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μParaflo™ Biochip for Nucleic Acid and Protein Analysis

  • Protocol
Microarrays

Part of the book series: Methods in Molecular Biology ((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.

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References

  1. Gao, X., Gulari, E., and Zhou, X. (2004) In situ synthesis of oligonucleotide microarrays. Biopolymers 73, 579–596.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  5. Ekins, R. P. (1989) Multi-analyte immunoassay. J. Pharm. Biomed. Anal. 7, 155–168.

    Article  CAS  Google Scholar 

  6. Mirzabekov, A. and Kolchinsky, A. (2002) Emerging array-based technologies in proteomics. Curr. Opin. Chem. Biol. 6, 70–75.

    Article  CAS  Google Scholar 

  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.

    Article  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  9. Ekins, R. P. (1998) Ligand assays: from electrophoresis to miniaturized microarrays. Clin. Chem. 44, 2015–2030.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  11. The chipping forecast. (1999) Nat. Genet. Suppl 21, 3–60.

    Article  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  14. Blanchard, A. P., Kaiser, R. J., and Hood, L. E. (1996) High-density oligonucleotide arrays. Biosens. Bioelectron 11, 687–690.

    Article  CAS  Google Scholar 

  15. Blanchard, A. P. and Hood, L. E. (1996) Sequence to array: probing the genome’s secrets. Nat. BioTechnol. 14, 1649.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  Google Scholar 

  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. 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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  Google Scholar 

  25. Frank, R. (2002) The SPOT-synthesis technique. Synthetic peptide arrays on membrane supports—principles and applications. J. Immunol. Methods 267, 13–26.

    Article  CAS  Google Scholar 

  26. Reimer, U., Reineke, U., and Schneider-Mergener, J. (2002) Peptide arrays: from macro to micro. Curr. Opin. Biotechnol. 13, 315–320.

    Article  CAS  Google Scholar 

  27. Lam, K. S. and Renil, M. (2002) From combinatorial chemistry to chemical microarray. Curr. Opin. Chem. Biol. 6, 353–358.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  34. Li, S., Bowerman, D., Marthandan, N., et al. (2004) Photolithographic synthesis of peptoids. J. Am. Chem. Soc. 126, 4088–4089.

    Article  CAS  Google Scholar 

  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.

    Article  Google Scholar 

  36. http://microrna.sanger.ac.uk/cgi-bin/sequences/browse.pl.

    Google Scholar 

  37. http://www.protocol-online.org/prot/Molecular_Biology/RNA/RNA_Extraction/Total_RNA_Isolation/.

    Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  44. Lee, R. C. and Ambros, V. (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science 294, 862–864.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  Google Scholar 

  54. Sioud, M. and Rosok, O. (2004) Profiling microRNA expression using sensitive cDNA probes and filter arrays. Biotechniques 37, 574–576, 578–580.

    CAS  Google Scholar 

  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.

    Article  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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. http://www.genisphere.com/pdf/array900_mirna_direct_manual_12_15_04.pdf.

    Google Scholar 

  60. http://las.perkinelmer.com; http://las.perkinelmer.com/content/manuals/mps545.pdf.

    Google Scholar 

  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.

    Article  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Biology and Biochemistry, University of Houston, Houston, TX

    Qi Zhu, Kyu-Yeon Jun & Xiaolian Gao

  2. Atactic Technologies Inc., Houston, TX

    Ailing Hong, Nijing Sheng, Xiaolin Zhang, Anna Matejko, Onnop Srivannavit & Xiaochuan Zhou

  3. Department of Chemical Engineering, University of Michigan, Ann Arbor, MI

    Erdogan Gulari

Authors
  1. Qi Zhu
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  2. Ailing Hong
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  3. Nijing Sheng
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  4. Xiaolin Zhang
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  5. Anna Matejko
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  6. Kyu-Yeon Jun
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  7. Onnop Srivannavit
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  8. Erdogan Gulari
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  9. Xiaolian Gao
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  10. Xiaochuan Zhou
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Editors and Affiliations

  1. Beckman Coulter, Inc., Brea, CA

    Jang B. Rampal

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© 2007 Humana Press Inc., Totowa, NJ

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Zhu, Q. et al. (2007). μParaflo™ Biochip for Nucleic Acid and Protein Analysis. In: Rampal, J.B. (eds) Microarrays. Methods in Molecular Biology, vol 382. Humana Press. https://doi.org/10.1007/978-1-59745-304-2_19

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  • DOI: https://doi.org/10.1007/978-1-59745-304-2_19

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-944-4

  • Online ISBN: 978-1-59745-304-2

  • eBook Packages: Springer Protocols

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