Article ID Journal Published Year Pages File Type
2048519 FEBS Letters 2012 6 Pages PDF
Abstract

We developed a rational scheme for designing DNA binding proteins. The scheme was applied for a zinc finger protein and the designed sequences were experimentally characterized with high DNA sequence specificity. Starting with the backbone of a known finger structure, we initially calculated amino acid sequences compatible with the expected structure and the secondary structures of the designed fingers were then experimentally confirmed. The DNA-binding function was added to the designed finger by reconsidering a section of the amino acid sequence and computationally selecting amino acids to have the lowest protein–DNA interaction energy for the target DNA sequences. Among the designed proteins, one had a gap between the lowest and second lowest protein–DNA interaction energies that was sufficient to give DNA sequence-specificity.

► A rational scheme for computationally designing DNA binding proteins is proposed. ► The structure and binding of the designed proteins were experimentally validated. ► A large energy gap between the lowest and the second sequences gives binding specificity.

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