Ex Parte Reppy et al

Board of Patent Appeals and Interferences

Sep 8, 2010

10354099 (B.P.A.I. Sep. 8, 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.
10/354,099 01/30/2003 Mary A. Reppy 22001-00005-US2 4958
30678 7590 09/08/2010
CONNOLLY BOVE LODGE & HUTZ LLP
1875 EYE STREET, N.W.
SUITE 1100
WASHINGTON, DC 20006
EXAMINER
LUNDGREN, JEFFREY S
ART UNIT PAPER NUMBER
1639
MAIL DATE DELIVERY MODE
09/08/2010 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 MARY A. REPPY, SARAH A. SPORN, and
CHARLES F. SALLER
__________

Appeal 2010-000277
Application 10/354,099
Technology Center 1600
__________

Before ERIC GRIMES, CAROL A. SPIEGEL and MELANIE L.
McCOLLUM, Administrative Patent Judges.

GRIMES, Administrative Patent Judge.

DECISION ON APPEAL1
This is an appeal under 35 U.S.C. § 134 involving claims to assay
methods. The Examiner has rejected the claims as indefinite and obvious.
We have jurisdiction under 35 U.S.C. § 6(b). We affirm.

1 The two-month time 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.
Appeal 2009-000277
Application 10/354,099

2
STATEMENT OF THE CASE
The Specification discloses a “method that measures fluorescent
changes in polydiacetylene films as they convert from the non-fluorescent
form … to the fluorescent forms” (Spec. 4). The Specification discloses an
assay method that comprises “contacting the sample to be tested with a two-
dimensional or three-dimensional array of a polydiacetylene backbone with
substrate (e.g. a ligand or reactive substrate)” (id. at 5). The Specification
discloses that the “change in fluorescence is measured or detected to indicate
the presence of the analyte” (id.).
Claims 20, 21, 25-37, 47, 48, and 50-66 are on appeal. Claims 20, 51,
and 53 are representative and read as follows:
20. A method for the detection of an analyte in a sample which
comprises contacting the sample to be tested with a two-dimensional array
of a polydiacetylene backbone having a substrate incorporated in the array,
wherein the array is coated onto a solid porous membrane support for
permitting said sample to pass through the membrane and wherein the
substrate has direct affinity for the analyte or can function as a binder to the
analyte or can react with the analyte and wherein the two-dimensional array
comprises a polymerized diacetylene array; and detecting a change in
fluorescence to indicate the presence of the analyte.

51. A method for detection of an analyte in a sample which comprises
contacting the sample to be tested with a two-dimensional array of a
polydiacetylene backbone having a substrate and fluorophore incorporated
in the array; wherein the substrate has direct affinity for the analyte or can
function as a binder to the analyte or can react with the analyte; and
detecting a change in fluorescence to indicate the presence of the analyte.

53. The method of claim 51 wherein the array is not supported on a
substrate.

Appeal 2009-000277
Application 10/354,099

3
The claims stand rejected as follows:
• Claim 53 under 35 U.S.C. § 112, second paragraph; and
• Claims 20, 21, 25-37, 47, 48, and 50-66 under 35 U.S.C. § 103(a) in
view of Saul2 and Charych.3
I.
The Examiner has rejected claim 53 under 35 U.S.C. § 112, second
paragraph, on the basis that claim 51 includes an “array … having a
substrate” while claim 53, which depends on claim 51, states that the array
“is not supported on a substrate” (Answer 3).
Appellants contend that the claims are not contradictory because
claim 51 “refers to the array having a substrate incorporated in the array. On
the other hand, claim 53 refers to the entire array as not be[ing] supported on
a substrate.” (Appeal Br.4 5).
We agree with the Examiner that claim 53 is indefinite. The
Specification defines a substrate as “[a] chemical or biological entity” (Spec.
6). The Specification also states that “arrays of diacetylenes or
polydiacetylenes may be used in the free form, or supported on glass,
ceramic, polymer, paper, metal, or other surfaces” (id. at 10).
Claim 51 recites an array that includes a substrate that binds or reacts
with an analyte; i.e., consistent with the Specification’s definition of a
“substrate.” Claim 53 incorporates the limitations of claim 51 but recites an
array that is “not supported on a substrate”; i.e., claim 53 uses “substrate” to
refer to a structure or surface that supports the array (cf. claim 20: “the array

2 Saul et al., US 5,415,999, May 16, 1995
3 Charych et al., US 6,022,748, Feb. 8, 2000
4 Supplemental Appeal Brief, filed March 16, 2009.
Appeal 2009-000277
Application 10/354,099

4
is coated onto a … support”). Since claim 53 appears to use the term
“substrate” to mean two different things and Appellants have not pointed to
support in the Specification for interpreting the term “substrate” to mean a
support for an array, we conclude that the scope of claim 53 would not be
clear to one of skill in the art.
II.
Issue
The Examiner has rejected claims 20, 21, 25-37, 47, 48, and 50-66
under 35 U.S.C. § 103(a) as being obvious in view of Saul and Charych.
The claims have been argued in two groups: claims 21, 25-37, 47, 48, and 50
stand or fall with claim 20; claims 52-66 therefore stand or fall with claim
51. 37 C.F.R. § 41.37(c)(1)(vii).
The Examiner finds that Saul discloses assays based on changes in the
fluorescence of a polydiacetylene material (Answer 3-4) and “each of Saul
and Charych are directed to the use of biosensors based on a polydiacetylene
material, wherein the signaling of the analyte/target is detected by the
production of optical/fluorescence signals” (id. at 6). The Examiner also
finds that Charych discloses “polydiacetylenes coated on porous membranes
as a biosensing support, wherein the backbone can take the form of a film”
(id.). The Examiner concludes that “[o]ne of ordinary skill in the art would
have been motivated to utilize the solid support of Charych in place of the
solid support of Saul because the solid support of Charych provides ease of
fabrication and use” (id. at 6).
Appellants contend that the cited references do not suggest an array
“coated onto a solid porous membrane support for permitting said sample to
Appeal 2009-000277
Application 10/354,099

5
pass through the membrane,” as recited in claim 20 (Appeal Br. 6) or a
“fluorophore incorporated in the array,” as recited in claim 51 (id. at 7).
The issue with respect to this rejection is: Does the evidence of
record support the Examiner’s conclusion that the cited references suggest
the limitations of claims 20 and 51, including an array “coated onto a solid
porous membrane support for permitting said sample to pass through the
membrane” and a “fluorophore incorporated in the array”?
Findings of Fact
1. Saul discloses sensors
comprising a fluorescent layer in conjunction with non-
covalently bound specific binding pair members, where the
fluorescent layer of particular interest is a conjugated
polyunsaturated lipid extended chain.… Assays are performed,
where a reagent is employed which modulates the fluorescent
properties of the fluorescent layer.… By employing a
fluorimeter, the fluorescence may be measured and related to
the amount of analyte.
(Saul, col. 2, ll. 44-57.)
2. Saul discloses that the fluorescent layer can be a polymerized
polydiacetylene lipid layer (id. at col. 14, l. 53).
3. Saul discloses that the
polymerized polyunsaturated lipid layer can serve as a
transducer for amplifying a signal resulting from an assay
component which affects the fluorescence of the layer. Thus, an
agent which may serve as a … fluorophore or which agent has
other properties which may affect the fluorescence can be
measured more sensitively, by the amplification resulting from
the interaction of such agent and the polymerized
polyunsaturated lipid layer.
(Id. at col. 3, ll. 1-9.)
Appeal 2009-000277
Application 10/354,099

6
4. Saul discloses that a ligand is “non-covalently associated with the
lipid lay to form the fluorescent production layer…. The ligand is … a
member of a specific binding pair which is … able to bind to the analyte.”
(Id. at col. 6, ll. 3-13.)
5. Charych discloses “the direct detection of analytes using color
changes in immobilized biopolymeric material that occur in response to
selective binding of analytes to their surface” (Charych, col. 5, ll. 16-19).
6. Charych discloses “polymerized biological materials immobilized
in porous glass that undergo conformational changes when exposed to
analytes, producing a detectable color change, although other
immobilization means are also contemplated” (id. at col. 5, ll. 21-24).
7. Charych discloses that, in some embodiments, “the biopolymeric
material comprises a plurality of self-assembling monomers selected from
the group consisting of diacetylenes, acetylenes,” etc. (id. at col. 3, ll. 21-
24).
8. Charych discloses “a means of immobilizing pre-formed liposomes
and other biopolymeric material … in a porous, robust metal oxide gel
matrix using the sol-gel method” (id. at col. 6, ll. 1-5).
9. Charych discloses that “the term ‘sol-gel method’ refers to any
method that results in the production of porous metal oxide glass” (id. at col.
7, ll. 23-24).
10. Charych discloses that “the optical clarity of the metal oxide gel
also makes it ideal for optical sensor applications” (id. at col. 6, ll. 15-16).
Analysis
Claim 20 is directed to a method for the detection of an analyte in a
sample which comprises, among other things, contacting the sample with a
Appeal 2009-000277
Application 10/354,099

7
two-dimensional array having a polydiacetylene backbone and having a
substrate incorporated in the array and detecting a change in fluorescence to
indicate the presence of the analyte. Claim 20 also requires that the array is
coated onto a solid porous membrane support to permit the sample to pass
through the membrane.
Saul discloses a method of detecting an analyte that is based on a
change of fluorescence of a polydiacetylene backbone in conjunction with a
member of a specific binding pair that is able to bind the analyte. Saul does
not disclose that its fluorescent layer is coated onto a porous membrane
support, but Charych discloses a similar assay method in which
biopolymeric material is immobilized in porous metal oxide glass. In view
of these disclosures, it would have been obvious to one of skill in the art to
coat Saul’s fluorescent layer onto the support of Charych, especially since
Charych discloses that it support is ideal for optical sensor applications.
Appellants argue that the “use of porous glass slides for the
techniques in Saul using a microscope would not be desirable since porous
glass tends to be cloudy, but clear or transparent slides are desirable in this
technique in Saul” (Appeal Br. 6). This argument is not persuasive because
Charych discloses its porous metal oxide glass has an optical clarity that
“makes it ideal for optical sensor applications” (FF 9).
Claim 51 is similar to claim 20 but does not require that the array is
coated onto a solid porous membrane support and requires a fluorophore
incorporated into the array.
Appellants argue that “Saul does not suggest a fluorophore
incorporated in the array” (Appeal Br. 7). This argument is not persuasive
Appeal 2009-000277
Application 10/354,099

8
because, as set forth above (FF 3), Saul expressly discloses that its assay
system can comprise a fluorophore incorporated into the fluorescent layer.
Conclusion of Law
The evidence of record supports the Examiner’s conclusion that the
cited references suggest the limitations of claims 20 and 51, including an
array “coated onto a solid porous membrane support for permitting said
sample to pass through the membrane” and a “fluorophore incorporated in
the array.”
SUMMARY
We affirm the rejection of claim 53 under 35 U.S.C. § 112, second
paragraph, and the rejection of claims 20, 21, 25-37, 47, 48, and 50-66 under
35 U.S.C. § 103(a).
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).

AFFIRMED

lp

Appeal 2009-000277
Application 10/354,099

9

CONNOLLY BOVE LODGE & HUTZ LLP
1875 EYE STREET, N.W.
SUITE 1100
WASHINGTON DC 20006