High-Throughput Profiling
of Peptide–RNA Interactions
Using Peptide Microarrays
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Abstract
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 (<i>K</i><sub>d</sub>) 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 <i>K</i><sub>d</sub> 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