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Molecular Diversity

, Volume 8, Issue 3, pp 177–187 | Cite as

High density peptide microarrays. In situ synthesis and applications

  • Xiaolian Gao
  • Jean Philippe Pellois
  • Younghwa Na
  • Younkee Kim
  • Erdogan Gulari
  • Xiaochuan Zhou
Article

Abstract

The technologies enabling the creation of large scale, miniaturized peptide or protein microarrays are emerging. The focuses of this review are the synthesis and applications of peptide and peptidomimetic microarrays, especially the light directed parallel synthesis of individually addressable high density peptide microarrays using a novel photogenerated reagent chemistry and digital photolithography (Gao et al., 1998, J. Am. Chem. Soc. 120, 12698; Pellois et al. 2002, Nat. Biotechnol. 20, 922). Concepts related to the synthesis are discussed, such as the reactions of photogenerated acids in the deprotection step of peptide synthesis or oligonucleotide synthesis, and the applications of high density peptide chips in antibody binding assays are discussed. Peptide chips provide versatile tools for probing antigen-antibody, protein-protein, peptide-ligand interactions and are basic components for miniaturization, automation, and system integration in research and clinical diagnosis applications.

antibody binding digital photolithography epitope screening miniaturization parallel synthesis peptide chip peptide microarray PGA PGR chemistry protein binding assay 

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References

  1. 1.
    Geysen, H. M., Meloen, R. H. and Barteling, S. J., Use of peptide synthesis to probe viral antigens for epitopes to a resolution of a single amino acid, Proc. Natl. Acad. Sci. USA, 81 (1984) 3998-4002.PubMedGoogle Scholar
  2. 2.
    Ekins, R. P., Multi-analyte immunoassay, J. Pharm. Biomed. Anal., 7 (1989) 155-168.PubMedGoogle Scholar
  3. 3.
    Lam, K. S., Salmon, S. E., Hersh, E. M., Hruby, V. J., Kazmierski, W. M. and Knapp, R. J., A new type of synthetic peptide library for identifying ligand-binding activity, Nature, 354 (1991) 82-84.PubMedGoogle Scholar
  4. 4.
    Houghten, R. A., Pinilla, C., Blondelle, S. E., Appel, J. R., Dooley, C. T. and Cuervo, J. H., Generation and use of synthetic peptide combinatorial libraries for basic research and drug discovery, Nature, 354 (1991) 84-86.PubMedGoogle Scholar
  5. 5.
    Frank, R., SPOT-synthesis: an easy technique for the positionally addressable, parallel chemical synthesis on a membrane support, Tetrahedron, 48 (1992) 9217-9232.Google Scholar
  6. 6.
    Fodor, S. P. A., Leighton, J., Pirrung, M. C., Stryer, L., Lu, A. T. and Solas, D., Light-directed, spatially addressable parallel chemical synthesis, Science, 251 (1991) 767-773.PubMedGoogle Scholar
  7. 7.
    Lebl, M., Solid-phase synthesis on planar supports, Biopolymers, 47 (1998) 397-404.Google Scholar
  8. 8.
    Beck-Sickinger, A. G. and Jung, G., From multiple peptide synthesis to peptide libraries, In G. Jung (Ed.), Combinatorial Peptide and Nonpeptide Libraries. A Handbook, pages: (1996) 79-109, VCH, New York.Google Scholar
  9. 9.
    Schena, M., Shalon, D. D., Davis, R. W. and Brown, P. O., Quantitative monitoring of gene expression patterns with a complementary DNA microarray, Science, 270 (1995) 467-460.Google Scholar
  10. 10.
    Lockhart, D. J., Dong, H., Byrne, M. C., Follettie, M. T., Gallo, M. V., Chee, M. S., Mittmann, M., Wang, C., Kobayashi, M., Horton, H. and Brown, E. L., Expression monitoring by hybridization to high-density oligonucleotide arrays, Nat. Biotech., 14 (1996) 1675-1680.Google Scholar
  11. 11.
    Special issue in DNA microarray data analysis. (2002) December, Nat. Genet.Google Scholar
  12. 12.
    Golub et al., Molecular classification of cancer: class discovery and class prediction by gene expression monitoring, Science, 286 (1999) 531-537.PubMedGoogle Scholar
  13. 13.
    Alizadeh et al., Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling, Nature, 403 (2000) 503-511.PubMedGoogle Scholar
  14. 14.
    Perou et al., Molecular portraits of human breast tumours, Nature, 17 (2000) 747-752.Google Scholar
  15. 15.
    Hughes, T. R. and Shoemaker, D. D., DNA microarrays for expression profiling, Curr. Opin. Chem. Biol., 5 (2001) 21-25.PubMedGoogle Scholar
  16. 16.
    Amin, R. P., Hamadeh, H. K., Bushel, P. R., Bennett, L., Afshari, C. A., Paules, R. S., Genomic interrogation of mechanism(s) underlying cellular responses to toxicants, Toxicology, 27 (2002) 555-563.Google Scholar
  17. 17.
    Wang, D. et al., Large-scale identification, mapping and genotyping of single nucleotide polymorphisms in human genome, Science, 280 (1998) 1077-1098.Google Scholar
  18. 18.
    Heller, M. J., DNA microarray technology: devices, systems, and applications, Annu. Rev. Biomed. Eng., 4 (2002) 129-153.PubMedGoogle Scholar
  19. 19.
    Schweitzer, B. and Kingsmore, S. F., Measuring proteins on microarrays, Curr. Opin. Biotechnol., 13 (2002) 14-19.PubMedGoogle Scholar
  20. 20.
    Zhu, H. and Snyder, M., Protein arrays and microarrays, Curr. Opin. Chem. Biol., 5 (2001) 40-45.PubMedGoogle Scholar
  21. 21.
    Kusnezow, W. and Hoheisel, J. D., Antibody microarrays: promises and problems, Biotechniques 2002 Dec. Suppl., (2002) 14-23.Google Scholar
  22. 22.
    Templin, M. F., Stoll, D., Schrenk, M., Traub, P. C., Vöhringer, C. F. and Joos, T. O., Protein microarray technology, Trends in Biotechnol., 20 (2002) 160–166.Google Scholar
  23. 23.
    Mutulis, F., Tysk, M., Mutule, I. and Wikberg, J. E., A simple and effective method for producing nonrandom peptide libraries using cotton as a carrier in continuous flow Peptide synthesizers, J. Comb. Chem., 13 (2003) 1-7.Google Scholar
  24. 24.
    Matysiak, S., Reuthner, F. and Hoheisel, J. D. Automating parallel peptide synthesis for the production of PNA library arrays, Biotechniques, 31, 896, 898, (2001) 900-902.Google Scholar
  25. 25.
    Pellois, J. P., Zhou, X., Srivannavit, O., Zhou, T., Erdogan, G. and Gao, X., Individually addressable parallel peptide synthesis on microchips, Nat. Biotechnol., 20 (2002) 922-926.PubMedGoogle Scholar
  26. 26.
    Houseman, B. T., Huh, J. H., Kron, S. J. and Mrksich, M., Peptide chips for the quantitative evaluation of protein kinase activity, Nat. Biotechnol., 20 (2002) 270-274.PubMedGoogle Scholar
  27. 27.
    Emili, A. Q. and Cagney, G., Large-scale functional analysis using peptide or protein arrays, Nat. Biotechnol., 18 (2000) 393-397.PubMedGoogle Scholar
  28. 28.
    Toepert, F., Knaute, T., Guffler, S., Pires, J.R., Matzdorf, T., Oschkinat, H. and Schneider-Mergener, J., Combining SPOT synthesis and native peptide ligation to create large arrays of WW protein domains, Angew. Chem. Int. Ed. Engl., 42 (2003) 1136-1140.PubMedGoogle Scholar
  29. 29.
    Winssinger, N., Harris, J. L., Backes, B. J. and Schultz, P. G., From split-pool libraries to spatially addressable microarrays and its application to functional proteomic profiling, Angew. Chem., Int. Ed., 40, (2001) 3152-3155.Google Scholar
  30. 30.
    Salisbury, C. M., Maly, D. J. and Ellman, J. A., Peptide microarrays for the determination of protease substrate specificity, J. Am. Chem. Soc., 124 (2002) 14868-14870.PubMedGoogle Scholar
  31. 31.
    Frank, R., The SPOT-synthesis technique. Synthetic peptide arrays on membrane supports-principles and applications, J. Immunol. Methods, 267 (2002) 13-26.PubMedGoogle Scholar
  32. 32.
    Reimer, U., Reineke, U. and Schneider-Mergener, J., Peptide arrays: from macro to micro, Curr. Opin. Biotechnol., 13 (2002) 315-320.PubMedGoogle Scholar
  33. 33.
    Lam, K. S., Liu, R., Miyamoto, S., Lehman, A. L. and Tuscano, J. M., Applications of one-read one-compound combinatorial libraries and chemical microarrays in signal transduction research, Acc. Chem. Res., 36(6) (2003) 370-377.PubMedGoogle Scholar
  34. 34.
    Bialek, K., Swistowski, A. and Frank, R., Epitope-targeted proteome analysis: towards a large-scale automated protein-protein-interaction mapping utilizing synthetic peptide arrays, Anal. Bioanal. Chem. [Epub ahead of print] PMID: (2003) 12677339.Google Scholar
  35. 35.
    Cho, C. Y., Morgan, E. J., Cherry, S. R., Stephans, J. C., Fodor, S. P. A., Adams, C. L., Sundaram, A., Jacobs, J. W. and Schultz, P. G., Unnatural biopolymer, Science 1993, 261 (1993) 1303-1305.Google Scholar
  36. 36.
    Gao, X., Yu, P. Y., LeProust, E., Sonigo, L., Pellois, J. P. and Zhang, H., Oligonucleotide synthesis using solution photogenerated acids, J. Am. Chem. Soc., 120 (1998) 12698-12699.Google Scholar
  37. 37.
    LeProust, E., Pellois, J. P., Yu, P., Zhang, H., Srivannavit, O., Gulari, E., Zhou, X. and Gao, X., Combinatorial screening method for synthesis optimization on a digital light-controlled microarray platform, J. Comb. Chem., 2 (2000) 349-354.PubMedGoogle Scholar
  38. 38.
    Pellois, J. P., Wang, W. and Gao, X., Peptide synthesis based on t-Boc chemistry and solution photogenerated acids, J. Comb. Chem., 2 (2000) 355-360.PubMedGoogle Scholar
  39. 39.
    Gao, X., LeProust, E., Zhang, H., Srivannavit, O., Gulari, E., Yu, P., Nishiguchi, C., Xiang, Q. and Zhou, X., Flexible DNA chip synthesis gated by deprotection using solution photogenerated acids, Nucleic Acids Res., 29 (2001) 4744-4750.PubMedGoogle Scholar
  40. 40.
    Gao et al., Affinity tag screening for antiflag peptide antibody binging using high density peptide chips, submitted for publication (2003).Google Scholar
  41. 41.
    Komolpis, K., Srivannavit, O. and Gulari, E., Light-directed simultaneous synthesis of oligopeptides on microarray substrate using a photogenerated acid, Biotechnol. Prog., 18 (2002) 641-646.PubMedGoogle Scholar
  42. 42.
    Devlin, J. J., Panganiban, L. C. and Devlin, P. E., Random peptide libraries: a source of specific protein binding molecules, Science, 249 (1990) 404-406.PubMedGoogle Scholar
  43. 43.
    Scott, J. K. and Smith, G. P., Searching for peptide ligands with an epitope library, Science, 249 (1990) 386-390.PubMedGoogle Scholar
  44. 44.
    Felici, F., Castagnoli, L., Musacchio, A., Jappelli, R. and Cesareni, G., Selection of antibody ligands from a large library of oligopeptides expressed on a multivalent exposition vector, J.Mol. Biol., 222 (1991) 301-310.PubMedGoogle Scholar
  45. 45.
    Cwirla, S. E., Peters, E. A., Barrett, R. W. and Dower, W. J., Peptides on phage: a vast library of peptides for identifying ligands, Proc. Natl. Acad. Sci. USA, 87 (1990) 6378-6382.PubMedGoogle Scholar
  46. 46.
    Furka, A., Chemical synthesis of peptide libraries: combinatorial peptide and nonpeptide libraries, In G. Jung (Ed.), A handbook, VCH, New York, (1996) pp. 111-138.Google Scholar
  47. 47.
    Xiao, X. Y., Li, R., Zhuang, H., Ewing, B., Karunaratne, K., Lillig, J., Brown, R. and Nicolaou, K. C., Solid-phase combinatorial synthesis using MicroKan reactors, Rf tagging, and directed sorting, Biotechnol Bioeng., 71 (2000) 44-50.PubMedGoogle Scholar
  48. 48.
    Boger, D. L., Fink, B. E. and Hedrick, M. P., Total synthesis of distamycin A and 2640 analogues, J. Am. Chem. Soc., 122 (2001) 6382-6394.Google Scholar
  49. 49.
    Kuruvilla, F. G., Shamji, A. F., Sternson, S. M., Hergenrother, P. J. and Schreiber, S. L., Dissecting glucose signalling with diversityoriented synthesis and small-molecule microarrays, Nature, 416 (2002) 653-657.PubMedGoogle Scholar
  50. 50.
    J. M. Stewartd amd J. D. Young (Eds.), Solid Phase Peptide Synthesis, Pierce Chemical Co., Rockford, IL, (1984).Google Scholar
  51. 51.
    Espanel, X., Walchli, S., Ruckle, T., Harrenga, A., Huguenin-Reggiani, M. and Hooft Van Huijsduijnen, R., Mapping of synergistic components of weakly interacting protein-protein motifs using arrays of paired peptides, J. Biol. Chem., 278 (2003) 15162-15167.PubMedGoogle Scholar
  52. 52.
    Beier, M. and Hoheisel, J. D., Production by quantitative photolithographic synthesis of individually quality checked DNA microarrays, Nucleic Acids Res., 28 (2000) 11e.Google Scholar
  53. 53.
    Pirrung, M. C. and Bradley, J.-C., Comparison of methods for photochemical phosphoramidite-based DNA synthesis, J. Org. Chem., 60 (1995) 6270-6276.Google Scholar
  54. 54.
    McGall, G. H., Barone, A. D., Diggelmann, M., Fodor, S. P. A., Gentalen, E. and Ngo, N., The efficiency of light-directed synthesis of DNA arrays on glass substrates, J. Am. Chem. Soc., 119 (1997) 5081-5090.Google Scholar
  55. 55.
    MacDonald, S. A., Willson, C. G. and Fréchet, J. M., Chemical amplification in high-resolution imaging systems, Acc. Chem. Res., 27 (1994) 151-157.Google Scholar
  56. 56.
    Willson, C. G., Organic resist materials, In L. F. Thompson, C. G., Willson and M. J. Bowden (Eds.), Introduction to Microlithography, Am. Chem. Soc., Washington D.C. (1994) pp. 138-267.Google Scholar
  57. 57.
    DeVoe, R. J., Olofson, P. M. and Sahyun, M. R. V., Photochemistry and photophysics of 'onium salts, Advances in Photochemistry, 17 (1992) 313-355.Google Scholar
  58. 58.
    Crivello, J. V., Shim, S.-Y, and Smith, B. W., Deep-UV chemically amplified dissolution-inhibited photoresists, Chem. Mater., 6 (1994) 2167-2171.Google Scholar
  59. 59.
    Beecher, J. E., McGall, G. H. and Goldberg, M., Polym. Mater. Sci. Eng., 76 (1997) 394-395.Google Scholar
  60. 60.
    Marshall, J. L., Telfer, S. J., Young, M. A., Lindholm, W. P., Minns, R. A. and Takiff, L., A silver-free, single-sheet imaging medium based on acid amplification, Science, 297 (2002) 1516-1521.PubMedGoogle Scholar
  61. 61.
    Cameron, J. F. and Fréchet, J. M. J., Photogeneration of organic bases from o-nitrobenzyl-derived carbamates, J. Am. Chem. Soc., 113 (1991) 4303-4313.Google Scholar
  62. 62.
    Pellois, J. P., Photogenerated Reagents and Light-Directed Parallel Synthesis of Peptide Microarrays, Thesis, Univ. of Houston, Houston (2002).Google Scholar
  63. 63.
    Serafinowski, P. J. and Garland, P. B., Novel photoacid generators for photodirected oligonucleotide synthesis, J. Am. Chem. Soc., 125 (2003) 962-965.PubMedGoogle Scholar
  64. 64.
    Gao, X. et al., In situ synthesis of oligonucleotide microarrays, Biopolymers, submitted (2003).Google Scholar
  65. 65.
    Garland, P. B. and Serafinowski, P. J., Effects of stray light on the fi-delity of photodirected oligonucleotide array synthesis, Nucleic Acids Res., 30 (2002) e99.PubMedGoogle Scholar
  66. 66.
    Singh-Gasson, S., Green, R. D., Yue, Y., Nelson, C., Blattner, F., Sussman, M. R. and Cerrina, F., Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array, Nat. Biotechnol., 17 (1999) 974-978.PubMedGoogle Scholar
  67. 67.
    Beier, M. and Hoheisel, J. D., Analysis of DNA-microarrays produced by inverse in situ oligonucleotide synthesis, J. Biotechnol., 94 (2002) 15-22.PubMedGoogle Scholar
  68. 68.
    Garner, H. R., Balog, R. P. and Luebke, K. J., The evolution of custom microarray manufacture, IEEE Eng. Med. Biol. Mag., 21 (2002) 123-125.PubMedGoogle Scholar
  69. 69.
    http://www.dlp.com/Google Scholar
  70. 70.
    Stephen, C. W. and Lane, D. P., Mutant conformation of p53. Precise epitope mapping using a filamentous phage epitope library, J. Mol. Biol., 225 (1992) 577-583.PubMedGoogle Scholar
  71. 71.
    Stephen, C.W., Helminen, P. and Lane, D. P., Characterization of epitopes on human p53 using phage displayed peptide libraries: insights into antibody-peptide interactions, J. Mol. Biol., 248 (1995) 58-78.PubMedGoogle Scholar
  72. 72.
    Jellis, C. L., Cradick, T. J., Rennert, P., Salinas, P., Boyd, J., Amirault, T. and Gray, G. S., Defining critical residues in the epitope for a HIVneutralizing monoclonal antibody using phage display and peptide array technologies, Gene, 137 (1993) 63-68.PubMedGoogle Scholar
  73. 73.
    Brannetti, B., Via, A., Cestra, G., Cesareni, G. and Helmer-Citterich, M., SH3-SPOT: an algorithm to predict preferred ligands to different members of the SH3 gene family, J. Mol. Biol., 298 (2000) 313-328.PubMedGoogle Scholar
  74. 74.
    Wegner, G. J., Lee, H. J. and Corn, R. M., Characterization and optimization of peptide arrays for the study of epitope-antibody interactions using surface plastmon resonance imaging, Anal. Chem., 74 (2002) 5161-5168.PubMedGoogle Scholar
  75. 75.
    Zubay, G., In vitro synthesis of protein in microbial systems, Ann. Rev. Genet., 7 (1973) 267-287.PubMedGoogle Scholar
  76. 76.
    Jermutus, L., Ryabova, L. A. and Pluckthun, A., Recent advances in producing and selecting functional proteins by using cell-free translation, Curr. Opin. Biotechnol., 9 (1998) 534-548.PubMedGoogle Scholar
  77. 77.
    Braun, P., Hu, Y., Shen, B., Halleck, A., Koundinya, M., Harlow, E. and LaBaer, J., Proteome-scale purification of human proteins from bacteria, Proc. Natl. Acad. Sci. USA, 99 (2002) 2654-2659.PubMedGoogle Scholar
  78. 78.
    Yokoyama, S., Protein expression systems for structural genomics and proteomics, Curr. Opin. Chem. Biol., 7 (2003) 39-43.PubMedGoogle Scholar
  79. 79.
    Li, S. and Roberts, R. W., A novel strategy for in vitro selection of peptide-drug conjugates, Chem. Biol., 10 (2003) 233-239.PubMedGoogle Scholar

Copyright information

© Kluwer Academic Publishers 2004

Authors and Affiliations

  • Xiaolian Gao
    • 1
  • Jean Philippe Pellois
    • 1
  • Younghwa Na
    • 1
  • Younkee Kim
    • 2
  • Erdogan Gulari
    • 3
  • Xiaochuan Zhou
    • 4
  1. 1.Department of ChemistryUniversity of HoustonHouston
  2. 2.Xeotron CoHouston
  3. 3.Department of Chemical EngineeringUniversity of MichiganAnn Arbor
  4. 4.Atactic Technologies Inc.Houston

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