Ex Parte Yu et al

Board of Patent Appeals and Interferences

Jan 4, 2012

10445996 (B.P.A.I. Jan. 4, 2012)

UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
__________

Ex parte ZHENGRONG YU, BRENDA F. BAKER, and HONGJIANG WU
__________

Appeal 2011-005123
Application 10/445,996
Technology Center 1600
__________

Before ERIC GRIMES, LORA M. GREEN, and MELANIE L.
McCOLLUM, Administrative Patent Judges.

McCOLLUM, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 involving claims to an
oligonucleotide detection or quantitation method. The Examiner has
rejected the claims as obvious. We have jurisdiction under 35 U.S.C. § 6(b).
We reverse.
STATEMENT OF THE CASE
Claims 16-29 are on appeal (App. Br. 2). We will focus on claim 16,
the only independent claim on appeal, which reads as follows:
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Application 10/445,996

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16. A method for detecting or quantitating an oligonucleotide in a
bodily fluid or extract wherein the oligonucleotide is 8 to 50 nucleosides in
length, comprising:
creating a test sample by contacting the bodily fluid or extract with a
probe, wherein:
the probe is complementary to the oligonucleotide; and
the probe comprises a detectable marker and a binding moiety,
wherein the detectable marker and the binding moiety are each
covalently bound to the probe;
contacting the test sample with a solid support wherein the solid
support comprises a binding partner of the binding moiety;
contacting the test sample with a single-strand-specific nuclease;
washing the test sample to remove detectable marker that is not
associated with the solid support;
detecting the presence or amount of detectable marker in the test
sample; and
thereby detecting or quantitating the oligouncleotide in the bodily
fluid or extract.
Claims 16, 17, 19, 26, and 27 stand rejected under 35 U.S.C. § 103(a)
as obvious over Temsamani
1
in view of Impraim
2
and VanAtta
3
(Ans. 6).
Claim 18 stands rejected under 35 U.S.C. § 103(a) as obvious over
Temsamani in view of Impraim, VanAtta, and de Serres
4
(Ans. 10).
Claims 20, 21, and 24 stand rejected under 35 U.S.C. § 103(a) as
obvious over Temsamani in view of Impraim, VanAtta, and Lind
5
(Ans. 11).

1
Temsamani et al., A Rapid Method for Quantitation of Oligodeoxy-
nucleotide Phosphorothioates in Biological Fluids and Tissues, 215
ANALYTICAL BIOCHEMISTRY 54-58 (1993).
2
Impraim et al., US 6,228,578 B1, May 8, 2001.
3
VanAtta et al., US 6,573,048 B1, Jun. 3, 2003.
4
de Serres et al., Development of a Novel Scintillation Proximity
Competitive Hybridization Assay for the Determination of Phosphorothioate
Antisense Oligonucleotide Plasma Concentrations in a Toxicokinetic Study,
233 ANALYTICAL BIOCHEMISTRY 228-233 (1996).
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3
Claims 22 and 23 stand rejected under 35 U.S.C. § 103(a) as obvious
over Temsamani in view of Impraim, VanAtta, and Cowsert
6
(Ans. 12).
Claims 24 and 25 stand rejected under 35 U.S.C. § 103(a) as obvious
over Temsamani in view of Impraim, VanAtta, and Prosnyak
7
(Ans. 13).
Claims 28 and 29 stand rejected under 35 U.S.C. § 103(a) as obvious
over Temsamani in view of Impraim, VanAtta, and Wang
8
(Ans. 14).
ISSUE
With respect to each ground of rejection, the issue is: Has the
Examiner set forth a prima facie case that Temsamani, Impraim, and
VanAtta suggest the method of claim 16?
FINDINGS OF FACT
1. VanAtta discloses an assay comprising “(1) hybridizing
labeled, degradable nucleic acid probe(s) to a target sequence, creating a
target-specific product from the probe(s), (2) degrading or separating the
target-complementary region from the labeled region of the probe(s), and
(3) detecting the presence of the labeled region” (VanAtta, col. 4, ll. 4-9).
2. VanAtta also discloses:
One aspect of the present invention provides a method for
detecting a target nucleic acid sequence in a sample whereby at
least one pair of nucleic acid probes anneals to the target

5
Lind et al., Structural characteristics of 2’-O-(2-methoxyethyl)-modified
nucleic acids from molecular dynamics simulations, 26 NUCLEIC ACIDS
RESEARCH 3694-3699 (1998).
6
Cowsert, US 5,945,290, Aug. 31, 1999.
7
Prosnyak et al., Substitution of 2-Aminoadenine and 5-Methylcytosine for
Adenine and Cytosine in Hybridization Probes Increases the Sensitivity of
DNA Fingerprinting, 21 GENOMICS 490-494 (1994).
8
Wang et al., US 6,900,013 B1, May 31, 2005.
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nucleic acid. The probes are characterized by two nucleic acid
regions which form a terminal probe-probe branch or stem after
the base pairing of the probes to the adjacent regions of the
target nucleic acid sequence. The regions of the probe which
are capable of forming the stem or probe-probe branch as
described herein are also referred to as “stem regions” or
“probe-probe regions”.
(Id. at col. 4, ll. 10-19.)
3. In addition, VanAtta discloses:
The probes have at least one crosslinking compound positioned
within the stem region of at least one of the probes of the probe
pair. . . . The covalent bond occurs after base pairing of the
probes to the target nucleic acid sequence, and thereby
permanently crosslinks the stem regions of the probe pair to
each other.
(Id. at col. 4, ll. 19-31.)
4. VanAtta also discloses that “the stem regions of the probes
contain a detectable moiety and a capture moiety which are bonded to the
end of the stem regions” (id. at col. 6, ll. 8-10).
5. In addition, VanAtta discloses that the “term „capture moiety‟
or „capture group‟ as used herein is a moiety that works in combination with
a detectable moiety, wherein one nucleic acid probe in a probe pair is
labeled with a detectable moiety and the other probe in a probe pair is
labeled with a capture moiety” (id. at col. 7, ll. 39-43).
ANALYSIS
Claim 16 requires contacting a bodily fluid or extract with a probe
comprising a detectable marker and a binding moiety. The Examiner relies
on VanAtta for disclosing a probe comprising a detectable marker and a
binding moiety (Ans. 7 & 15). As noted by the Examiner, VanAtta discloses
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that “the stem regions of [a pair of] probes contain a detectable moiety and a
capture moiety which are bonded to the end of the stem regions” (Findings
of Fact (FF) 2 & 4). However, VanAtta discloses that “one nucleic acid
probe in a probe pair is labeled with a detectable moiety and the other probe
in a probe pair is labeled with a capture moiety” (FF 5). Although these
probes are subsequently cross-linked to form a unitary structure (FF 3), we
agree with Appellants that VanAtta does not disclose or suggest contacting
this unitary structure, which is already hybridized to target nucleic acid
(FF 3), with bodily fluid or extract (App. Br. 5), nor has the Examiner
adequately explained how or why this unitary structure would be utilized in
the methods of Temsamani and Impraim to provide the method of claim 16.
CONCLUSION
The Examiner has set not forth a prima facie case that Temsamani,
Impraim, and VanAtta suggest the method of claim 16. We therefore
reverse the obviousness rejections.

REVERSED

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