PATENT CLAIM ANALYSIS

Application Number: 15962127
Application Type: Utility
Filing Date: 2018-04
Publication Date: 2018-08
Patent Classification: ["530", "327000"]

Abstract:
A method for designing a protein capable of binding in an RNA base selective manner or RNA base sequence specific manner is provided. The protein of the present invention is a protein containing one or more of PPR motifs (preferably 2 to 14 PPR motifs) each consisting of a polypeptide of 30- to 38-amino acid length represented by the 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, 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  is a combination corresponding to a target RNA base or base sequence.

Claim (Index 13):
The method according to  claim 11 , wherein the target RNA base sequence for the candidate PPR protein is predicted on the basis of any of the propositions (3-1) to (3-16) for the combination of the three amino acids A1, A4 and Lii or on the basis of any of the propositions (2-1) to (2-12) for the combination of the two amino acids A4 and Lii:\n (2-1) when A4 and Lii are asparagine and aspartic acid, respectively, the motif can selectively bind to U; (2-2) when A4 and Lii are asparagine and asparagine, respectively, the motif can selectively bind to C; (2-3) when A4 and Lii are threonine and asparagine, respectively, the motif can selectively bind to A; (2-4) when A4 and Lii are threonine and aspartic acid, respectively, the motif can selectively bind to G; (2-5) when A4 and Lii are serine and asparagine, respectively, the motif can selectively bind to A; (2-6) when A4 and Lii are glycine and aspartic acid, respectively, the motif can selectively bind to G; (2-7) when A4 and Lii are asparagine and serine, respectively, the motif can selectively bind to C; (2-8) when A4 and Lii are proline and aspartic acid, respectively, the motif can selectively bind to U; (2-9) when A4 and Lii are glycine and asparagine, respectively, the motif can selectively bind to A; (2-10) when A4 and Lii are methionine and aspartic acid, respectively, the motif can selectively bind to U; (2-11) when A4 and Lii are leucine and aspartic acid, respectively, the motif can selectively bind to C; and (2-12) when A4 and Lii are valine and threonine, respectively, the motif can selectively bind to U, (3-1) when the three amino acids A 1 , A 4 , and L ii  are valine, asparagine, and aspartic acid, respectively, the PPR motif can selectively bind to U (uracil); (3-2) when the three amino acids A 1 , A 4 , and L ii  are valine, threonine, and asparagine, respectively, the PPR motif can selectively bind to A (adenine); (3-3) when the three amino acids A 1 , A 4 , and L ii  are valine, asparagine, and asparagine, respectively, the PPR motif can selectively bind to C (cytosine); (3-4) when the three amino acids A 1 , A 4 , and L ii  are glutamic acid, glycine, and aspartic acid, respectively, the PPR motif can selectively bind to G (guanine); (3-5) when the three amino acids A 1 , A 4 , and L ii  are isoleucine, asparagine, and asparagine, respectively, the PPR motif can selectively bind to C or U; (3-6) when the three amino acids A 1 , A 4 , and L ii  are valine, threonine, and aspartic acid, respectively, the PPR motif can selectively bind to G; (3-7) when the three amino acids A 1 , A 4 , and L ii  are lysine, threonine, and aspartic acid, respectively, the PPR motif can selectively bind to G; (3-8) when the three amino acids A 1 , A 4 , and L ii  are phenylalanine, serine, and asparagine, respectively, the PPR motif can selectively bind to A; (3-9) when the three amino acids A 1 , A 4 , and L ii  are valine, asparagine, and serine, respectively, the PPR motif can selectively bind to C; (3-10) when the three amino acids A 1 , A 4 , and L ii  are phenylalanine, threonine, and asparagine, respectively, the PPR motif can selectively bind to A; (3-11) when the three amino acids A 1 , A 4 , and L ii  are isoleucine, asparagine, and aspartic acid, respectively, the PPR motif can selectively bind to U or A; (3-12) when the three amino acids A 1 , A 4 , and L ii  are threonine, threonine, and asparagine, respectively, the PPR motif can selectively bind to A; (3-13) when the three amino acids A 1 , A 4 , and L ii  are isoleucine, methionine, and aspartic acid, respectively, the PPR motif can selectively bind to U or C; (3-14) when the three amino acids A 1 , A 4 , and L ii  are phenylalanine, proline, and aspartic acid, respectively, the PPR motif can selectively bind to U; (3-15) when the three amino acids A 1 , A 4 , and L ii  are tyrosine, proline, and aspartic acid, respectively, the PPR motif can selectively bind to U; and (3-16) when the three amino acids A 1 , A 4 , and L ii  are leucine, threonine, and aspartic acid, respectively, the PPR motif can selectively bind to G.

Metadata:
- Claim Count in Document: 20.0
- Percentile: 91.0
- Lexical Diversity: 2.5
- Patent Class: 530.0
- Transitional Phrase Type: none
- Component Type: 0
- Foreign Priority: True
- Related Applications: ['15335243', '14352697', '14785952', '13989676', '15415216']

Analysis Scores:
- 35 USC 101 Eligibility (BERT): 0.726445540213217
- 35 USC 102 Novelty (BERT): 0.646710508572347
- Combined Prediction Score: 0.71847203704913
- Mean Citation Score: 497.161108
- Max Citation Score: 740.08636
- Similarity Product: 550.0050124348378

Labels:
- Claim Label 101: 1
- Claim Label 102: 1
- Claim Label 103: 1
- Claim Label 112: 0
- Combined Label: 1
- Label 101 Adjusted: 1

Dataset: test