Ex Parte Wang et al

Board of Patent Appeals and Interferences

Sep 22, 2010

09636243 (B.P.A.I. Sep. 22, 2010)

UNITED STATES PATENT AND TRADEMARK OFFICE
UNITED STATES DEPARTMENT OF COMMERCE
United States Patent and Trademark Office
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APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO.
09/636,243 08/10/2000 Bryan S. Wang 8325-1004 (M4-US1) 6438
20855 7590 09/22/2010
ROBINS & PASTERNAK
1731 EMBARCADERO ROAD
SUITE 230
PALO ALTO, CA 94303
EXAMINER
WESSENDORF, TERESA D
ART UNIT PAPER NUMBER
1639
MAIL DATE DELIVERY MODE
09/22/2010 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 BRYAN S. WANG and CARL O. PABO
____________

Appeal 2010-008082
Application 09/636,243
Technology Center 1600
____________

Before ERIC GRIMES, DONALD E. ADAMS, and
JEFFREY N. FREDMAN, Administrative Patent Judges.

ADAMS, Administrative Patent Judge.

DECISION ON APPEAL1
This appeal under 35 U.S.C. § 134 involves claims 5, 6, 20, and 21,
the only claims pending in this application. We have jurisdiction under 35
U.S.C. § 6(b).

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 2010-008082
Application 09/636,243

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STATEMENT OF THE CASE
The claims are directed to a zinc finger complex. Claim 5 is
representative and is reproduced in the “Claims Appendix” of Appellants’
Brief (App. Br. 12).
Claims 5, 6, 20, and 212 stand rejected under 35 U.S.C § 103(a) as
unpatentable over the combination of Pomerantz3 and Krylov.4
We reverse.
ISSUE
Does the preponderance of evidence support a conclusion that the
combination of Pomerantz and Krylov suggests non-naturally occurring
peptide linkers of 30 amino acids or less in length?
FINDINGS OF FACT
FF 1. Claim 5 requires non-naturally occurring peptide linkers of 30 amino
acids or less in length (Claim 5).
FF 2. The Examiner finds that “Pomerantz shows at the bottom panel [of
Figure 1, page 968] that the dimerization domain is from 41 to 65 residues
(i.e., 24 amino acid residues) in length” (Ans. 6).

2 In the Final Rejection the Examiner included claim 21 in this rejection
(Fin. Rej. 2). Nevertheless, while the Examiner recognizes that claim 21 is
on appeal (Ans. 2), the Examiner failed to include this claim in the statement
of the rejection (Ans. 3). Appellants, however, identify claim 21 as part of
the rejection of record (see App. Br. 3 and Reply Br. 2). Accordingly, we
find the Examiner’s failure to include claim 21 in the statement of the
rejection to be a typographical error and have included claim 21 in our
deliberations on the rejection before us on Appeal.
3 Joel L. Pomerantz, et al., Structure-Based Design of a Dimeric Zinc Finger
Protein, 37 BIOCHEMISTRY 965-970 (1998).
4 Dmitry Krylov et al., A thermodynamic scale for leucine zipper stability
and dimerization specificity: e and g interhelical interactions, 13 EMBO J.
2849-2861 (1994).
Appeal 2010-008082
Application 09/636,243

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FF 3. Pomerantz constructed a fusion protein (ZFGD1) comprising zinc
fingers 1 and 2 of Zif268 with a linker and a dimerization element consisting
of residues 41-100 of GAL4 (Pomerantz 967: col. 1, ll. 38-39; see also Ans.
7).
FF 4. Pomerantz teaches that while “[s]tructural information is not
available for residues 66-100 of GAL4 . . . these residues were included
because they are known to form part of the GAL4 dimerization domain”
(Pomerantz 967: col. 1, ll. 40-42).
FF 5. Pomerantz’s Figure 1 A provides a schematic of the ZFGD1
construct:

The foregoing schematic “indicat[es] the domain structure and linker region
of ZFGD1” (Pomerantz 968: Figure 1).
FF 6. The Examiner finds that Krylov “teaches a [sic] coiled coil heptads,
which is 24 amino acids long commencing from letter d (leucine) of the
coiled-coil repeating heptad sequence (at most 29 of the coiled-coil
interacting domain)” (Ans. 10).
FF 7. The Examiner finds that Krylov teaches:
(B) The amino acid sequence of the leucine zipper region of
VBP is presented using the single-letter code. Below the VBP
sequence is the nomenclature for the positions in a coiled coil.
The sequence starts at the first ‘leucine’ position as defined
previously (Vinson et a[l.] 1989) and is grouped into heptads
(g, a, b, [c], d, e, f).

(Ans. 10, quoting Krylov 2850: Fig 1. legend.)
Appeal 2010-008082
Application 09/636,243

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FF 8. Krylov teaches that “[t]he protein sequence of the first four leucine
zipper heptads of . . . bZIP protein VBP [the chicken version of the
mammalian DBP] is presented in Figure 1B” reproduced below:

“The amino acid sequence of the leucine zipper region of VBP . . . is
presented using the single-letter code. Below the VBP sequence is the
nomenclature for the positions in a coiled coil” (Krylov 2850: Fig. 1,
legend).
ANALYSIS
Claim 5 requires non-naturally occurring peptide linkers of 30 amino
acids or less in length (FF 1).
Contrary to the Examiner’s assertion (FF 2) we agree with Appellants’
contention that “[t]he GAL4 dimerization domain used in Pomerantz is fully
50 amino acids in length . . . [and] this does not include a 9 amino acid
peptide linker used to join the zinc fingers to the dimerization domain”
(App. Br. 5; FF 3-5).
Contrary to the Examiner’s assertions (FF 6-7) we agree with
Appellants’ contention that “Krylov’s dimerization domains are at least 3[3]
amino acids in length (4 heptads and 3 N-terminus amino acids and 2 C-
terminal amino acids)” (App. Br. 6; FF 8; see also Reply Br. 8). The
Examiner asserts that Krylov’s leucine zipper dimerization domain begins
with the leucine present in the first heptad of Krylov’s VBP protein (FF 6).
Appeal 2010-008082
Application 09/636,243

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In support of this assertion the Examiner asserts that Krylov teaches that
“[t]he sequence starts at the first ‘leucine’ position as defined previously
(Vinson et a[l.] 1989) and is grouped into heptads (g, a, b, [c], d, e, f)” (FF
7). The Examiner does not, however, establish that “the first ‘leucine’
position” defined by Vinson et al., is the leucine set forth in Krylov’s first
heptad. In this regard, we note that Krylov states that “[t]he leucine
positions are italicized” (Krylov 2850: Fig. 1, legend). We find that
Appellants have the better argument, specifically that “the italized [sic] ‘I’
residue of Figure 1B . . . acts as ‘leucine’ before the first heptad” (see Reply
Br. 8).
The Examiner has provided no evidence or reasoning which suggests
the use of peptide linkers of 30 amino acids or less in length in the zinc
finger complex. Without such evidence or reasoning, we are constrained to
reverse the rejection.
CONCLUSION OF LAW
The preponderance of evidence fails to support a conclusion that the
combination of Pomerantz and Krylov suggests non-naturally occurring
peptide linkers of 30 amino acids or less in length.
The rejection of claims 5, 6, 20, and 21 under 35 U.S.C § 103(a) as
unpatentable over the combination of Pomerantz and Krylov is reversed.

REVERSED

Appeal 2010-008082
Application 09/636,243

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ROBINS & PASTERNAK
1731 EMBARCADERO ROAD
SUITE 230
PALO ALTO, CA 94303