Ex parte Adams

Board of Patent Appeals and Interferences

Jul 31, 2000

08361024 (B.P.A.I. Jul. 31, 2000)

Application for patent filed December 21, 1994. According to appellant, this application is a1
continuation of application no. 07/925,059 filed August 4, 1992, now abandoned.
THIS OPINION WAS NOT WRITTEN FOR PUBLICATION
The opinion in support of the decision being entered today (1) was not written for publication in a law journal
and (2) is not binding precedent of the Board.
Paper No. 38
UNITED STATES PATENT AND TRADEMARK OFFICE
____________
BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
____________
Ex parte CRAIG W. ADAMS
____________
Appeal No. 1997-1668
Application No. 08/361,0241
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ON BRIEF
____________
Before WILLIAM F. SMITH, SPIEGEL, and SCHEINER, Administrative Patent Judges.
SPIEGEL, Administrative Patent Judge.
DECISION ON APPEAL
This is a decision on appeal under 35 U.S.C. § 134 from the examiner's final
rejection of claims 1-7, which are all of the claims pending in this application.
Claims 1 and 5 are illustrative and read as follows.
Appeal No. 1997-1668
Application No. 08/361,024
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1. A kit comprising reagents for amplification of at least one target
sequence comprising at least one region having a defined nucleic acid
sequence, the kit comprising at least one Blocker moiety, at least one
Primer moiety, and at least one End-Run moiety, where the Blocker moiety
is capable of hybridizing to the nucleic acid sequence, the Primer moiety is
capable of hybridizing to the nucleic acid sequence such that the Primer
moiety abuts the hybridized Blocker moiety or is capable of extending to the
hybridized Blocker moiety, and the End-Run moiety comprises a sequence
which is complementary to at least a portion of the Blocker moiety.
[Emphasis added.]
5. A kit comprising components for conducting a reaction for
amplifying or detecting a target sequence of a polynucleotide, said reaction
comprising the steps:
a) treating said polynucleotide with at least three oligonucleotide
moieties wherein said at least three oligonucleotide moieties include:
i) a first oligonucleotide moiety comprising a
nucleotide sequence complementary to and capable of
hybridizing to the polynucleotide;
ii) a second oligonucleotide moiety complementary to
and capable of hybridizing to the polynucleotide such that the
second oligonucleotide moiety abuts the first oligonucleotide
moiety when the first oligonucleotide moiety is hybridized to
the polynucleotide or such that the second oligonucleotide is
capable of extending to the first oligonucleotide moiety when
the first oligonucleotide moiety is hybridized to the
polynucleotide; and
iii) a third oligonucleotide moiety comprising a
sequence which is complementary to at least a portion of the
first oligonucleotide moiety;
b) providing conditions for hybridizing the first moiety and the second
moiety to the polynucleotide;
c) providing conditions for ligating the hybridized first moiety to the
hybridized second moiety to form a ligation product; and
d) providing conditions for hybridizing and chain extending the third
moiety,
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Application No. 08/361,024
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said components being capable of buffering said reaction to a pH of
6 - 9 and capable of promoting ligase and polymerase specificity and
processivity. [Emphasis added.]
The references relied on by the examiner are:
Mullis et al. (Mullis) 4,683,195 Jul. 28, 1987
Landegren et al. (Landegren) 4,988,617 Jan. 29, 1991
Claims 1-7 stand rejected under 35 U.S.C. § 103 as being unpatentable over
Landegren in view of Mullis. We REVERSE.
In reaching our decision in this appeal we have given careful consideration to the
appellant's specification and claims and to the respective positions articulated by the
appellant and the examiner. We make reference to the examiner's answer (Paper No. 37,
mailed July 23, 1996) for the examiner's reasoning in support of the rejection and to the
appellant's brief (Paper No. 36, filed April 22, 1996) for the appellant's arguments
thereagainst.
OPINION
To establish a prima facie case of obviousness, there must be both some
suggestion or motivation to modify the reference or combine reference teachings and a
reasonable expectation of success. Furthermore, the prior art must teach or suggest all
the claim limitations. In re Vaeck, 947 F.2d 488, 493, 20 USPQ2d 1438, 1442
(Fed. Cir. 1991).
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Application No. 08/361,024
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Landegren describes an assay for determining the nucleic acid sequence in a
region of a nucleic acid test substance having a known normal sequence and a known
possible mutation at a target nucleotide position involving use of two probes (i.e.,
primers), i.e., a target probe and an adjacent probe, capable of hybridizing to immediately
adjacent parts of a complementary test substance. The target probe has an end region
nucleotide which is complementary to the normal or mutation nucleotide at the
corresponding target nucleotide position. When the target probe and the adjacent probe
hybridize to one strand of the nucleic acid test substance in the presence of a linking
agent, e.g., a ligase, the target probe and the adjacent probe will link (i.e., ligate) only if the
target nucleotide is correctly base paired with the target probe. Determining the presence
or absence of ligation indicates whether the target nucleotide is normal or a mutation. See
col. 2, line 34 - col. 3, line 20. Landegren discloses a kit comprising a target probe, an
adjacent probe and a ligase (col. 3, lines 39-52).
Mullis describes a process known as the polymerase chain reaction (PCR)
comprising treating separated complementary strands of a nucleic acid with a molar
excess of two oligonucleotide primers, selected such that each primer hybridizes to the 3'
terminus of a different strand of the double-stranded molecule, and extending the
hybridized primers by a polymerase. The duplexes formed by the extension are then
separated and each newly formed nucleic acid sequence becomes the template of the
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other primer for another polymerase extension reaction. Each time the process is
repeated the amount of newly formed nucleic acid sequences doubles. See col. 2, line 46
- col. 3, line 33. Mullis discloses adding a labeled probe capable of hybridizing to the
sequence being detected/amplified or a mutation thereof (col. 3, lines 25-27) and a kit
comprising the two oligonucleotide primer (col. 3, lines 34-55).
According to the examiner,
[i]t would have been obvious to add a third oligonucleotide into the kit [of
Landegren] for the detection of the ligated product of the first and second
oligonucleotides, as Mullis et al. discloses detecting a nucleic acid product
by using a probe having a sequence complementary to the target nucleic
acid to be detected (col. 3, lines 3-33; in particular, lines 25-27) (answer,
page 4).

The flaw in the examiner's analysis is that the ligated product is not the same as the
first Blocker oligonucleotide. Thus, the "detection" probe might have a sequence
complementary to the second Primer oligonucleotide moiety of the ligated product.
However, all of the claims on appeal require the third End-Run oligonucleotide to
comprises a sequence which is complementary to at least a portion of the first Blocker
oligonucleotide. The examiner has not pointed out, and we do not find, where either
Landegren or Mullis disclose or suggest this limitation, i.e., that the End-Run
oligonucleotide be complementary to at least a portion of the Blocker oligonucleotide.
The mere fact that the prior art could be so modified would not have made the modification
obvious unless the prior art suggests the desirability of the modification. That is not the
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case here. Accordingly, we conclude that the examiner has not established a prima facie
case of obviousness.
The rejection of claims 1-7 over Landegren in view of Mullis is reversed.
CONCLUSION
To summarize, the decision of the examiner to reject claims 1-7 under 35 U.S.C. §
103 as being unpatentable over Landegren in view of Mullis is reversed.
REVERSED
WILLIAM F. SMITH )
Administrative Patent Judge )
)
)
)
) BOARD OF PATENT
CAROL A. SPIEGEL ) APPEALS
Administrative Patent Judge ) AND
) INTERFERENCES
)
)
)
TONI R. SCHEINER )
Administrative Patent Judge )
Appeal No. 1997-1668
Application No. 08/361,024
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WILLIAM H. MAY
BECKMAN INSTRUMENTS INC.
2500 HARBOR BLVD.
FULLERTON, CA 92634
CAS/jlb