Agilent Technologies, Inc.

Patent Trials and Appeals Board

Sep 29, 2020

2020001122 (P.T.A.B. Sep. 29, 2020)

UNITED STATES PATENT AND TRADEMARK OFFICE
UNITED STATES DEPARTMENT OF COMMERCE
United States Patent and Trademark Office
Address: COMMISSIONER FOR PATENTS
P.O. Box 1450
Alexandria, Virginia 22313-1450
www.uspto.gov
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO.
15/010,973 01/29/2016 JOEL MYERSON 20140284-02 8331
22878 7590 09/29/2020
Agilent Technologies, Inc.
Global IP Operations
5301 Stevens Creek Blvd
Santa Clara, CA 95051
EXAMINER
KAUP, SAHANA S
ART UNIT PAPER NUMBER
1639
NOTIFICATION DATE DELIVERY MODE
09/29/2020 ELECTRONIC
Please find below and/or attached an Office communication concerning this application or proceeding.
The time period for reply, if any, is set in the attached communication.
Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the
following e-mail address(es):
Agilentdocketing@cpaglobal.com
ipopsadmin@agilent.foundationip.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
__________

Ex parte JOEL MYERSON and BO U. CURRY
__________

Appeal 2020-001122
Application115/010,973
Technology Center 1600
__________

Before ANTON FETTING, ULRIKE W. JENKS, and
RACHEL H. TOWNSEND, Administrative Patent Judges.

TOWNSEND, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134(a) involving claims to a
method of producing an array of proteins from an array of expression
cassettes, which have been rejected as obvious.2 We have jurisdiction under
35 U.S.C. § 6(b).
We affirm.

1 We use the word “Appellant” to refer to “applicant” as defined in 37
C.F.R. § 1.42. Appellant identifies the real party in interest as Agilent
Technologies, Inc. (Appeal Br. 2.)
2 The provisional obviousness-type double patenting rejections made by the
Examiner have been rendered moot by the abandonment of Application
14/550,713.
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STATEMENT OF THE CASE
Claims 1–20 are on appeal. Claim 1 is illustrative and reads as
follows:
1. A method comprising:
a) providing an array of expression cassettes;
b) providing a planar absorbent support comprising an in
vitro transcription and translation (NTT) mix impregnated
therein;
c) placing the planar absorbent support in contact with
the array of expression cassettes; and
d) incubating the planar absorbent support and array
under conditions by which the expressed cassettes are
transcribed and translated by the impregnated NTT
components, thereby producing an array of protein in, within or
at the surface of the planar absorbent support.
(Appeal Br. 15.)

The prior art relied upon by the Examiner is:
Name Reference Date
Taussig et al. US 2008/0293591 A1 Nov. 27, 2008
Jacobson et al. US 2012/0220497 A1 Aug. 30, 2012
Bertozzi et al. US 2012/0244601 A1 Sept. 27, 2012
Hudson et al. US 2013/0252849 A1 Sept. 26, 2013
M. He et al., Printing protein arrays from DNA arrays, 5(2) Nature , 175–
177 (2008)

The following grounds of rejection by the Examiner are before us on
review:
Claims 1, 7, 8, and 12 under 35 U.S.C. § 102 (a)(1) and (a)(2) as
anticipated by Taussig.
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Claims 1, 7, 10, and 12 under 35 U.S.C. § 102 (a)(1) and (a)(2) as
anticipated by He.
Claims 2–5 and 18–20 under 35 U.S.C. § 103 as unpatentable over
Taussig and Hudson.
Claim 6 under 35 U.S.C. § 103 as unpatentable over Taussig, Hudson,
and Bertozzi.
Claims 9, 11, and 13–17 under 35 U.S.C. § 103 as unpatentable over
Taussig and Jacobson.
DISCUSSION
Anticipation
A. Taussig
The Examiner finds that Taussig teaches a protein expression system,
including a sandwich embodiment that meets the claimed limitations. (Final
Action 2.) In particular, the Examiner states that in the sandwich
embodiment that Taussig teaches, the DNA molecule templates are
immobilized in an array to a first surface, a membrane filter that is
presoaked with a cell-free expression system extract (referred to as an IVTT)
is placed on top of the immobilized DNA array, and a second surface
comprising protein capture reagents is placed on top of the filter. (Id. at 2–3
(citing Taussig ¶¶63, 69, and Example 1).) The Examiner explains that the
pre-soaked membrane filter includes “transcriptional promoters,
transcriptional regulatory sequences, untranslated leader sequences,
sequences encoding cleavage sites, recombination sites, transcriptional
terminators or ribosome entry sites, cistrons, and open reading frames (e.g.,
para 0023-0024, pg. 2).” (Id. at 3.)
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Appellant focuses only on the limitations of claim 1. Claims 7, 8, and
12 have not been argued separately and therefore fall with claim 1. 37
C.F.R. § 41.37(c)(1)(iv).
Appellant argues that the claims on appeal require “protein capture by
the IVTT impregnated planar absorbent support by virtue of protein
production in, within or at the surface of the support” and the rejection is in
error because Taussig “does not describe protein capture or production
within or at the surface of an IVTT impregnated planar absorbent support.”
(Appeal Br. 6; Reply Br. 5.) According to Appellant, the three layer
sandwich assay described in Taussig “does not disclose or suggest
production of a protein array in, within or at the surface of an IVTT
impregnated planar absorbent support” and because the protein capture
surface is separated from the DNA array surface by a membrane, it does not
“disclose placing the planar absorbent support in contact with the array of
expression cassettes.” (Appeal Br. 6; Reply Br. 5.) We disagree.
Appellant’s claim 1 requires that after “an array of expression
cassettes” is incubated with “a planar absorbent support” that has an in vitro
transcription and translation mix impregnated therein, “an array of protein”
is produced “in, within or at the surface of the planar absorbent support.”
Thus, the claim 1 does not literally recite “protein capture.” Instead it
simply recites producing an array of protein “in, within or at the surface of”
the planar absorbent support that has an IVTT mix impregnated therein.
The term “array” is defined in Appellant’s Specification, in terms of a
two-dimensional arrangement but not in terms of protein capture. (Spec. 4
(“The term ‘array’ is intended to describe a two-dimensional arrangement of
addressable regions bearing oligonucleotides associated with that region.”).)
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Thus an “array of expression cassettes” as required in claim 1, step a) is
simply a two dimensional arrangement of addressable regions bearing
expression cassettes. And “an array of protein” required in claim 1, step d)
is simply a two dimensional arrangement of addressable regions bearing
proteins.
Taussig teaches a planar absorbent support that includes an IVTT
matrix impregnated therein. In particular, Taussig states that “cell-free
protein synthesis . . . occurs within a protein permeable material (e.g.,
membrane filter)” where that filter is “pre-soaked with a coupled cell-free
lysate for protein synthesis.” (Taussig ¶ 63 (emphasis added).)
We find further that Taussig teaches production of protein “in, within
or at the surface” of that planar absorbent support. Taussig describes the
“cell-free” system that is impregnated in the protein permeable material is
“capable of performing protein synthesis by transcription and translation.”
(Id. ¶ 28.) Taussig further explains that the cell-free system “provide[s] an
environment in which the conditions of protein synthesis can be adjusted and
controlled through addition of exogenous biomolecules or molecules” (id. ¶
30) and can include agents that “interact with the arrayed proteins [that are
present on a first support surface] or encode said interacting additional
agents (e.g., nucleic acids capable of being transcribed and/or translated into
protein by the cell-free system)” (id. ¶ 32). Taussig further teaches that the
protein produced within the permeable membrane ends up at the surface of
the membrane through diffusion. Taussig states: “The individual DNA
molecules direct the synthesis of proteins 4, which subsequently diffuse
through the filter to the second support surface 3 where they are
immobilized in situ.” (Id. ¶ 63 (emphasis added).)
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It is true that Taussig teaches that the protein produced through
transcription and translation by the impregnated IVTT components of the
protein permeable material is “captured” on a protein capturing surface by
“interaction with the capture reagent.” (Id.; see also id. ¶ 28.) Nevertheless,
the protein is produced “within [the] protein permeable material” and
diffuses to the surface of that membrane prior to being captured on another
support surface. (Id. ¶ 63.)
We note further that Taussig teaches the capture of the protein so
diffused is in an array “that is complementary to” the DNA array on the first
support surface because “protein diffusion within the plane of the membrane
is limited.” (Id.) Given that protein capture is in a complementary array, we
find that the protein produced that diffuses to the surface of the membrane
must be in a similar complementary array. Thus, contrary to Appellant’s
argument, we find Taussig describes production of a protein array as
claimed. That this array of protein at the surface of the protein permeable
support is not captured with a capturing reagent does not preclude finding
the claimed limitations, which do not require capture, are met.
Furthermore, contrary to Appellant’s argument, we find Taussig
describes placing the planar absorbent support as claimed in contact with the
array of expression cassettes. In particular, Taussig describes that the
membrane filter that is first soaked with cell-free lysate is “placed between
the DNA array slide and the protein capturing slide “and a tight contact
between the surfaces was made.” (Taussig ¶ 69.)
In light of the foregoing, we agree with the Examiner that Taussig
anticipates the method as recited in claim 1.
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B. He
Like Taussig, He teaches a sandwich assay in which a planar
absorbent support, i.e., a permeable membrane, carries a cell-free lysate,
capable of performing coupled transcription and translation, that is
positioned between a DNA array and a capture slide. (He 175.) As with
Taussig, the protein that is synthesized during the incubation, diffuses
through the membrane to its surface and then is immobilized on the capture
slide surface. (Id.)
Here, again, Appellant focuses its arguments only on the limitations of
claims 1. Claims 7, 10, and 12 have not been argued separately and
therefore fall with claim 1. 37 C.F.R. § 41.37(c)(1)(iv).
Appellant’s arguments as to why He does not anticipate claim 1 are
the same as those it made with respect to Taussig. (Appeal Br. 8–9; Reply
Br. 7–8.) We do not find Appellant’s arguments persuasive for the same
reasons discussed above with respect to Taussig.

Obviousness
Appellant’s arguments against the Examiner’s obviousness rejections
stem from its contention that Taussig does not anticipate the method of
producing the protein array recited in claim 1. (See Appeal Br. 10–11.)
However, for the reasons discussed above, we disagree with Appellant’s
proposition. Consequently, we affirm the Examiner’s rejections of
a) claims 2–5 and 18–20 under 35 U.S.C. § 103 as unpatentable over
Taussig and Hudson;
b) claim 6 under 35 U.S.C. § 103 as unpatentable over Taussig,
Hudson, and Bertozzi; and
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c) claims 9, 11, and 13–17 under 35 U.S.C. § 103 as unpatentable over
Taussig and Jacobson.
DECISION SUMMARY
In summary:
Claims
Rejected
35 U.S.C.
§
Reference(s)/Basis Affirmed Reversed
1, 7, 8, 12 102 Taussig 1, 7, 8, 12
1, 7, 10, 12 102 He 1, 7, 10, 12
2–5, 18–20 103 Taussig, Hudson 2–5, 18–20
6 103 Taussig, Hudson,
Bertozzi
6
9, 11, 13–17 103 Taussig, Jacobson 9, 11, 13–17
Overall
Outcome
1–20

TIME PERIOD FOR RESPONSE
No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a). See 37 C.F.R.
§ 1.136(a)(1)(iv).

AFFIRMED