Ex Parte Haseltine et al

Board of Patent Appeals and Interferences

Sep 8, 2010

10386575 (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
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APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO.
10/386,575 03/11/2003 Cynthia A. Haseltine 02307O-125300US 1798
20350 7590 09/08/2010
TOWNSEND AND TOWNSEND AND CREW, LLP
TWO EMBARCADERO CENTER
EIGHTH FLOOR
SAN FRANCISCO, CA 94111-3834
EXAMINER
SALMON, KATHERINE D
ART UNIT PAPER NUMBER
1634
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 CYNTHIA A. HASELTINE and
STEPHEN C. KOWALCZYKOWSKI
__________

Appeal 2010-005032
Application 10/386,575
Technology Center 1600
__________

Before ERIC GRIMES, JEFFREY N. FREDMAN, and STEPHEN
WALSH, Administrative Patent Judges.

WALSH, Administrative Patent Judge.

DECISION ON APPEAL1
This is an appeal under 35 U.S.C. § 134(a) involving claims to
methods for performing nucleic acid amplification and nucleic acid

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 2010-005032
Application 10/386,575

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engineering using a multimeric protein. The Patent Examiner rejected the
claims as obvious. We have jurisdiction under 35 U.S.C. § 6(b). We affirm.

STATEMENT OF THE CASE
The invention concerns the use of single stranded DNA binding
proteins in nucleic acid amplification reactions. (Spec. [04]). The
Specification states that “[s]ingle-stranded DNA (ssDNA) binding proteins
(SSBs) are essential in most intracellular interactions that involve DNA,
including replication, repair, and recombination.” (Id. at [05]).
Claims 6, 9-12, 15, and 16, which are all the pending claims, are on
appeal. Claim 6 is representative and reads as follows:
6. A method of performing nucleic acid amplification, said
method comprising contacting a single stranded DNA with a multimeric
protein, wherein each unit of said multimeric protein has at least 95%
sequence identity to SEQ ID NO: 1, and wherein said multimeric protein
binds single stranded DNA.

The Examiner rejected the claims under 35 U.S.C. § 103(a) as
unpatentable over She,2 GenBank,3 and Nielson.4
Claims 9-12, 15 and 16 have not been argued separately and therefore
stand or fall with claim 6. 37 C.F.R. § 41.37(c)(1)(vii).

2 Qunxin She et al., The complete genome of the crenarchaeon Sulfolobus
solfataricus P2, 98 PROC. NATL. ACAD. SCI., no. 14, 7835-40 (2001).
3 GenBank Accession No. AAK42515 (2001).
4 US Patent No. 5,449,603 issued to Kirk B. Nielson et al., Sep. 12, 1995.
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Application 10/386,575

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OBVIOUSNESS
The Issue
The Examiner’s position is that She disclosed the complete genome of
the crenarchaeon Sulfolobus solfataricus P2. (Ans. 3). The Examiner found
that She described Sulfolobus solfataricus as “a model for research on
mechanisms of DNA replication, the cell cycle, chromosomal integration,
transcription, RNA processing, and translation.” (Id.). The Examiner also
found that She taught the single-strand-specific DNA-binding (SSB) protein
Sso2364, having 148 amino acids, required for DNA replication and repair.
(Id.). She did not disclose the specific amino acids of SEQ ID NO:1 or the
method of performing nucleic acid amplification recited in instant claim 6.
(Id.).
The Examiner found that GenBank disclosed the amino acid sequence
for a SSB having 100% identity to SEQ ID NO:1. (Id. at 4). Additionally,
the Examiner found that Nielson taught that SSB proteins can be used to
minimize secondary structure in ssDNA, facilitate polymerase enzyme
passage along a DNA template, and decrease the amount of nonspecific
hybridization between nucleic acids. (Id.).
According to the Examiner, it would have been obvious to a person of
ordinary skill in the art at the time the invention was made to use the
crenarchaeon Sulfolobus solfataricus P2 as a SSB protein as taught by She
with the amino acid sequence disclosed by GenBank in methods of nucleic
acid amplification using SSB proteins as taught by Nielson with a reasonable
expectation of success. (Id. at 5). The Examiner found the ordinary artisan
would have been motivated to do so because Neilson taught advantages to
using SSBs, and preferably heat stable SSBs like She’s. (Id.) According to
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the Examiner, the SSB in the prior art inherently multimerizes on binding to
ssDNA. (Fin. Rej. 6).
Appellants do not dispute that the prior art disclosed a SSB having an
amino acid sequence which was 100% identical to SEQ ID NO:1. Rather,
Appellants contend that “[n]one of the three references teach or suggest an
SSB protein that binds single stranded DNA in multimeric form.” (App. Br.
5). Appellants assert that “because the SSB protein may be present in a
solution in either a monomeric form or a multimeric form, ‘the protein being
multimeric’ is not an inherent property, because this property does not exist
in a permanent, invariable manner….” (App. Br. 8; Reply Br. 2).
Appellants further assert that the combined prior art would not have
provided a skilled artisan at the time of the invention a reasonable
expectation of successfully achieving the claimed method because success
would have required the selection of the right solution conditions favoring
the multimeric presence of the SSB protein. (Id.). Appellants contend that
“even if the SSB protein’s being multimeric is deemed an inherent property
under the condition that the protein binds ssDNA, it still cannot be relied
upon to make the obviousness rejection, because such inherent feature was
far from being established at the time this invention was made.” (Id. at 9.)
The issue with respect to this rejection is whether the evidence
supports the Examiner’s finding that the SSB protein disclosed in the prior
art inherently formed a multimer on binding ssDNA.

Appeal 2010-005032
Application 10/386,575

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Findings of Fact disclosed
1. We agree with the Examiner’s findings concerning the explicit
teachings of She, GenBank and Nielson. (See Ans. 3-5).
2. The instant Specification discloses that under normal PCR conditions
SSO SSB protein binds as a multimer to ssDNA. (Spec. [25]-[27]).

Principle of Law
“From the standpoint of patent law, a compound and all of its
properties are inseparable; they are one and the same thing.” In re Papesch,
315 F.2d 381, 391 (CCPA 1963). “Inherency is not necessarily coterminous
with the knowledge of those of ordinary skill in the art. Artisans of ordinary
skill may not recognize the inherent characteristics or functioning of the
prior art.” MEHL/Biophile Int’l Corp. v. Milgraum, 192 F.3d 1362, 1365
(Fed. Cir. 1999).

Analysis
Appellants’ contentions are not convincing. The prior art disclosed an
SSB having an amino acid sequence which was 100% identical to the
sequence SEQ ID NO:1. (Ans. 4). As the claimed method requires a
multimeric protein having at least 95% sequence identity to SEQ ID NO:1,
the SSO SSB of the prior art having 100% sequence identity to SEQ ID
NO:1 would inherently have the same properties as the protein of the
claimed method, including having a multimeric form on binding ssDNA.
See Papesch, 315 F.2d at 391.
Moreover, insofar as Appellants assert that the combined prior art
would not have provided a skilled artisan at the time of the invention a
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reasonable expectation of successfully achieving a method of performing
nucleic acid amplification using a multimeric protein, we remain
unpersuaded. (App. Br. 8). Appellants contend that success would have
required the selection of the right solution conditions favoring the
multimeric presence of the SSB protein. (Id.). There is no evidence that
under the ordinary prior art conditions used for nucleic acid amplification,
the prior art SSB could have functioned without being in multimeric form.
The evidence supports the Examiner’s finding that the SSB disclosed by She
and GenBank, and now used in Appellants’ method, is a multimer under the
same conditions as disclosed in Nielson. (See Ans. 8-9, 16). It appears that
under certain conditions of acrylamide analytical procedures that Appellants
refer to, the protein is a monomer. Those methods do not show that when
used under the conditions in Neilson’s method the SSB could do anything
other than multimerize. The discussion of additional references raised both
by Appellants and the Examiner cannot change the properties of the SSB
protein. (See App. Br. 5-9; Reply Br. 3-7; Ans. 9-19). Put another way,
debate in the art at the time of the invention does not displace the evidence
of inherency. See, e.g, MEHL/Biophile, 192 F.3d at 1365.

CONCLUSION OF LAW
The evidence supports the Examiner’s finding that the SSB protein
disclosed in the prior art inherently forms a multimer when it binds ssDNA.

SUMMARY
We affirm the rejection of claims 6, 9-12, 15, and 16 under 35 U.S.C.
§ 103(a) as unpatentable over She, GenBank, and Nielson.
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Application 10/386,575

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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

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EIGHTH FLOOR
SAN FRANCISCO CA 94111-3834