Patent ID: 8401798
Filing Date: 2013-03-19
Classification: C12Q,G16B

Abstract:
1. A method of constructing a frequency lookup table for an expression system, wherein the frequency lookup table comprises a plurality of codons, the method comprising: (A) constructing a plurality of polynucleotides, wherein the plurality of polynucleotides comprises five or more polynucleotides, each respective polynucleotide in the plurality of polynucleotides encoding a respective single polypeptide sequence the entirety of which is at least ninety-five percent identical to the entirety of the respective single polypeptide sequence encoded by each other polynucleotide in the plurality of polynucleotides, wherein (i) a first, second and third polynucleotide in the plurality of polynucleotides each comprises a first synonymous codon in a plurality of synonymous codons, wherein the plurality of synonymous codons encode the same amino acid, (ii) the first synonymous codon is present in the first polynucleotide with a first frequency relative to all other codons in the plurality of synonymous codons in the first polynucleotide, (iii) the first synonymous codon is present in the second polynucleotide with a second frequency relative to all other codons in the plurality of synonymous codons in the second polynucleotide, (iv) the first synonymous codon is present in the third polynucleotide with a third frequency relative to all other codons in the plurality of synonymous codons in the third polynucleotide, and (v) the first frequency is different than the second frequency and the third frequency is between the first frequency and the second frequency; (B) expressing each respective polynucleotide in the plurality of polynucleotides individually in said expression system using the same vector and the same promoter; (C) measuring an expression property value of each respective polynucleotide in the plurality of polynucleotides in the expression system thereby constructing a dataset, wherein said dataset comprises, for each respective polynucleotide in the plurality of polynucleotides, a representation of codon occurrence in the respective polynucleotide and the measured expression property value of the respective polynucleotide; and (D) computing said frequency lookup table for said expression system based on the dataset, wherein the frequency lookup table provides a corresponding codon frequency range or target frequency for each of two or more codons in the plurality of codons.