Microarrays pp 287-312 | Cite as

μParaflo™ Biochip for Nucleic Acid and Protein Analysis

  • Qi Zhu
  • Ailing Hong
  • Nijing Sheng
  • Xiaolin Zhang
  • Anna Matejko
  • Kyu-Yeon Jun
  • Onnop Srivannavit
  • Erdogan Gulari
  • Xiaolian Gao
  • Xiaochuan Zhou
Part of the Methods in Molecular Biology book series (MIMB, volume 382)

Abstract

We describe in this chapter the use of oligonucleotide or peptide microarrays (arrays) based on microfluidic chips. Specifically, three major applications are presented: (1) microRNA/small RNA detection using a microRNA detection chip, (2) protein binding and function analysis using epitope, kinase substrate, or phosphopeptide chips, and (3) protein-binding analysis using oligonucleotide chips. These diverse categories of customizable arrays are based on the same biochip platform featuring a significant amount of flexibility in the sequence design to suit a wide range of research needs. The protocols of the array applications play a critical role in obtaining high quality and reliable results. Given the comprehensive and complex nature of the array experiments, the details presented in this chapter is intended merely as a useful information source of reference or a starting point for many researchers who are interested in genomeor proteome-scale studies of proteins and nucleic acids and their interactions.

Key Words

Aptamer microarray digital photolithography epitope-antibody profiling epitope screening kinase profiling assay microfluidic biochip micro-RNA detection oligoncleotide microarray peptide microarray microfluidics parallel synthesis phosphopeptide-protein binding photogenerated acid picoarray protein-binding 

References

  1. 1.
    Gao, X., Gulari, E., and Zhou, X. (2004) In situ synthesis of oligonucleotide microarrays. Biopolymers 73, 579–596.CrossRefGoogle Scholar
  2. 2.
    Zhou, X., Cai, S., Hong, A., et al. (2004) Microfluidic PicoArray synthesis of oligodeoxynucleotides and simultaneous assembling of multiple DNA sequences. Nucleic Acids Res. 32, 5409–5417.CrossRefGoogle Scholar
  3. 3.
    Gao, X., Pellois, J. P., Na, Y., Kim, Y., Gulari, E., and Zhou, X. (2004) High density peptide microarrays. In situ synthesis and applications. Mol. Divers 8, 177–187.CrossRefGoogle Scholar
  4. 4.
    Hinds, D. A., Stuve, L. L., Nilsen, G. B., et al. (2005) Whole-genome patterns of common DNA variation in three human populations. Science 307, 1072–1079.CrossRefGoogle Scholar
  5. 5.
    Ekins, R. P. (1989) Multi-analyte immunoassay. J. Pharm. Biomed. Anal. 7, 155–168.CrossRefGoogle Scholar
  6. 6.
    Mirzabekov, A. and Kolchinsky, A. (2002) Emerging array-based technologies in proteomics. Curr. Opin. Chem. Biol. 6, 70–75.CrossRefGoogle Scholar
  7. 7.
    Schena, M., Shalon, D. D., Davis, R. W., and Brown, P. O. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 460–467.CrossRefGoogle Scholar
  8. 8.
    Lockhart, D. J., Dong, H., Byrne, M. C., et al. (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotech. 14, 1675–1680.CrossRefGoogle Scholar
  9. 9.
    Ekins, R. P. (1998) Ligand assays: from electrophoresis to miniaturized microarrays. Clin. Chem. 44, 2015–2030.Google Scholar
  10. 10.
    Stoll, D., Templin, M. F., Bachmann, J., and Joos, T. O. (2005) Protein microarrays: applications and future challenges. Curr. Opin. Drug. Discov. Devel. 8, 239–252.Google Scholar
  11. 11.
    The chipping forecast. (1999) Nat. Genet. Suppl 21, 3–60.CrossRefGoogle Scholar
  12. 12.
    Fodor, S. P., Leighton, P. A. J., Pirrung, M. C., Stryer, L., and Solas, D. (1991) Light-directed spatially addressable parallel chemical synthesis. Science 251, 767–773.CrossRefGoogle Scholar
  13. 13.
    Maskos, U. and Southern, E. M. (1992) Parallel analysis of oligodeoxyribonucleotide (oligonucleotide) interactions. I. Analysis of factors influencing oligonucleotide duplex formation. Nucleic Acids Res. 20, 1675–1678.CrossRefGoogle Scholar
  14. 14.
    Blanchard, A. P., Kaiser, R. J., and Hood, L. E. (1996) High-density oligonucleotide arrays. Biosens. Bioelectron 11, 687–690.CrossRefGoogle Scholar
  15. 15.
    Blanchard, A. P. and Hood, L. E. (1996) Sequence to array: probing the genome’s secrets. Nat. BioTechnol. 14, 1649.CrossRefGoogle Scholar
  16. 16.
    Gao, X., Yu, P. Y., LeProust, E., Sonigo, L., Pellois, J. P., and Zhang, H. (1998) Oligonucleotide synthesis using solution photogenerated acids. J. Am. Chem. Soc. 120, 12,698–12,699.CrossRefGoogle Scholar
  17. 17.
    Singh-Gasson, S., Green, R. D., Yue, Y., et al. (1999) Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nat. Biotech. 17, 974–978.CrossRefGoogle Scholar
  18. 18.
    Gao, X., LeProust, E., Zhang, H., et al. (2001) Flexible DNA chip synthesis gated by deprotection using solution photogenerated acids. Nucleic Acids Res. 29, 4744–4750.CrossRefGoogle Scholar
  19. 19.
    Hughes, T. R., Mao, M., Jones, A. R., et al. (2001) Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat. Biotechnol. 19, 342–347.CrossRefGoogle Scholar
  20. 20.
    Bulter, J. H., Cronin, M., Anderson, K. M., et al. (2001) In situ synthesis of oligonucleotide arrays by using surface tension. J. Am. Chem. Soc. 123, 8887–8894.CrossRefGoogle Scholar
  21. 21.
    McGall, G. H. and Fidanza, J. A. (2001) DNA Microarrays: photolithographic synthesis of high-density oligonucleotide arrays: in Methods and Protocols in Molecular Biology, vol. 170 (Rampal, J. B., ed.), Humana, Totowa, NJ, pp. 71–101.Google Scholar
  22. 22.
    Luebke1, K. J., Balog, R. P., and Garner, H. R. (2003) Prioritized selection of oligodeoxyribonucleotide probes for efficient hybridization to RNA transcripts. Nucleic Acids Res. 31, 750–758.CrossRefGoogle Scholar
  23. 23.
    Tesfu, E., Maurer, K., Ragsdale, S. R., and Moeller, K. D. (2004) Building addressable libraries: the use of electrochemistry for generating reactive Pd(II) reagents at preselected sites on a chip. J. Am. Chem. Soc. 126, 6212–6213.CrossRefGoogle Scholar
  24. 24.
    Srivannavit, O., Gulari, M., Gulari, E., et al. (2004) Design and fabrication of microwell array chips for a solution-based, photogenerated acid-catalyzed parallel oligonucleotide DNA synthesis. Sensors Actuators A 116, 150–160.CrossRefGoogle Scholar
  25. 25.
    Frank, R. (2002) The SPOT-synthesis technique. Synthetic peptide arrays on membrane supports—principles and applications. J. Immunol. Methods 267, 13–26.CrossRefGoogle Scholar
  26. 26.
    Reimer, U., Reineke, U., and Schneider-Mergener, J. (2002) Peptide arrays: from macro to micro. Curr. Opin. Biotechnol. 13, 315–320.CrossRefGoogle Scholar
  27. 27.
    Lam, K. S. and Renil, M. (2002) From combinatorial chemistry to chemical microarray. Curr. Opin. Chem. Biol. 6, 353–358.CrossRefGoogle Scholar
  28. 28.
    Panse, S., Dong, L., Burian, A., et al. (2004) Profiling of generic anti-phosphopeptide antibodies and kinases with peptide microarrays using radioactive and fluorescence-based assays. Mol. Divers 8, 291–299.CrossRefGoogle Scholar
  29. 29.
    Pease, A. C., Solas, D., Sullivan, E. J., Cronin, M. T., Holmes, C. P., and Fodor, S. P. (1994) Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc. Natl. Acad. Sci. USA 91, 5022–5026.CrossRefGoogle Scholar
  30. 30.
    Holmes, C. P., Adams, C. L., Kochersperger, L. M., Mortensen, R. B., and Aldwin, L. A. (1995) The use of light-directed combinatorial peptide synthesis in epitope mapping. Biopolymers 37, 199–211.CrossRefGoogle Scholar
  31. 31.
    Pellois, J. P., Wang, W., and Gao, X. (2000) Peptide synthesis based on t-Boc chemistry and solution photogenerated acids. J. Comb. Chem. 2, 355–360.CrossRefGoogle Scholar
  32. 32.
    Pellois, J. P., Zhou, X., Srivannavit, O., Zhou, T., Gulari, E., and Gao, X. (2002) Individually addressable parallel peptide synthesis on microchips. Nat. Biotechnol. 20, 922–926.CrossRefGoogle Scholar
  33. 33.
    Komolpis, K., Srivannavit, O., and Gulari, E. (2002) Light-directed simultaneous synthesis of oligopeptides on microarray substrate using a photogenerated acid. Biotechnol. Prog. 18, 641–646.CrossRefGoogle Scholar
  34. 34.
    Li, S., Bowerman, D., Marthandan, N., et al. (2004) Photolithographic synthesis of peptoids. J. Am. Chem. Soc. 126, 4088–4089.CrossRefGoogle Scholar
  35. 35.
    Li, S., Marthandan, N., Bowerman, D., Garner, H. R., and Kodadek, T. (2005) Photolithographic synthesis of cyclic peptide arrays using a differential deprotection strategy. Chem. Commun. (Camb) 2005, 581–583.CrossRefGoogle Scholar
  36. 36.
    http://microrna.sanger.ac.uk/cgi-bin/sequences/browse.pl.Google Scholar
  37. 37.
    http://www.protocol-online.org/prot/Molecular_Biology/RNA/RNA_Extraction/Total_RNA_Isolation/.Google Scholar
  38. 38.
    Sun, X. J., Crimmins, D. L., Myers, M. G. Jr., Miralpeix, M., and White, M. F. (1993) Pleiotropic insulin signals are engaged by multisite phosphorylation of IRS-1. Mol. Cell Biol. 13, 7418–7428.Google Scholar
  39. 39.
    Hers, I., Bell, C. J., Poole, A. W., et al. (2002) Reciprocal feedback regulation of insulin receptor and insulin receptor substrate tyrosine phosphorylation by phosphoinositide 3-kinase in primary adipocytes. Biochem. J. 368, 875–884.CrossRefGoogle Scholar
  40. 40.
    Lehr, S., Kotzka, J., Herkner, A., et al. (2000) Identification of major tyrosine phosphorylation sites in the human insulin receptor substrate Gab-1 by insulin receptor kinase in vitro. Biochemistry 39, 10,898–10,907.CrossRefGoogle Scholar
  41. 41.
    Lehr, S., Kotzka, J., Herkner, A., et al. (1999) Identification of tyrosine phosphorylation sites in human Gab-1 protein by EGF receptor kinase in vitro. Biochemistry 38, 151–159.CrossRefGoogle Scholar
  42. 42.
    Yokote, K., Mori, S., Hansen, K., et al. (1994) Direct interaction between Shc and the platelet-derived growth factor beta-receptor. J. Biol. Chem. 269, 15,337–15,343.Google Scholar
  43. 43.
    Lagos-Quintana, M., Rauhut, R., Lendeckel, W., and Tuschl, T. (2001) Identification of novel genes coding for small expressed RNAs. Science 294, 853–858.CrossRefGoogle Scholar
  44. 44.
    Lee, R. C. and Ambros, V. (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science 294, 862–864.CrossRefGoogle Scholar
  45. 45.
    Thomson, J. M., Parker, J., Perou, C. M., and Hammond, S. M. (2004) A custom microarray platform for analysis of microRNA gene expression. Nat. Methods 1, 47–53.CrossRefGoogle Scholar
  46. 46.
    Nelson, P. T., Baldwin, D. A., Scearce, L. M., Oberholtzer, J. C., Tobias, J. W., and Mourelatos, Z. (2004) Microarray-based, high-throughput gene expression profiling of microRNAs. Nat. Methods 1, 155–161.CrossRefGoogle Scholar
  47. 47.
    Liang, R. Q., Li, W., Li, Y., et al. (2005) An oligonucleotide microarray for microRNA expression analysis based on labeling RNA with quantum dot and nanogold probe. Nucleic Acids Res. 33, E17.CrossRefGoogle Scholar
  48. 48.
    Shingara, J., Keiger, K., Shelton, J., et al. (2005) An optimized isolation and labeling platform for accurate microRNA expression profiling. RNA 11, 1461–1470.CrossRefGoogle Scholar
  49. 49.
    Barad, O., Meiri, E., Avniel, A., et al. (2004) MicroRNA expression detected by oligonucleotide microarrays: system establishment and expression profiling in human tissues. Genome Res. 14, 2486–2494.CrossRefGoogle Scholar
  50. 50.
    Liu, C. G., Calin, G. A., Meloon, B., et al. (2004) An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. Proc. Natl. Acad. Sci. USA 101, 9740–9744.CrossRefGoogle Scholar
  51. 51.
    Babak, T., Zhang, W., Morris, Q., Blencowe, B. J., and Hughes, T. R. (2004) Probing microRNAs with microarrays: tissue specificity and functional inference. RNA 10, 1813–1819.CrossRefGoogle Scholar
  52. 52.
    Baskerville, S. and Bartel, D. P. (2005) Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 11, 241–247.CrossRefGoogle Scholar
  53. 53.
    Miska, E. A., Alvarez-Saavedra, E., Townsend, M., et al. (2004) Microarray analysis of microRNA expression in the developing mammalian brain. Genome Biol. 5, R68.CrossRefGoogle Scholar
  54. 54.
    Sioud, M. and Rosok, O. (2004) Profiling microRNA expression using sensitive cDNA probes and filter arrays. Biotechniques 37, 574–576, 578–580.Google Scholar
  55. 55.
    Sun, Y., Koo, S., White, N., et al. (2004) Development of a micro-array to detect human and mouse microRNAs and characterization of expression in human organs. Nucleic Acids Res. 32, E188.CrossRefGoogle Scholar
  56. 56.
    Krichevsky, A. M., King, K. S., Donahue, C. P., Khrapko, K., and Kosik, K. S. (2003) A microRNA array reveals extensive regulation of microRNAs during brain development. RNA 9, 1274–1281.CrossRefGoogle Scholar
  57. 57.
    Lau, N. C., Lim, L. P., Weinstein, E. G., and Bartel, D. P. (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294, 858–862.CrossRefGoogle Scholar
  58. 58.
    See Protocol listed in http://www.protocol-online.org/prot/Molecular_Biology/RNA/microRNA/microRNA_Cloning/ and http://web.wi.mit.edu/bartel/pub/protocols/miRNAcloning.pdf.Google Scholar
  59. 59.
    http://www.genisphere.com/pdf/array900_mirna_direct_manual_12_15_04.pdf.Google Scholar
  60. 60.
    http://las.perkinelmer.com; http://las.perkinelmer.com/content/manuals/mps545.pdf.Google Scholar
  61. 61.
    Bulyk, M. L., Gentalen, E., Lockhart, D. J., and Church, G. M. (1999) Quantifying DNA-protein interactions by double-stranded DNA arrays. Nat. Biotechnol. 17, 536–537.CrossRefGoogle Scholar
  62. 62.
    Bulyk, M. L., Huang, X., Choo, Y., and Church, G. M. (2001) Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proc. Natl. Acad. Sci. USA 98, 7158–7163.CrossRefGoogle Scholar
  63. 63.
    Krylov, A. S., Zasedateleva, O. A., Prokopenko, D. V., Rouviere-Yaniv, J., and Mirzabekov, A. D. (2001) Massive parallel analysis of the binding specificity of histone-like protein HU to single-and double-stranded DNA with generic oligodeoxyribonucleotide microchips. Nucleic Acids Res. 29, 2654–2660.CrossRefGoogle Scholar
  64. 64.
    Bulyk, M. L., Johnson, P. L., and Church, G. M. (2002) Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res. 30, 255–261.CrossRefGoogle Scholar
  65. 65.
    Wang, J., Bai, Y., Li, T., and Lu, Z. (2003) DNA microarrays with unimolecular hairpin double-stranded DNA probes: fabrication and exploration of sequencespecific DNA/protein interactions. J. Biochem. Biophys. Methods 55, 215–232.CrossRefGoogle Scholar
  66. 66.
    Wang, J. K., Li, T. X., Bai, Y. F., and Lu, Z. H. (2003) Evaluating the binding affinities of NF-kappaB p50 homodimer to the wild-type and single-nucleotide mutant Ig-kappaB sites by the unimolecular dsDNA microarray. Anal. Biochem. 316, 192–201.CrossRefGoogle Scholar
  67. 67.
    Mukherjee, S., Berger, M. F., Jona, G., et al. (2004) Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nat. Genetics 36, 1331–1339.CrossRefGoogle Scholar
  68. 68.
    Yamamoto-Fujita, R. and Kumar, P. K. (2005) Aptamer-derived nucleic acid oligos: applications to develop nucleic acid chips to analyze proteins and small ligands. Anal. Chem. 77, 5460–5466.CrossRefGoogle Scholar
  69. 69.
    Collett, J. R., Cho, E. J., Lee, J. F., et al. (2005) Functional RNA microarrays for high-throughput screening of antiprotein aptamers. Anal. Biochem. 338, 113–123.CrossRefGoogle Scholar

Copyright information

© Humana Press Inc., Totowa, NJ 2007

Authors and Affiliations

  • Qi Zhu
    • 1
  • Ailing Hong
    • 2
  • Nijing Sheng
    • 2
  • Xiaolin Zhang
    • 2
  • Anna Matejko
    • 2
  • Kyu-Yeon Jun
    • 1
  • Onnop Srivannavit
    • 2
  • Erdogan Gulari
    • 3
  • Xiaolian Gao
    • 1
  • Xiaochuan Zhou
    • 2
  1. 1.Department of Biology and BiochemistryUniversity of HoustonHouston
  2. 2.Atactic Technologies Inc.Houston
  3. 3.Department of Chemical EngineeringUniversity of MichiganAnn Arbor

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