Federal Circuit Finds That a Variant Polypeptide Sequence Infringes Under the Doctrine of Equivalents
In a pair of cross-appeals from the International Trade Commission, the Federal Circuit affirmed the Commission’s ruling that one of CJ CheilJedang Corp.’s engineered bacterial strains infringed Ajinomoto’s patent, while another strain did not infringe.
Ajinomoto’s patent claim is related to methods of cultivating E. coli bacteria that have been genetically engineered to increase their production of aromatic L-amino acids during fermentation. The claim recites, among other limitations, (1) a protein that “consists of the sequence of SEQ ID NO: 2” and (2) enhancing the activity of the protein by “replacing the native promoter [for the protein] … with a more potent promoter.”
An expert had testified that CJ’s first bacterial strain produced a protein 85% to 95% identical in structure to Ajinomoto’s SEQ ID NO: 2. Thus, the claim was not literally infringed, and the Federal Circuit applied the “function-way-result” for infringement under the doctrine of equivalents. The Federal Circuit affirmed the finding that both proteins had been shown to function as export proteins, both performed membrane transport in substantially the same way, and both achieved the result of exporting L-tryptophan out of the cell. Accordingly, the Federal Circuit affirmed the finding of infringement under the doctrine of equivalents.
While narrowing amendments to the claims during prosecution can bar infringement under doctrine of equivalents, this bar does not apply for an amendment that has no more than a tangential relationship to the equivalent in question. Here, the Federal Circuit found that there was no bar to the doctrine of equivalents. The patentee had pursued two alternative claim formats, one related to DNA sequences, and one related to protein sequences. The patentee had narrowed the DNA sequence format to limit the variety of proteins that could be encoded by the DNA, but left the protein sequence format claims unaltered. The Federal Circuit found that the rationale of the amendment was to “limit the scope of proteins within the claim’s scope so that it no longer included the prior art [protein],” and that this amendment was “unrelated to differences among the several DNA sequences that encode a given protein.” As such, the Federal Circuit concluded that the amendment was only tangentially related to the protein sequence claim format, and was not a surrender of protein claim scope under the doctrine of equivalents.
In a dissent, Judge Dyk observed that the original claim covered variation in the protein sequence, and the purpose of the amendment was to exclude prior art proteins. In Judge Dyk’s opinion, the amendment was more than merely tangentially related to the accused equivalent, which was a variant of the recited protein sequence.
CJ’s second bacterial strain contained a point mutation in the native promoter. Referring to the prosecution history, the Federal Circuit noted that CJ’s change of a single nucleotide (to produce the point mutant) did not infringe Ajinomoto’s claim to “replacing the native promoter… with a more potent promoter.” During prosecution, Ajinomoto’s original claim had more broadly recited “alteration of expression regulation sequence of said DNA,” but that original claim was narrowed in response to the Examiner’s finding of enablement for replacing the promoter, but not for changes in expression regulation sequences outside of the promoter. The Federal Circuit construed “replacing” a promoter to substitute the entire native promoter with a different promoter, and concluded that CJ’s single nucleotide change did not do so.
In dicta, the Federal Circuit speculated that the applicants may have surrendered more than was necessary to overcome the Examiner’s rejection. The Federal Circuit posited that if the applicants had just changed “expression regulation sequence” to “native promoter,” such an amendment might have sufficed to overcome the Examiner’s rejection.
 See Festo Corp. v. Shoketsu Kinzoku Kogyo Kabushiki Co., 535 U.S. 722, 740 (2002).
 Slip opinion at p. 21
 Slip opinion at p. 22