Opinion
No. C 01-0415 SI.
February 25, 2004
Plaintiff Carnegie Mellon University has moved for summary judgment that defendants' plasmid pLSG5 and its use infringe claims 4-11, 15-22 and 29 of U.S. Patent No. 6,017,745 ("the '745 patent") under the doctrine of equivalents. Defendants have filed a counter-motion for summary judgment of non-infringement. Having carefully considered the arguments of counsel and the papers submitted, the Court hereby DENIES plaintiff's motion and GRANTS defendants' motion, for the reasons set forth below.
BACKGROUND
1. Procedural history
In 1996, plaintiffs Carnegie Mellon University ("Carnegie Mellon") and Three Rivers Biologicals, Inc. sued several defendants in this court (Case No. C 95-3524 SI) alleging infringement of U.S. Patent No. 4,767,708 (the "'708 patent") and U.S. Patent No. 5,126,270 (the "'270 patent"), both entitled "Enzyme Amplification and Purification." Those patents related to recombinant plasmids for the controlled expression of an enzyme identified in the '708 patent as "DNA polymerase I"; processes related to the construction of such plasmids; and processes related to the culturing of host cells containing such plasmids. Patents '708 and '270, as well as patent '745, the patent-in-suit, all derive from the same original application. The Patent and Trademark Office ("PTO") issued the '708 patent from a "parent" application, No. 06/638,638 ("`638 application"), filed on August 7, 1984; the '270 patent from a "continuation" application filed on November 5, 1987; and the '745 patent from another "continuation" application filed on May 9, 1992. The '745 patent issued on January 25, 2000.
In the previous suit, on August 19, 1999 this Court granted a summary judgment motion filed by the Roche defendants, finding the '270 patent invalid for lack of an adequate supporting written description as required by 35 U.S.C. § 112. Also in the previous suit, on June 27, 2001 this Court granted the Roche defendants' motion for summary judgment on their counterclaim for declaratory judgment that claims 1-19, 22-40 and 43-35 of the '708 patent are invalid for failure to comply with the written description requirement.
Hoffman-La Roche Inc., Roche Molecular Systems, Inc., Roche Diagnostic Systems, Inc., Roche Biomedical Laboratories, Inc., The Perkin-Elmer Corp., and Laboratory Corporation of America Holdings (collectively the "Roche defendants").
The current lawsuit, filed in 2001, alleges infringement by the Roche defendants of plaintiff Carnegie Mellon's '745 patent. On September 29, 2003, this Court granted defendants' motion for summary judgment that claims 1-3, 12-14, 23-28, and 30-33 of the '745 patent are invalid under the written description requirement of 35 U.S.C. § 112. Claims 4-11 and 15-22 depend on the invalidated claims but remain presumptively valid. See 35 U.S.C. § 282 (all dependent claims are presumed valid even if dependent on an invalid claim). Thus the current motions remain for this Court to decide.
This overview of DNA technology is excerpted from the Federal Circuit's decision in In re O'Farrell, 853 F.2d 894, 895-97 (Fed. Cir. 1988).
Proteins are biological molecules of enormous importance. Proteins include enzymes that catalyze biochemical reactions, major structural materials of the animal body, and many hormones. Numerous patents and applications for patents in the field of biotechnology involve specific proteins or methods for making and using proteins. Many valuable proteins occur in nature only in minute quantities, or are difficult to purify from natural sources. Therefore, a goal of many biotechnology projects is to devise methods to synthesize useful quantities of specific proteins by controlling the mechanism by which living cells make proteins.
Protein molecules are composed of long chains of amino acids. To make a protein molecule, a cell needs information about the sequence in which the amino acids must be assembled. The cell uses DNA — deoxyribonucleic acid — to store this information. DNA molecules do not participate directly in the synthesis of proteins, but instead act as a permanent "blueprint" for the synthesis of a protein.
DNA is comprised of building blocks called nucleotides that are linked together to form a strand Due to the orientation of nucleotides, each strand of DNA has a 5' end and a 3' end. The sequence and combination of nucleotides in DNA determines the sequence of amino acids in a particular protein. DNA predominantly exists in long-stranded structures called chromosomes, but can also be found in smaller circular structures called plasmids. The specific region of DNA that codes for the sequence of a particular protein is called a gene.
In order to make a selected protein by expressing its cloned gene in bacteria, several technical hurdles must be overcome. First the particular gene coding for the specific protein must be isolated for cloning. Next the isolated gene must be introduced into the host bacterium. This can be done by incorporating the gene into a cloning vector. A cloning vector is a piece of DNA that can be introduced into bacteria and will then replicate itself as the bacterial cells grow and divide. Plasmids are often used as cloning vectors due to their small size and ability to replicate in host cells. A recombinant plasmid is a plasmid that has been artificially constructed (i.e. cloned), rather than isolated from nature. Recombinant DNA technology can be used to modify plasmids by splicing in cloned genes and other useful segments of DNA containing control sequences.
The '745 patent is directed to recombinant plasmids containing a gene that encodes the useful enzyme DNA polymerase I. This particular gene is commonly referred to as the "polA" gene, and the enzyme it encodes, DNA polymerase I, is also known as the "pol I" enzyme.
LEGAL STANDARD
A. Summary judgment"Summary judgment is appropriate in a patent case, as in other cases, when there is no genuine issue as to any material fact and the moving party is entitled to judgment as a matter of law."Nike Inc. v. Wolverine World Wide, Inc., 43 F.3d 644, 646 (Fed. Cir. 1994).
A motion for summary judgment may be granted when "the pleadings, depositions, answers to interrogatories, and admissions on file, together with the affidavits, if any, show that there is no genuine issue as to any material fact and that the moving party is entitled to a judgment as a matter of law." Fed.R.Civ.P. 56(c). The moving party bears the initial burden of "informing the district court of the basis for its motion" and identifying the matter that "it believes demonstrate[s] the absence of a genuine issue of material fact." Celotex Corp. V. Catrett, 477 U.S. 317, 323 (1986). If the moving party meets this burden, the nonmoving party must then set forth "specific facts showing that there is a genuine issue for trial." Fed.R.Civ.P. 56(e); see also T.W. Elec. Serv., Inc. v. Pacific Elec. Contractors Ass'n, 809 F.2d 626, 630 (9th Cir. 1987). "Rule 56(c) requires the moving party to show not only the absence of a disputed issue of fact but also that he is entitled to judgment as a matter of law . . . [T]herefore, the court must . . . consider the burden of proof on the issue and where it will rest at trial . . . Where the moving party has the burden — the plaintiff on a claim for relief or the defendant on an affirmative defense — his showing must be sufficient for the court to hold that no reasonable trier of fact could find other than for the moving party." Calderone v. United States, 799 F.2d 254, 259 (6th Cir. 1986) (quotations omitted).
The evidence presented by the parties in support of or opposition to a motion for summary judgment must be admissible.See Fed.R.Civ.P. 56(e). In evaluating this evidence, the court does not make credibility determinations or weigh conflicting evidence, and draws all inferences in the light most favorable to the nonmoving party. T.W. Elec. Serv., 809 F.2d at 630-31 (citing Matsushita Elec. Indus. Co. V. Zenith Radio Corp., 475 U.S. 574 (1986)); Ting v. United States, 927 F.2d 1504, 1509 (9th Cir. 1991).
B. Doctrine of equivalents
"A device that does not literally infringe a claim may nonetheless infringe under the doctrine of equivalents if every element in the claim is literally or equivalently present in the accused device." See Sage Prods., Inc. v. Devon Indus., Inc., 126 F.3d 1420, 1423 (Fed. Cir. 1997). The doctrine of equivalents must be applied on an element-by-element basis, rather than to the whole invention.See Warner-Jenkinson Co. v. Hilton Davis Chem. Co., 117 S.Ct. 1040, 1049 (1997). Thus, "[u]nder the doctrine of equivalents, a claim limitation not literally met may be satisfied by an element of the accused product if the differences between the two are `insubstantial' to one of ordinary skill in the art." Boehringer Ingelheim Vetmedica v. Schering Plough Corp., 320 F.3d 1339, 1351 (Fed. Cir. 2003) (citations omitted). "While no particular linguistic framework controls the inquiry, the insubstantial differences inquiry may be guided by determining whether the element in the accused device `performs substantially the same function in substantially the same way to obtain the same result' as the claim limitation." Id. (citations omitted).
Although equivalence is a factual matter normally reserved for the jury, the trial court should grant summary judgment in any case where no reasonable fact finder could find equivalence. See Warner-Jenkinson, 117 S.Ct. at 1053 n. 8 ("Where the evidence is such that no reasonable jury could determine two elements to be equivalent, district courts are obliged to grant partial or complete summary judgment.").
DISCUSSION
1. Descriptions of the claims
Claim 4, rewritten in independent form, provides for a recombinant plasmid
[a] containing a DNA coding sequence for the expression of DNA polymerase activity,
[b] wherein said DNA coding sequence is derived from a source that encodes a bacterial DNA DNA polymerase,
[c] said source not containing an amber mutation affecting expression of said DNA polymerase activity,
[d] such that when said plasmid is transformed into a bacterial host system the host system can grow and divide thereby replicating said plasmid[,]
[e] wherein said DNA polymerase activity includes Nick-translation activity[,]
[f] wherein said Nick-translation activity is under operable control of a conditionally controllable foreign promoter, said foreign promoter being functional to express said Nick-translation activity in said host system [,]
[g] wherein the bacterial host system and the bacterial source are each E. Coli; and wherein the Nick-translation activity includes polymerase and 5'-3' exonuclease activities.
Claim 15, rewritten in independent form, provides for a recombinant plasmid
[a] containing a DNA coding sequence for the expression of DNA polymerase activity,
[b] wherein said DNA coding sequence is derived from a source that encodes a bacterial DNA polymerase,
[c] said source not containing an amber mutation affecting expression of said DNA polymerase activity,
[d] such that when said plasmid is transformed into a bacterial host system the host system can grow and divide for at least 20 generations thereby replicating said plasmid[,]
[e] wherein said DNA polymerase activity includes Nick-translation activity[,]
[f] wherein said Nick-translation activity is under operable control of a conditionally controllable foreign promoter, said foreign promoter being functional to express said Nick-translation activity in said host system[,]
[g] wherein the bacterial host system and the bacterial source are each E. coli; and wherein the Nick-translation activity includes polymerase and 5'-3' exonuclease activities.
Defendants' Counter-Motion and Oppo., Appendix A. Plaintiff argues that Defendants' plasmid pLSG5 infringes claims 4-11 and 15-22 of its '745 Patent. Claims 5-11 depend on Claim 4 and Claims 16-22 depend on Claim 15, so this Court has included only Claims 4 and 15.
Method claim 29 depends from independent claim 23, and they read as follows:
Claim 23. A method of producing an enzyme possessing DNA polymerase activity comprising the steps of:
transforming a recombinant plasmid having a DNA coding sequence for the expression of DNA polymerase activity that is under operable control of a conditionally controllable foreign promoter into a bacterial host system, said DNA polymerase coding sequence derived from a source that encodes a bacterial DNA polymerase, said source not containing an amber mutation affecting expression of said, DNA polymerase activity; and
allowing the host system to grow and divide for at least twenty generations thereby replicating said plasmid.
Claim 29. The method of claim 23 wherein the bacterial host system and the bacterial source are each E. Coli.2. Comparison of E. coli and Thermus aquaticus
"Enzymes encoded by bacterial PolA genes have proven to be valuable tools for scientific research, particularly in the polymerase chain reaction (PCR), a technique first described in 1985 that has become central to molecular biology. In PCR, reagents (including a DNA polymerase) are subjected to multiple repetitive cycles of heating and cooling to achieve rapid selective amplification of a target DNA sequence." Abramson Decl., attached as Ex. 2 to Rabinowitz Decl., at 3: 21-25. " E. coli DNA polymerase I has been used to perform PCR, but this enzyme is inactivated by heating ( i.e., it is not thermostable) and must be replenished for each PCR cycle." Id. at 25-27. In contrast, " Thermus aquaticus (" Taq") DNA polymerase, when suitably purified, is thermostable (survives high temperatures) and need not be replenished during a PCR amplification." Id. at 4:3-5. Thus the "introduction [of Taq] for PCR greatly improved the specificity, yield, sensitivity and length of products that can be amplified in PCR and facilitated automation of the PCR technique." Id. at 4: 5-7.
Plaintiffs' patent limits the bacterial agent to E. coli, but defendants' process substitutes T. aquaticus for E. coli. Since the "essential inquiry" for this Court is whether "the accused product or process contain[s] elements identical or equivalent to each claimed element of the patented invention,"Warner-Jenkinson, 117 S.Ct. at 1054, the "essential inquiry" for this Court is whether defendants' use of T. aquaticus is equivalent to use of E. coli and thus constitutes infringement under the doctrine of equivalents. Claim 4 of the '745 Patent is limited to plasmids "wherein the bacterial host system and the bacterial source are each E. coli, and wherein the Nick-translation activity includes polymerase and 5'-3' exonuclease activities." As an initial mater, then, this Court must compare these properties of E. coli to those of T. aquaticus.
Defendants' "[p]lasmid pLSG5 encodes the enzyme Thermus aquaticus DNA polymerase (`Taq polymerase'), which [defendant] Roche sells under the designation `AmpliTaq® DNA Polymerase.' All AmpliTaq® DNA Polymerase ever sold by Roche or by Cetus was expressed from plasmid pLSG5." White Decl. at 1:23-26, attached to Colen Decl. as Tab B. "AmpliTaq® DNA Polymerase possesses polymerase activity and 5'-3' exonuclease activity, but lacks 3'-5' exonuclease activity. A detailed description of plasmid pLSG5 appears in U.S. Patent No. 5,079,352 at col. 41, line 40 to col. 42, line 31." Id. at 2:1-3. One of plaintiff's experts agreed that "DNA Polymerase I from Thermus aquaticus has also been identified without identifying 3'-5' exonnuclease [sic] [activity] as shown by Laywer et al." Benkovic Affidavit, attached to Rabinowitz Decl. as Ex. 1, at 4: 22-24. The 3'-5' exonuclease activity possessed by E. coli polymerase I and lacking in the DNA polymerase I from Thermus aquaticus is referred to as the "`proofreading'" function. Id. At 4: 16.
Furthermore, "pLSG5 contains the DNA coding sequence from T. aquaticus for the expression of Nick-translation activity, and the leftward promoter of phage lambda, a negatively regulated promoter, which DNA coding sequence encodes T. aquaticus DNA polymerase I. The DNA coding sequence of pLSG5 reported in the Lawyer et al. article [attached as Ex. F of the Colen Decl.] does not contain an amber mutation effecting [sic] expression of the DNA polymerase." Low's February Decl. at 3, ¶ 10.
3. Application of the doctrine of equivalents
In this case, the asserted claims of the '745 patent include the specific limitation that the bacterial source for the recombinant plasmid be E. coli. Plaintiffs contend that defendants' [p]lasmid pLSG5 infringes under the doctrine of equivalents, because the substitution of T. aquaticus for E. coli was an "unimportant and insubstantial" change, citingWarner-Jenkinson. However, this Court must be mindful that "the application of the doctrine [of equivalents], even as to an individual element, is not allowed such broad play as to effectively eliminate that element in its entirety."Warner-Jenkinson, 117 S.Ct. 1040, 1049.
Each side argues that an application of the "`triple identity' test," Warner-Jenkinson, 117 S.Ct. at 1054, supports its position. This test requires analysis of "the function served by a particular claim element, the way that element serves the function, and the result thus obtained by the element." Id.
Thus plaintiff argues:
For purposes of the claimed invention, the DNA coding sequence of plasmid pLSG5 derived from T. aquaticus performs the same function as the DNA coding sequence derived from E. coli (expresses a DNA polymerase having Nick-translation activity) in the same way (under the operable control of a conditionally controllable foreign promoter) to achieve the same result (permit the host system to grow and divide to replicate the plasmid when transformed into the E. coli host system).
Defendants' plasmid pLSG5 performs the same function (expresses a DNA polymerase having Nick-translation activity) in the same way (under the operable control of a conditionally controllable foreign promoter) to accomplish the same result (permit the host system to grow and divide and replicate the plasmid when transformed into an E. coli host system).
Plaintiff's Motion at 8:22-9:8. Based on what plaintiff regards as defendants' "insubstantial substitution of T. aquaticus for E. coli," plaintiff's motion at 8:14, plaintiff argues that, "[f]or purposes of the claimed invention, i.e., a plasmid for expressing DNA polymerase activity which includes Nick-translation activity, the claimed and accused sequences produce the same result and hence are not substantially different." Plaintiff's Reply in Support at 8:22-24. Plaintiff essentially argues that "a DNA coding sequence derived from E. coli is the recited claim limitation, and Defendants' DNA coding sequence derived from T. aquaticus is its equivalent." Id. at 3: 5-7.
Defendants respond that "[t]he function of the coding sequence in plasmid pLSG5 is to encode Taq DNA polymerase, and the result is that the host cell produces large amounts of recombinant Taq DNA polymerase . . . By contrast, the function of the coding sequence in the equivalently asserted product claims is to encode E. coli DNA polymerase I, and the result is elevated production by the host cell of recombinant E. coli DNA polymerase I." Defendants' Counter-Motion at 12: 14-20.
Both parties cite the Federal Circuit's recent decision inBoehringer Ingelheim Vetmedica, Inc. v. Schering-Plough Corp., 320 F.3d 1339 (Fed. Cir. 2003), a patent infringement suit concerning "[a] method of growing and isolating swine infertility and respiratory system virus, ATCC-VR2332." Id. at 1344. A jury found patent infringement under the doctrine of equivalents when a competitor's method of in vitro culturing paralleled Boehringer's method but used ATCC-VR2525, a different strain of the same virus, id. at 1350. The Federal Circuit affirmed.Id. at 1354.
In Boehringer, the Federal Circuit emphasized "the basic principle that the relevant analysis is `of the role played by each element in the context of the specific patent claim.'" Id. citing Warner-Jenkinson, 117 S.Ct. at 1040. The court found that although "ATCC-VR2332 is a pathogenic virus . . . while VR2525 is not," "what happens when the virus is administered to a pig is irrelevant to the assessment of whether the two viral strains are equivalent in the in vitro culture method defined by [the relevant patent] claim." Id. "The jury was presented with expert testimony from which it could conclude that VR2525 plays the same role as VR2332 in performance of the claimed method. The fact that, in other contexts, VR2525 can perform other functions in different ways to yield a different result is not relevant." Id. The Federal Circuit also noted that "the jury was presented with expert testimony that the two viral genomes are highly similar overall and that any differences between the two are insignificant." Id. at 1352. Thus "[a] reasonable jury could easily rely on this testimony to conclude that the genetic differences between VR2525 and ATCC-VR2332 areinsubstantial in the context of the claimed method." Id. (emphasis added).
Comparing T. aquaticus and E. coli "in the context of the claimed method," Boehringer, 320 F.3d at 1352, "the function of the E. coli DNA coding sequence is to express an E. coli DNA polymerase that has Nick-translation activity, i.e, E. coli DNA polymerase I. In contrast, the function of the Thermus aquaticus DNA coding sequence of plasmid pLSG5 is to express Taq DNA polymerase." Reply at 6:19-23. Moreover, while inBoehringer "the two viral genomes [were] highly similar overall and . . . any differences between the two [were] insignificant," Boehringer, at 1352, in this case E. coli and T. aquaticus are substantially different and do not even belong to the same bacterial family. Reply at 7: 8-10.
This Court finds that the defendants' substitution of T. aquaticus for E. coli was not "`insubstantial' to one of ordinary skill in the art" and that it does not "`perform substantially the same function in substantially the same way to obtain the same result' as the claim limitation." Boehringer, at 1351 (citations omitted). To find otherwise would require this Court to eliminate the E. coli limitations from the '745 patent, which, under Warner-Jenkinson, this Court cannot do. "It is important to ensure that the application of the doctrine [of equivalents], even as to an individual element, is not allowed such broad play as to effectively eliminate that element in its entirely." Warner Jenkinson, 117 S.Ct. At 1049.
The Supreme Court has instructed that, "[w]here the evidence is such that no reasonable jury could determine two elements to be equivalent, district courts are obliged to grant partial or complete summary judgment." Id. at 1053, n. 8. Applying the doctrine of equivalents to the case at hand in order to allow the substitution of T. aquaticus for E. coli would "entirely vitiate" the E. coli claim element. Id. In such a situation, the Supreme Court has instructed that "partial or complete summary judgment should be rendered by the court, as there would be no further material issue for jury to resolve." Id. (emphasis in original).
4. Claim 29
Claim 29 is a method claim, namely "[t]he method of claim 23 wherein the bacterial host system and the bacterial source are each E. coli."'745 Patent. Defendants allege, and plaintiffs concede, that defendants "have never practiced the `transforming' step of claim 29 with plasmid pLSG5 during the term of the '745 Patent." Defendants' Counter-Motion and Oppo. At 15:26-27. Thus "[Plaintiff] withdraws Claim 29 from its motion in view of the facts represented in the Declaration of Stuart M. Palmer, but reserves the right to reassert Claim 29 should Defendants', or any party acting on their behalf, transform pLSG5, or its equivalent, into a bacterial host after January 25, 2000, the issue date of the '745 Patent." Plaintiff's Reply at 2, n. 6. Defendant continues to move for summary judgment of non-infringement with regard to Claim 29 and this Court grants defendants' motion, since plaintiff concedes that defendants have not infringed Claim 29 of the '745 Patent.
CONCLUSION
For the foregoing reasons, the Court DENIES plaintiff's motion for summary judgment and GRANTS defendants' counter-motion for summary judgment. [Docket ##84, 97]
IT IS SO ORDERED.