Ex Parte Hobbs et al

Board of Patent Appeals and Interferences

Sep 17, 2010

10285810 - (D) (B.P.A.I. Sep. 17, 2010)

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.
10/285,810 10/31/2002 Susan K. Hobbs STAN-252 (S01-116) 3173
77974 7590 09/20/2010
Stanford University Office of Technology Licensing
Bozicevic, Field & Francis LLP
1900 University Avenue
Suite 200
East Palo Alto, CA 94303
EXAMINER
CHEU, CHANGHWA J
ART UNIT PAPER NUMBER
1641
MAIL DATE DELIVERY MODE
09/20/2010 PAPER
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.
PTOL-90A (Rev. 04/07)

UNITED STATES PATENT AND TRADEMARK OFFICE
____________________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
____________________

Ex parte SUSAN K. HOBBS, MARK D. BEDNARSKI, YI-SHAN YANG,
SAMIRA GUCCIONE,
and
GONGYI SHI,
Appellants1
____________________

Appeal 2010-001999
Application 10/285,810
Technology Center 1600
____________________

Before CAROL A. SPIEGEL, DONALD E. ADAMS, and
STEPHEN WALSH, Administrative Patent Judges.

SPIEGEL, Administrative Patent Judge.

DECISION ON APPEAL2

1 The real party in interest is the Board of Trustees of the Leland Stanford
Junior University (Appellants' Brief filed 2 November 2007 ("Br.") at 3).
This decision also cites the Examiner's Answer mailed 17 August 2009
("Ans.") and the Specification of Application 10/285,810 ("Spec.").
2 The two-month period for filing an appeal or commencing a civil action, as
recited in 37 C.F.R. § 1.304, or for filing a request for rehearing, as recited
in 37 C.F.R. § 41.52, begins to run from the "MAIL DATE" (paper delivery
mode) or the "NOTIFICATION DATE" (electronic delivery mode) shown
on the PTOL-90A cover letter attached to this decision.
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2
Appellants appeal under 35 U.S.C. § 134 from an Examiner's final
rejection of all pending claims, claims 1, 4, 6, and 7 (Br. 3; Ans. 3). We
have jurisdiction under 35 U.S.C. § 134. We AFFIRM.
I. Statement of the Case
The subject matter on appeal is directed to a device comprising a
polymerized diacetylene thin film containing a specific binding moiety
(ligand) arrayed on a surface. Claim 1 is illustrative and reads (Ans. 3,
emphasis and paragraphing added):
1. A device for identifying and characterizing
an analyte, said device comprising:
(a) a substrate; and
(b) a polymerized diacetylene
monomolecular film deposited as plurality of
spots on at least a portion of said substrate surface,
wherein each of said spots comprises a unique
specific binding moiety at least a portion of said
substrate surface, wherein said polymerized
monomolecular film comprises a mixture
consisting of cross-linking self-assembling
diacetylene monomers and amphipathic molecules
comprising a specific binding moiety;
wherein said device is stable to the laser
intensities employed in matrix-associated laser
desorption/ionization mass spectroscopy (MALDI-
MS).

The Examiner has rejected claims 1, 4, 6, and 7 as indefinite and
anticipated.3 We address these rejections in order. However, as an initial

3 The Examiner has withdrawn the rejections of claims 1, 4, 6, and 7 as
indefinite under 35 U.S.C. § 112, second paragraph, based on the recitation
of "unique specific binding moiety" and "amphipathic" in claims 1, 4, and 7;
and, of claims 1, 4, 6, and 7 as obvious under 35 U.S.C. § 103(a) over
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matter, we note that Appellants have requested the Board to allow entry of
an amendment filed January 22, 2007 after a Final rejection (Br. 3-4).
Denial of entry of amendments submitted after Final rejection is a
petitionable matter under 37 C.F.R. § 1.182.
II. Indefiniteness
The Examiner rejected claims 1, 4, 6, and 7 as indefinite under 35
U.S.C. § 112, second paragraph, because it is unclear what particular
structure is meant by the recitation of "a unique specific binding moiety at
least a portion of said substrate" in claim 1, step (b) (Ans. 4). Appellants
state that "the cited phrase contains a typographical error, the specification
uses the intended phrase 'over at least a portion of the substrate' multiple
times" (Br. 6). Since the claim language is in error and, therefore, does not
"particularly point out and distinctly claim the subject matter which
applicant regards as the invention" as required by § 112, second paragraph,
we sustain the rejection of claim 1 and its dependent claims.
III. Anticipation
A. Statement of the rejection
The Examiner rejected claims 1, 4, 6, and 7 under 35 U.S.C. § 102(e)
as anticipated by Charych4 (Ans. 5).
The Examiner found that Charych teaches a device for identifying and
characterizing an analyte comprising a polymerized diacetylene
monomolecular film deposited on a substrate in a plurality of spots, wherein

Barraud et al. in view of Wilson et al. (See the final Office action mailed 20
July 2006 at 2-3, 5-6; Ans. 2-6).
4 US Patent 6,306,598 B1, Nucleic Acid-Coupled Colorimetric Analyte
Detectors, issued 23 October 2001, to Deborah H. Charych and Ulrich Jonas,
based on Application 09/337,973, filed 21 June 1999 ("Charych").
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each spot comprises a mixture of cross-linked self-assembly
pentacosadiynoic acid monomers and amphipathic lipid molecules having a
specific binding moiety bound thereto (Ans. 5).
Appellants argue that Charych fails to teach a polymerized
diacetylene monomolecular film as claimed (Br. 7). Appellants further
argue "that while Charych assertedly tests and uses monolayers in
developing the invention, Charych unambiguously teaches the disadvantages
of using monolayers as compared to bilayers for the purpose of detecting
and characterizing analyte" (id. at 8) and, thus, explicitly teaches away from
a monomolecular film (id. at 7).
Since Appellants do not separately argue any of the dependent claims,
we decide this appeal on the basis of claim 1. 37 C.F.R. § 41.37(c)(1)(vii).
Thus, at issue is whether Charych discloses the claimed invention such that a
skilled artisan could take its teachings in combination with his own
knowledge of the particular art and be in possession of the invention.
B. Findings of Fact
The following findings of fact ("FF") are supported by a
preponderance of the evidence of record.
A. The Specification
[1] The Specification defines a "polymerized monomolecular film" as
follows:
the term "film[]" refers to a material deposited or
used in a thin section or in a layer form, where the
film is a single molecule thick. The thin films of
the invention are comprised of two components, a
ligand (or specific binding moiety) containing
amphipathic molecule[], and a self-assembling
monomer. … "self-assembling monomers" and
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"lipid monomers" refer to molecules that
spontaneously associate to form molecular
assemblies. … Generally, the ratio in the film of
ligand containing molecules to self-assembling
monomers will be at least 0.1, about 1, about 10,
about 15, or about 20 mole percent. (Spec. 6, ¶
20.)

[2] Preferred self-assembling diacetylene monomers ("SAMs") include
the fatty acids 10,12-pentacosadiynoic acid and 5,7-pentacosadiynoic
acid (id. at 6, ¶ 21).
[3] Preferred amphipathic molecules (i.e., molecules having a hydrophilic
head group for binding a specific binding moiety, either directly or
through a linker, and a hydrophobic tail group for self-assembly into
films) include lipids such as fatty acids (id. at 6, ¶ 22 to 8, ¶ 29).
[4] The solid support surface or substrate may be any convenient
substrate that is hydrophobic or substantially hydrophobic (id. at 11, ¶
38), and may be modified with one or more different layers of
compounds to provide desired properties, e.g., an aluminum oxide
surface derivatized with octadecyltriethyoxysilane (id. at 11, ¶¶ 40-41).
[5] Figure 1B of the Specification is a schematic representation of an
exemplary device comprising specific binding moiety terminated head
groups immobilized and displayed within a polymerized diacetylene
backbone deposited on a modified hydrophobic aluminum oxide
substrate as spots of thin films (Spec. 3, ¶ 9). The films were formed
by spreading a mixture of SAM with and without terminally-linked
specific binding moieties (i.e., from right to left: biotin, hydroxyl, and
integrin antagonist) on a bead of water covering a hydrophobic
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surface and then polymerizing the monomers with UV radiation (id. at
19, ¶¶ 70-71). Figure 1B is reproduced below.

{Figure 1B illustrates an exemplary device according to the Specification.}

B. Charych
[6] In one embodiment, Charych is directed to methods and compositions
related to the specific detection of nucleic acid hybridization via
recognition of a single stranded sample nucleic acid with a single
stranded probe nucleic acid, which is covalently attached to the
surface of a biopolymeric material (Charych col. 20, ll. 18-23).
[7] The biopolymeric material may comprise liposomes, films, and
multilayers, as well as other nanostructures (id. at col. 21, ll. 49-53).
[8] The biopolymeric material may further comprise one or more dopants,
including diacetylene derivatives, to optimize desired properties, such
as response, sensitivity, and amenability to immobilization, and may
be organized as films, monolayers, and bilayers (id. at col. 16, ll. 4-10,
23-26; col 27, ll. 56-col. 28, l. 9).
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[9] According to Charych,
FIGS. 40-50 show various embodiments of
nucleic acid-coupled biopolymeric material
generation and use. In particular, FIG. 41A shows
various nucleic acid derivatized biopolymeric
materials. Likewise, FIG. 41B shows additional
nucleic acid derivatized biopolymeric materials. …
[Id. at col. 6, ll. 54-58.]

[10] Figure 40 illustrates colorimetric detection of DNA hybridization. A
visibly blue film formed by UV irradiation-induced polymerization of
lipids comprising diacetylene monomers is transferred to a
hydrophobized solid support (i.e., a device) (id. at col. 22, ll. 15-30).
When hybridization (i.e., specific binding) occurs between the
specific binding moiety (ss-p-DNA) associated with the
polydiacetylene monolayer immobilized on the support and its
complementary ss-s-DNA (i.e., analyte), the color of the film changes
from blue to red. Figure 40 is reproduced below.

{Figure 40 of Charych illustrates detection of DNA
hybridization of a ss-p-DNA attached to a
polydiacetylene lipid monolayer on a solid support.}
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[11] Figure 45 illustrates one method of linking a single-stranded DNA
molecule to a diacetylene monomer to form a biopolymeric material
and is reproduced below.

{Figure 45 of Charych depicts a nucleic acid-linked
biopolymeric material.}

[12] Example 9 describes synthesizing an array of single-stranded probe
DNA ("ss-p-DNA") sequences at different spots on a polydiacetylene
layer immobilized on a solid substrate as shown in Figure 46 (a
device) (id. at col. 67, ll. 55-col. 68, l. 61). Figure 46 is reproduced
below:
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{Figure 46 of Charych depicts generating a multivalent
sensor for detecting multiple different
single-stranded DNA analytes in one step.}

[13] Example 9 also describes generating biopolymeric materials with
different properties, e.g., analyte affinities (e.g., different ss-p-DNAs),
and then immobilizing the biopolymeric materials to specific portions
of a device in order to generate an array for identifying and
characterizing a broad range of analytes (id. at col. 68, ll. 32-39).
[14] According to Charych, biopolymeric material may be immobilized on
a variety of solid supports by a variety of methods (id. at col. 42, ll.
43-44), including (a) using an inkjet printer with multiple cartridges
loaded with different biopolymeric materials to "print" patterned
arrays of any desired shape and size (id. at col. 42, ll. 64-col. 43, l. 6)
and (b) filling a printing cartridge with a liposome solution, printing a
thin film of the liposome material, and then photopolymerizing the
printed liposomes (id. at col. 43, ll. 7- 31).
[15] Example 8 provides a generic method for immobilizing biopolymeric
materials, including liposomes, films, and other nanostructures, to
silicon chips and gels (id. at col. 67, ll. 1-53).
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[16] According to Charych, monolayers and films (or multilayers) made
from amphiphilic (amphipathic) materials are planar membranes and
form a two-dimensional architecture (id. at col. 22. ll. 63-65), whereas
liposomes are three-dimensional vesicles that enclose an aqueous
space (id. at col. 23, ll. 8-10).
[17] The Examiner found that Charych’s device is suitable for mass
spectroscopy analysis (Ans. 5.).
C. Legal principles
A reference anticipates a claim if it discloses the claimed invention
such that a skilled artisan could take its teachings in combination with his
own knowledge of the particular art and be in possession of the invention.
In re LeGrice, 301 F.2d 929, 939 (CCPA 1962). See also In re Donohue,
766 F.2d 531, 533 (Fed. Cir. 1985). Anticipation requires a prior art
reference to describe every limitation in a claim either explicitly or
implicitly. In re Schreiber, 128 F.3d 1473, 1477 (Fed. Cir. 1997). A
specific example is not required to establish anticipation. In re Petering,
301 F.2d 676 (CCPA 1962); In re Schaumann, 572 F.2d 312, 316 (CCPA
1978). Where the claimed and prior art products are identical or
substantially identical, the burden is on Appellant to prove otherwise. In re
Best, 562 F.2d 1252, 1255 (CCPA 1977); In re Spada, 911 F.2d 705, 709
(Fed. Cir. 1990); In re Fitzgerald, 619 F.2d 67, 70 (CCPA 1980).
"A reference is no less anticipatory if, after disclosing the invention,
the reference then disparages it. Thus, the question whether a reference
'teaches away' from the invention is inapplicable to an anticipation analysis."
Celeritas Techs., Ltd. v. Rockwell Int'l. Corp., 150 F.3d 1354, 1361 (Fed. Cir.
1998).
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D. Analysis
Here, Example 9 of Charych discloses the device of claim 1 such that
a skilled artisan could take its teachings in combination with his own
knowledge of the particular art and be in possession of the invention.
LeGrice, 301 F.2d at 939; Donohue, 766 F.2d at 533. Charych discloses a
device comprising an array of ss-p-DNAs in a polydiacetylene layer
immobilized on a solid substrate (FF 12-13). Appellants do not dispute that
it is within ordinary skill in the art to immobilize biopolymeric materials in
an array on a solid substrate. Indeed, Charych discloses several methods of
doing so (FF 14-15; Example 8).
Appellants argue that Charych "is directed to membranes containing
'polydiacetylene sensors composed of fully conjugated polymer backbones
embedded in lipid bilayers" and fails to teach or suggest a polymerized
diacetylene monomolecular film as claimed (Br. 7). However, Charych
teaches that its biopolymeric material may be in the form of liposomes, films
(including mono- and multi-layers), and other nanostructures (FF 7, 15;
Example 8); and, Example 9 expressly discloses a film structure comprising
a polydiacetylene layer (FF 12; Fig. 46). Moreover, as pointed out by the
Examiner (Ans. 8), Charych expressly teaches mixing the diacetylene
monomer with a dopant, such as a diacetylene derivative, to optimize desired
properties, including sensitivity and response (FF 8). Furthermore,
Appellants note that the Examiner points out that the instant claim language
recites a "monomolecular" film, not a "monolayer" film (Br. 7). The
Specification defines a "polymerized monomolecular film" as a "material
deposited or used in a thin section or in a layer form, where the film is a
single molecule thick" (FF 1). The Specification neither defines the
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thickness of a single molecule nor expressly limits the layer form to a
monolayer. We also note in passing that Charych states that monolayers and
films (or multilayers) made from amphiphilic materials are planar
membranes and form a two-dimensional architecture (FF 16). Thus,
Charych fairly teaches linking a specific binding moiety (ss-p-DNA) to the
same diacetylene monomer in the presence of a diacetylene derivative
dopant to form a crosslinked biopolymeric material film having a two-
dimensional architecture (i.e., a monomolecular film) on a support
(substrate) (FF 10-16). Therefore, this argument is not persuasive of
patentability.
Appellants further argue "that while Charych assertedly tests and uses
monolayers in developing the invention, Charych unambiguously teaches the
disadvantage[s] of using monolayers as compared to bilayers for the purpose
of detecting and characterizing analyte" (Br. 8) and, thus, explicitly teaches
away from a monomolecular film (id. at 7). This argument is also
unpersuasive of patentability. It is irrelevant for purposes of anticipation if
the reference teaching the invention additionally teaches that the anticipating
subject matter is sub-par. Celeritas, 150 F.3d at 1361.
We note that Appellants have not provided any evidence establishing
that the claimed device and the device of Charych are not the same or
substantially the same. Best, 562 F.2d at 1255; Spada, 911 F.2d at 709;
Fitzgerald, 619 F.2d at 70.
E. Conclusion
Based on the foregoing, we will sustain the rejection of claims 1, 4, 6,
and 7 under § 102(e) as anticipated by Charych. We find that whether
Charych discloses the claimed invention such that a skilled artisan could
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take its teachings in combination with his own knowledge of the particular
art and be in possession of the invention.
IV. Order
Upon consideration of the record, and for the reasons given, it is
ORDERED that the decision of the Examiner to reject claims 1, 4, 6,
and 7 as indefinite under 35 U.S.C. § 112, second paragraph, is AFFIRMED;
FURTHER ORDERED that the decision of the Examiner to reject
claims 1, 4, 6, and 7 under 35 U.S.C. § 102(e) as anticipated by Charych is
AFFIRMED; and,
FURTHER ORDERED that no time period for taking any subsequent
action in connection with this appeal may be extended under 37 C.F.R. §
1.136(a)(1)(vi).
AFFIRMED

cdc
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