Aptamers biosensors for pharmaceutical compounds

Combinatorial Chemistry and High Throughput Screening

Volumn 13, Issue 7, 2010, Pages 641-649

  Tombelli, Sara ^a   Mascini, Marco ^a,b  

^a UNIVERSITY OF FLORENCE   (Italy)

^b NATIONAL INSTITUTE OF BIOSTRUCTURES AND BIOSYSTEMS   (Italy)

Author keywords

Aptamers; Biosensors; Cholic acid; Cocaine; Codeine; Neomycin B; Oxytetracycline

Indexed keywords

4,4' METHYLENEDIANILINE; ADENOSINE; ANTINEOPLASTIC AGENT; ANTITHROMBIN; APTAMER; ARC 183; ARGININE; AS 1411; BIOTIN; CHENODEOXYCHOLIC ACID; CHOLIC ACID; COCAINE; CODEINE; DOPAMINE; DOXYCYCLINE; FLAVINE MONONUCLEOTIDE; FRAMYCETIN; LITHOCHOLIC ACID; MOENOMYCIN A; MORPHINE; NEOMYCIN; OXYTETRACYCLINE; PEGAPTANIB; S ADENOSYLHOMOCYSTEINE; STREPTOMYCIN; TETRACYCLINE; THEBAINE; THEOPHYLLINE; TRENBOLONE; UNCLASSIFIED DRUG; UNINDEXED DRUG;

ADVANCED CANCER; BINDING COMPETITION; BIOSENSOR; CHEMOLUMINESCENCE; CLINICAL TRIAL; CONFORMATIONAL TRANSITION; CYCLIC POTENTIOMETRY; DNA LIBRARY; DNA SEQUENCE; DRUG DNA INTERACTION; DRUG STRUCTURE; ELECTRODE; HUMAN; INBORN ERROR OF METABOLISM; MOLECULAR INTERACTION; NUCLEOTIDE SEQUENCE; PAIN; POTENTIOMETRY; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; PROTEIN TARGETING; REVIEW; SEQUENCE ANALYSIS;

EID: 77955731511     PISSN: 13862073     EISSN: None     Source Type: Journal    
DOI: 10.2174/1386207311004070641     Document Type: Review

References (57)

1. Mayer, G. The chemical biology of aptamers. Angew. Chem. Int. Ed., 2009, 48, 2672-2689.
2. Ellington, A. D.; Szostak, J. W. In vitro selection of RNA molecules that bind specific ligands. Nature, 1990, 346, 818-822.
3. Tuerk, C.; Gold, L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science, 1990, 249, 505-510.
4. Pedergranst, P. S.; Epstein, D. M. The Aptamer Handbook, Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, 2006.
5. Burmeister, P. E.; Lewis, S. D.; Silva, R. F.; Preiss, J. R.; Horwitz, L. R. Direct in vitro selection of a 2'-O-methyl aptamer to VEGF. Chem. Biol., 2005, 12, 25-33.
6. Lee, J. F.; Stovall, G. M.; Ellington, D. A. Aptamer therapeutics advance. Curr. Opin. Chem. Biol., 2006, 10, 282-289.
7. Willis, M. C.; Collins, B. D.; Zhang, T.; Green, L. S.; Sebesta, D. P.; Bell, C.; Kellogg, E.; Gill, S. C.; Magallanez, A.; Knauer, S.; Bendele, R. A.; Gill, P. S.; Janjic, N. Liposome-anchored vascular endothelial growth factor aptamers. Bioconjug. Chem., 1998, 9, 573-582.
8. Ng, E. W.; Shima, D. T.; Calias, P.; Cunningham, E. T.; Guyer, D. R.; Adamis, A. P. Pegaptanib, a targeted anti-VEGF aptamer for ocular vascular disease. Nat. Rev. Drug Discov., 2006, 5, 123-132.
9. Levy-Nissenbaum, E.; Radovic-Moreno, A. F.; Wang, A. Z.; Langer, R.; Farokhzad, O. C. Nanotechnology and aptamers: applications in drug delivery. Trends Biotechnol., 2008, 26, 442-449.
10. Green, L. S.; Jellinek, D.; Jenison, R.; Ostman, A.; Heldin, C. H.; Janjic, N. Inhibitory DNA ligands to platelet-derived growth factor B-chain. Biochemistry, 1996, 35, 14413-14424.
11. Rusconi, C. P.; Roberts, J. D.; Pitoc, G. A.; Nimjee, S. M.; White, R. R. Antidote-mediated control of an anticoagulant aptamer in vivo. Nat. Biotechnol., 2004, 22, 1423-1428.
12. Willner, I.; Zayats, M. Electronic aptamer-based sensors. Angew. Chem. Int. Ed., 2007, 46, 6408-6418.
13. Song, S.; Wang, L.; Li, J.; Zhao, J.; Fan, C. Aptamer-based biosensors. Trends Analyt. Chem., 2008, 27, 108-117.
14. De-los-Santos-Alvarez, N.; Lobo-Castanon, M.; Miranda-Ordieres, A. J.; Tunon-Blanco, P. Aptamers as recognition elements for labelfree analytical devices. Trends Analyt. Chem., 2008, 27, 437-446.
15. Nguyen, T.; Hilton, J. P.; Lin, Q. Emerging applications of aptamers to micro-and nanoscale biosensing. Microfluid. Nanofluidics, 2009, 6, 347-362.
16. Sefah, K.; Phillips, J. A.; Xiong, X.; Meng, L.; Van Simaeys, D.; Chen, H.; Tan, W. Nucleic acid aptamers for biosensors and bioanalytical applications. Analyst, 2009, 134, 1765-1775.
17. Cheng, A. K. H.; Sen, D.; Yu, H.-Z. Design and testing of aptamerbased electrochemical biosensors for proteins and small molecules. Bioelectrochemistry, 2009, 77, 1-12.
18. Tombelli, S.; Mascini M. Aptamers as molecular tools for bioanalytical methods. Curr. Opin. Mol. Therap., 2009, 11, 179-188.
19. Klussmann, S., Ed. The aptamer Handbook, Wiley-VCH Verlag GmbH & Co. KGaA: Weinheim, 2006.
20. Mascini, M. Ed. Aptamers in bioanalysis, John Wiley & Sons, Inc.: Hoboken, New Jersey, 2008.
21. Deng, Q.; Watson, C. J.; Kennedy, R. T. Highly sensitive assay for the measurement of serotonin in microdialysates using capillary high-performance liquid chromatography with electrochemical detection. J. Chromat. A, 2003, 1005, 123-132.
22. Deng, Q.; German, I.; Buchanan, D. D.; Kennedy, R. T. Retention and separation of adenosine and analogues by affinity chromatography with an aptamer stationary phase. Anal. Chem., 2001, 73, 5415-5421.
23. Stojanovic, M. N.; Landry, D. W. Aptamer-based colorimetric probe for cocaine. J. Am. Chem. Soc., 2002, 124, 9678-9679.
24. Stojanovic, M. N.; de Prada, P.; Landry, D. W. Aptamer-based folding fluorescent sensor for cocaine. J. Am. Chem. Soc., 2001, 123, 4928-4931.
25. Brockstedt, U.; Uzarowska, A.; Montpetit, A.; Pfau, W.; Labuda, D. In vitro evolution of RNA aptamers recognizing carcinogenic aromatic amines. Biochem. Biophys. Res. Commun., 2004, 313, 1004-1008.
26. Jhaveri, S. D.; Kirby, R.; Conrad, R.; Maglott, E. J.; Bowser, M.; Kennedy, R. T.; Glick, G.; Ellington, A. D. Designed signaling aptamers that transduce molecular recognition to changes in fluorescence intensity. J. Am. Chem. Soc., 2000, 122, 2469-2473.
27. Wang, J.; Jiang, Y.; Zhou, C.; Fang, X. Aptamer Based ATP Assay Using a Luminescent Light Switching Complex. Anal. Chem., 2005, 77, 3542-3546.
28. Frauendorf, C.; Jaschke, A. Detection of small organic analytes by fluorescing molecular switches. Bioorg. Med. Chem., 2001, 9, 2521-2524.
29. Geiger, A.; Burgstaller, P.; Von der Eltz, H.; Roeder, A.; Famulok, M. RNA aptamers that bind L-arginine with sub-micromolar dissociation constants and high enantioselectivity. Nucleic Acids Res., 1996, 24, 1029-1036.
30. Harada, K.; Frankel, A. D. Identification of two novel arginine binding DNAs. EMBO J., 1995, 14, 5798-5811.
31. Wallis, M. G.; Von Ahsen, U.; Schroeder, R.; Famulok, M. A novel RNA motif for neomycin recognition. Chem. Biol., 1995, 2, 543-552.
32. Famulok, M.; Huttenhofer, A. In vitro selection analysis of neomycin binding RNAs with a mutagenized pool of variants of the 16S rRNA decoding region. Biochemistry, 1996, 35, 4265-4270.
33. Seetharaman, S.; Zivarts, M.; Sudarsan, N.; Breaker, R. R. Immobilized RNA switches for the analysis of complex chemical and biological mixtures. Nature Biotechnol., 2001, 19, 336-341.
34. Bachler, M.; Schroeder, R.; von Ahsen, U. StreptoTag: a novel method for the isolation of RNA-binding proteins. RNA, 1999 5, 1509-1516.
35. Berens, C.; Thain, A.; Schroeder, R. A tetracycline-binding RNA aptamer. Bioorg. Med. Chem., 2001, 9, 2549-2556.
36. Wilson, C.; Nix, J.; Szostak, J. W. Functional requirements for specific ligand recognition by a biotin-binding RNA pseudoknot. Biochemistry, 1998, 37, 14410-14419.
37. Schurer, H.; Stembera, K.; Knoll, D.; Mayer, G.; Blind, M.; Forster, H. H.; Famulok, M.; Welzel, P.; Hahn, U. Aptamers that bind to the antibiotic moenomycin A. Bioorg. Med. Chem., 2001, 9, 2557-2563.
38. Gebhardt, K.; Shokraei, A.; Babaie, E.; Lindqvist, B. H. RNA aptamers to S-adenosylhomocysteine: kinetic properties, divalent cation dependency, and comparison with anti-S-adenosylhomocysteine antibody. Biochemistry, 2000, 39, 7255-7265.
39. Niazi, J. H.; Lee, S. J.; Kim, Y. S.; Gu, M. B. ssDNA aptamers that selectively bind oxytetracycline. Bioorg. Med. Chem., 2008, 16, 1254-1261.
40. Win, M. N.; Klein, J. S.; Smolke, C. D. Codeine-binding RNA aptamers and rapid determination of their binding constants using a direct coupling surface plasmon resonance assay. Nucleic Acids Res., 2006, 34, 5670-5682.
41. Kato, T.; Takemura, T.; Yano, K.; Ikebukuro, K.; Karube, I. In vitro selection of DNA aptamers which bind to cholic acid. Biochim. Biophys. Acta., 2000, 1493, 12-18.
42. Mannironi, C.; Di Nardo, A.; Fruscoloni, P.; Tocchini-Valentini, G. P. In vitro selection of dopamine RNA ligands. Biochemistry, 1997, 36, 9726-9734.
43. Kato, T.; Yano, K.; Ikebukuro, K.; Karube, I. Bioassay of bile acids using an enzyme-linked DNA aptamer. Analyst, 2000, 125, 1371-1373.
44. Weber, C. C.; Link, N.; Fux, C.; Zisch, A. H.; Weber, W.; Fussenegger, M. Broad-spectrum protein biosensors for classspecific detection of antibiotics. Biotechnol. Bioeng., 2005, 89, 9-17.
45. Kim, Y. S.; Niazi, J. H.; Gu, M. B. Specific detection of oxytetracycline using DNA aptamer-immobilized interdigitated array electrode chip. Anal. Chim. Acta, 2009, 634, 250-254.
46. De-los-Santos-Alvarez, N.; Lobo-Castañon, M. J.; Miranda-Ordieres, A. J.; Tuñon-Blanco, P. Modified-RNA aptamer-based sensor for competitive impedimetric assay of neomycin B. J. Am. Chem. Soc., 2007, 129, 3808-3809.
47. Cowan, J. A.; Ohyama, T.; Wang, D. Q.; Natarajan, K. Recognition of a cognate RNA aptamer by neomycin B: quantitative evaluation of hydrogen bonding and electrostatic interactions. Nucleic Acids Res., 2000, 28, 2935-2942.
48. De-los-Santos-Alvarez, N.; Lobo-Castañon, M. J.; Miranda-Ordieres, A. J.; Tuñon-Blanco, P. SPR sensing of small molecules with modified RNA aptamers: detection of neomycin B. Biosens. Bioelectron., 2009, 24, 2547-2553.
49. Stojanovic, M. N.; de Prada, P.; Landry, D. W. Fluorescent sensors based on aptamer self-assembly. J. Am. Chem. Soc., 2000, 122, 11547-11548.
50. Baker, B. R.; Lai, R. Y.; Wood, M. S.; Doctor, E. H.; Heeger, A. J.; Plaxco, K. W. 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., 2006, 128, 3138-3139.
51. Lai, R. Y.; Plaxco, K. W.; Heeger, A. J. Aptamer-based electrochemical detection of picomolar platelet-derived growth factor directly in blood serum. Anal. Chem., 2007, 79, 229-233.
52. Golub, E.; Pelossof, G.; Freeman, R.; Zhang, H.; Willner, I. Electrochemical, photoelectrochemical, and surface plasmon resonance detection of cocaine using supramolecular aptamer complexes and metallic or semiconductor nanoparticles. Anal. Chem., 2009, 81, 9291-9298.
53. Sharon, E.; Freeman, R.; Tel-Vered, R.; Willner, I. Impedimetric or ion-sensitive field-effect transistor (ISFET)-aptasensors based on the self-assembly of Au nanoparticle-functionalized supramolecular aptamer nanostructures. Electroanalysis, 2009, 21, 1291-1296.
54. Zuo, X.; Xiao, Y.; Plaxco, K. W. 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., 2009, 131, 6944-6945.
55. Liu, J.; Mazumdar, D.; Lu, Y. A simple and sensitive "Dip Stick" test in serum based on lateral flow separation of aptamer-linked nanostructures. Angew. Chem. Int. Ed., 2006, 45, 7955-7959.
56. Li, Y.; Qi, H.; Peng, Y.; Yang, J.; Zhang, C. Electrogenerated chemiluminescence aptamer-based biosensor for the determination of cocaine. Electrochem. Commun., 2007, 9, 2571-2575.
57. Shlyahovsky, B.; Li, D.; Weizmann, Y.; Nowarski, R.; Kotler, M.; Willner, I. Spotlighting of cocaine by an autonomous aptamerbased machine. J. Am. Chem. Soc., 2007, 129, 3814-3815.