Ex Parte Heeger et al

Board of Patent Appeals and Interferences

Mar 30, 2011

11193318 (B.P.A.I. Mar. 30, 2011)

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.
11/193,318 07/29/2005 Alan J. Heeger UCSB-510CIP2 7183
24353 7590 03/30/2011
BOZICEVIC, FIELD & FRANCIS LLP
1900 UNIVERSITY AVENUE
SUITE 200
EAST PALO ALTO, CA 94303
EXAMINER
CROW, ROBERT THOMAS
ART UNIT PAPER NUMBER
1634
MAIL DATE DELIVERY MODE
03/30/2011 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 ALAN J. HEEGER, CHUNHAI FAN and KEVIN PLAXCO
____________

Appeal 2010-008307
Application 11/193,318
Technology Center 1600
____________

Before TONI R. SCHEINER, DONALD E. ADAMS, and
FRANCISCO C. PRATS, Administrative Patent Judges.

ADAMS, Administrative Patent Judge.

DECISION ON APPEAL

This appeal under 35 U.S.C. § 134 involves claims 23-41, 58-65, and
68.1 We have jurisdiction under 35 U.S.C. § 6(b).

1 “[C]laims 42-57 and 66-67 have been withdrawn from consideration as
being drawn to a non-elected invention” (App. Br. 3).
Appeal 2010-008307
Application 11/193,318

2
STATEMENT OF THE CASE
The claims are directed to a detector for determining the presence of a
target. Claims 23, 26, and 32 are representative and are reproduced in the
“CLAIMS APPENDIX” of Appellants’ Brief (App. Br. 21-22).
The rejections presented by the Examiner follow:
1. Claims 23-25, 27-41, 58-65, and 68 stand rejected under 35 U.S.C.
§ 103(a) as unpatentable over the combination of Blackburn2 and Lizardi.3
2. Claim 26 stands rejected under 35 U.S.C. § 103(a) as unpatentable over
the combination of Blackburn, Lizardi, and Rothberg.4
We reverse.
The Combination of Blackburn and Lizardi:
ISSUE
Does the preponderance of evidence on this record support a
conclusion of obviousness?
FACTUAL FINDINGS
FF 1. Blackburn does not teach a detector wherein the end of the probe
bearing the redox moiety moves closer to the electrode upon binding the
target (Ans. 5).
FF 2. Lizardi teaches “a single switch probe nucleic acid molecule having
two alternative conformations in the presence or absence of a target
molecule” (id.).

2 Blackburn et al., US 6,264,825 B1, issued July 24, 2001.
3 Lizardi et al., US 5,312,728, issued May 17, 1994.
4 Rothberg et al., US 2002/0012930 A1, published January 31, 2002.
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Application 11/193,318

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FF 3. The open and closed conformation of Lizardi’s single switch probe
nucleic acid molecule is illustrated in Lizardi’s figures 12 and 13,
reproduced below:

“FIG. 12 is a schematic representation of the probe of [Lizardi’s] Example
V, containing a switch in a[ ] closed state. FIG. 13 is a schematic
representation of the probe of [Lizardi’s] Example V, containing a switch in
an open state” (Lizardi, col. 6, ll. 34-37).
FF 4. The Examiner’s proposes to combine the prior art by immobilizing
the end defined by element 35 of Lizardi’s probe (see FF 3, FIG. 12) to
Blackburn’s detector (Ans. 6).
FF 5. The Examiner finds that by modifying Blackburn as described in FF
4, “end 32 [of Lizardi] would move closer to end 35, as depicted n Figure
13, thereby meeting the limitations of the claim because the redox moiety is
now closer to the electrode” (Ans. 6).
FF 6. Lizardi discloses that the probe (see FF 3, FIG. 12) binds a target
sequence and undergoes a conformational change (see FF 3, FIG. 13) that
results in the creation of a ribozyme (FF 3, FIG 13, element 36). This
ribozyme then cleaves the 3’ end of the probe (FF 3, FIG. 13, element 35)
Appeal 2010-008307
Application 11/193,318

4
away from the remainder of the probe (see Lizardi, col. 14, ll. 3-41; see also
App. Br. 11-12; Reply Br. 6-7).
ANALYSIS
The Examiner finds that the combination of prior art suggests
immobilizing Lizardi’s probe at element 35 to Blackburn’s detector, thereby
providing an arrangement wherein element 35 of Lizardi’s probe will move
closer to element 32 when Lizardi’s probe binds target (FF 1-5). According
to the Examiner the proposed modification will meet the limitations of
Appellants’ claimed invention because the redox moiety would be closer to
the electrode (FF 5). We are not persuaded. Lizardi teaches that upon
binding a target the probe will undergo a conformational change resulting in
the cleavage of the end defined by element 35 (FF 6). Therefore, contrary to
the Examiner’s assertion, the proposed modification “will result in an
inoperable probe” (App. Br. 12; Reply Br. 6).
The Examiner acknowledges Appellants’ contention that the proposed
combination of Blackburn and Lizardi “renders Blackburn et al inoperable
for its intended purpose” (Ans. 23). Nevertheless, the Examiner fails to
explain how the proposed modification will result in a detector that does not
self-cleave Lizardi’s probe from Blackburn’s detector (see Ans. 23-24). In
this regard, we are not persuaded by the Examiner’s assertion that Lizardi “is
merely relied upon for a specific type of hairpin loop structure, not a method
of detection. Thus, any additional method steps taught by Lizardi et al are
not relied upon for the structural modification of the apparatus of
Blackburn” (Ans. 29). As Appellants explain “the specific type of hairpin
loop structure described in Lizardi et al. and relied on by the Examiner, i.e.,
that shown in Figs. 12 and 13, is one which based on its sequence forms a
Appeal 2010-008307
Application 11/193,318

5
ribozyme structure upon binding of the probe to target” (Reply Br. 7).
Stated differently, what the Examiner refers to as Lizardi’s “additional
method steps” are, in fact, inherent to the specific hairpin loop structure
taught by Lizardi (see Ans. 29). Lastly, we recognize Appellants’
contention that, notwithstanding the Examiner’s assertions to the contrary,
“of all the probes described by Lizardi et al. only the probe depicted in
Figures 12 and 13 (which specifically show a probe structurally configured
to form a ribozyme) provide a structure in which the two ends move closer
together upon target binding” (Reply Br. 7; Cf. Ans. 29-30).
In sum, we find that the preponderance of evidence on this record falls
in favor of Appellants.
CONCLUSION OF LAW
The preponderance of evidence on this record fails to support a
conclusion of obviousness. The rejection of claims 23-25, 27-41, 58-65, and
68 under 35 U.S.C. § 103(a) as unpatentable over the combination of
Blackburn and Lizardi is reversed.

The Combination of Blackburn, Lizardi, and Rothberg:
ISSUE
Does the preponderance of evidence on this record support a
conclusion of obviousness?
FACTUAL FINDINGS
FF 7. The Examiner relies on the combination of Blackburn and Lizardi as
discussed above (Ans. 15).
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Application 11/193,318

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FF 8. The Examiner finds that the combination of Blackburn and Lizardi
fails to suggest “loops in the target and the probe in the second position (i.e.,
during hybridization)” (id.).
FF 9. The Examiner finds that Rothberg teaches “probes hybridized to
targets wherein the probe and the target have a loop during hybridization”
(id.).
FF 10. The Examiner finds that Rothberg “teach the loop in the target has
the added advantage of allowing detection of single nucleotide
polymorphisms” (id.).
ANALYSIS
In essence, Appellants contend that Rothberg fails to make up for the
deficiencies in the combination of Blackburn and Lizardi (see App. Br. 17-
18; Reply Br. 11-12). We agree and the rejection is reversed.
CONCLUSION OF LAW
The preponderance of evidence on this record fails to support a
conclusion of obviousness. The rejection of claim 26 under 35 U.S.C.
§ 103(a) as unpatentable over the combination of Blackburn, Lizardi, and
Rothberg is reversed.

REVERSED

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