A method for preparing a protein comprising designing a protein that can bind to an RNA molecule in an RNA base-selective or RNA base sequence-specific manner, the method comprising: designing a protein that specifically binds to RNA having a specific sequence by paying attention to the combination of amino acids A 1, A 4, and L ii or the combination of amino acids A 4 and L ii, wherein the protein contains one or more of PPR motifs each consisting of a polypeptide of 30- to 38-amino acid length represented by the formula 1: (HelixA)-X-(HelixB)-L (Formula 1) (wherein: Helix A is a moiety of 12-amino acid length capable of forming an α-helix structure, and is represented by the formula 2: A 1 - A 2 -A 3 - A 4 - A 5 - A 6 - A 7 - A 8 - A 9 - A 10 - A 11 - A 12 (Formula 2) wherein, in the formula 2, A 1 to A 12 independently represent an amino acid; X does not exist, or is a moiety of 1- to 9-amino acid length; Helix B is a moiety of 11- to 13-amino acid length capable of forming an α-helix structure; and L is a moiety of 2- to 7-amino acid length represented by the formula 3; L vii - L vii -L v -L iv -L iii -L ii -L i (Formula 3) wherein, in the formula 3, the amino acids are numbered "i" (-1), "ii" (-2), and so on from the C-terminus side, provided that L iii to L vii may not exist), and combination of three amino acids A 1, A 4 and L ii, or combination of two amino acids A 4, and L ii of one PPR motif contained in the protein is a combination corresponding to a target RNA base or a specific RNA base constituting a target base sequence. designing a protein that specifically binds to RNA having a specific sequence by paying attention to the combination of amino acids A 1, A 4, and L ii or the combination of amino acids A 4 and L ii, wherein the protein contains one or more of PPR motifs each consisting of a polypeptide of 30- to 38-amino acid length represented by the formula 1: (HelixA)-X-(HelixB)-L (Formula 1) (wherein: Helix A is a moiety of 12-amino acid length capable of forming an α-helix structure, and is represented by the formula 2: A 1 - A 2 -A 3 - A 4 - A 5 - A 6 - A 7 - A 8 - A 9 - A 10 - A 11 - A 12 (Formula 2) wherein, in the formula 2, A 1 to A 12 independently represent an amino acid; X does not exist, or is a moiety of 1- to 9-amino acid length; Helix B is a moiety of 11- to 13-amino acid length capable of forming an α-helix structure; and L is a moiety of 2- to 7-amino acid length represented by the formula 3; L vii - L vii -L v -L iv -L iii -L ii -L i (Formula 3) wherein, in the formula 3, the amino acids are numbered "i" (-1), "ii" (-2), and so on from the C-terminus side, provided that L iii to L vii may not exist), and combination of three amino acids A 1, A 4 and L ii, or combination of two amino acids A 4, and L ii of one PPR motif contained in the protein is a combination corresponding to a target RNA base or a specific RNA base constituting a target base sequence. wherein, in the formula 2, A 1 to A 12 independently represent an amino acid; X does not exist, or is a moiety of 1- to 9-amino acid length; Helix B is a moiety of 11- to 13-amino acid length capable of forming an α-helix structure; and L is a moiety of 2- to 7-amino acid length represented by the formula 3; wherein, in the formula 3, the amino acids are numbered "i" (-1), "ii" (-2), and so on from the C-terminus side, provided that L iii to L vii may not exist), and combination of three amino acids A 1, A 4 and L ii, or combination of two amino acids A 4, and L ii of one PPR motif contained in the protein is a combination corresponding to a target RNA base or a specific RNA base constituting a target base sequence.