Analytical Applications of Aptamers

Marco Mascini

Analytical Applications of Aptamers

Abstract

Aptamers are single stranded DNA or RNA ligands which can be selected for different targets starting from a libraryof molecules containing randomly created sequences. Aptamers have been selected to bind very different targets,from proteins to small organic dyes. Aptamers are proposed as alternatives to antibodies as biorecognition elementsin analytical devices with ever increasing frequency. This in order to satisfy the demand for quick, cheap, simple andhighly reproducible analytical devices, especially for protein detection in the medical field or for the detection of smallermolecules in environmental and food analysis. In our recent experience, DNA and RNA aptamers, specific for threedifferent proteins Tat, IgE and thrombin , have been exploited as bio-recognition elements to develop specificbiosensors aptasensors . These recognition elements have been coupled to piezoelectric quartz crystals and surfaceplasmon resonance SPR devices as transducers where the aptamers have been immobilized on the gold surfaceof the crystals electrodes or on SPR chips, respectively

Keywords

aptamers,Biosensors,Thrombin,IgE,HIV TAT protein

References

1. W. James, Encyclopaedia of Analytical Chemistry, Mayers R.A. editor, 4848-4871 (2000).
2. A.D. Ellington, and J.W. Szostak, “In vitro selection of RNA molecules that bind specific ligands”, Nature 346, 818-822 (1990).
3. C. Tuerk, and L. Gold, “Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase”, Science 249, 505-510 (1990).
4. S. Jayasena, “An emerging class of molecules that rival antibodies in diagnostics”, Clin. Chem. 45, 1628-1650 (1999).
5. C.K. O’Sullivan, “Aptasensors-The future of biosensing?”, Anal. Bioanal. Chem. 372, 44-48 (2002).
6. E. Luzi, M. Minunni, S. Tombelli, M. Mascini, “New trends in affinity sensing: aptamers for ligand binding“, Trends in Anal. Chem. 22, 810- 818 (2003).
7. S. Tombelli, M. Minunni, M. Mascini, “Analytical applications of aptamers”, Biosens. & Bioelectron. 20, 2424- 2434 (2005).
8. S.L. Clark, V.T. Remcho, “Aptamers as analytical reagents“, Electrophoresis 23, 1335- 1340 (2002).

9. K.M. You, S.H. Lee, A. Im, S.B. Lee, “Aptamers as functional nucleic acids: in vitro selection and biotechnological applications“, Biotechnol. Bioprocess Eng. 8, 64-75 (2003).
10. M. Famulok, G. Mayer, M. Blind, “Nucleic acid aptamers – From selection in vitro to application in vivo”, Acc.Chem. Res. 33, 591- 599 (2000).
11. W. Pieken, D.B. Olsen, F. Benseler, H. Aurup, F. Eckstein, “Kinetic characterization of ribonuclease-resistant 2’-modified hammer head ribozymes”, Science 253, 314-317 (1991).
12. M. Michaud, E. Jourdan, C. Ravelet, A Villet, A. Ravel, C. Grosset, E: Peyrin, “Immobilized DNA aptamers as target-specific chiral stationary phases for resolution of nucleoside and amino acid derivative enantiomer”. Anal. Chem. 76, 1015-1020 (2004).
13. I. German, D.D. Buchanan, R.T. Kennedy, “Aptamers as ligands in affinity probe capillary electrophoresis” Anal. Chem. 70, 4540-4545 (1998).
14. R.B. Kotia, L. Li, L.B. McGown, “Separation of nontarget compounds by DNA aptamers”, Anal. Chem. 72, 827-831 (2000).
15. L.W. Dick and L.B. McGown, “Aptamerenhanced laser desorption/ionization for affinity mass spectrometry”, Anal. Chem. 76, 3037- 3041 (2004).
16. J.R. Cole, L.W. Dick, E.J. Morgan, L.B. McGown, “Affinity Capture and Detection of Immunoglobulin E in Human Serum Using an Aptamer-Modified Surface in Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry”, Anal. Chem. 79, 273-279 (2007).
17. L.C. Bock, L.C. Griffin, J.A. Latham, E.H. Vermaas, and J.J. Toole, “Selection of singlestranded DNA molecules that bind and inhibit human thrombin”, Nature 355, 564-566 (1992).
18. R. Yamamoto, M. Katahira, S. Nishikawa, T. Baba, K. Taira, P.K.R. Kumar, “A novel RNA motif that binds efficiently and specifically to the Ttat protein of HIV and inhibits the transactivation by Tat of transcription in vitro and in vivo“, Genes to Cells 5, 371-388 (2000
19. R. Yamamoto, and P.K.R. Kumar, “Mol).ecular beacon aptamer fluoresces in the presence of Tat protein of HIV- 1”, Genes to Cells 5, 389- 396 (2000).
20. E. Brys, S. Tombelli, M. Minunni, M. Mascini, A.P.F. Turner, “Approaches to allergy detection using aptasensors” Smart Biosensor Technology, CRC Press, 118, 539-565 (2006).
21. T.W. Wiegand, P.B. Williams, S.C. Dreskin, M.H. Jouvin, J.P. Kinet, D. Tasset, “High-affinity oligonucleotide ligands to human IgE inhibit binding to Fc epsilon receptor I”, J. Immunol. 157, 221-230 (1996).
22. M.A. Shuman and P.W. Majerus, “The measurement of thrombin in clotting blood by radioimmunoassay”, J. Clin. Invest. 58, 1249- 1258 (1976).
23. E. Baldrich, A. Restrepo, and C. K. O’Sullivan, “Aptasensor development: elucidation of critical parameters for optimal aptamer performance”, Anal. Chem. 76, 7053-7063 (2004).
24. T. Hianik, V. Ostatná, Z. Zajacová, E. Stoikova, and G. Evtugyn, “Detection of aptamer-protein interactions using QCM and electrochemical indicator methods”, Bioorganic & Medicinal Chemistry Letters 15, 291-295 (2005).
25. K. Ikebukuro, C. Kiyohara, and K. Sode, “Electrochemical sensing of protein using two aptamers in sandwich manner”, Biosensors & Bioelectronics 20, 2168-2172 (2005).
26. T.M.A. Gronewold, S. Glass, E. Quandt, and M. Famulok, “Monitoring complex formation in the bloodcoagulation cascade using aptamercoated SAW sensors”, Biosensors & Bioelectronics 20, 2044-2052 (2005).
27. R.F. Macaya, P. Schultze, F.W. Smith, J.A. Roe, and J. Feigon, “Thrombin-Binding DNA Aptamer Forms a Unimolecular Quadruplex Structure in Solution”, PNAS 90, 3745-3749 (1993).
28. L.R. Paborsky, S.N. McCurdy, L.C. Griffin, J.J. Toole, and L.L. Leung, “The single-stranded DNA aptamer binding site of human thrombin”, J. Biol. Chem. 268, 20808-20811 (1993).
29. S. Centi, S. Tombelli, M. Minunni, M. Mascini, “Aptamer-Based Detection of Plasma Proteins by an Electrochemical Assay Coupled to Magnetic Beads” Anal. Chem. 79, 1466-1473 (2007).
30. H.C. Chang, F. Samaniego, B.C. Nair, L. Buonaguro, B. Ensoli, “HIV-1 Tat protein exits from cells via a leaderless secretory pathway and binds to extracellular matrix-associated heparan sulfate proteoglycans through its basic region”, AIDS 11, 1421-1430 (1997).
31. P. Mucha, A. Szyk, P. Rekowski, J. Barciszewski, “Structural requirements for conserved Arg52 residue for interaction of the human immunodeficiency virus type 1 transactivation responsive element with trans-activator of transcription protein (49–57): Capillary electrophoresis mobility shift assay”, Journal of Chromatography A 968, 211- 220 (2002).
32. S. Tombelli, M. Mascini, A.P.F. Turner, “Improved procedures for immobilisation of oligonucleotides on goldcoated piezoelectric quartz crystals”, Biosensors & Bioelectronics, 17, 929-936 (2002).
33. R. Hamilton and N. Adkinson, “Clinical laboratory assessment of IgE-dependent hypersensitivity”, Journal of Allergy and Clinical Immunology 111, 687–701 (2003).
34. C.A. Holland, A.T. Henry, H.C. Whinna, and F.C. Church, “Effect of oligodeoxynucleotide thrombin aptamer on thrombin inhibition by heparin cofactor II and antithrombin”, FEBS Lett. 484, 87–91 (2000).

Details

Primary Language

English

Subjects

-

Journal Section

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Authors

Marco Mascini This is me

Publication Date

December 1, 2008

Submission Date

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Acceptance Date

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Published in Issue

Year 2008 Volume: 36 Number: 4

IZ

https://izlik.org/JA83NH44PS

Cite

RIS / Bibtex

APA

Mascini, M. (2008). Analytical Applications of Aptamers. Hacettepe Journal of Biology and Chemistry, 36(4), 273-282. https://izlik.org/JA83NH44PS

AMA

1.Mascini M. Analytical Applications of Aptamers. HJBC. 2008;36(4):273-282. https://izlik.org/JA83NH44PS

Chicago

Mascini, Marco. 2008. “Analytical Applications of Aptamers”. Hacettepe Journal of Biology and Chemistry 36 (4): 273-82. https://izlik.org/JA83NH44PS.

EndNote

Mascini M (December 1, 2008) Analytical Applications of Aptamers. Hacettepe Journal of Biology and Chemistry 36 4 273–282.

IEEE

[1]M. Mascini, “Analytical Applications of Aptamers”, HJBC, vol. 36, no. 4, pp. 273–282, Dec. 2008, [Online]. Available: https://izlik.org/JA83NH44PS

ISNAD

Mascini, Marco. “Analytical Applications of Aptamers”. Hacettepe Journal of Biology and Chemistry 36/4 (December 1, 2008): 273-282. https://izlik.org/JA83NH44PS.

JAMA

1.Mascini M. Analytical Applications of Aptamers. HJBC. 2008;36:273–282.

MLA

Mascini, Marco. “Analytical Applications of Aptamers”. Hacettepe Journal of Biology and Chemistry, vol. 36, no. 4, Dec. 2008, pp. 273-82, https://izlik.org/JA83NH44PS.

Vancouver

1.Marco Mascini. Analytical Applications of Aptamers. HJBC [Internet]. 2008 Dec. 1;36(4):273-82. Available from: https://izlik.org/JA83NH44PS