Antibodies have traditionally been used for isolating affinity reagents to new molecular targets, but alternative protein scaffolds are increasingly being used for the directed evolution of proteins with novel molecular recognition properties. We have designed a combinatorial library based on the DNA binding domain of the human retinoid-X-receptor (hRXRalpha). We chose this domain because of its small size, stable fold, and two closely juxtaposed recognition loops. We replaced the two loops with segments of random amino acids, and used mRNA display to isolate variants that specifically recognize adenosine triphosphate (ATP), demonstrating a significant alteration of the function of this protein domain from DNA binding to ATP recognition. Many novel independent sequences were recovered with moderate affinity and high specificity for ATP, validating this scaffold for the generation of functional molecules.
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