Rational design of DNA sequence-specific zinc fingers |
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Authors: | Kono Hidetoshi Imanishi Miki Negi Shigeru Tatsutani Kazuya Sakaeda Yui Hashimoto Ayaka Nakayama Chie Futaki Shiroh Sugiura Yukio |
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Affiliation: | Molecular Modeling and Simulation, Quantum Beam Science Directorate, Japan Atomic Energy Agency, Kizugawa, Kyoto, Japan. kono.hidetoshi@jaea.go.jp |
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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. |
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