA 9, 377-383.
8. Stojanovic, M. N., and Kolpashchikov, D. M. (2004) Modular aptameric sensors, J. Am. Chem. Soc. 126, 9266-9270.
9. Wang, X.-L., Li, F., Su, Y.-H., Sun, X, Li, X.-B., Schluesener, H. J., Tang, F., and Xu, S.-Q. (2004) Ultrasensitive detection of protein using an aptamer-based exonuclease protection assay, Anal. Chem. 76, 5605-5610.
10. Tombelli, S., Minunni, M., and Mascini, M. (2005) Analytical applications of aptamers, Biosens. Bioelectron. 20, 2424-2434.
11. Soukup, G. A. (2004) Aptamers meet allostery, Chem. Biol. 11, 1031-1032.
12. Wu, L., and Curran, J. F. (1999) An allosteric synthetic DNA, Nucleic Acid Res. 27, 1512-1516.
13. Vuyisich, M., and Beal, P. A. (2002) Controlling protein activity with ligand- regulated RNA aptamers, Chem. Biol. 9, 907-913.
14. Buskirk, A. R., Landrigan, A., and Liu, D. R. (2004) Engineering a ligand-dependent RNA transcriptional activator, Chem. Biol. 11, 1157-1163.
15. Nutiu, R., and Li, Y. (2004) Structure-switching signaling aptamers: transducing molecular recognition into fluorescence signaling, Chem.-Eur. J. 10, 1868-1876.
16. Cong, X., and Nielsen-Hamilton, M. (2005) Allosteric aptamers: targeted reversibly attenuated probes, Biochemistry 44, 7945-7954.
17. Fitzwater, T., and Polisky, B. (1996) A SELEX primer, Methods Enzymol. 267, 275-301.
18. Pollard, J., Bell, S. D., and Ellington, A. D. (2000) Design, synthesis, and amplification of DNA pools for in vitro selection, in Current Protocols in Nucleic Add Chemistry, pp 9.2.1-9.2-23, Wiley, New York.
19. Jhaveri, S. D, and Ellington, A. D. (2000) In vitro selection of RNA aptamers to a protein target by filter immobilization, in Current Protocols in Nucleic Acid Chemistry, pp 9.3.1-9.3.25, Wiley, New York.
20. Cox, J. C., Hayhurst, A., Hesselberth, J., Bayer, T. S., Georgiou, G., and Ellington, A. D. (2002) Automated selection of aptamers against protein targets translated in vitro: from gene to aptamer, Nucleic Acid Res. 30, e108, 1-14.
21. Jelinek, D., Green, L. S., Bell, C., and Janjic, N. (1994) Inhibition of receptor binding by high-affinity RNA ligands to vascular endothelial growth factor, Biochemistry 33, 10450-10456.
22. 165), J. Biol. Chem. 273, 20556-20567.
23. Dirks, R. M., and Pierce, N. A. (2003) A partition function algorithm for nucleic acid secondary structure including pseudoknots, J. Comput. Chem. 24, 1664-1677.
24. Dirks, R. M., and Pierce, N. A (2004) An algorithm for computing nucleic acid base pairing probabilities including pseudoknots, J. Comput. Chem. 25, 1295-1304.
25. Han, K., and Byun, Y. (2003) PseudoViewer2: visualization of RNA pseudoknots of any type. Nucleic Acid Res. 31, 3432-3440.
26. Strachan, N. J. C., and Ogden, I. D. (2000) A sensitive microsphere coagulation ELISA for Escherichia coli O157:H7 using Russell's viper venom, FEMS Microbiol. Lett. 186, 79-84.
27. Gowda, D. C., Jackson, C. M., Hensley, P., and Davidson, E. A. (1994) Factor X activating glycoprotein of Russell's viper venom. Polypeptide composition and characterization of the carbohydrate moieties, J. Biol. Chem. 269, 10644-10650.
28. Doellgast, G. J., Triscott, M. X., Beard, G. A., Bottoms, J. D., Cheng, T., Roh, B. H., Roman, M. G., Hall, P. A., and Brown, J. E. (1993) Sensitive enzyme-linked immunosorbent assay for detection of Clostridium botulinum neurotoxins A, B, and E using signal amplification via enzyme-linked coagulation assay, J. Clin. Microbiol. 31, 2402-2409.
29. Fish, G., Haller, J. A., Ho, A. C., Klein, M., Loewenstein, J., Martin, D., Orth, D., Rosen, R. B., Sanislo, S., Schwartz, S. D., et al. (2003) Anti-vascular endothelial growth factor therapy for subfoveal choroidal neovascularization secondary to age related macular degeneration. Phase II study results, Ophthalmology 110, 979-986.
30. Dell, S. D., Denu, J. M., Dixon, J. E., and Ellington, A. D. (1998) RNA molecules that bind to and inhibit the active site of tyrosine phosphatase, J. Biol. Chem. 273, 14309-14314.