Aptamers - Basic research, drug development, and clinical applications

Applied Microbiology and Biotechnology

Volumn 69, Issue 4, 2005, Pages 367-374

  Proske, Daniela ^a   Blank, Michael ^a   Buhmann, Raymund ^b   Resch, Ansgar ^a  

^a NascaCell Technologies AG   (Germany)

^b INSTITUTE OF EPIDEMIOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DNA SEQUENCES; DRUG PRODUCTS; PROTEINS; PURIFICATION; RNA;

APTAMER TECHNOLOGY; DRUG DISCOVERY; ENDOTHELIAL GROWTH; RNA SEQUENCIES;

BIOTECHNOLOGY;

APTAMER; BACTERIUM LYSATE; DNA; FLUORESCEIN ISOTHIOCYANATE; PEGAPTANIB;

DRUG DEVELOPMENT;

AFFINITY CHROMATOGRAPHY; CLINICAL RESEARCH; DNA BINDING; DNA MICROARRAY; DNA SEQUENCE; DRUG DESIGN; DRUG INDUSTRY; FOOD AND DRUG ADMINISTRATION; HIGH THROUGHPUT SCREENING; MOLECULAR RECOGNITION; NICK END LABELING; PHOTOCHEMICAL QUENCHING; PROTEIN BINDING; PROTEIN DENATURATION; PROTEIN FUNCTION; PROTEIN PURIFICATION; PROTEIN TARGETING; RETINA MACULA AGE RELATED DEGENERATION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SHORT SURVEY;

ANIMALS; APTAMERS, NUCLEOTIDE; DRUG DESIGN; HUMANS; RATS; RESEARCH; VASCULAR ENDOTHELIAL GROWTH FACTOR A;

BACTERIA (MICROORGANISMS);

EID: 28444484636     PISSN: 01757598     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00253-005-0193-5     Document Type: Short Survey

References (69)

1. Antisoma (2005) Promising phase I data for Antisoma's AS1411 revealed at ASCO http://www.archemix.com/press/pr_jun04.html Archemix announce submission on an IND for thrombin inhibitor ARC183
2. Baldrich E, Restrepo A, O'Sullivan CK (2004) Aptasensor development: elucidation of critical parameters for optimal aptamer performance. Anal Chem 76:7053-7063
3. Blank M, Weinschenk T, Priemer M, Schluesener H (2001) Systematic evolution of a DNA aptamer binding to rat brain tumor microvessels. Selective targeting of endothelial regulatory protein pigpen. J Biol Chem 276:16464-16468
4. Blind M, Kolanus W, Famulok M (1999) Cytoplasmic RNA modulators of an inside-out signal-transduction cascade. Proc Natl Acad Sci U S A 96:3606-3610
5. Blind M, Grättinger M, Mayer G (2002) Nucleic acid biotools: accelerating the discovery of lead compounds. Screening 6:35-37
6. Bock C, Coleman M, Collins B, Davis J, Foulds G, Gold L, Greef C, Heil J, Heilig JS, Hicke B, Hurst MN, Husar GM, Miller D, Ostroff R, Petach H, Schneider D, Vant-Hull B, Waugh S, Weiss A, Wilcox SK, Zichi D (2004) Photoaptamer arrays applied to multiplexed proteomic analysis. Proteomics 4:609-618
7. Brody EN, Willis MC, Smith JD, Jayasena S, Zichi D, Gold L (1999) The use of aptamers in large arrays for molecular diagnostics. Mol Diagn 4:381-388
8. Burgstaller P, Girod A, Blind M (2002) Aptamers as tools for target prioritization and lead identification. Drug Discov Today 7:1221-1228
9. Burmeister PE, Lewis SD, Silva RF, Preiss JR, Horwitz LR, Pendergrast PS, McCauley TG, Kurz JC, Epstein DM, Wilson C, Keefe AD (2005) Direct in vitro selection of a 2′-O-methyl aptamer to VEGF. Chem Biol 12:25-33
10. Chen CH, Chernis GA, Hoang VQ, Landgraf R (2003) Inhibition of heregulin signaling by an aptamer that preferentially binds to the oligomeric form of human epidermal growth factor receptor-3. Proc Natl Acad Sci U S A 100:9226-9231
11. Conrad R, Ellington AD (1996) Detecting immobilized protein kinase C isozymes with RNA aptamers. Anal Biochem 242:261-265
12. Cox JC, Ellington AD (2001) Automated selection of anti-protein aptamers. Bioorg Med Chem 9:2525-2531
13. Davis KA (1998) Staining of cell surface CD4 with 2′-F-pyrimidin- containing RNA aptamers for flow cytometry. Nucleic Acids Res 26:3915-3924
14. Drolet DW, Moon-McDermott L, Romig TS (1996) An enzyme-linked oligonucleotide assay. Nat Biotechnol 14:1021-1025
15. Ellington AD, Szostak JW (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346:818-822
16. Eulberg D, Buchner K, Maasch C, Klussmann S (2005) Development of an automated in vitro selection protocol to obtain RNA-based aptamers: identification of a biostable substance P antagonist. Nucleic Acids Res 33:e45
17. Eyetech Study Group (2002) Preclinical and phase 1A clinical evaluation of an anti-VEGF pegylated aptamer (EYE001) for the treatment of exudative age related macular degeneration. Retina 22:143-152
18. Eyetech Study Group (2003) Antivascular endothelial growth factor therapy for subfoveal choroidal neovascularization secondary to age related macular degeneration: phase II study results. Ophthalmology 110:979-986
19. Farokhzad OC, Jon S, Khademhosseini A, Tran TN, Lavan DA, Langer R (2004) Nanoparticle-aptamer bioconjugates: a new approach for targeting prostate cancer cells. Cancer Res 64:7668-7672
20. FDA (2004) http://www.fda.gov/bbs/topics/news/2004/new01146.html
21. Floege J, Ostendorf T, Janssen U, Burg M, Radeke HH, Vargeese C, Gill SC, Green LS, Janjic N (1999) Novel approach to specific growth factor inhibition in vivo: antagonism of platelet-derived growth factor in glomerulonephritis by aptamers. Am J Pathol 154:169-179
22. Fredrikson S (2002) Protein detection using proximity-dependent DNA ligation assays. Nat Biotechnol 20:473-477
23. Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Crucial CM, Remor M, Hofert C, Schelder M, Brajenovic M, Ruffner H, Merino A, Klein K, Hudak M, Dickson D, Rudi T, Gnau V, Bauch A, Bastuck S, Huhse B, Leutwein C, Heurtier MA, Copley RR, Edelmann A, Querfurth E, Rybin V, Drewes G, Raida M, Bouwmeester T, Bork P, Seraphin B, Kuster B, Neubauer G, Superti-Furga G (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415:141-147
24. Geiger A, Burgstaller P, von der Eltz H, Roeder A, Famulok M (1996) RNA aptamers that bind L-arginine with sub-micromolar dissociation constants and high enantioselectivity. Nucleic Acids Res 24:1029-1036
25. Gold L, Polisky B, Uhlenbeck O, Yarus M (1995) Diversity of oligonucleotide functions. Annu Rev Biochem 64:763-797
26. Green LS, Bell C, Janjic N (2001) Aptamers as reagents for high-throughput screening. BioTechniques 30:1094-1110
27. Hamaguchi N, Ellington A, Stanton M (2001) Aptamer beacons for the direct detection of proteins. Anal Biochem 294:126-131
28. Han M (2001) Quantum-dot-tagged microbeads for multiplexed optical coding of biomolecules. Nat Biotechnol 19: 631-635
29. Harris S, Foord SM (2000) Transgenic knock-outs: functional genomics and therapeutic target selection. Pharmacogenomics 1:433-443
30. Heilig J (2004) Abstract book 2nd annual Nucleic Acid World Summit Boston
31. Heyduk E, Heyduk T (2005) Nucleic acid-based fluorescence sensors for detecting proteins. Anal Chem 77:1147-1156
32. Hicke BJ, Marion C, Chang F, Gould T, Lynott CK, Parma D, Schmidt PG, Warren S (2001) Tenascin-C aptamers are generated using tumor cells and purified protein. J Biol Chem 276:48644-48654
33. Ikebukuro K, Kiyohara C, Sode K (2005) Novel electrochemical sensor system for protein using the aptamers in sandwich manner. Biosens Bioelectron 20:2168-2172
34. Jayasena SD (1999) Aptamers: an emerging class of molecules that rival antibodies in diagnostics. Clin Chem 45:1628-1650
35. Kimoto M, Sakamoto K, Shirouzu M, Hirao I, Yokoyama S (1998) RNA aptamers that specifically bind to the Ras-binding domain of Raf-1. FEBS Lett 441:322-326
36. Kohler G, Milstein C (1975) Continuous cultures of fused cells secreting antibody of predefined specificity. Nature 256:496-497
37. Kohn DB, Bauer G, Rice CR, Rothschild JC, Carbonaro DA, Valdez P, Hao Q, Zhou C, Bahner I, Kearns K, Brody K, Fox S, Haden E, Wilson K, Salata C, Dolan C, Wetter C, Aguilar-Cordova E, Church J (1999) A clinical trial of retroviral-mediated transfer of a rev-responsive element decoy gene into CD34(+) cells from the bone marrow of human immunodeficiency virus-1-infected children. Blood 94:368-371
38. Konopka K, Lee NS, Rossi J, Duzgunes N (2000) Rev-binding aptamer and CMV promoter act as decoys to inhibit HIV replication. Gene 255:235-244
39. Liss M, Petersen B, Wolf H, Prohaska E (2002) An aptamer-based quartz crystal protein biosensor. Anal Chem 74:4488-4495
40. Lorger M, Engstler M, Homann M, Göringer HU (2003) Targeting the variable surface of African trypanosomes with variant surface glycoproteins-specific serum stable RNA aptamers. Eukaryot Cell 2:84-94
41. Lupold SE, Hicke BJ, Lin Y, Coffey DS (2002) Identification and characterization of nuclease-stabilized RNA molecules that bind human prostate cancer cells via the prostate-specific membrane antigen. Cancer Res 62:4029-4033
42. Mannironi C, Di Narbo A, Fruscoloni P, Tocchini-Valentini GP (1997) In vitro selection of dopamine RNA ligands. Biochemistry 36:9726-9734
43. Marro ML, Daniels DA, McNamee A, Andrew DP, Chapman TD, Jiang MS, Wu Z, Smith JL, Patel KK, Gearing KL (2005) Identification of potent and selective RNA antagonist of the IFN-γ-inducible CXCL10 chemokine. Biochemistry 44:8449-8460
44. Martell RE, Nevins JR, Sullenger BA (2002) Optimizing aptamer activity for gene therapy applications using expression cassette SELEX. Mol Ther 6:30-34
45. Mayer G, Blind M, Nagel W, Bohm T, Knorr T, Jackson CL, Kolanus W, Famulok M (2001) Controlling small guanine-nucleotide-exchange factor function through cytoplasmic RNA intramers. Proc Natl Acad Sci U S A 98:4961-4965
46. Murphy MB, Fuller ST, Richardson PM, Doyle SA (2003) An improved method for the in vitro evolution of aptamers and applications in protein detection and purification. Nucleic Acids Res 31(18):e110
47. Nickens DG, Patterson JT, Burke DH (2003) Inhibition of HIV-1 reverse transcriptase by RNA aptamers in Escherichia coli. RNA 9:1029-1033
48. Nieuwlandt D, Wecker M, Gold L (1995) In vitro selection of RNA ligands to substance P. Biochemistry 24:5651-5659
49. Nimjee SM, Rusconi CP, Harrington RA, Sullenger BA (2005a) The potential of aptamers as anticoagulants. Trends Cardiovasc Med 15:41-45
50. Nimjee SM, Rusconi CP, Sullenger BA (2005b) Aptamers: an emerging class of therapeutics. Annu Rev Med 56:555-583
51. Nutiu R, Li Y (2004) Structure-switching signaling aptamers: transducing molecular recognition into fluorescence signaling. Chemistry 10:1868-1876
52. Opalinska JB, Gewirtz AM (2002) Nucleic-acid therapeutics: basic principles and recent applications. Nat Rev Drug Discov 1:503-514
53. Petach H, Gold L (2002) Dimensionality is the issue: use of photoaptamers in protein microarrays. Curr Opin Biotechnol 13:309-314
54. Proske D, Höfliger M, Soll RM, Beck-Sickinger AG, Famulok M (2002) A Y2 receptor mimetic aptamer directed against neuropeptide Y. J Biol Chem 277:11416-11422
55. Rinquist S, Parma D (1998) Anti-L-selectin oligonucleotide ligands recognize CD62L-positive leucocytes: binding affinity and specificity of univalent and bivalent ligands. Cytometry 33:394-405
56. Romig TS, Bell C, Drolet DW (1999) Aptamer affinity chromatography: combinatorial chemistry applied to protein purification. J Chromatogr B Biomed Sci Appl 731:275-284
57. Rossi JJ (1999) Ribozymes, genomics and therapeutics. Chem Biol 6:R33-R37
58. Rusconi CP, Yeh A, Lyerly HK, Lawson JH, Sullenger BA (2000) Blocking the initiation of coagulation by RNA aptamers to factor VIIa. Thromb Haemost 84:841-848
59. Rusconi CP, Scardino E, Layzer J, Pitoc GA, Ortel TL, Monroe D, Sullenger BA (2002) RNA aptamers as reversible antagonists of coagulation factor IXa. Nature 419:90-94
60. Rusconi CP, Roberts JD, Pitoc GA, Nimjee SM, White RR, Quick G Jr, Scardino E, Fay WP, Sullenger BA (2004) Antidote-mediated control of an anticoagulant aptamer in vivo. Nat Biotechnol 22:1373-1384
61. Seiwert SD, Stines Nahreini T, Aigner S, Ahn NG, Uhlenbeck OC (2000) RNA aptamers as pathway-specific MAP kinase inhibitors. Chem Biol 7:833-843
62. Shi H, Hoffman BE, Lis JT (1999) RNA aptamers as effective protein antagonists in a multicellular organism. Proc Natl Acad Sci U S A 96(18):10033-10038
63. Thompson JD (2002) Applications of antisense and siRNAs during preclinical development. Drug Discov Today 7:912-917
64. Tuerk C, Gold L (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249: 505-510
65. Tuschl T (2002) Expanding small RNA interference. Nat Biotechnol 20:446-448
66. Tuschl T, Zamore PD, Lehmann R, Bartel DP, Sharp PA (1999) Targeted mRNA degradation by double-stranded RNA in vitro. Genes Dev 13:3191-3197
67. Vicens MC, Sen A, Vanderlaan A, Drake TJ, Tan W (2005) Investigation of molecular beacon aptamer-based bioassay for platelet-derived growth factor detection. Chembiochem 6:900-907
68. Yamamoto R, Baba T, Kumar PK (2000a) Molecular beacon aptamer fluoresces in the presence of Tat protein of HIV-1. Genes Cells 5:389-396
69. Yamamoto R, Katahira M, Nishikawa S, Baba T, Taira K, Kumar PK (2000b) A novel RNA motif that binds efficiently and specifically to the Tat protein of HIV and inhibits the transactivation by Tat of transcription in vitro and in vivo. Genes Cells 5(5):371-388