Dna-binding protein using ppr motif, and use thereof

A method for preparing a protein that can bind in a DNA base-selective manner or a DNA base sequence-specific manner, comprising:

• providing a nucleic acid sequence encoding a protein;
• cloning said nucleic acid sequence;
• and
• preparing a transformant which produces the protein,
• wherein the protein contains one or more PPR motifs having a structure of the following formula 1:
• (Helix A)-X-(Helix B)-L (Formula 1)
• (wherein, in the formula 1:
• Helix A is a part that can form an α-helix structure;
• X does not exist, or is a part consisting of 1 to 9 amino acids;
• Helix B is a part that can form an α-helix structure;
• and
• L is a part consisting of 2 to 7 amino acids),
• wherein,
• under the following definitions:
• the first amino acid of Helix A is referred to as Number 1 amino acid (Number 1 AA), the fourth amino acid as Number 4 amino acid (Number 4 AA), and
• when a next PPR motif (Mn+1) contiguously exists on the C-terminus side of the PPR motif (Mn) (when there is no amino acid insertion between the PPR motifs), the −2nd amino acid counted from the end (C-terminus side) of the amino acids constituting the PPR motif (Mn);
• when a non-PPR motif consisting of 1 to 20 amino acids exists between the PPR motif (Mn) and the next PPR motif (Mn+1) on the C-terminus side, the amino acid locating upstream of the first amino acid of the next PPR motif (Mn+1) by 2 positions, i.e., the −2nd amino acid;
• or
• when any next PPR motif (Mn+1) does not exist on the C-terminus side of the PPR motif (Mn), or 21 or more amino acids constituting a non-PPR motif exist between the PPR motif (Mn) and the next PPR motif (Mn+1) on the C-terminus side, the 2nd amino acid counted from the end (C-terminus side) of the amino acids constituting the PPR motif (Mn)
• is referred to as Number “ii” (−2) amino acid (Number “ii” (−2) AA),
• one PPR motif (Mn) contained in the protein is a PPR motif having a specific combination of amino acids corresponding to a target DNA base or target DNA base sequence as the three amino acids of Number 1 AA, Number 4 AA, and Number “ii” (−2) AA.