Ex Parte Borns

Board of Patent Appeals and Interferences

Oct 29, 2010

10702400 (B.P.A.I. Oct. 29, 2010)

UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
__________

Ex parte MICHAEL BORNS
__________

Appeal 2010-005232
Application 10/702,400
Technology Center 1600
__________

Before ERIC GRIMES, LORA M. GREEN, 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 a mixture
of DNA polymerases. The Examiner has rejected the claims for lack of

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 2010-005232
Application 10/702,400

2
adequate description, nonenablement, and obviousness. We have
jurisdiction under 35 U.S.C. § 6(b). We reverse.
STATEMENT OF THE CASE
Claims 1, 2, 5-8, 22, 27, 31, 33, and 40-442 are on appeal. Claim 1 is
the only independent claim and reads as follows:
1. A blend of two or more DNA polymerases, comprising at least one
fusion polypeptide DNA polymerase and at least one non-fusion polypeptide
DNA polymerase,
wherein said fusion polypeptide DNA polymerase has a proofreading
activity and consists of a first polypeptide covalently linked to a second
polypeptide, wherein said first polypeptide is a DNA polymerase selected
from archaeal DNA polymerases and eubacterial DNA polymerases, and the
second polypeptide is a DNA binding polypeptide, wherein the first and
second polypeptides are not fused to each other in nature; and wherein said
non-fusion polypeptide is a DNA polymerase selected from archaeal DNA
polymerases and eubacterial DNA polymerases, said non-fusion polypeptide
having a proofreading activity.

The claims stand rejected as follows:3
• Claims 1, 2, 5-8, 22, 27, 31, 33, and 40-44 under 35 U.S.C. § 112,
first paragraph, for lack of adequate written description (Answer 4);

2 Claims 56-65 are also pending, but stand withdrawn from consideration.
(App. Br. 6.)
3 The Examiner has also provisionally rejected the claims for obviousness-
type double patenting (Answer 13-15). Appellant has not argued the merits
of the double-patenting rejections but requests that the provisional rejections
be held in abeyance until one of the conflicting applications is otherwise in
condition for allowance (Appeal Br. 24-25). Because we reverse the other
rejections on appeal, it would be premature to address the merits of the
provisional double-patenting rejections. See Ex parte Moncla, 95 USPQ2d
1884, 1885 (BPAI 2010).
Appeal 2010-005232
Application 10/702,400

3
• Claims 1, 2, 5-8, 22, 27, 31, 33, and 40-44 under 35 U.S.C. § 112,
first paragraph, for lack of enablement (Answer 5); and
• Claims 1, 2, 5, 6, 22, 27, and 40-44 under 35 U.S.C. § 103(a) as
obvious based on Barnes4 and Komori5 (Answer 10).
I.
The Examiner has rejected all of the claims on appeal for lack of
adequate written description in the Specification, on the basis that the
“specification states at page 8, line 26, under ‘Definitions’ that the ‘blend’ of
the invention has a greater than 10% increase in proofreading activity . . . as
compared to the non-chimeric (non-fusion) component of the blend”
(Answer 4) but
[t]here is no disclosure of any particular structure to
function/activity relationship in the specification or knowledge
in the art that would put one in possession of the genus of
blends of variant DNA polymerases having a proofreading
activity, wherein the blend has a greater than 10% increase in
proofreading activity relative to the non-chimeric (non-fusion)
polymerase.
(Id. at 5.)
Similarly, the Examiner has rejected all of the claims on appeal for
lack of enablement, on the basis that the Specification “does not reasonably
provide enablement for any blend of two or more DNA polymerases
comprising at least one fusion polypeptide DNA polymerase . . . wherein

4 Barnes US 5,436,149, Jul. 25, 1995
5 Kayoko Komori et al., Functional interdependence of DNA polymerizing
3’→5’ exonucleolytic activities in Pyrococcus furiosus DNA polymerase I,
13 PROTEIN ENGINEERING NO. 1, 41-47 (200).
Appeal 2010-005232
Application 10/702,400

4
said blend has a greater than 10% increase in proofreading activity as
compared to the non-chimeric component of the blend” (id. at 5-6).
We will reverse both of these rejections. None of the claims on
appeal is directed to a blend of DNA polymerases that have a greater than
10% increase in proofreading activity as compared to the non-chimeric DNA
polymerase in the blend. The Specification states that “[a]s used herein, a
‘blend’ refers to a combination of two or more DNA polymerases
comprising at least one chimeric DNA polymerase and at least one non-
chimeric DNA polymerase” (Spec. 8: 17-19). The Specification also states:
A “blend” of the invention has a >10% increase in one or more
of the following activities . . . as compared to the non-chimeric
component of the blend for a genomic and / or plasmid
template.: processivity, efficiency, template length amplifi-
cation capability, GC-rich target amplification efficiency,
specificity, thermostability, intrinsic hot start capability, proof-
reading activity, fidelity, DNA binding activity, strand displace-
ment activity, nucleotide binding and recognition, and salt
resistance.
(Id. at 8: 26 to 9: 3.)
The Examiner has not adequately explained why the Specification’s
definition of “blend” requires reading the term to mean a mixture that has a
greater than 10% increase in proofreading activity relative to the non-
chimeric polymerase in the mixture. “[W]hile it is true that claims are to be
interpreted in light of the specification and with a view to ascertaining the
invention, it does not follow that limitations from the specification may be
read into the claims.” Sjolund v. Musland, 847 F.2d 1573, 1582 (Fed. Cir.
1988).
Appeal 2010-005232
Application 10/702,400

5
The rejections of claims 1, 2, 5-8, 22, 27, 31, 33, and 40-44 for lack of
adequate written description and lack of enablement are reversed.
II.
The Examiner has rejected claims 1, 2, 5, 6, 22, 27, and 40-44 under
35 U.S.C. § 103(a) based on Barnes and Komori (Answer 10). The
Examiner finds that Barnes teaches a mixture of DNA polymerases (id.) and
Komori teaches mutant DNA polymerases from Pyrococcus furiosus (id. at
11). The Examiner concludes that it would have been obvious “to use either
of the Pfu DNA polymerase mutants . . . taught by Komori et al. in the
formulation taught by Barnes et al.” (id.).
The Examiner interprets Komori’s mutant DNA polymerase to meet
the claim limitation requiring one of the polymerases in the claimed mix to
be a “fusion polypeptide” (claim 1), because “a ‘fusion polypeptide’ is any
polypeptide that comprises ‘fused’ polypeptides . . . [and the] polymerase
mutants taught by Komori et al. comprise multiple polypeptide domains (i.e.
Polymerase, DNA binding and exonuclease domains) ‘fused’ together”
(Answer 31). The Examiner interprets Komori’s mutant DNA polymerase
to meet the claim limitation requiring the fusion polypeptide to consist of
“first and second polypeptides [that] are not fused to each other in nature”
(claim 1), because “the mutant polymerase taught by Komori . . . is a
polymerase comprising sequences that do not exist in nature” (Answer 33).
Appellant argues that the Examiner’s interpretation is unreasonably
broad, because the “terms ‘fusion polypeptide’ or ‘fusion protein’ are terms
of art and would be understood by one of skill in the art to mean a protein
created by joining two or more genes that code for separate proteins or the
Appeal 2010-005232
Application 10/702,400

6
domains of separate proteins” (Appeal Br. 22). Appellant also argues that
the Examiner’s interpretation is inconsistent with the Specification because
those of skill in the art use the terms “chimera” and “fusion polypeptide”
interchangeably, and the Specification defines a chimera as “two or more
amino acid sequences . . . from unrelated proteins, joined to form a new
functional protein” (id. at 23, quoting Specification 15: 16-19).
We agree with Appellant that a “fusion polypeptide . . . [that] consists
of . . . a DNA polymerase . . . [and] a DNA binding polypeptide” (claim 1)
cannot reasonably be interpreted to encompass a DNA polymerase that is not
fused to another polypeptide. The Specification defines a chimera is “a
fusion of a first amino acid sequence (protein) comprising a wild type or
mutant DNA polymerase of the invention, joined to a second amino acid
sequence defining a polypeptide the modulates one or more activities of the
DNA polymerase” (Spec. 15: 9-12, emphases added). This passage supports
Appellant’s position that “chimera” and “fusion protein” or “fusion
polypeptide” are used interchangeably.
The Specification also states that a “‘chimera’ according to the
invention contains two or more amino acid sequences . . . from unrelated
proteins, joined to form a new functional protein” (Spec. 15: 16-19). Thus,
when the claim term “fusion polypeptide” is read in light of the
Specification, it cannot reasonably be interpreted to read on a protein, like a
DNA polymerase, that naturally has different functional domains. The claim
language requires a polypeptide in which sequences that are normally found
in different proteins have been fused into a single polypeptide. The
Examiner has pointed to no protein in either Barnes or Komori that meets
Appeal 2010-005232
Application 10/702,400

7
this criterion, and therefore has not shown that the claimed composition
would have been obvious based on those references.
SUMMARY
We reverse the rejection of claims 1, 2, 5-8, 22, 27, 31, 33, and 40-44
under 35 U.S.C. § 112, first paragraph, for lack of adequate written
description and lack of enablement. We also reverse the rejection of claims
1, 2, 5, 6, 22, 27, and 40-44 under 35 U.S.C. § 103(a).

REVERSED

lp

AGILENT TECHOLOGIES INC, IN CARE OF
CPA GLOBAL
P. O. BOX 52050
MINNEAPOLIS MN 55402