High-throughput profiling of peptide-RNA interactions using peptide microarrays

Jaeyoung Pai, Taejin Yoon, Nam Doo Kim, Im Soon Lee, Jaehoon Yu, Injae Shin

Research output: Contribution to journalArticlepeer-review

36 Citations (Scopus)


A rapid and quantitative method to evaluate binding properties of hairpin RNAs to peptides using peptide microarrays has been developed. The microarray technology was shown to be a powerful tool for high-throughput analysis of RNA-peptide interactions by its application to profiling interactions between 111 peptides and six hairpin RNAs. The peptide microarrays were also employed to measure hundreds of dissociation constants (Kd) of RNA-peptide complexes. Our results reveal that both hydrophobic and hydrophilic faces of amphiphilic peptides are likely involved in interactions with RNAs. Furthermore, these results also show that most of the tested peptides bind hairpin RNAs with submicromolar Kd values. One of the peptides identified by using this method was found to have good inhibitory activity against TAR-Tat interactions in cells. Because of their great applicability to evaluation of nearly all types of RNA-peptide interactions, peptide microarrays are expected to serve as robust tools for rapid assessment of peptide-RNA interactions and development of peptide ligands against RNA targets.

Original languageEnglish
Pages (from-to)19287-19296
Number of pages10
JournalJournal of the American Chemical Society
Issue number46
Publication statusPublished - 2012 Nov 21

All Science Journal Classification (ASJC) codes

  • Catalysis
  • General Chemistry
  • Biochemistry
  • Colloid and Surface Chemistry


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