Ex Parte Sorge et al

Board of Patent Appeals and Interferences

Feb 24, 2012

09896923 (B.P.A.I. Feb. 24, 2012)

UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
__________

Ex parte JOSEPH A. SORGE, CONNIE JO HANSEN,
and HOLLY HOGREFE
__________

Appeal 2011-007501
Application 09/896,923
Technology Center 1600
__________

Before DEMETRA J. MILLS, ERIC GRIMES, and LORA M. GREEN,
Administrative Patent Judges.

GRIMES, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 involving claims to a kit or
composition comprising a DNA polymerase. The Examiner has rejected the
claims as obvious. We have jurisdiction under 35 U.S.C. § 6(b). We
reverse.
STATEMENT OF THE CASE
The Specification discloses “DNA polymerase enzymes with reduced
discrimination for non-conventional nucleotides. The enzymes of the
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invention are useful in many applications calling for the detectable labeling
of nucleic acids and are particularly useful in DNA sequencing applications”
(Spec. 1).
Claims 1, 7-14, 18-22, 28-35, 39-41, 43, and 107 are on appeal.
Claim 1 is representative and reads as follows:
1. A composition for identifying a nucleotide at a given position of a
template DNA molecule, said composition comprising:
a Family B DNA polymerase deficient in 3′ to 5′ exonuclease activity
comprising the amino acid sequence of one of SEQ ID NOs: 2 and 62-78,
except
a first mutation at amino acid D or E or both in the exo I (DXE) motif
within said SEQ ID NO, and
a second mutation at an amino acid selected from the group consisting
of: amino acid L, P, and both L and P in Region II (DXXSLYPSII, SEQ ID
NO:7) within said SEQ ID NO, wherein said second mutation confers a
reduction in discrimination.

Claim 22, the only other independent claim, is directed to a “kit for
identifying a nucleotide at a given position of a template DNA molecule”
which comprises the same DNA polymerase specified in claim 1.
The Examiner has rejected claims 1, 7-14, 18-22, 28-35, 39-41, 43,
and 107 under 35 U.S.C. § 103(a) as being obvious in view of Mathur,
1

Riedl,
2
and Gardner.
3
The Examiner finds that Mathur discloses a
“thermostable DNA polymerase I from Pyrococcus furiosus … [which]
comprises the amino acid sequence of [instantly claimed] SEQ ID NO: 68”
and also discloses the corresponding polynucleotide sequence (Answer 3).

1
Mathur, US 5,545,552, issued August 13, 1996.
2
Riedl et al., US 5,882,904, issued March 16, 1999.
3
Gardner et al., 27 NUCLEIC ACIDS RESEARCH 2545-2553 (1999).
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The Examiner finds that Riedl discloses “a mutant Thermococcus barosii
DNA polymerase (Family B) with reduced 3’-5’ exonuclease … [and] a
reduced discrimination against dideoxynucleotides or ribonucleotides,”
which has a mutation of D or E in the DXE motif, as recited in the claims
(id. at 3-4).
The Examiner finds that Gardner discloses a Vent DNA polymerase
that also contains a mutation of D or E in the DXE motif (id. at 4). The
Examiner finds that Gardner discloses “a Family B consensus motif A,
comprising 8 amino acids, DhxSLYPS, which are involved in nucleotide
sugar recognition,” as well as “a Y412V variant, within this region, which
relaxed the specificity (reduced discrimination) of the Vent DNA
polymerase” (id.). The Examiner finds that Gardner suggests that “the larger
amino acid group [i.e., tyrosine (Y) at position 412] acts as a steric gate to
block access … to the binding site” by the ribonucleotide sugar (id. at 4-5).
The Examiner concludes that one of ordinary skill in the art would
have been motivated to mutate Mathur’s DNA polymerase of SEQ ID
NO:68, as described in Gardner, “for use as a DNA polymerase for
sequencing reactions” (id. at 5), and that it would have been obvious to
mutate the positions adjacent to position Y412 (the L and P of the
DXXSLYPSII sequence) “as a means of confirming the basis of the
reduction in nucleotide discrimination as due to steric hindrance.
Additionally mutation of these adjacent residues … would allow even
greater reductions in nucleotide discrimination due to the potential for even
less steric hindrance.” (Id. at 6.)
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Appellants argue that none of the cited references identify the L and P
residues of the DXXSLYPSII motif as targets for reducing nucleotide
discrimination (Reply Br. 2) and that one of skill in the art would not have
had an expectation of successfully creating a DNA polymerase having a
reduction in nucleotide discrimination by mutating those residues (id. at
2-3).
We agree with Appellants that the Examiner has not adequately
shown that the cited references would have made obvious the DNA
polymerase of independent claims 1 and 22. Gardner discloses a mutational
analysis of a Family B (Vent
TM
) DNA polymerase (Gardner 2545, right
col.). Gardner discloses that DNA polymerases have conserved regions
referred to as Motif B and Motif A (id.); the DXXSLYPSII sequence recited
in claim 1 corresponds to Motif A and the tyrosine residue (Y) in that
sequence is referred to as Y412 (see id. at 2546, legend to Fig. 1).
Gardner discloses that the Y412V variant (i.e., a variant having valine
substituted for Y412) showed a two-fold increase in incorporation of
ddATP, and a 200-fold increase in incorporation of the ribonucleotide ATP,
relative to the wild-type polymerase (id. at Table 2). Gardner discloses that
previous studies suggested that Y412 “could potentially play a role in 2’-
deoxyribonucleotide/ribonucleotide discrimination” because the bulk of the
tyrosine residue could block the hydroxyl group of a ribonucleotide from the
binding site (id. at 2551, left col.).
The Examiner has not adequately explained how Gardner, or the other
cited references, would have made obvious a DNA having the L or P
mutation required by claims 1 and 22. Although the DXXSLYPSII motif
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was known to be part of a conserved motif, and Gardner disclosed that
mutating the Y residue in this motif (Y412) could affect nucleotide
discrimination, neither Gardner nor the other cited references provides any
suggestion to mutate the L or P residues adjacent to Y412. Further, although
Gardner suggests that Y412 is involved in nucleotide discrimination, it does
not suggest that the adjacent L and P residues are also involved. Thus, none
of the cited references provides one of skill in the art with a reasonable
expectation that a mutation at L or P, or both, in the DXXSLYPSII motif
would confer “a reduction in discrimination” as required in claims 1 and 22.
Thus, we reverse the rejection of independent claims 1 and 22, and
dependent claims 7-14, 18-21, 28-35, 39-41, 43, and 107 as being obvious in
view of Mathur, Riedl, and Gardner.
SUMMARY
We reverse the rejection of claims 1, 7-14, 18-22, 28-35, 39-41, 43,
and 107 under 35 U.S.C. § 103(a).

REVERSED

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