High-Throughput Profiling of Peptide–RNA Interactions Using Peptide Microarrays

Jaeyoung Pai †, Taejin Yoon †, Nam Doo Kim ‡, Im-Soon Lee §, Jaehoon Yu *, and Injae Shin *†

^† National Creative Research Center for Biofunctional Molecules, Department of Chemistry, Yonsei University, Seoul 120-749, Korea

^‡ New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 706-010, Korea

^§ Department of Biological Sciences, Konkuk University, Seoul 143-701, Korea

 Department of Chemistry and Education, Seoul National University, Seoul 151-742, Korea

J. Am. Chem. Soc., Article ASAP

DOI: 10.1021/ja309760g

Publication Date (Web): October 30, 2012

Copyright © 2012 American Chemical Society

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 (K_d) 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 K_d 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.