Functional RNA microarrays for high-throughput screening of antiprotein aptamers

James R. Collett, Eun Jeong Cho, Jennifer F. Lee, Matthew Levy, Allysia J. Hood, Christine Wan, Andrew D. Ellington

Research output: Contribution to journalArticle

76 Scopus citations

Abstract

High-throughput methods for generating aptamer microarrays are described. As a proof-of-principle, the microarrays were used to screen the affinity and specificity of a pool of robotically selected antilysozyme RNA aptamers. Aptamers were transcribed in vitro in reactions supplemented with biotinyl-guanosine 5′-monophosphate, which led to the specific addition of a 5′ biotin moiety, and then spotted on streptavidin-coated microarray slides. The aptamers captured target protein in a dose-dependent manner, with linear signal response ranges that covered seven orders of magnitude and a lower limit of detection of 1 pg/mL (70 fM). Aptamers on the microarray retained their specificity for target protein in the presence of a 10,000-fold (w/w) excess of T-4 cell lysate protein. The RNA aptamer microarrays performed comparably to current antibody microarrays and within the clinically relevant ranges of many disease biomarkers. These methods should also prove useful for generating other functional RNA microarrays, including arrays for genomic noncoding RNAs that bind proteins. Integrating RNA aptamer microarray production with the maturing technology for automated in vitro selection of antiprotein aptamers should result in the high-throughput production of proteome chips.

Original languageEnglish (US)
Pages (from-to)113-123
Number of pages11
JournalAnalytical Biochemistry
Volume338
Issue number1
DOIs
StatePublished - Mar 1 2005

Keywords

  • Functional RNA
  • High-throughput screening
  • Microarray
  • Protein detection
  • Proteomics
  • RNA aptamer

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Molecular Biology
  • Cell Biology

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  • Cite this

    Collett, J. R., Cho, E. J., Lee, J. F., Levy, M., Hood, A. J., Wan, C., & Ellington, A. D. (2005). Functional RNA microarrays for high-throughput screening of antiprotein aptamers. Analytical Biochemistry, 338(1), 113-123. https://doi.org/10.1016/j.ab.2004.11.027