Rational design of DNA sequence-specific zinc fingers

河野 秀俊; 今西 未来*; 根木 滋*; 辰谷 和弥*; 栄田 優衣*; 橋本 彩加*; 中山 千絵*; 二木 史朗*; 杉浦 幸雄*

FEBS Letters, 586(6), p.918 - 923, 2012/03

https://doi.org/10.1016/j.febslet.2012.02.025

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 that expected structure and the designed fingers were experimentally confirmed their expected secondary structures. The DNA-binding function was then 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.