Identification of small peptides that interact specifically with a small organic dye

Using a 'one-bead one-peptide' combinatorial peptide library method, we have been able to identify peptide ligands that interact specifically with various macromolecular targets such as monoclonal antibodies, streptavidin, avidin, MHC-Class molecules, proteases, growth factor receptors, and gpIIb/IIIa integrin. In this paper, we test the hypothesis that small peptides that interact specifically with a small organic molecule can also be identified using this combinatorial peptide method. Using a small organic dye molecule, indigo carmine, as a color probe to screen a random L-heptapeptide and two D-hexa and octapeptide libraries, we were able to identify a specific peptide binding motif. Potential applications of this technology are described.