Dimensionality is the issue: Use of photoaptamers in protein microarrays

Current Opinion in Biotechnology

Volumn 13, Issue 4, 2002, Pages 309-314

  Petach, Helen ^a   Gold, Larry ^a  

^a NONE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBODY; APTAMER; REAGENT;

ACCURACY; DNA MICROARRAY; ENZYME LINKED IMMUNOSORBENT ASSAY; INTERMETHOD COMPARISON; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN DETERMINATION; PROTEOMICS; REVIEW; TWO DIMENSIONAL GEL ELECTROPHORESIS;

ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; ENZYME-LINKED IMMUNOSORBENT ASSAY; INDICATORS AND REAGENTS; LIGANDS; MOLECULAR PROBES; PHOTOCHEMISTRY; PROTEIN ARRAY ANALYSIS; PROTEINS; PROTEOMICS; SENSITIVITY AND SPECIFICITY;

EID: 0036669413     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0958-1669(02)00329-4     Document Type: Review

References (51)

1. Jayasena S.D. Aptamers: an emerging class of molecules that rival antibodies in diagnostics. Clin Chem. 45:1999;1628-1650.
2. Brody E., Gold L. Aptamers as therapeutic and diagnostic agents. Rev Mol Technol. 74:2000;5-13.
3. Butler J.E. Solid supports in enzyme-linked immunosorbent assay and other solid-phase immunoassays. Methods. 22:2000;4-23.
4. Nord K., Nord O., Uhlén M., Kelley B., Ljungqvist C., Nygren P. Recombinant human factor VIII-specific affinity ligands selected from phage-displayed combinatorial libraries of protein A. Eur J Biochem. 268:2001;4269-4277.
5. Roberts R.W., Szostak J.W. RNA-peptide fusions for the in vitro selection of peptides and proteins. Proc Natl Acad Sci USA. 94:1997;12297-12302.
6. McGuiness B.T., Walter G., Fitzgerald K., Shuler P., Mahoney W., Duncan A.R., Hoogenboom H.R. Phage display repertoires for selection of large numbers of bispecific antibody fragments. Nat Biotechnol. 14:1996;1149-1154.
7. Gao C., Mao S., lo C.L., Wirsching P., Lerner R.A., Janda K.D. Making artificial antibodies: a format for phage display of combinatorial heterodimeric arrays. Proc Natl Acad Sci USA. 96:1999;6025-6030.
8. Eaton B.E., Gold L., Zichi D.A. Let's get specific: the relationship between specificity and affinity. Chem Biol. 2:1995;633-638.
9. Srinivasan J., Leclerc F., Xu W., Ellington A.D., Cedergren R. A docking and modelling strategy for peptide-RNA complexes: applications to BIV Tat-TAR and HIV Rev-RBE. Fold Des. 1:1996;463-472.
10. L-binding proteins from a mix of tissue-specific mRNA display libraries. J Biol Chem. 276:2001;20898-20906.
11. Weng S., Gu K., Hammond P.W., Lohse P., Rise C., Wagner R.W., Wright M.C., Kuimelis R.G. Generating addressable protein microarrays with PROfusion covalent mRNA-protein fusion technology. Proteomics. 2:2002;48-57. The feasibility of using mRNA-protein fusion technology to create large-scale protein microarrays was demonstrated. Each mRNA-protein fusion is a protein covalently bound to its encoding mRNA in which a unique epitope is displayed on the protein moiety. The displayed proteins retain their binding functionality after immobilization.
12. Cho G., Keefe A.D., Liu R., Wilson D.S., Szostak J.W. Constructing high complexity synthetic libraries of long ORFs using in vitro selection. J Mol Biol. 297:2000;309-319.
13. Golden M.C., Collins B.D., Willis M.C., Koch T.H. Diagnostic potential of PhotoSELEX-evolved ssDNA aptamers. J Biotechnol. 81:2000;167-178. The selection of two ssDNA photoaptamers to the cognate protein, bFGF, was demonstrated. The yield for the photoaptamer crosslinking to cognate protein was 81% and 50% for the two photoaptamers, while the dissociation constants measured by filter-binding studies were 560 pM and 16 pM, respectively. Specificity was assessed by measuring the lack of photo-crosslinking of the photoaptamer to serum proteins in a 10% serum sample, as assessed by SDS-PAGE analysis.
14. Drolet D.W., Jenison R.D., Smith D.E., Pratt D., Hicke B.J. A high-throughput platform for systematic evolution of ligands by exponential enrichment (SELEX). Comb Chem High Throughput Screen. 2:1999;271-278.
15. Brody E.N., Willis M.C., Smith J.D., Jayasena S., Zichi D., Gold L. The use of aptamers in large arrays for molecular diagnostics. Mol Diagn. 4:1999;381-388.
16. O'Farrell P.H. High-resolution two-dimensional electrophoresis of proteins. J Biol Chem. 250:1975;4007-4021.
17. Gygi S., Rist B., Gerber S., Turecek F., Gelb M., Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol. 17:1999;994-999.
18. Hanash S. 2-D or not 2-D - Is there a future for 2-D gels in proteomics? Proteomics. 1:2001;635-637.
19. Madoz-Gurpide J., Wang H., Misek D., Brichory F., Hanash S.M. Protein based microarrays: a tool for probing the proteome of cancer cells and tissues. Proteomics. 1:2001;1279-1287.
20. Rabilloud T. Two-dimensional gel electrophoresis in proteomics: old, old fashioned, but it still climbs up the mountains. Proteomics. 2:2002;3-10.
21. Washburn M.P., Wolters D., Yates J.R. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol. 19:2001;242-247.
22. Liebler D.C. Introduction to Proteomics: Tools for the New Biology. 2002;Humana Press, New Jersey.
23. King H.C., Sinha A.A. Gene expression profile analysis by DNA microarrays: promise and pitfalls. J Am Med Assoc. 286:2001;2280-2288.
24. Stoll D., Templin M.F., Schrenk M., Traub P.C., Vohringer C.F., Joos T.O. Protein microarray technology. Front Biosci. 7:2002;c13-c32.
25. MacBeath G., Schreiber S.L. Printing proteins as microarrays for high-throughput function determination. Science. 289:2000;1760-1763.
26. Zhu H., Bilgin M., Bangham R., Hall D., Casamayor A., Bertone P., Lan N., Jansen R., Bidlingmaier S., Houfek T., et al. Global analysis of protein activities using proteome chips. Science. 293:2001;2101-2105.
27. Jones M.B., Krutzsch H., Shu H., Zhao Y., Liotta L.A., Kohn E.C., Petricoin E.F. Proteomic analysis and identification of new biomarkers and therapeutic targets for invasive ovarian cancer. Proteomics. 2:2002;76-84.
28. Liotta L.A., Kohn E.C., Petricoin E.F. Clinical proteomics - Personalized molecular medicine. J Am Med Assoc. 286:2001;2211-2214.
29. Petricoin E.F., Ardekani A.M., Hitt B.A., Levine P.J., Fusaro V.A., Steinberg S.M., Mills G.B., Simone C., Fishman D.A., Kohn E.C., et al. Use of proteomic patterns in serum to identify ovarian cancer. Lancet. 359:2002;572-577. Proteomic patterns were identified for ovarian cancer serum samples by immobilizing serum proteins onto Ciphergen microarray surfaces that reproducibly separate proteins based on chromatographic properties. Those proteins were then analyzed using surface-enhanced laser desorption and ionization time-of-flight (SELDI-TOF). Fifty unaffected patient sera were compared to fifty cancer patient sera to identify proteomic patterns on the microarrays. The results yielded much higher PPV than a single analyte comparison.
30. Liotta L., Petricoin E. Molecular profiling of human cancer. Nature. 1:2000;48-56.
31. Huang R.-P., Huang R., Fan Y., Lin Y. Simultaneous detection of multiple cytokines from conditioned media and patient's sera by an antibody-based protein array system. Anal Biochem. 294:2001;55-62.
32. Huang R.-P. Detection of multiple proteins in an antibody-based protein microarray system. J Immunol Methods. 255:2001;1-13.
33. Arenkov P., Kukhtin A., Gemmell A., Voloshchuk S., Chupeeva V., Mirzabekov A. Protein microchips: use for immunoassay and enzymatic reactions. Anal Biochem. 278:2000;123-131.
34. Sreekumar A., Nyati M.K., Varambally S., Barrette T.R., Ghosh D., Lawrence T.S., Chinnaiyan A.M. Profiling of cancer cells using protein microarrays: discovery of novel radiation-regulated proteins. Cancer Res. 61:2001;7585-7593.
35. Knezevic V., Leethanakul C., Bichsel V.E., Worth J.M., Prabhu V.V., Gutkind J.S., Liotta L.A., Munson P.J., Petricoin E.F., Krizman D.B. Proteomic profiling of the cancer microenvironment by antibody arrays. Proteomics. 1:2001;1271-1278.
36. Mezzasoma L., Bacarese-Hamilton T., DiCristina M., Rossi R., Bistoni F., Crisanti A. Antigen microarrays for serodiagnosis of infectious diseases. Clin Chem. 48:2002;121-130.
37. Wiese R., Belosludtsev Y., Powdrill T., Thompson P., Hogan M. Simultaneous multianalyte ELISA performed on a microarray platform. Clin Chem. 47:2001;1451-1457.
38. Moody M.D., VanArsdell S.W., Murphy K.P., Orencole S.F., Burns C. Array-based ELISAs for high-throughput analysis of human cytokines. Biotechniques. 31:2001;186-194.
39. Mendoza L.G., McQuary P., Mongan A., Gangadharan R., Brignac S., Eggers M. High-throughput microarray-based enzyme-linked immunosorbent assay (ELISA). Biotechniques. 27:1999;778-788.
40. Haab B.B., Dunham M.J., Brown P.O. Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Genome Biology. 2:2001;4.1-4.13. A dual labeling procedure was applied to antibody microarrays in which two samples (Cy3-labeled antigens and Cy5-labeled reference antigens) were mixed and applied to the array for differential analysis to quantify analyte binding to the array. A total of 110 antibodies were immobilized and at least 20% of captured antibodies retained their binding activities.
41. Hanes J., Jermutus L., Weber-Bornhauser S., Bosshard H.R., Plückthun A. Ribosome display efficiently selects and evolves high-affinity antibodies in vitro from immune libraries. Proc Natl Acad Sci USA. 95:1998;14130-14135.
42. Hanes J., Plückthun A. In vitro selection and evolution of functional proteins by using ribosome display. Proc Natl Acad Sci USA. 94:1997;4937-4942.
43. Figeys D., Pinto D. Proteomics on a chip: promising developments. Electrophoresis. 22:2001;208-216.
44. -21 moles).
45. Srinivas P.R., Srivastava S., Hanash S., Wright G.L. Proteomics in early detection of cancer. Clin Chem. 47:2001;1901-1911.
46. Jensen K.B., Atkinson B.L., Willis M.C., Koch T.H., Gold L. Using in vitro selection to direct the covalent attachment of human immunodeficiency virus type 1 Rev protein to high-affinity RNA ligands. Proc Natl Acad Sci USA. 92:1995;12220-12224.
47. Gold L, Zichi D, Jenison R, Schneider D: Method and Apparatus for the Automated Generation of Nucleic Acid Ligands. PCT Publication WO 00/43534 2000.
48. Cox J.C., Ellington A.D. Automated selection of anti-protein aptamers. Bioorg Med Chem. 9:2001;2525-2531.
49. Hopfield J.J. Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity. Proc Natl Acad Sci USA. 71:1974;4135-4139.
50. Meisenheimer K.M., Meisenheimer P.L., Koch T.A. Nucleoprotein photo-crosslinking using halopyrimidine-substituted RNAs. Methods Enzymol. 318:2000;88-104.
51. Seetharaman S., Zivarts M., Sudarsan N., Breaker R.R. Immobilized RNA switches for the analysis of complex chemical and biological mixtures. Nat Biotechnol. 19:2001;336-341. RNA engineered to function as an 'RNA switch', was immobilized onto gold surfaces using thiol attachment directly to gold-coated silicon, followed by washing with 6-mercapto-1-hexanol to form a self-assembling thiol monolayer around the immobilized RNA. The mercapto-hexanol monolayer is important for removing non-specifically bound RNA and ensuring proper folding of the RNA. The RNA switch functionality of the RNA molecule was retained following immobilization.