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`UNITED STATES DISTRICT COURT
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`SOUTHERN DISTRICT OF CALIFORNIA
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`THE SCRIPPS RESEARCH
`INSTITUTE,
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` Case No.: 16-CV-661 JLS (BGS)
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`ORDER ON CLAIM
`CONSTRUCTION
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`Plaintiff,
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`v.
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`ILLUMINA, INC.,
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`(ECF Nos. 54, 55)
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`Defendant.
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`In March 2016, Plaintiff The Scripps Research Institute brought suit against
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`Defendant Illuminia, Inc. alleging infringement of U.S. Patent No. 6,060,596 (“the ’596
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`patent”), entitled “Encoded Combinatorial Chemical Libraries.” Presently before the Court
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`is claim construction. The Court held a claim construction hearing on January 30, 2018.
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`The ’596 patent generally relates to a library of bifunctional molecules, each
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`molecule having a chemical polymer and an identifier oligonucleotide sequence that
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`defines the structure of the chemical polymer. See U.S. Patent No. 6,060,596 (filed May
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`9, 2000).) The libraries are used in the manufacture of DNA microarrays. (ECF No. 55,
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`at 5.)1 Each DNA bead in a microarray contains many copies of specific DNA sequences
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`(known as “probes,” “oligonucleotides,” or “oglios.”) (Id. at 5–6.) These probes “can be
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`used to bind to and detect a complementary DNA or RNA sample.” (Id. at 6.) Scripps
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`asserts claims 1, 3, 10, and 16, and the Parties dispute six terms within claim 1. Defendant
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`filed a claim construction brief, (“Def. CC Brief,” ECF No. 54), as did Plaintiff, (“Pl. CC
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`Brief,” ECF No. 55). Both Parties also filed a response, (“Def. Response,” ECF No. 56;
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`“Pl. Response,” ECF No. 57).
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`LEGAL STANDARD
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`“A determination of infringement involves a two-step analysis. ‘First, the claim
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`must be properly construed to determine its scope and meaning. Second, the claim as
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`properly construed must be compared to the accused device or process.’” Omega Eng’g,
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`Inc. v. Raytek Corp., 334 F.3d 1314, 1320 (Fed. Cir. 2003) (quoting Carroll Touch, Inc. v.
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`Electro Mech. Sys., Inc., 15 F.3d 1573, 1576 (Fed. Cir. 1993)).
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`The first step, commonly known as claim construction, is presently before the Court.
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`Claim construction is a matter of law for the Court’s determination. Markman v. Westview
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`Instruments, Inc., 517 U.S. 370, 388 (1996) (“[J]udges, not juries, are the better suited to
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`find the acquired meaning of patent terms.”).
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`Words of a claim are “generally given their ordinary and customary meaning.”
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`Vitronics Corp. v. Conceptronic, Inc., 90 F.3d 1576, 1582 (Fed. Cir. 1996). “[T]he
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`ordinary and customary meaning of a claim term is the meaning that the term would have
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`to a person of ordinary skill in the art in question at the time of the invention, i.e., as of the
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`effective filing date of the patent application.” Phillips v. AWH Corp., 415 F.3d 1303,
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`1313 (Fed. Cir. 2005) (en banc). Because the inquiry into the meaning of claim terms is
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`an objective one, “a court looks to those sources available to the public that show what a
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`1 Pin citations to docketed material refer to the CM/ECF numbers electronically stamped at the top of each
`page.
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`person of skill in the art would have understood disputed claim language to mean.”
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`Innova/Pure Water, Inc. v. Safari Water Filtration Sys., Inc., 381 F.3d 1111, 1116 (Fed.
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`Cir. 2004). “Those sources include the words of the claims themselves, the remainder of
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`the specification, the prosecution history, and extrinsic evidence concerning relevant
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`scientific principles, the meaning of technical terms, and the state of the art.”2 Id. (citing
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`Vitronics, 90 F.3d at 1582–83).
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`Claim construction begins with an analysis of the words of the claims themselves.
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`See Scanner Techs. Corp. v. ICOS Vision Sys. Corp., 365 F.3d 1299, 1303 (Fed. Cir. 2004)
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`(holding that claim construction “begins and ends” with a claim’s actual words). “In some
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`cases, the ordinary meaning of claim language as understood by a person of skill in the art
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`may be readily apparent even to lay judges, and claim construction in such cases involves
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`little more than the application of the widely accepted meaning of commonly understood
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`words.” Phillips, 415 F.3d at 1314. However, the meaning of a claim term as understood
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`by ordinarily skilled artisans often is not immediately apparent. Id. In those situations, the
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`court looks to “sources available to the public that show what a person of skill in the art
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`would have understood disputed claim language to mean.” Id. Or, when a patentee
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`“chooses to be his own lexicographer and use terms in a manner other than their ordinary
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`meaning,” the court can use the patentee’s meaning “as long as the special definition of the
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`term is clearly stated in the patent specification or file history.” Vitronics, 90 F.3d at 1582.
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`In examining the claims themselves, “the context in which a term is used can be
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`highly instructive.” Phillips, 415 F.3d at 1314. Moreover, “[o]ther claims of the patent in
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`question, both asserted and unasserted can . . . be valuable sources of enlightenment as to
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`the meaning of a claim term.” Id. (citing Vitronics, 90 F.3d at 1582). “Because claim
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`terms are normally used consistently throughout the patent, the usage of a term in one claim
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`2 The first three sources are considered “intrinsic evidence” of claim meaning. See generally Phillips, 415
`F.3d at 1314–17.
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`Case 3:16-cv-00661-JLS-BGS Document 77 Filed 04/10/18 PageID.1276 Page 4 of 18
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`can often illuminate the meaning of the same term in other claims.” Id. Conversely, under
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`the doctrine of claim differentiation, “‘different words or phrases used in separate claims
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`are presumed to indicate that the claims have different meanings and scope.’” Andersen
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`Corp. v. Fiber Composites, LLC, 474 F.3d 1361, 1369 (Fed. Cir. 2007) (quoting Karlin
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`Tech., Inc. v. Surgical Dynamics, Inc., 177 F.3d 968, 971–72 (Fed. Cir. 1999)).
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`“Importantly, the person of ordinary skill in the art is deemed to read the claim term
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`not only in the context of the particular claim in which the disputed term appears, but in
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`the context of the entire patent, including the specification.” Phillips, 415 F.3d at 1313.
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`“The specification acts as a dictionary when it expressly defines terms used in the claims
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`or when it defines them by implication.” Vitronics, 90 F.3d at 1582. “In addition to
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`providing contemporaneous technological context for defining claim terms, the patent
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`applicant may also define a claim term in the specification ‘in a manner inconsistent with
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`its ordinary meaning.’” Metabolite Labs., Inc. v. Lab. Corp. of Am., 370 F.3d 1354, 1360
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`(Fed. Cir. 2004). “Usually, [the specification] is dispositive; it is the single best guide to
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`the meaning of a disputed term.” Vitronics, 90 F.3d at 1582; accord Phillips, 415 F.3d at
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`1317 (“It is . . . entirely appropriate for a court, when conducting claim construction, to
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`rely heavily on the written description for guidance as to the meaning of the claims.”).
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`Patent claims should ordinarily be construed to encompass the preferred
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`embodiments described in the specification, for “[a] claim construction that excludes a
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`preferred embodiment . . . ‘is rarely, if ever, correct.’” SanDisk Corp. v. Memorex Prods.,
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`Inc., 415 F.3d 1278, 1285 (Fed. Cir. 2005) (quoting Vitronics, 90 F.3d at 1583). However,
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`a court should not import limitations from the specification into the claims, Phillips, 415
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`F.3d at 1323 (“[A]lthough the specification often describes very specific embodiments of
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`the invention, we have repeatedly warned against confining the claims to those
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`embodiments.”), absent a specific reference in the claims themselves, Reinshaw PLC v.
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`Marposs Societa’ per Azioni, 158 F.3d 1243, 1248 (Fed. Cir. 1998) (“[A] party wishing to
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`use statements in the written description to confine or otherwise affect a patent’s scope
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`must, at the very least, point to a term or terms in the claim with which to draw in those
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`statements.”).
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`The patent’s prosecution history, if in evidence, may also shed light on claim
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`construction. Vitronics, 90 F.3d at 1582. “This history contains the complete record of all
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`proceedings before the Patent and Trademark Office [(“PTO”)], including any express
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`representations made by the applicant regarding scope of the claims.” Id. “Like the
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`specification, the prosecution history provides evidence of how the PTO and the inventor
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`understood the patent.” Phillips, 415 F.3d at 1317. Although the prosecution history
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`“often lacks the clarity of the specification,” it is nevertheless useful to show “how the
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`inventor understood the invention and whether the inventor limited the invention in the
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`course of prosecution, making the claim scope narrower than it would otherwise be.” Id.
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`“In most situations, an analysis of the intrinsic evidence alone will resolve any
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`ambiguity in a disputed claim term. In such circumstances, it is improper to rely on
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`extrinsic evidence.” Vitronics, 90 F.3d at 1583. Thus, expert testimony on the proper
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`construction of disputed claim terms “may only be relied upon if the patent documents,
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`taken as a whole, are insufficient to enable the court to construe disputed claim terms.” Id.
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`at 1585.
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`However, Vitronics does not state a rule of admissibility, nor does it “prohibit courts
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`from examining extrinsic evidence, even where the patent document is itself clear.” Pitney
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`Bowes, Inc. v. Hewlett-Packard Co., 182 F.3d 1298, 1308 (Fed. Cir. 1999). As the Federal
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`Circuit has made clear:
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`[B]ecause extrinsic evidence can help educate the court regarding the field of
`the invention and can help the court determine what a person of ordinary skill
`in the art would understand claim terms to mean, it is permissible for the
`district court in its sound discretion to admit and use such evidence.
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`Phillips, 415 F.3d at 1319; accord Key Pharms. v. Hercon Labs. Corp., 161 F.3d 709, 716
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`(Fed. Cir. 1998) (“[T]rial courts generally can hear expert testimony for background and
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`education on the technology implicated by the presented claim construction issues, and
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`trial courts have broad discretion in this regard.”). The court is not “barred from
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`considering any particular sources or required to analyze sources in any specific sequence,
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`as long as those sources are not used to contradict claim meaning that is unambiguous in
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`light of the intrinsic evidence.” Phillips, 415 F.3d at 1324; see also Biagro W. Sales, Inc.
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`v. Grow More, Inc., 423 F.3d 1296, 1302 (Fed. Cir. 2005) (“Extrinsic evidence, such as
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`expert testimony, may be useful in claim construction, but it should be considered in the
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`context of the intrinsic evidence.”).
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`DISCUSSION
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`The Parties dispute the meaning of six claim terms or phrases in claim 1 of the ’596
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`patent.
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`I.
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`The ’596 Patent
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`The ’596 patent is titled “Encoded Combinatorial Chemical Libraries.” Claim 1 of
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`the patent is reproduced below:
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`A bifunctional molecule according to the formula A–B–C, wherein A is a
`polymer comprising a linear series of chemical units represented by the
`formula (Xn)a, wherein X is a single chemical unit in polymer A, B is a linker
`molecule operatively linked to A and C. and identifier oligonucleotide C is
`represented by the formula (Zn)a, wherein a unit identifier nucleotide sequence
`Z within oligonucleotide C identifies the chemical unit X at position n; and
`wherein n is a position identifier for both X in polymer A and Z in
`oligonucleotide C having the value of 1+i where i is an integer from 0 to 10,
`such that when n is 1, X or Z is located most proximal to the linker, and a is
`an integer from 4 to 50.
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`’596 patent, at 43:1–14.
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`The patent is directed to methods for creating encoded combinatorial chemical
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`libraries made up of many bifunctional molecules. These molecules are made of both a
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`chemical polymer and an identifier oligonucleotide sequence that defines the structure of
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`the chemical polymer. ’596 patent, abstract. The chemical polymer can be, for example,
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`a series of amino acids, and the identifier oligonucleotide is a series of nucleotides (e.g.,
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`adenosine (A), guanine (G), cytosine (C), and thymine (T)). Id. at 4:44–55; 6:12–24. The
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`bifunctional molecules are built by starting with the linker, (“B”) and adding chemical units
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`(X) to one end and identifier nucleotide sequences (Z) to the other end. Id. at 10:18–25.
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`For example: X1–B–Z1. Id. at 6:1. The series of chemical units (Xs) are called “polymer
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`A” and the series of unit identifiers (Zs) are called “identifier oligonucleotide C.” Id. at
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`4:31–36; 5:56–61. A and C are joined by “linker molecule B.” Id. at 8:20–24. Thus, the
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`formula is depicted as A–B–C. One can determine the structure of the first chemical unit
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`(X1) by reading the first unit identifier (Z1). Id. at 2:66–3:1 (“The identity of the active
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`molecule is determined by reading the genetic tag, i.e., the identifier oligonucleotide
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`sequence.”). “n” is a position identifier for both X and Z. Id. at 43:10–12. “n” has a value
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`of 1+i where i is an integer from 0 to 10. Id. In the example above, X1–B–Z1, n = 1,
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`meaning X and Z are located “most proximal to the linker [B].” Id. at 43:13. The term
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`“a”, the formulas “(Zn)a” and “(Xn)a”, and other terms are construed herein.
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`II. Disputed Terms
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`The Parties dispute in which order the Court should review the terms. (See generally
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`“Joint Hearing Statement,” ECF No. 50.) Because the dispute regarding the construction
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`of “a” is intertwined with the construction of “(Zn)a” and “(Xn)a”, the Court evaluates these
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`three terms together, and then proceeds with the remaining terms.
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`A. “a”, “(Zn)a”, and “(Xn)a”
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`Plaintiff would construe “a” as: “the length of polymer A or identifier
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`oligionucleotide C and is an integer from 4 to 50.” (“Joint CC Worksheet,” ECF No. 50-2,
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`at 8–9.) Defendant would construe “a” as: “an integer from 4 to 50 that is further defined
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`in the context of the formulas (Zn)a and (Xn)a.” (Id.) These proposed constructions do not
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`speak to the crux of the matter. The real dispute is the proper construction of “a” within
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`the constructions of “(Zn)a” and “(Xn)a.” Defendant proposes “(Xn)a” be construed as: “A
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`representation of polymer A, where ‘a’ is the number of chemical units of X forming the
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`polymer A.” (Id. at 3–4 (emphasis added).) Similarly, Defendant proposes “(Zn)a” be
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`construed as: “A representation of identifier oligonucleotide C, where ‘a’ is the number of
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`chemical unit identifiers in the oligonucleotide.” (Id. at 7–8 (emphasis added).)
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`Generally, Defendant argues “a” is defined as the number of chemical units (X) and
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`the number of corresponding unit identifiers (Z). Plaintiff argues “a” is not limited to the
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`number of chemical units but refers to the length of polymer A and oligonucleotide C.
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`Plaintiff would construe “(Xn)a” as: “the formula that represents polymer A comprising a
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`linear series of chemical units, where ‘a’ is the length of polymer A and is an integer from
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`4 to 50, ‘X’ and ‘n’ are defined by Claim 1 and require no further construction.” (Id. at 3–
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`4 (emphasis added).) Plaintiff would construe “(Zn)a” as: “the formula that represents
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`identifier oligonucleotide C, where ‘a’ is the length of identifier oligonucleotide C and is
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`an integer from 4 to 50, ‘Z’ and ‘n’ are defined by Claim 1 and require no further
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`construction.” (Id. at 7–8 (emphasis added).)
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`To sum up the arguments with an illustration, both Parties interpret Figure 2.
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`See ’596 patent, fig. 2 (with additions, in color). Plaintiff argues “a” for oligonucleotide
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`C in Figure 2 has a value of 18 which is the “total number of A, T, C, and G bases that
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`comprise
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`identifier oligonucleotide C.”
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`(“Metzker Decl.,” ECF No. 55-2,
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`¶ 53.) Plaintiff argues “a” for polymer A in Figure 2 has a value of 3, “which is the length
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`of the polymer of glycine and methionine residues.” (Id.) Defendant argues “a” for
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`oligonucleotide C in Figure 2 has a value of 3 “because there are 3 chemical unit identifiers
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`in the oligonucleotide.” (“Chelsky Decl.,” ECF No. 54-18, ¶ 27.) Defendant agrees with
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`Plaintiff that “a” is 3 for polymer A. (Id. ¶ 37.)3
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`At the claim construction hearing, Plaintiff requested leave to present supplemental
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`briefing and documents. In the supplemental briefs, the Parties again summarize their
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`proposed construction: Plaintiff argues “a” is the length of polymer A and identifier
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`oligonucleotide C. (“Pl. Supp. Br.,” ECF No. 66, at 3.) Plaintiff argues “polymer A is
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`determined by counting the number of monomers” and “the length of an oligonucleotide is
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`measured in nucleotide bases.” (Id.) Plaintiff does not propose these units of measurement
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`be officially added to the claim construction for “a” but argues a person of ordinary skill
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`in the art reading the patent would understand that length is measured in these units. (Id.
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`at 5.)
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`Plaintiff submitted 37 C.F.R. § 1.823 as an exhibit to its brief. This regulation
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`provides what shall be included in a sequence listing. The sequence listing, which sets
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`“forth the nucleotide and/or amino acid sequence and associated information,” shall
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`include “length” in “an integer expressing the number of bases or amino acid residues.” 37
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`C.F.R. § 1.823(b). Plaintiff argues this regulation, which governs “submission of sequence
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`listings of oligonucleotides and polypeptides,” “expressly required that the length be
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`measured by the number of nucleotide bases or amino acid residues, respectively.” (Pl.
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`Supp. Br. 4.) Plaintiff argues one can read this federal regulation, which dictates how
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`sequences must be described in a patent, to determine how to measure the length of a
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`polypeptide of oligonucleotide. (Id. at 5.) Defendant argues this regulation is not relevant
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`to interpreting the formula “(Xn)a” because the patent’s sequence listing relates to
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`3 Defendant previously brought a motion to dismiss, which dealt with the term “a.” As it does in the
`present claim construction, Defendant argued the patent defines “a” to be the number of chemical units in
`polymer A and the number of corresponding unit identifiers in identifier oligonucleotide C. (ECF No. 30-
`1, at 15.) The Court denied Defendant’s motion to dismiss, finding it “cannot say at this stage that
`Defendant’s construction is correct as a matter of law.” (ECF No. 34, at 10.) The Court held that passages
`from the patent illustrate “a” can be defined by the number of chemical units, it does not specify it must
`be so defined. (Id.) The Court noted that the Parties would have another opportunity to contest the
`meaning of “a” at the claim construction phrase. (Id. at 13.)
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`Case 3:16-cv-00661-JLS-BGS Document 77 Filed 04/10/18 PageID.1282 Page 10 of 18
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`oligonucleotide C, not polymer A. (“Def. Supp. Br.,” ECF No. 67, at 7; see ’596 patent, at
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`29.) As to the construction of “(Xn)a”, Defendant does not disagree that the patent describes
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`“a” as “the length of the polymer A.” ’596 patent, at 4:39–42 (“[T]he length of the polymer
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`can vary, defined by a.”). But Defendant reaffirms its position that “length” is measured
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`in chemical units. (Def. Supp. Br. 4 (citing ’569 patent, at 9:9–11 (in Va, “‘a’ is an exponent
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`to V and represents the number of chemical units of X forming the polymer A, i.e., the
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`length of polymer A.”)).)
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`The Court agrees with Defendant’s construction. Critically, Plaintiff cannot point
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`to evidence or to any part of the patent that would allow “a” to be two different integers or
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`measured by two different units for polymer A and oligonucleotide C. Instead, “a” is
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`specifically defined as “an integer”—indicating it is the same for both “(Xn)a” and “(Zn)a”.
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`See ’596 patent, at 4:43–44 (for Polymer A, “‘a’ is an integer from 4 to 50”); id. at 5:63–
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`65 (for oligonucleotide C, “‘a’ is an integer as described previously to connote the number
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`of chemical unit identifiers in the oligonucleotide”). As Defendant points out, “when
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`Scripps wanted to represent two different things (like chemical units (X) and chemical unit
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`identifiers (Z)), it did so by using different variables for each of them in claim 1.” (Def.
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`Supp. Br. 10.) Had Plaintiff intended “a” to represent different values with different units
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`of measurement for polymer A and for oligonucleotide C, it should have specified this, or
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`used two different variables. Plaintiff’s proposed construction leaves open the units of
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`measurement, which will result in two different values for “a” due to the two different units
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`of measurement indicated by Plaintiff in its briefing (monomers and nucleotide bases). (Pl.
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`Supp. Br. 5 (stating “‘a’ need not have the same value in the case of polymer A and
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`oligonucleotide C for a given bifunctional molecule.”).) This is not supported by the patent
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`language nor by 37 C.F.R. § 1.823(b). Plaintiff has not defined “a” with any form of clarity
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`in the sequence listing or in the specification, thus the Court declines to construe “a” based
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`on Plaintiff’s proposed lexicography. And, 37 C.F.R. § 1.823(b), even read in connection
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`Case 3:16-cv-00661-JLS-BGS Document 77 Filed 04/10/18 PageID.1283 Page 11 of 18
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`with the patent’s sequence listing, does not provide that an integer can represent two
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`different lengths with two different units of measurement.
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`The Court construes “a” as “an integer from 4 to 50 that is further defined in the
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`context of the formulas (Zn)a and (Xn)a.”4 The Court construes “(Xn)a” as “a representation
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`of polymer A, where ‘a’ is the number of chemical units of X forming the polymer A.”
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`The Court construes “(Zn)a” as “a representation of identifier oligonucleotide C, where ‘a’
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`is the number of chemical unit identifiers in the oligonucleotide.”
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`B. “B is a linker molecule operatively linked to A and C”
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`Plaintiff would construe this term as “single molecule B that performs the function
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`of operatively linking a single polymer A to single identifier oligonucleotide C.” (Joint
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`CC Worksheet 4.) Defendant would construe this term as “linker molecule B (1) links to
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`A and to C, (2) allows for alternative addition of nucleotides and amino acids to itself, and
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`(3) is capable of coupling to and decoupling from a solid support without cleaving either
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`the polypeptide or oligonucleotide from linker molecule B.” (Id. at 4–5.) Alternatively, if
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`the Court does not accept this, Defendant proposes “a molecule B that performs the
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`function of operatively linking a chemical moiety A to an identifier oligonucleotide C.”
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`(Id. at 5.)
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`In February 2017, the Patent Trial and Appeal Board (“PTAB”) construed the
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`present term. See Illuminia, Inc. v. The Scripps Research Institute, No. IPR2016-01619
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`(P.T.A.B. Feb. 13, 2017) (hereinafter “Illuminia”). Defendant proposes the Court construe
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`the term exactly as the PTAB construed it.
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`The Court agrees with the PTAB’s construction. The decision is reasoned,
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`4 The Court notes that Plaintiff’s proposed construction of “a” specifically (not in the context of the two
`formulas) is not technically incorrect. Plaintiff proposes “a” be construed as “the length of polymer A or
`identifier oligionucleotide C and is an integer from 4 to 50.” (Joint CC Worksheet 8–9.) Defendant would
`construe “a” as: “an integer from 4 to 50 that is further defined in the context of the formulas (Zn)a and
`(Xn)a.” (Id.) Both Parties agree “a” is “the length” of polymer A and oligonucleotide C, thus, both
`proposed constructions are correct. But, Defendant’s construction for “a” as consistent with the
`constructions of (Zn)a and (Xn)a.
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`Case 3:16-cv-00661-JLS-BGS Document 77 Filed 04/10/18 PageID.1284 Page 12 of 18
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`persuasive, and provides the Court with guidance on the construction of the term. (See id.
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`at 9–17.) Further, the PTAB noted, because the ’596 patent expired in 2012, its review of
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`the patent “is similar to that of a district court’s review.” Id. at 9; see In re Rambus,
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`Inc., 694 F.3d 42, 46 (Fed. Cir. 2012) (“[T]he Board’s review of the claims of
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`an expired patent is similar to that of a district court’s review.” (citations omitted)). The
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`PTAB applied the principles set forth in Phillips, 415 F.3d at 1312–13. Illuminia, at 10.
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`The PTAB concluded the term “B is a linker molecule operatively linked to A and C” to
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`mean “that linker molecule B (1) links to A and to C, (2) allows for alternative addition of
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`nucleotides and amino acids to itself, and (3) is capable of coupling to and decoupling from
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`a solid support without cleaving either the polypeptide or oligonucleotide from linker
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`molecule B.” Illuminia, at 17. In sum, the PTAB looked at the language of the claim
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`language, the “disclosure in the specification” and the “narrowing statements” made by
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`Plaintiff during prosecution. Id.; see also id. (“[T]he arguments made to distinguish the
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`prior art constitute a clear and unequivocal disavowal of linker molecules that fail to allow
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`for alternative addition (or synthesis) of an oligonucleotide and amino acid onto the linker
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`molecule, while separately allowing for coupling and decoupling of the linker molecule
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`from a solid support.”).
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`The Court agrees and adopts the PTAB’s construction as to this term. See
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`Evolutionary Intelligence, LLC v. Spring Nextel Corp., No. C-13-04513, 2014 WL
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`4802426, at *4 (N.D. Cal. Sept. 26, 2014) (stating PTAB decisions are not binding on the
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`court but they may “inform” the court’s ultimate reasoning). The term is construed as
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`“linker molecule B (1) links to A and to C, (2) allows for alternative addition of nucleotides
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`and amino acids to itself, and (3) is capable of coupling to and decoupling from a solid
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`support without cleaving either the polypeptide or oligonucleotide from linker molecule
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`B.”
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`C. “bifunctional molecule”
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`Plaintiff would construe this term as “a single molecule of the formula A–B–C,
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`16-CV-661 JLS (BGS)
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`Case 3:16-cv-00661-JLS-BGS Document 77 Filed 04/10/18 PageID.1285 Page 13 of 18
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`whereby one molecule of chemical moiety A and one molecule of identifier
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`oligonucleotide C are operatively linked by one molecule of linker B.” (Pl. CC Brief 18.)
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`Defendant argues this preamble term is not limiting and “is merely a descriptive name to
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`the set of limitations in the body of the claim.” (Def. CC Brief 28.) If the Court determines
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`the term is limiting, Defendant would construe the term as “a molecule that can be
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`represented by the formula A–B–C, where A is a chemical moiety, B is a linker molecule
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`operatively linked to A and C, and C is an identifier oligonucleotide comprising a sequence
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`of nucleotides that identifies the structure of chemical moiety A.” (Id.)
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`A preamble is an introductory phrase that may summarize the invention, its relation
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`to the prior art, or its intended use or properties. E. I. du Pont de Nemours & Co. v.
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`Monsanto Co., 903 F. Supp. 680, 693 (D. Del. 1995) (quoting 8 Donald S. Chisum, Chisum
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`on Patents § 8.06 (Matthew Bender ed. 3d ed.)), aff’d, 92 F.3d 1208 (Fed. Cir.
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`1996) (unpublished). A recurrent problem in construing patent claims is whether language
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`in a claim is a limitation of the claim’s scope or merely a non-limiting statement of intended
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`use or effect. Chisum, § 8.06. “If the preamble adds no limitations to those in the body of
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`the claim, the preamble is not itself a claim limitation and is irrelevant to proper
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`construction of the claim.” IMS Tech., Inc. v. Haas Automation, Inc., 206 F.3d 1422, 1434
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`(Fed. Cir. 2000) (citing Pitney Bowes, 182 F.3d at 1305).
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`Whether to treat a preamble as a limitation is a determination “resolved only on
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`review of the entirety of the patent to gain an understanding of what the inventors actually
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`invented and intended to encompass by the claim.” Corning Glass Works v. Sumitomo
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`Electric U.S.A., Inc., 868 F.2d 1251, 1257 (Fed. Cir. 1989); see also Applied Materials,
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`Inc. v. Advanced Semiconductor Materials Am., Inc., 98 F.3d 1563, 1572–73 (Fed. Cir.
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`1996) (“Whether a preamble stating the purpose and context of the invention constitutes a
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`limitation of the claimed process is determined on the facts of each case in light of the
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`overall form of the claim, and the invention as described in the specification and
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`illuminated in the prosecution history.”).
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`16-CV-661 JLS (BGS)
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`Case 3:16-cv-00661-JLS-BGS Document 77 Filed 04/10/18 PageID.1286 Page 14 of 18
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`In general, a preamble limits the invention if it recites essential structure or steps, or
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`if it is “necessary to give life, meaning, and vitality” to the claim. Pitney Bowes, 182 F.3d
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`at 1305. Conversely, a preamble is not limiting “where a patentee defines a structurally
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`complete invention in the claim body and uses the preamble only to state a purpose or
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`intended use for the invention.” Rowe v. Dror, 112 F.3d 473, 478 (Fed. Cir. 1997). “[A]
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`preamble generally is not limiting when the claim body describes a structurally complete
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`invention such that deletion of the preamble phrase does not affect the structure or steps of
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`the claimed invention.” IMS Tech., 206 F.3d at 1434 (holding preamble phrase “control
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`apparatus” does not limit claim scope where it merely gives a name to the structurally
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`complete invention).
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`The Court finds the phrase “a bifunctional molecule” is not limi