title: Rational design of DNA sequence-specific zinc fingers.
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.
authors.affiliation: Molecular Modeling and Simulation, Quantum Beam Science Directorate, Japan Atomic Energy Agency, Kizugawa, Kyoto, Japan. kono.hidetoshi@jaea.go.jp
authors.forename: Hidetoshi
authors.initials: H
authors.lastname: Kono
authors.forename: Miki
authors.initials: M
authors.lastname: Imanishi
authors.forename: Shigeru
authors.initials: S
authors.lastname: Negi
authors.forename: Kazuya
authors.initials: K
authors.lastname: Tatsutani
authors.forename: Yui
authors.initials: Y
authors.lastname: Sakaeda
authors.forename: Ayaka
authors.initials: A
authors.lastname: Hashimoto
authors.forename: Chie
authors.initials: C
authors.lastname: Nakayama
authors.forename: Shiroh
authors.initials: S
authors.lastname: Futaki
authors.forename: Yukio
authors.initials: Y
authors.lastname: Sugiura
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D001665:Binding Sites; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D011487:Protein Conformation; D015202:Protein Engineering / Q000379:methods*; D017510:Protein Folding; D016335:Zinc Fingers / Q000235:genetics*
chemical_list: D004268:DNA-Binding Proteins