The combinatorial method has been applied to determine peptide ligands to the duplex DNA by using the solid-state pentapeptide library and the target-DNA conjugated magnetic beads. Seventy-one sequences were determined as ligands for AT duplex. Interestingly, hydrophobic amino acids such as Phe, Ile and Gly were most frequently determined. Relative binding affinity of the selected pentapeptides with the various DNA sequences was estimated by ethidium displacement assay in 10 mM SHE buffer. FQGII constituted of amino acids that were most frequently determined in the random screening showed highest binding affinity to the duplex DNA.
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