Oxford Nanopore Technologies Ltd.v.University of Washington

Patent Trial and Appeal Board

Sep 15, 2014

13069187 (P.T.A.B. Sep. 15, 2014)

Trials@uspto.gov Paper 12
Tel: 571-272-7822 Entered: September 15, 2014

UNITED STATES PATENT AND TRADEMARK OFFICE
_______________
BEFORE THE PATENT TRIAL AND APPEAL BOARD
_______________
OXFORD NANOPORE TECHNOLOGIES LTD.,
Petitioner,
v.
UNIVERSITY OF WASHINGTON and
UAB RESEARCH FOUNDATION,
Patent Owner.
_______________

Case IPR2014-00512
Patent 8,673,550 B2
_______________

Before FRANCISCO C. PRATS, JACQUELINE WRIGHT BONILLA, and
SHERIDAN K. SNEDDEN, Administrative Patent Judges.

PRATS, Administrative Patent Judge.

DECISION
Denying Institution of Inter Partes Review
37 C.F.R. § 42.108

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I. INTRODUCTION
A. Statement of the Case
Oxford Nanopore Technologies Ltd. (“Petitioner”) filed a Petition
(Paper 1, “Pet.”) requesting inter partes review of claims 1–13, 16–20, 23–
31, and 34–41 of U.S. Patent No. 8,673,550 B2 (Ex. 1001, “the ’550
patent”). The University of Washington and UAB Research Foundation
(collectively, “Patent Owner”) filed a Preliminary Response. Paper 10
(“Prelim. Resp.”). We have jurisdiction under 35 U.S.C. § 314.
The standard for instituting an inter partes review is set forth in 35
U.S.C. § 314(a), which states:
THRESHOLD.—The Director may not authorize an inter
partes review to be instituted unless the Director determines
that the information presented in the petition filed under section
311 and any response filed under section 313 shows that there
is a reasonable likelihood that the petitioner would prevail with
respect to at least 1 of the claims challenged in the petition.

Upon consideration of the Petition and the Preliminary Response, we
conclude that Petitioner has not established a reasonable likelihood that it
would prevail in showing the unpatentability of at least one of the claims
challenged in its Petition. Accordingly, we decline to institute an inter
partes review as to claims 1–13, 16–20, 23–31, and 34–41 of the ’550
patent.
B. Related Proceedings
Concurrently with the Petition under consideration herein, Petitioner
has filed another Petition advancing additional challenges to the claims of
the ’550 patent. Pet. 1; Case No. IPR2014-00513.
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C. Proposed Grounds of Unpatentability
Petitioner contends that the challenged claims are unpatentable under
35 U.S.C. § 103(a) based on the following specific grounds (Pet. 4–8, 18–
56):1
Reference[s] Claims challenged
Akeson2 in combination with any one
of Butler,3 Gundlach Grant,4 Gundlach
Supp.,5 Wong,6 or Faller7

1–13, 16–19, 23–31, and
34–41

1 Petitioner supports its challenge with a Declaration, executed March 18,
2014, by Daniel Branton, Ph.D. (“Branton Decl.”) (Ex. 1012), and a
Declaration, executed March 17, 2014, by Dr. Roland Benz (“Benz Decl.”)
(Ex. 1013).
2 US 2006/0063171 A1 (published Mar. 23, 2006) (Ex. 1009).
3 Thomas Butler, Nanopore Analysis of Nucleic Acids (2007) (Ph.D.
dissertation, University of Washington, Seattle, Washington) (Ex. 1003).
4 Jens Gundlach, Ph.D., Engineering MspA for Nanopore Sequencing,
NHGRI Grant Application, No. 1R21HG004145-01, awarded September 25,
2006 (Ex. 1005).
5 Jens Gundlach, Ph.D., NHGRI Grant Supplement No. 5R21HG004145-02,
awarded August 20, 2007 (Ex. 1006).
6 Risa Wong, Engineering Mycobacterium smegmatis Porin A (MspA) for
DNA Analysis, University of Washington Summer Research Poster Session,
pamphlet cover, program description, schedule of events, abstract and poster
(August 16, 2007) (Ex.1008).
7 Michael Faller et al., The Structure of a Mycobacterial Outer-Membrane
Channel, 303 SCIENCE 1189–1192 (2004) (Ex. 1010).
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Reference[s] Claims challenged
Any one of Akeson, Butler, Gundlach
Grant, Gundlach Supp., or Wong, in
combination with Stahl8
20

D. The ’550 patent
The ’550 patent discloses using a “Mycobacterium smegmatis porin
(Msp)” to detect analytes in liquid media. Ex. 1001, 7:54–8:55. The ’550
patent explains that a porin is a tunnel-forming multimeric protein through
which nutrients pass in mycobacteria. Id. at 7:53–55, 18:32–57 . Wild-type
M. smegmatis porins include MspA, MspB, MspC, and MspD. Id. at 18:59–
61. The ’550 patent discloses that wild-type or mutant Msp porins may be
used in its analytical methods. Id. at 7:60–64.
The ’550 patent discloses that the tunnel of an Msp porin includes two
sections, a “vestibule,” and a “constriction zone.” Id. at 27:15–16.
The ’550 patent states that a “‘vestibule’ refers to the cone-shaped
portion of the interior of an Msp porin whose diameter generally decreases
from one end to the other along a central axis, where the narrowest portion
of the vestibule is connected to the constriction zone. A vestibule may also
be referred to as a ‘goblet.’” Id. at 27:9–14; see also id. at Fig. 1 (showing
structure of wild-type MspA porin).

8 Claudia Stahl et al., MspA provides the main hydrophilic pathway through
the cell wall of Mycobacterium smegmatis, 40 MOLECULAR MICROBIOLOGY
451–464 (2001) (Ex. 1011).
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A “‘constriction zone’ refers to the narrowest portion of the tunnel of
an Msp porin, in terms of diameter, that is connected to the vestibule.” Id. at
27:35–37.
As to its analytical methods, the ’550 patent explains that, when an
Msp porin is placed in a lipid bilayer that separates first and second
conductive liquid media, application of an electrical field can cause an
analyte to be driven into, and/or through, the porin. Id. at 7:53–8:16. The
’550 patent explains further:
The electric field moves an analyte such that it interacts with
the tunnel. By “interacts,” it is meant that the analyte moves
into and, optionally, through the tunnel, where “through the
Msp tunnel” (or “translocates”) means to enter one side of the
tunnel and move to and out of the other side of the tunnel.

Id. at 28:1–6.
The analyte may be detected by “measuring an ion current as the
analyte interacts with an Msp porin tunnel to provide a current pattern,
wherein the appearance of a blockade in the current pattern indicates the
presence of the analyte.” Id. at 8:13–16. Thus, a “‘blockade’ is evidenced
by a change in ion current that is clearly distinguishable from noise
fluctuations and is usually associated with the presence of an analyte
molecule at the pore’s central opening.” Id. at 33:38–41. “More
particularly, a ‘blockade’ refers to an interval where the ionic current drops
below a threshold of about 5–100% of the unblocked current level, remains
there for at least 1.0 µs, and returns spontaneously to the unblocked level.”
Id. at 33:43–46.
The ’550 patent discloses that “an analyte may be a nucleotide, a
nucleic acid, an amino acid, a peptide, a protein, a polymer, a drug, an ion, a
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pollutant, a nanoscopic object, or a biological warfare agent. Optionally, an
analyte is a polymer, such as a protein, a peptide, or a nucleic acid.” Id. at
8:45–49.
The ’550 patent discloses that the negatively charged amino acids in
the tunnel of the wild-type MspA were thought to inhibit DNA entry into the
porin. Id. at 42:15–19. Thus, the ’550 patent describes embodiments in
which negative amino acids in the constriction zone, vestibule, and around
the entrance of wild-type MspA are replaced with positively charged
residues, so as to allow more optimal translocation of single-stranded DNA
through the porin. Id. at 42:19–22, 45:45–46:13.
The ’550 patent also discloses that the Msp porins used in it methods
can include a “molecular motor” which allows analytes to move “into or
through the tunnel with a translocation velocity or an average translocation
velocity that is less than the translocation velocity or average translocation
velocity at which the analyte translocates into or through the tunnel in the
absence of the molecular motor.” Id. at 14:36–42. The ’550 patent discloses
that the molecular motor “may be an enzyme, such as a polymerase, an
exonuclease, or Klenow fragment.” Id. at 14: 43–44.
Claims 1, 16, 17, and 23, the independent claims under challenge,
illustrate the claimed subject matter, and read as follows:
1. A method for detecting the presence of an
analyte, comprising:

applying an electric field sufficient to translocate
an analyte from a first conductive liquid
medium to a second conductive liquid
medium in liquid communication through a
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Mycobacterium smegmatis porin (Msp)
having a vestibule and a constriction zone
that define a tunnel; and

measuring an ion current, wherein a 5% or more
reduction in the ion current for at least 1.0
µs compared to an ion current level for the
Msp without an analyte present indicates the
presence of the analyte in the first medium.

16. A method of modifying the conductance
through the tunnel of a Mycobacterium smegmatis porin
(Msp) comprising removing, adding, or replacing at least
one amino acid in the vestibule or the constriction zone
of a wild-type Msp to define a conductive tunnel that is
distinct from the tunnel defined by the wild-type Msp.

17. A system comprising a Mycobacterium
smegmatis porin (Msp) having a vestibule and a
constriction zone that define a tunnel,

wherein the tunnel is positioned between a first
conductive liquid medium and a second
conductive liquid medium allowing liquid
communication between the first and second
conductive liquid media,

wherein at least one conductive liquid medium
comprises an analyte, and

wherein the system is operative to detect the
analyte when the system is subjected to an
electric field sufficient to translocate the
analyte from one conductive liquid medium
to the other.

23. A mutant Mycobacterium smegmatis porin A
(MspA) comprising:
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a vestibule and a constriction zone that define a
tunnel, and

at least a first mutant MspA monomer comprising
a mutation at position 93 and a mutation at
position 90, position 91, or both positions 90
and 91.
II. ANALYSIS
A. Claim Construction
The Board interprets claims in an unexpired patent using the “broadest
reasonable construction in light of the specification of the patent in which
[they] appear[].” 37 C.F.R. § 42.100(b); see also Office Patent Trial
Practice Guide, 77 Fed. Reg. 48,756, 48,766 (Aug. 14, 2012). Under that
standard, claim terms are given their ordinary and customary meaning, as
would be understood by one of ordinary skill in the art in the context of the
entire disclosure. In re Translogic Tech. Inc., 504 F.3d 1249, 1257 (Fed.
Cir. 2007). Based on our review of the Petition and Preliminary Response,
we conclude that none of the terms in the claims requires an express claim
construction at this time.
B. Prior art status of redacted copies of Gundlach Grant (Ex. 1005) and
Gundlach Supp. (Ex. 1006)
Petitioner contends, and Patent Owners do not dispute presently, that
the redacted copies of the Gundlach Grant (Ex. 1005) and Gundlach Supp.
(Ex. 1006) are copies of grant applications submitted by Jens Gundlach, one
of the inventors of the ’550 patent, to the National Human Genome Research
Institute (“NHGRI”). Pet. 11–12; Prelim. Resp 1-2. Petitioner states that,
on December 13, 2013, Petitioner’s counsel obtained the copies of these
grant applications, entered as Exhibits 1005 and 1006, respectively, which
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Petitioner submitted to the Board in support of the instant Petition. Id.
(citing Ex. 1007).
Petitioner contends that Gundlach Grant and Gundlach Supp. became
publicly available under the Freedom of Information Act (“FOIA”) on the
dates the grants were awarded, September 25, 2006, and August 20, 2007,
respectively. Id. (citing E.I. duPont de Nemours & Co. v. Cetus Corp, 19
USPQ2d 1174, 1182 n.7 (N.D. Cal. 1990)). Therefore, Petitioner contends,
Gundlach Grant and Gundlach Supp. constitute prior art as to the claims of
the ’550 patent under 35 U.S.C. § 102(b). Id.
Patent Owners respond that, under the rules governing the release of
grant applications in response to requests from the public, the submitter of a
grant application is given the opportunity to remove confidential material
from the grant application before a copy of the application is released to the
public requester. Prelim. Resp. 2–3 (citing 45 C.F.R. §§ 5.65(d)(1)–(d)(3)).
Thus, Patent Owners contend, because the portions of a grant considered to
be confidential can change over time, “a redacted document obtained via a
FOIA request made at a given point in time does not necessarily reflect the
redactions that might have been made if the request had been made earlier.”
Id. at 3.
Moreover, Patent Owners contend, Petitioner “offers no proof that the
redacted copies obtained on December 13, 2013, well after the critical date
for the ’550 patent, would have been the same as copies obtained pursuant to
a FOIA request filed on the grant dates.” Id. at 3–4. Thus, Patent Owners
contend, the instant situation is the same as that confronted by the Board in
Medtronic, Inc. v. NuVasive, Inc., IPR2014-00076, Paper 13, Decision
(mailed April 8, 2014), in which the Board declined to institute trial based
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on a document obtained by FOIA request well after the filing date of the
patent at issue in that proceeding. Id. at 4–5.
Petitioner does not persuade us that the redacted copies of the
Gundlach Grant (Ex. 1005) and Gundlach Supp. (Ex. 1006), obtained by a
FOIA request in 2013, constitute prior art under 35 U.S.C. § 102(b).
The question here is whether either the redacted copy of Gundlach
Grant or Gundlach Supp., as obtained in 2013, constitutes a “printed
publication” under § 102(b). In this regard, “the key inquiry is whether the
reference was made ‘sufficiently accessible to the public interested in the
art’ before the critical date.” Voter Verified, Inc. v. Premier Election
Solutions, 698 F.3d 1374, 1380 (Fed. Cir. 2012). Here, both copies of the
Gundlach Grant and Gundlach Supp. filed with the Board contain significant
redactions, with a number of the redactions described in the documents as
being “[p]roprietary info.” See Ex. 1005, 29–30; Ex. 1006, 11–13.9 In the
Gundlach Supp. copy, for example, information regarding the specific
mutants used in the described experiments is redacted. Ex. 1006, 11–13.
Thus, as Patent Owners argue, an opportunity existed, at all times after grant
award dates, to remove confidential proprietary information from the grant
applications. Prelim. Resp. 2. Thus, both Gundlach Grant and Gundlach
Supp. were subject to significant revision before disclosure to the public, and
could have been subject to a great deal more redaction in earlier years as
compared to redactions occurring in 2013.

9 In citing to Gundlach Grant and Gundlach Supp., Exhibits 1005 and 1006,
respectively, we cite to the Exhibit page numbers inserted by Petitioner at
the bottom right corner of each page.
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Accordingly, because of the opportunity for redaction, the copies of
Gundlach Grant and Gundlach Supp. obtained on December 13, 2013,
presented as Exhibits 1005 and 1006, demonstrate what was available to the
public on December 13, 2013, based on Petitioner’s FOIA request of
November 8, 2013. Prelim. Resp. 3–4. Exhibits 1005 and 1006 do not
establish, however, what would have been publicly available any time prior
to Petitioner’s FOIA request.
To that end, Petitioner has not explained adequately why the copies
obtained on December 13, 2013, would have contained the same disclosures
had the documents been obtained via FOIA requests occurring at any time
before the critical date under § 102(b), i.e., more than a year before the
effective filing date of the ’550 patent. Indeed, Petitioner points to no clear
or specific evidence suggesting that any disclosures in Gundlach Grant and
Gundlach Supp. relevant to the challenges advanced in the Petitioner would
have been considered non-confidential had the documents been requested
and released prior to the critical date under § 102(b). Thus, we are not
persuaded that there is a reasonable likelihood that Petitioner would prevail
in establishing that Gundlach Grant and Gundlach Supp. constitute prior art
to the claims of the ’550 patent under 35 U.S.C. § 102(b).
We acknowledge Petitioner’s reliance on E.I. du Pont de Nemours &
Co. v. Cetus Corp., 19 USPQ2d at 1182 n.7, in which a district court in the
Northern District of California concluded that a grant proposal to a different
agency was a printed publication because it was available upon FOIA
request, was indexed by title, author, institution, and grant number, and was
cited by grant number on a prior art document that any researcher in the art
would have been familiar with. Here, however, Petitioner does not assert or
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point to any specific evidence suggesting that Gundlach Grant or Gundlach
Supp. was catalogued or indexed in a meaningful way such as in the manner
described in the E.I. du Pont case, nor does Petitioner direct us to any
undisputed § 102(b) prior art which cites Gundlach Grant or Gundlach Supp.
In sum, for the reasons discussed, we are not persuaded that Petitioner
has shown a reasonable likelihood that it will prevail on its contention that
Gundlach Grant and Gundlach Supp. constitute prior art to the claims of the
’550 patent under 35 U.S.C. § 102(b). As such, we decline to institute trial
as to the grounds based on those documents.
C. Obviousness over Akeson in view of any one of Butler, Gundlach
Grant, Gundlach Supp., Wong, or Faller
Petitioner challenges claims 1–13, 16–19, 23–31, and 34–41 as
obvious over Akeson (Ex. 1009) in view of any one of Butler (Ex. 1003),
Gundlach Grant (Ex. 1005), Gundlach Supp. (Ex. 1006), Wong (Ex. 1008),
or Faller (Ex. 1010). Pet. 21. As noted above, we are not persuaded that
Petitioner has shown that the redacted copies of the Gundlach Grant and
Gundlach Supp., obtained in 2013, constitute prior art to the claims of the
’550 patent, and, therefore, decline to institute trial as to grounds based on
Akeson combined with either Gundlach Grant or Gundlach Supp.
As to the challenges based on Akeson combined with any one of
Butler, Wong, or Faller, Petitioner contends that Akeson describes processes
and systems including all of the features of independent claims 1, 16, 17,
and 23, except for the use of an Msp porin required by those claims. See
Pet. 22 (“Akeson discloses each and every element of claim 1, except the use
of an Msp porin.”); see also id. at 34 (“[O]ne of skill in the art would have
been motivated to modify the system described in Akeson to incorporate a
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mutant MspA porin having an amino acid replacement in the vestibule or the
constriction zone.”) (discussing claim 16); id. at 35 (“Akeson discloses a
system capable of detecting an analyte, which comprises each and every
element of claim 17, except the use of an Msp porin.”); id. at 39 (“[T]he
only issue with respect to claim 23 is whether it would have been obvious to
modify the system described in Akeson by making MspA mutants
comprising mutations at the specified positions.”).
To address that deficiency in Akeson, Petitioner contends:
One of skill in the art would have been motivated to
modify the system described in Akeson to incorporate the Msp
porin, which has a short constriction zone as disclosed in any
one of Butler; . . . Wong; and Faller, given the teaching in
Akeson (via its incorporation by reference of the ‘782 patent) of
the desirability of using porins with short constriction zones to
improve monomer resolution. (“To determine current
modulation attributable to individual monomers, one may use
channels containing a limiting aperture that is much shorter
than the full length of the overall channel[.]” Ex. 1024 at col.
13, lines 10-13).

Pet. 22 (citing Ex. 1012 at ¶¶ 241-242 (Branton Decl.)). Moreover,
Petitioner contends, an ordinary artisan “would view the use of an Msp porin
in the method outlined in Akeson as nothing more than the predictable use of
a prior art element according to its established function.” Id. at 23 (citing
Ex. 1012 ¶¶ 241–242).
In KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 415 (2007), although
the Supreme Court emphasized “an expansive and flexible approach” to the
obviousness question, the Court also reaffirmed the importance of
determining “whether there was an apparent reason to combine the known
elements in the fashion claimed by the patent at issue.” Id. at 418. A
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determination that claims would have been obvious to an ordinary artisan
“cannot be sustained by mere conclusory statements; instead, there must be
some articulated reasoning with some rational underpinning to support the
legal conclusion of obviousness.” Id.; see also, Unigene Laboratories, Inc.
v. Apotex, Inc., 655 F.3d 1352, 1360 (Fed. Cir. 2011) (“Obviousness requires
more than a mere showing that the prior art includes separate references
covering each separate limitation in a claim under examination.”).
In the instant case, we are not persuaded that the Petition has
advanced a rational underpinning sufficient to support the obviousness
challenges to independent claims 1, 16, 17, and 23. Petitioner contends that
column 13, lines 10–13 of the ’782 patent, which Akeson incorporates by
reference, teaches the desirability of using porins with short constriction
zones to improve monomer resolution. Pet. 22 (citing Ex. 1024, 13:10-13).
We acknowledge, as discussed in the Petition, that Akeson describes a
system in which a biological nanopore protein, alpha-hemolysin (“αHL”), is
placed between two containers of conductive media, thereby allowing
detection of DNA as it passes through the nanopore protein in response to an
applied electric field. Pet. 21–22; see also Ex. 1009 ¶¶ 79–81. We also
acknowledge Akeson’s statement that “[a]ll publications, patents, and patent
applications mentioned in this specification are herein incorporated by
reference to the same extent as if each independent publication or patent
application was specifically and individually indicated to be incorporated by
reference.” Ex. 1009 ¶ 98. We further acknowledge that, alongside
approximately ten other patents and published patent applications, Akeson
lists the ’782 patent (Ex. 1024) as describing “[s]uitable nanopores.” Ex.
1009 ¶ 44.
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In addressing the issue of incorporation by reference, however, the
Federal Circuit has stated that the “host document must identify with
detailed particularity what specific material it incorporates and clearly
indicate where that material is found in the various documents.” Zenon
Environmental, Inc. v. U.S. Filter Corp., 506 F.3d 1370, 1378 (Fed. Cir.
2007) (citing Cook Biotech Inc. v. Acell, Inc., 460 F.3d 1365, 1376 (Fed. Cir.
2006)). In the instant case, although Petitioner urges that Akeson
incorporates by reference the disclosure at column 13, lines 10–13 of the
’782 patent, the Petition does not direct us to any express or specific
disclosure in Akeson mentioning that passage with detailed particularity.
See, e.g., Pet. 21-23. Nor does the Petition direct us to any clear or specific
disclosure in Akeson suggesting that Akeson sought to incorporate by
reference any teachings in the ’782 patent as to the physical properties
Akeson required of its nanopores. See id. Accordingly, we are not
persuaded that the Petition has shown that, because Akeson incorporates the
’782 patent as a whole by reference, among many other references, Akeson
in effect can be considered as positively teaching the subject matter
disclosed at column 10, lines 10–13 of the ’782 patent. As to the actual
teaching at column 10, lines 10–13 of the ’782 patent, the Petition does not
list the ’782 patent as a reference relied upon to show unpatentability in its
listed grounds. See, e.g., Pet. 10–11.
Moreover, although the Petition contends that Akeson would have
suggested substituting Akeson’s αHL porin for a porin with a limiting
aperture that is much shorter than the overall length of the channel, (see Pet.
22), the Petition fails to identify the specific teachings in Butler, Wong, or
Faller explaining why Msp porins possess that structural attribute. We note
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that paragraph 240 of the Branton Declaration includes approximately six
pages of claim charts explaining the disclosures of Butler, Wong, and Faller
with specificity, including the structural attributes of Msp porins. Ex. 1012
¶ 240. We note also that paragraphs 241 and 242 of the Branton
Declaration, cited as support for the obviousness rationale (see Pet. 22–23),
advance a number reasons allegedly explaining why the teachings in Butler,
Wong, and Faller would have prompted an ordinary artisan to use an Msp
porin in Akeson’s system.
Nonetheless, essentially none of the discussion in the cited paragraphs
of the Branton Declaration, allegedly explaining why an ordinary artisan
would have combined Akeson with Butler, Wong, or Faller, appears in the
Petition. We decline to import the extensive discussion regarding
obviousness from the declarations of Petitioner’s experts into the Petition,
based solely on the Petition’s citation of certain paragraphs within the
declarations. As stated in 37 C.F.R. § 42.6(a)(3), “[a]rguments must not be
incorporated by reference from one document into another document.”
Moreover, we agree with our colleagues’ reasoning in Conopco, Inc. v. The
Procter & Gamble Company, in that “[w]e decline to consider information
presented in a supporting declaration, but not discussed in a petition,
because, among other reasons, doing so would encourage the use of
declarations to circumvent the page limits that apply to petitions.” IPR2013-
00510, slip op. at 8 (PTAB February 12, 2014) (Paper 9).
In asserting that claim 16 would have been obvious, the Petition cross-
references to another rationale advanced for modifying Akeson’s system, in
which the Petition asserts that an ordinary artisan would have been
motivated to modify Akeson’s system to incorporate a mutant MspA porin,
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“because it was well known at the time that mutations to MspA porins could
be made that would improve analyte translocation.” Pet. 29 (citing Ex.
1012, ¶¶ 291–293); see also id. at 34 (discussing claim 16, cross-referencing
to “Section VIII(B)(11)” (discussion at page 29 of Petition)).
As to combining Akeson with either Butler or Wong, however, the
Petition does not discuss, with any specificity, the teachings in Butler and
Wong that would have prompted an ordinary artisan to use a mutant Msp
porin in Akeson’s system. Although the Petition cites Butler and Wong as
disclosing MspA mutants (Pet. 29), the Petition does not discuss the systems
described in those references with any specificity. Nor does the Petition
compare Akeson’s system to the systems of Butler and Wong, so as to
present a motive, based on a rational underpinning, explaining why an
ordinary artisan would have considered it obvious to use the mutants of
Butler or Wong in Akeson’s system. The mere fact that Butler and Wong
might describe some type of apparatus that uses mutant Msp porins does not,
by itself, persuade us that an ordinary artisan would considered it obvious to
use mutant Msp porins in Akeson’s system.
As to the combination of Akeson and Faller, we acknowledge the
Petition’s assertion that Faller teaches that mutating a particular residue in an
Msp porin should result in a protein with decisively increased translocation
activity. See Pet. 30 (citing Ex. 1010, 4). Nonetheless, the Petition does not
identify any clear or specific teaching in the cited prior art, or in the
knowledge available to an ordinary artisan, explaining why an ordinary
artisan would have considered a mutated porin having that property
desirable, or even useful, in Akeson’s system. We are not persuaded,
therefore, that the Petition explains convincingly why an ordinary artisan
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would have been prompted to use such a porin in Akeson’s system.
In sum, we are not persuaded that the Petition has advanced sufficient
reasoning, based on a rational underpinning, to support its obviousness
challenges to independent claims 1, 16, 17, and 23, based on Akeson
combined with Butler, Wong or Faller. Accordingly, we decline to institute
trial as to claims 1, 16, 17, and 23, and their dependent claims, based on
those obviousness grounds.
D. Obviousness of claim 20 over Stahl in view of any one of Akeson,
Butler, Gundlach Grant, Gundlach Supp., or Wong
Claim 20 reads as follows:
20. The system of claim 17, wherein the Msp comprises a
mutant porin comprising:
a vestibule having a length from about 2 to about 6 nm
and a diameter from about 2 to about 6 nm, and
a constriction zone having a length from about 0.3 to
about 3 nm and a diameter from about 0.3 to about
3 nm,
and wherein the mutant porin comprises at least a first
mutant MspA paralog or homolog monomer.

Ex. 1001, 105:30–37.
Petitioner contends that claim 20 would have been obvious over Stahl
(Ex. 1011) in view of any one of Akeson, Butler, Gundlach Grant, Gundlach
Supp., or Wong. Pet. 58. Specifically, Petitioner contends that an ordinary
artisan would have been motivated “to modify the systems described in any
one of Akeson, Butler, Gundlach Grant, Gundlach Supp., and Wong to
incorporate a MspA paralog or homolog falling within the specified length
and diameter ranges, such as the MspA homologs disclosed in Stahl, i.e.,
MspB, MspC, and MspD.” Id. at 59 (citing Ex. 1012 ¶¶ 429–430 (Branton
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Patent 8,673,550 B2

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Decl.)). Moreover, Petitioner contends, an ordinary artisan “would view the
use of the MspA paralogs of Stahl in the method outlined in Akeson, Butler,
Gundlach Grant, Gundlach Supp., and Wong as nothing more than the
predictable use of a prior art element according to its established function.
Id. (citing Ex. 1012 ¶¶ 429-430).
As noted above, we are not persuaded that Petitioner has shown that
the redacted copies of the Gundlach Grant (Ex. 1005) and Gundlach Supp.
(Ex. 1006), obtained in 2013, constitute prior art to the claims of the ’550
patent. Thus, we decline to institute trial as to grounds based on Stahl
combined with either Gundlach Grant or Gundlach Supp.
As to the remaining challenges to claim 20, we first note Petitioner’s
assertion that § VIII(B)(1) of the Petition discusses the disclosure, by each of
Akeson, Butler, and Wong, of systems capable of detecting an analyte by
employing “an electric field applied to the systems with three components, a
first conductive liquid medium that contains the analyte, a second liquid
conductive medium, and a biological nanopore connecting the two media.”
Pet. 58. Section VIII(B)(1) of the Petition, however, discusses only the
elements in Akeson’s system to the level of detail asserted, and does not
discuss the systems of Butler or Wong with any specificity. See Pet. 21–23
(§ VIII (B)(1)).
Moreover, the Petition does not articulate adequately clear or specific
reasoning, or evident underlying rational underpinning, to support its
assertion that an ordinary artisan would have been motivated to modify the
systems of Akeson, Butler, or Wong, to include MspA homologs disclosed
by Stahl. See Pet. 59. The Petition also does not articulate adequately clear
or specific reasoning, or evident underlying rational underpinning,
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Patent 8,673,550 B2

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explaining why making that modification would have amounted to nothing
more than the predictable use of a known prior art element according to its
established function. See id. Rather, the Petition cites only to ¶¶ 429 and
430 of the Branton Declaration in support of those contentions. See id.
We acknowledge that ¶¶ 429 and 430 of the Branton Declaration
advance a number of reasons allegedly explaining why an ordinary artisan
would have combined the teachings of Stahl with the teachings of Akeson,
Butler, and Wong. See Ex. 1012 ¶¶ 429-430. As discussed above, however,
we decline to import the extensive discussion regarding obviousness from
the declarations of Petitioner’s experts into the Petition, based solely on the
Petition’s citation of certain paragraphs within the declarations. See 37
C.F.R. § 42.6(a)(3); see also Conopco, Inc. v. The Procter & Gamble
Company, IPR2013-00510, slip op. at 8 (PTAB February 12, 2014) (Paper
9).
In sum, for the reasons discussed, we are not persuaded that the
Petition has advanced sufficient reasoning, based on a rational underpinning,
to support its obviousness challenges to claim 20, based on Stahl combined
with Akeson, Butler, Wong or Faller. Accordingly, we decline to institute
trial as to claim 20, based on those grounds.
III. CONCLUSION
For the foregoing reasons, we are not persuaded that there is a
reasonable likelihood that Petitioner would prevail with respect to at least
one of the claims of the ’550 patent challenged in the grounds of
unpatentability advanced in the Petition.
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IV. ORDER
It is
ORDERED that the petition is denied as to all challenged claims and
no trial is instituted.

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Patent 8,673,550 B2

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For PETITIONER:

Steven Lendaris
Robert Scheinfeld
BAKER BOTTS LLP
steven.lendaris@bakerbotts.com
robert.scheinfeld@bakerbotts.com

For PATENT OWNERS:
Dorothy P. Whelan
Sean P. Daley
FISH & RICHARDSON P.C.
Whelan@fr.com
Daley@fr.com