DNA-binding ligands from peptide libraries containing unnatural amino acids

An unnatural peptide-based library bound on a solid support, was screened for double-stranded-DNA (dsDNA)-binding ligands. For this purpose, fluorescein and rhodamine were used to label the single-stranded oligodeoxynucleotides, Beads containing products with affinity to dsDNA turned red in visible light and fluoresced yellow in UV light. A similar technique can be used for the selection of ligands which bind to a hairpin RNA, using a monolabelled oligoribonucleotide. The screening process revealed a high structure-affinity relationship in the successful products, Only six out of the twelve unnatural amino acids were selected, with the repeated appearance of AlaU, Sar and the secondary amino acids (Hyp, Inp). The affinity and selectivity for the target was determined using a DNase I protection assay.