Analytical applications of aptamers

Biosensors and Bioelectronics

Volumn 20, Issue 12, 2005, Pages 2424-2434

  Tombelli, S ^a   Minunni, M ^a   Mascini, M ^a  

^a UNIVERSITY OF FLORENCE   (Italy)

Author keywords

Affinity chromatography; Aptamers; Biosensors; SELEX

Indexed keywords

AMPLIFICATION; DIAGNOSIS; DNA; ENZYMES; OLIGOMERS; REACTION KINETICS; RNA; TOXIC MATERIALS;

APTAMERS; HYBRIDIZATION; MOLECULAR RECOGNITION; RANDOM SEQUENCES;

BIOSENSORS;

APTAMER;

ACOUSTICS; AFFINITY CHROMATOGRAPHY; ANALYTIC METHOD; BIOSENSOR; CAPILLARY ELECTROPHORESIS; CHROMATOGRAPHY; DNA SEQUENCE; GENE AMPLIFICATION; MASS SPECTROMETRY; POLYMERASE CHAIN REACTION; REVIEW; RNA SEQUENCE; SYSTEMATIC EVOLUTION OF LIGANDS BY EXPONENTIAL ENRICHMENT;

EID: 18044372281     PISSN: 09565663     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bios.2004.11.006     Document Type: Review

References (77)

1. S. Baskerville, M. Zapp, and A.D. Ellington Anti-Rex aptamers as mimics of the Rex-binding element J. Virol. 73 1999 4962 4971
2. M. Berezovski, R. Nutiu, Y. Li, and S.N. Krylov Affinity analysis of a protein-aptamer complex using nonequilibrium capillary electrophoresis of equilibrium mixtures Anal. Chem. 75 2003 1382 1386
3. L.C. Bock, L.C. Griffin, J.A. Latham, E.H. Vermaas, and J.J. Toole Selection of single-stranded DNA molecules that bind and inhibit human thrombin Nature 355 1992 564 566
4. E.N. Brody, and L. Gold Aptamers as therapeutic and diagnostic agents Rev. Mol. Biotechnol. 74 2000 5 13
5. W. Cao Recent developments in ligase-mediated amplification and detection Trends Biotechnol. 22 2004 38 44
6. S.L. Clark, and V.T. Remcho Aptamers as analytical reagents Electrophoresis 23 2002 1335 1340
7. S.L. Clark, and V.T. Remcho Electrochromatographic retention studies on a flavin-binding RNA aptamer sorbent Anal. Chem. 75 2003 5692 5696
8. J.C. Cox, and A.D. Ellington Automated selection of anti-proteins aptamers Bioorg. Med. Chem. 9 2001 2525 2531
9. J.C. Cox, A. Hayhurst, J. Hesselberth, E.A. Davidson, L.J. Sooter, T.S. Bayer, G. Georgiou, and A.D. Ellington Automated selection of aptamers against protein targets translated in vitro: from gene to aptamer Nucl. Acids Res. 30 2002 e108
10. J.C. Cox, M. Rajendran, T. Riedel, E.A. Davidson, L.J. Sooter, T.S. Bayer, M. Schmitz-Brown, and A.D. Ellington Automated acquisition of aptamer sequences Comb. Chem. High. T. Scr. 5 2002 289 299
11. Q. Deng, I. German, D.D. Buchanan, and R.T. Kennedy Retention and separation of adenosine and analogues by affinity chromatography with an aptamer stationary phase Anal. Chem. 73 2001 5415 5421
12. Q. Deng, C.J. Watson, and R.T. Kennedy Aptamer affinity chromatography for rapid assay of adenosine in microdialysis samples collected in vivo J. Chromatogr. A 1005 2003 123 130
13. L.W. Dick, and L.B. McGown Aptamer-enhanced laser desorption/ionization for affinity mass spectrometry Anal. Chem. 76 2004 3037 3041
14. A.D. Ellington, and J.W. Szostak In vitro selection of RNA molecules that bind specific ligands Nature 346 1990 818 822
15. A.D. Ellington, and J.W. Szostak Selection in vitro of single-stranded DNA molecules that fold into specific ligand-binding structures Nature 355 1992 850 852
16. M. Famulok, G. Mayer, and M. Blind Nucleic acid aptamers - from selection in vitro to application in vivo Acc. Chem. Res. 33 2000 591 599
17. M. Famulok, and J.W. Szostak Stereospecific recognition of tryptophan agarose by in vitro selected RNA J. Am. Chem. Soc. 14 1992 3990 3991
18. S. Fredriksson, M. Gullberg, J. Jarvius, C. Olsson, K. Pietras, S.M. Gustafsdottir, A. Ostman, and U. Landegren Protein detection using proximity-dependent DNA ligation assays Nat. Biotechnol. 20 2002 473 477
19. L.M. Furtado, H. Su, and M. Thompson Interactions of HIV-1 TAR RNA with Tat-derived peptides discriminated by on-line acoustic wave detector Anal. Chem. 71 1999 1167 1175
20. A. Geiger, P. Burgstaller, H. Von der Eltz, A. Roeder, and M. Famulok RNA aptamers that bind l-arginine with sub-micromolar dissociation constants and high enantioselectivity. Nucl. Acids Res. 24 1996 1029 1036
21. I. German, D.D. Buchanan, and R.T. Kennedy Aptamers as ligands in affinity probe capillary electrophoresis Anal. Chem. 70 1998 4540 4545
22. M.C. Golden, B.D. Collins, M.C. Willis, and T.H. Koch Diagnostic potential of PhotoSELEX-evolved ssDNA aptamers J. Biotechnol. 81 2000 167 178
23. L.S. Green, D. Jellinek, R. Jenison, A. Ostman, C.H. Heldin, and N. Janjic Inhibitory DNA ligands to platelet-derived growth factor B-chain Biochemistry 45 1996 14413 14424
24. N. Hamaguchi, A. Ellington, and M. Stanton Aptamer beacons for the direct detection of proteins Anal. Biochem. 294 2001 126 131
25. K. Harada, and A.D. Frankel Identification of two novel arginine binding DNAs EMBO J. 23 1995 5798 5811
26. O. Heidenreich, and F. Eckstein Hammerhead ribozyme-mediated cleavage of the long terminal repeat RNA of human immunodeficiency virus type 1 J. Biol. Chem. 267 1992 1904 1909
27. T. Herman, and D. Patel Adaptive recognition by nucleic acid aptamers Science 287 2000 820 825
28. J.R. Hesselberth, D. Miller, J. Robertus, and A.D. Ellington In vitro selection of RNA molecules that inhibit the activity of Ricin A-chain J. Biol. Chem. 275 2000 4937 4942
29. B.J. Hicke, S.R. Watson, A. Koenig, C.K. Lynott, R.F. Bargatze, Y.-F. Chang, S. Ringquist, L. Moon-McDermott, S. Jennings, T. Fitzwater, H.-L. Han, N. Varki, I. Albinana, M.C. Willis, A. Varki, and D. Parma DNA aptamers block l-selectin function in vivo inhibition of human lymphocyte trafficking in SCID mice J. Clin. Invest. 98 12 1996 2688 2692
30. H.-A. Ho, and M. Leclerc Optical sensors based on hybrid aptamer/conjugated polymer complexes J. Am. Chem. Soc. 126 2004 1384 1387
31. S. Jayasena Aptamers: an emerging class of molecules that rival antibodies in diagnostics Clin. Chem. 45 1999 1628 1650
32. R.D. Jenison, S.C. Gill, A. Pardi, and B. Polisky High-resolution molecular discrimination by RNA Science 263 1994 1425 1429
33. S.D. Jhaveri, R. Kirby, R. Conrad, E.J. Maglott, M. Bowser, R.T. Kennedy, G. Glick, and A.D. Ellington Designed signaling aptamers that transduce molecular recognition to changes in fluorescence intensity J. Am. Chem. Soc. 122 2000 2469 2473
34. Y. Jiang, X. Fang, and C. Bai Signaling aptamer/protein binding by a molecular light switch complex Anal. Chem. 76 2004 5230 5235
35. R. Kirby, E.J. Cho, B. Gehrke, T. Bayer, Y.S. Park, D.P. Neikirk, J.T. McDevitt, and A.D. Ellington Aptamer-based sensor arrays for the detection and quantitation of proteins Anal. Chem. 76 2004 4066 4075
36. S.J. Klug, A. Huttenhofer, and M. Famulok In vitro selection of RNA aptamers that bind special elongation factor SelB, a protein with multiple RNA-binding sites, reveals one major interaction domain at the carboxyl terminus RNA 5 1999 1180 1190
37. R.B. Kotia, L. Li, and L.B. McGown Separation of nontarget compounds by DNA aptamers Anal. Chem. 72 2000 827 831
38. + T lymphocyte function J. Immunol. 160 1998 5209 5212
39. W. Kusser Chemically modified nucleic acid aptamers for in vitro selections: evolving evolution J. Biotechnol. 74 2000 27 38
40. L.A. Lasky Selectin-carbohydrate interactions and the initiation of the inflammatory response Annu. Rev. Biochem. 64 1995 113 140
41. M. Lee, and D.R. Walt A fiber-optic microarray biosensor using aptamers as receptors Anal. Biochem. 282 2000 142 146
42. J.J. Li, X. Fang, and W. Tan Molecular aptamer beacons for real-time protein recognition Biochem. Biophys. Res. Commun. 292 2002 31 40
43. M. Liss, B. Petersen, H. Wolf, and E. Prohaska An aptamer-based quartz crystal protein biosensor Anal. Chem. 74 2002 4488 4495
44. E. Luzi, M. Minunni, S. Tombelli, and M. Mascini New trends in affinity sensing: aptamers for ligand binding Trends Anal. Chem. 22 2003 810 818
45. K.A. Marshall, and A.D. Ellington In vitro selection of RNA aptamers Meth. Enzymol. 318 2000 193 214
46. T.G. McCauley, N. Hamaguchi, and M. Stanton Aptamer-based biosensor arrays detection and quantification of biological macromolecules Anal. Biochem. 319 2003 244 250
47. S.D. Mendonsa, and M.T. Bowser In vitro evolution of functional DNA using capillary electrophoresis J. Am. Chem. Soc. 126 2004 20 21
48. M. Michaud, E. Jourdan, C. Ravelet, A. Villet, A. Ravel, C. Grosset, and E. Peyrin Immobilized DNA aptamers as target-specific chiral stationary phases for resolution of nucleoside and amino acid derivative enantiomers Anal. Chem. 76 2004 1015 1020
49. M. Michaud, E. Jourdan, A. Villet, A. Ravel, C. Grosset, and E. Peyrin A DNA aptamer as a new target-specific chiral selector for HPLC J. Am. Chem. Soc. 125 2003 8672 8679
50. Minunni, M., Tombelli, S., Gullotto, A., Luzi, E., Mascini, M., 2004. Development of biosensors with aptamers as bio-recognition element: the case of HIV-1 Tat protein. Biosens. Bioelectron. 20, 1149-1156.
51. P. Mucha, A. Szyk, P. Rekowski, and J. Barciszewski Structural requirements for conserved Arg52 residue for interaction of the human immunodeficiency virus type 1 trans-activation responsive element with the trans-activator of transcription protein (49-57): capillary electrophoresis mobility shift assay J. Chromatogr. A 968 2002 211 220
52. M.B. Murphy, S.T. Fuller, P.M. Richardson, and S.A. Doyle An improved method for the in vitro evolution of aptamers and applications in protein detection and purification Nucl. Acids Res. 31 2003 18e110
53. R. Nutiu, and Y. Li Structure-switching signalling aptamers J. Am. Chem. Soc. 125 2004 4771 4778
54. C.K. O'Sullivan Aptasensors - the future of biosensing? Anal. Bioanal. Chem. 372 2002 44 48
55. D.J. Patel, and A.K. Suri Structure, recognition and discrimination in RNA aptamer complexes with cofactors, amino acids, drugs and aminoglycoside antibiotics Rev. Mol. Biotechnol. 74 2000 39 60
56. V. Pavski, and X.C. Le Detection of human immunodeficiency virus type 1 reverse transcriptase using aptamers as probes in affinity capillary electrophoresis Anal. Chem. 73 2001 6070 6076
57. W. Pieken, D.B. Olsen, F. Benseler, H. Aurup, and H.F. Eckstein Kinetic characterization of ribonuclease-resistant 2′-modified hammerhead ribozymes Science 253 1991 314 317
58. M. Rajendran, and A.D. Ellington Nucleic acids for reagentless biosensors Optical Biosensors: Present and Future 2002 Ligler and Taitt Edition pp. 369-396
59. F. Ristoratore, A. Spagnuolo, F. Aniello, M. Branno, F. Fabbrini, and R. Di Lauro Expression and functional analysis of Cititf1, an ascidian NK-2 class gene, suggest its role in endoderm development Development 126 1999 5149 5159
60. T.S. Romig, C. Bell, and D.W. Drolet Aptamer affinity chromatography: combinatorial chemistry applied to protein purification J. Chromatogr. B 731 1999 275 284
61. C.A. Savran, S.M. Knudsen, A.D. Ellington, and S.R. Manalis Micromechanical detection of proteins using aptamer-based receptor molecules Anal. Chem. 76 2004 3194 3198
62. M.D. Schlensog, T.M.A. Gronewold, M. Tewes, M. Famulok, and E. Quandt A Lowe-wave biosensor using nucleic acids as ligands Sens. Actuators B 10 2004 308 315
63. H. Schurer, K. Stembera, D. Knoll, G. Mayer, M. Blind, H. Foerster, M. Famulok, P. Welzel, and U. Hahn Aptamers that bind to the antibiotic moenomycin A Bioorg. Med. Chem. 92 2001 2557 2563
64. M.N. Stojanovic, and D.W. Landry Aptamer-based colorimetric probe for cocaine J. Am. Chem. Soc. 124 2002 9678 9679
65. L.Q. Sun, M.J. Cairns, E.G. Saravolac, A. Baker, and W.L. Gerlach Catalytic nucleic acids: from lab to applications Pharmacol. Rev. 52 2000 325 347
66. V. Tereshko, E. Skripkin, and D.J. Patel Encapsulating streptomycin within a small 40-mer RNA Chem. Biol. 10 2003 175 187
67. C. Tuerk, and L. Gold Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase Science 249 1990 505 510
68. D.I. Van Ryk, and S. Venkatesan Real-time kinetics of HIV-1 Rev-Rev response element interactions J. Biol. Chem. 274 1999 17452 17463
69. J.D. Wen, C.W. Gray, and D.M. Gray SELEX selection of high-affinity oligonucleotides for bacteriophage Ff gene 5 protein Biochemistry 40 2001 9300 9310
70. R.R. White, B.A. Sullenger, and C.P. Rusconi Developing aptamers into therapeutics J. Clin. Invest. 106 2000 929 934
71. T.W. Wiegand, P.B. Williams, S.C. Dreskin, M.-H. Jouvin, J.-P. Kinet, and D. Tasset High-affinity oligonucleotide ligands to human IgE inhibit binding to Fc epsilon receptor I J. Immunol. 157 1996 221 230
72. K.P. Williams, X.H. Liu, T.N.M. Schumacher, H.Y. Lin, D.A. Ausiello, P.S. Kim, and D.P. Bartel Bioactive and nuclease-resistant l-DNA ligand of vasopressin Proc. Natl. Acad. Sci. 94 1997 11285 11290
73. C. Wilson, J. Nix, and J.W. Szostak Functional requirements for specific ligand recognition by a biotin-binding RNA pseudoknot Biochemistry 37 1998 14410 14419
74. D.S. Wilson, and J.W. Szostak In vitro selection of functional nucleic acids Annu. Rev. Biochem. 68 1999 611 647
75. R. Yamamoto, and P.K.R. Kumar Molecular beacon aptamer fluoresces in the presence of Tat protein of HIV-1 Genes to Cells 5 2000 389 396
76. K.M. You, S.H. Lee, A. Im, and S.B. Lee Aptamers as functional nucleic acids: in vitro selection and biotechnological applications Biotechnol. Bioprocess. Eng. 8 2003 64 75
77. J.M. Zimmerman, and L.J. Maher In vivo selection of spectinomycin-binding RNAs Nucl. Acids Res. 30 2002 5425 5435