Ex Parte Samuelson et al

Board of Patent Appeals and Interferences

Apr 1, 2009

10958900 (B.P.A.I. Apr. 1, 2009)

UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
__________

Ex parte LYNNE A. SAMUELSON,
FERDINANDO BRUNO, SUKANT K. TRIPATHY,
SUSAN TRIPATHY, RAMASWAMY NAGARAJAN,
JAYANT KUMAR, and WEI LIU
__________

Appeal 2008-5699
Application 10/958,900
Technology Center 1600
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Decided:1 April 1, 2009
__________

Before TONI R. SCHEINER, LORA M. GREEN, and
JEFFREY N. FREDMAN, Administrative Patent Judges.

FREDMAN, Administrative Patent Judge.

1 The two-month time period for filing an appeal or commencing a
civil action, as recited in 37 C.F.R. § 1.304, begins to run from the
decided date shown on this page of the decision. The time period
does not run from the Mail Date (paper delivery) or Notification
Date (electronic delivery).

Appeal 2008-5699
Application 10/958,900

DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 involving claims to a method
of identifying a nucleic acid complexed with polyaniline, which the
Examiner has rejected as failing the enablement requirement. We have
jurisdiction under 35 U.S.C. § 6(b). We affirm.
Statement of the Case
The Claims
Claims 51, 52, 54, and 55 are on appeal. We will focus on claim 51,
which is representative and reads as follows:

51. A method for identifying a target polynucleotide,
comprising the steps of:
a) contacting said target polynucleotide with a probe that
includes a polynucleotide template complexed with a conductive
polymer, said polymer being a polyaniline whereby said probe
binds to the target polynucleotide by hybridization, said
hybridization modifying at least one electromagnetic property of
the conductive polymer wherein the electromagnetic property is an
electrical or optical property, and said target polynucleotide being
complementary, or substantially complementary, to a sequence, or
a portion of said sequence, of the probe nucleotide; and
b) detecting said modified electromagnetic property, said
modified property being a change in optical and/or electrical
properties of the conductive polymer during or after hybridization
with the target, and thereby identifying the target polynucleotide,
and discriminating between complementary targets and a target
having one or more mismatches.

The Issue
The Examiner rejected claims 51, 52, 54, and 55 under 35 U.S.C. §
112, first paragraph as failing to comply with the enablement requirement
(Ans. 3-12).
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The Examiner finds that the “specification is essentially silent as to
how one is to detect, much less quantitate, hybridization events wherein said
detection is based upon a change in UV-visible absorption, circular
dichroism, or cyclic voltammetry” (Ans. 6). The Examiner finds that “the
specification does not teach how one of skill in the art is to avoid and/or
overcome art-recognized difficulties. Indeed, the specification is silent as to
how any specific nucleic acid is to be detected” (id. at 11). The Examiner
finds that “[i]n view of the breadth of scope clamed, the limited guidance
provided, the unpredictable nature of the art to which the claimed invention
is directed, and in the absence of convincing evidence to the contrary, the
claims are deemed to be non-enabled by the disclosure” (id. at 12).
Appellants contend that “the specification describes the claimed
subject matter in such a way as to enable one skilled in the art, for example,
biosensors, to make and/or use the invention” (App. Br. 5). Appellants
specifically contend that “[p]ages 13-17 teach hybridization, and particularly
pages 15-17 teach contacting a target polynucleotide with a probe which
includes a polynucleotide/conductive polymer complex that can bind to the
target by hybridization for modifying at least one electromagnetic property
of the conducting polymer” (App. Br. 5).
In view of these conflicting positions, we frame the enablement issue
before us as follows:
Did the Examiner err in finding that it would have required undue
experimentation on how to use the method of identifying a target
polynucleotide by using a probe that includes a polynucleotide complexed
with polyaniline?
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Application 10/958,900

Findings of Fact (FF)
Breadth of the Claims
1. The Examiner interprets the claims as encompassing:
[U]tilizing probes of virtually any length, and that any
amount of polyaniline can be present, and only needs to be
bound to the probe at a place and condition such that when
hybridization occurs, some change in an electrical or optical
property takes place. In accordance with step b), the method
is to allow one to identify single nucleotide mismatches, no
mater [sic] how large the sequence, where the mismatch
occurs, or how large or small any change in electrical or
optical property takes place.

(Ans. 5.)
Presence of Working Examples
2. The Specification teaches “formation of a polyelectrolyte
complex of DNA-polyaniline” (Spec. 25, l. 6).
3. The Specification teaches that the “secondary structure of DNA
was readily controlled by . . . changing the extent of oxidation of
polyaniline. . . . The neutralization of polyaniline minimized the electrostatic
interaction between the DNA and polyaniline resulting in the uncoiling of
DNA, back to its native state” (Spec. 26, ll. 3-9).
Amount of Direction or Guidance Presented
4. The Specification teaches that “the chirality and electrical
properties of polyaniline combined with the selectivity of DNA may be
useful in the design of highly specific biosensors” (Spec. 25, ll. 26-28).
5. The Specification teaches “a method of identifying a target
polynucleotide by contacting the target polynucleotide with a probe which
includes a polynucleotide/conductive polymer complex that can bind to a
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Application 10/958,900

target polynucleotide by hybridization. Hybridization of the probe to the
target polynucleotide modifies at least one electromagnetic property of the
conductive polymer” (Spec. 15, ll. 22-26).
6. Figure 8 of the Specification is reproduced below:

“Fig. 8 is a schematic representation of polyaniline bound to a DNA double
helix” (Spec. 5, l. 12).
7. The Specification teaches that the polynucleotide binding
incorporates “noncanonical base-pairing schemes such as triple helix
formation . . . and quadruplex formation” (Spec. 18, ll. 9-12).
8. The Specification teaches that “changing the oxidation state of
polyaniline bound to a DNA duplex changes the linear length of a helical
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Application 10/958,900

turn and, therefore, could be used to study the binding properties of DNA
regulatory proteins” (Spec. 4, ll. 14-16).
State of the Art and Unpredictability of the Art
9. The Examiner finds that “the example does not disclose any
nucleic acid hybridization event” (Ans. 6).
10. Zhang2 teaches
Although kinds of synthesizing methods have been
established, preparation of one-dimensional nano-structured
PANI with controllable morphologies and sizes, especially
well oriented arrays on a large scale is still a major
challenge. Furthermore, the exact formation mechanisms of
the nanostructures need to be elucidated from a scientific
point of view, which will be of great importance in
morphological control of PANI and other polymers prepared
by precipitation polymerization.

(Zhang 17, col. 2.)
11. The Examiner finds that “the use of polyaniline, even some
nine years post filing, is an area of technology that has yet to be developed
such that reproducible and useful polyaniline structures are developed and
used” (Ans. 8).
Quantity of Experimentation necessary
12. The Examiner finds that “after ‘tremendous efforts’ have been
expended, the art has yet to developed to where the actual usefulness of
polyaniline on DNA has been realized” (Ans. 13).
13. The Examiner finds that

2 Zhang et al., Synthesis and applications of one-dimensional
nano-structured polyaniline: An overview, 134 MATERIALS
SCIENCE AND ENGINEERING B 9-19 (2006).
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Application 10/958,900

[M]uch time and effort has been exerted with the
result being that more work needs to be done before
one will be able to reproducibly manufacture
polyaniline on DNA (nano-structured PANI), or any
other substrate, with a predictable morphology.
Similarly, more time and effort will need to be
expended before one will be able to use the PANI in a
method that has utility.

(Ans. 7-8.)
Principles of Law
“In order to satisfy the enablement requirement of section 112, an
applicant must describe the manner of making and using the invention ‘in
such full, clear, concise, and exact terms as to enable any person skilled in
the art ... to make and use the same ....’ 35 U.S.C. § 112, para. 1.”
Rasmusson v. SmithKline Beecham Corp., 413 F.3d 1318, 1322 (Fed. Cir.
2005).
The Court has explained that “‘the how to use prong of section 112
incorporates as a matter of law the requirement of 35 U.S.C. § 101 that the
specification disclose as a matter of fact a practical utility for the
invention.’” In re Cortright, 165 F.3d 1353, 1356 (Fed. Cir. 1999), quoting
In re Ziegler, 992 F.2d 1197, 1200 (Fed. Cir. 1993). “Patent protection is
granted in return for an enabling disclosure . . . , not for vague intimations of
general ideas that may or may not be workable.” Genentech, Inc. v. Novo
Nordisk, A/S, 108 F.3d 1361, 1366 (Fed. Cir. 1997). “Tossing out the mere
germ of an idea does not constitute enabling disclosure. While every aspect
of a generic claim certainly need not have been carried out by an inventor, or
exemplified in the specification, reasonable detail must be provided in order
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to enable members of the public [skilled in the art] to understand and carry
out the invention.” Id. (emphasis added).
Factors to be considered in determining whether a
disclosure would require undue experimentation . . . include
(1) the quantity of experimentation necessary, (2) the
amount of direction or guidance presented, (3) the presence
or absence of working examples, (4) the nature of the
invention, (5) the state of the prior art, (6) the relative skill
of those in the art, (7) the predictability or unpredictability
of the art, and (8) the breadth of the claims.

In re Wands, 858 F.2d 731, 737 (Fed. Cir. 1988).
The Examiner has the initial burden to establish a reasonable basis to
question the enablement provided for the claimed invention. See In re
Wright, 999 F.2d 1557, 1561-62 (Fed. Cir. 1993) (Examiner must provide a
reasonable explanation as to why the scope of protection provided by a
claim is not adequately enabled by the disclosure).
Analysis
The Specification provides substantial teachings regarding methods of
making polyaniline-DNA complexes, including working examples (FF 2-3).
The Examiner’s rejection is focused not on the “how to make” prong of
enablement, but on the “how to use” prong (see Ans. 11).
Claim 51 is drawn to a method of “identifying a target
polynucleotide” (Claim 51). The Specification identifies this specific use for
the polyaniline/DNA complex; as a biosensor for hybridization (FF 4-8).
However, the Specification does not explain or exemplify how DNA which
is bound to polyaniline can function as a biosensor (see FF 6, where figure 8
of the Specification shows the double stranded DNA surrounded by the
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polyaniline). The Specification does not explain how DNA, which is
encased in polyaniline, will be capable of binding to a target polynucleotide
by hybridization (FF 6).
The Examiner cites Zhang, who generically discusses challenges in
polyaniline formation and use (FF 10). The Examiner reasonably concludes
that it is unpredictable whether the encased polyaniline-DNA complex
would permit hybridization or protein binding. The Examiner also
reasonably concludes that in the absence of any teaching of specific
protocols or methods on how to use the DNA-polyaniline complex in the
Specification, the quantity of experimentation would be large (FF 11-13).
Balancing the Wands factors, we agree with the Examiner that undue
experimentation would have been required to use the claimed invention.
With a Specification that only teaches methods of making the DNA-
polyaniline complex (FF 2-8), with no guidance as to how to functionally
hybridize a target polynucleotide to a probe that is in a DNA-polyaniline
complex (FF 9-11), the significant experimentation required for use the
polyaniline-DNA complex in the claimed method, and the unpredictability
of the prior art, we conclude that it would require an undue amount of
experimentation to use the polyaniline-DNA complex in a method of
identifying a target polynucleotide as set forth in the claim 51.
We are not persuaded by Appellants’ argument that the Specification
describes “how a probe comprising a polynucleotide/conductive polymer
complex binds to a target polynucleotide” (App. Br. 4). In fact, while
Appellants cite pages 13-17 of the Specification to teach probe binding,
these pages simply state that such binding will occur. The Specification
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Application 10/958,900

does not explain the steric mechanism by which a polynucleotide, when
encased with polyaniline as shown in Figure 8 of the Specification, will be
capable of hybridization. The Specification does not teach any specifics on
how to use the DNA-polyaniline as a biosensor (FF 9-11). Nor does the
Specification provide any specific teachings which overcome the issues
regarding how to bind probes or regulatory proteins to DNA which is
encased in polyaniline (FF 9, 11).
In rebuttal to the Examiner’s reasonable prima facie case, Appellants
have provided no specific evidence regarding methods of using the DNA-
polyaniline complex for hybridization or protein binding. At best,
Appellants argue that the methods may be used. See In re Pearson, 494 F.2d
1399, 1405 (CCPA 1974) (“Attorney’s argument in a brief cannot take the
place of evidence.”).
Conclusions of Law
The Examiner did not err in finding that it would have required undue
experimentation on how to use the method of identifying a target
polynucleotide by using a probe that includes a polynucleotide complexed
with polyaniline.
SUMMARY
In summary, we affirm the rejection of claim 51 under 35 U.S.C. §
112, first paragraph enablement. Pursuant to 37 C.F.R.
§ 41.37(c)(1)(vii)(2006), we also affirm the rejection of claims 52, 54, and
55 as these claims were not argued separately.
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)(iv)(2006).
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Application 10/958,900

AFFIRMED

cdc

U.S. ARMY SOLDIER BIOLOGICAL CHEMICAL COMMAND,
SOLDIER SYSTEMS CTR, TERESSA CROUSE, LEGAL OFFICE
KANSAS STREET
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