Ex Parte Lee

Board of Patent Appeals and Interferences

Sep 27, 2011

11957334 (B.P.A.I. Sep. 27, 2011)

UNITED STATES PATENT AND TRADEMARK OFFICE
UNITED STATES DEPARTMENT OF COMMERCE
United States Patent and Trademark Office
Address: COMMISSIONER FOR PATENTS
P.O. Box 1450
Alexandria, Virginia 22313-1450
www.uspto.gov
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO.
11/957,334 12/14/2007 Ming-Chou Lee 054769-9940 9129
30542 7590 09/27/2011
FOLEY & LARDNER LLP
P.O. BOX 80278
SAN DIEGO, CA 92138-0278
EXAMINER
MYERS, CARLA J
ART UNIT PAPER NUMBER
1634
MAIL DATE DELIVERY MODE
09/27/2011 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 MING-CHOU LEE
__________

Appeal 2011-006060
Application 11/957,334
Technology Center 1600
__________

Before DONALD E. ADAMS, DEMETRA J. MILLS, and ERIC GRIMES,
Administrative Patent Judges.

GRIMES, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 involving claims to methods
of amplifying nucleic acids. The Examiner has rejected the claims as
obvious. We have jurisdiction under 35 U.S.C. § 6(b). We affirm.
STATEMENT OF THE CASE
The Specification discloses that a “method for target nucleic acid
detection has been described under the name ‘Scorpion’” (Spec. 4,¶ 0017).
The Specification discloses that “there is a significant loss of fluorescent
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label from the amplicon generated from certain Scorpion primers by
cleavage of the fluorophore from Scorpion when a nucleic acid polymerase
having 5’ to 3’ exonuclease activity is used” (id.). The Specification
discloses “a Scorpion design that effectively retains the fluorophore on the
amplicon during amplification with a nucleic acid polymerase having
endonuclease or 5’ to 3’ exonuclease activity. This modified Scorpion
primer [is] referred to as ‘DQS’ (Dye-Quencher-Switched)” (id. at 5,
¶ 0018).
The relevant part of the Specification’s Figure 1 is shown below:

The figure shows a Scorpion primer (Fig. 1A) having a fluorophore (F) at
the 5' end and a quencher (Q) between the primer and probe regions, and a
DQS Scorpion primer (Fig. 1B) having the quencher at the 5' end and the
fluorophore between the primer and probe regions.
Claims 1-14 are on appeal. The claims have not been argued
separately and therefore stand or fall together. 37 C.F.R. § 41.37(c)(1)(vii).
Claim 1 is representative and reads as follows:
1. A method of avoiding loss of a fluorescent label from an amplicon
generated by amplification of target nucleic acid using a polymerase with
endonuclease or 5' exonuclease activity, comprising the steps of:
(a) amplifying a target nucleic acid to generate an extension product
using a pair of primers wherein one of the primers of the pair is a Scorpion
primer comprising, a fluorophore, a quencher, and in 5' to 3' order, a probe
region, a linker region and a primer region,
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wherein the quencher is located at or near the 5' end of the probe
region, the primer region is complementary to the target nucleic acid, and
the probe region hybridizes to a complementary sequence in said extension
product of the primer region;
(b) separating said extension product of step (a) by electrophoresis;
and
(c) detecting said extension product of the target nucleic acid by
detecting said fluorophore, wherein said fluorophore is retained on said
extension product.

Issue
The Examiner has rejected claims 1-14 under 35 U.S.C. § 103(a) as
being obvious in view of Whitcombe1 and Slepnev.2 The Examiner finds
that Whitcombe discloses a method of “amplifying a target nucleic acid to
generate an extension product with a … Scorpion primer … wherein the
quencher is at the 5' end” (Answer 3). The Examiner finds that “the
amplification reaction is performed in the presence of Taq DNA polymerase
which is known to have 5'-exonuclease activity” (id. at 4). The Examiner
reasons that Whitcombe’s method inherently “avoids loss of a fluorescent
label from an amplicon” (id.) because the quencher, not the fluorophore, is at
the 5' end.
The Examiner finds that Slepnev discloses methods for detecting
“products that are produced in amplification methods that use a fluorophore
labeled primer … [by] separating the products … by capillary
electrophoresis, and … detecting the incorporated fluorophore” (id. at 5).
The Examiner further finds that Slepnev discloses that its method “provides

1 Whitcombe et al., US 6,636,145 B1, Dec. 4, 2001
2 Slepnev, US Patent Application Publication 2003/0235844 A1, Dec. 25,
2003
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numerous advantageous [sic], including … the quantitative determination of
amplification products and the ability to generate a profile of each of the
distinctly-sized amplification products” (id.). The Examiner concludes that
it would have been obvious “to have modified the method of Whitcombe …
by separating the extension products using capillary electrophoresis and
detecting the presence of the incorporated fluorophore in the separated
extension products in order to achieve the advantages set forth by Slepnev”
(id. at 5-6).
Appellant argues that the method of claim 1 would not have been
obvious in view of Whitcombe and Slepnev because both references teach
away from combining their teachings (Appeal Br. 7-9) and because
Appellant identified a problem in the art that is solved by the claimed
invention (id. at 8-9).
The issue presented is: Does the evidence of record support the
Examiner’s conclusion that claim 1 would have been obvious in view of the
cited references?
Findings of Fact
1. Whitcombe discloses a system “used in the detection of target
nucleic acid sequences” (Whitcombe, col. 1, ll. 4-7).
2. Whitcombe discloses “a nucleic acid primer comprising (i) a
template binding region and (ii) a tail comprising a linker and a target
binding region such that in use the target binding region hybridises to a
complementary sequence in an extension product of the primer” (id. at
col. 4, ll. 10-14).
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3. Whitcombe discloses that “preferably a blocking moiety is sited
between the template binding region of the primer and the tail region, which
moiety prevents … copying of the tail region of the primer” (id. at col. 4, ll.
18-21).
4. Whitcombe discloses “the tailed primers of the invention are
referred to as Scorpions primers” (id. at col. 7, ll. 46-48).
5. Figure 1 of Whitcombe is shown below:

Figure 1 shows
the template binding region … indicated by the shaded arrow,
the tail region compris[ing] a blocking group indicated by H,
also shown are a quencher [Q] and fluorophore [F], the target
binding region is in the region indicated by the solid line
between the quencher and fluorophore.

(Id. at col. 11, ll. 20-25.)
6. Whitcombe discloses that “[q]uenching is achieved by the random
folding of the tail bringing the fluorophore/quencher (F/Q) pair into
proximity by chance” (id. at col. 8, ll. 52-54).
7. Figure 3 of Whitcombe is shown below:

Figure 3 shows “hybridisation of the target binding region [of the Scorpion
primer] to a complementary sequence in the primer extension product
corresponding to the target region” (id. at col. 11, ll. 29-31); the signal is
switched-on by the “loss of quenching caused by hybridisation of the probe”
(id. at col. 8, ll. 57-58).
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8. Whitcombe discloses that “[i]n order to maximise this quenching,
it is preferred but not essential to have the fluorophore in the middle of the
molecule with the quencher at the 5' end” (id. at col. 8, ll. 54-57).
9. Whitcombe discloses that the “Scorpions primers of this invention
are particularly suited to real time assays since signal generation is rapid and
requires only a unimolecular interaction” (id. at col. 8, ll. 24-26).
10. Whitcombe discloses that the “range of assays which can be
performed using the Scorpions primers is extensive. Detection may, for
example, be effected after PCR amplification…. [P]ositive fluorescence
signals are so high and backgrounds so low, that fluorescence can be
observed by eye.” (Id. at col. 8, ll. 12-17.)
11. Slepnev discloses “methods of monitoring the amplification of
one or more nucleic acid sequences of interest … in real time” (Slepnev 2,
¶ 0012).
12. Slepnev’s method comprises contacting a sample with primers,
amplifying, separating the nucleic acids, and detecting a detectable marker
(id. at 2, ¶ 0013).
13. Slepnev discloses that “[s]eparation is preferably performed by
capillary electrophoresis (CE)” (id. at 11, ¶ 0120).
14. Slepnev discloses that “[i]n one embodiment, the different
primers can be labeled with the same fluorescent marker. In that instance,
the primers for the different amplification products are selected such that the
sizes of the amplified products are distinct.” (Id. at 8, ¶ 0090.)
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15. Slepnev discloses that its methods “permit improved
determination of the abundance of one or more target nucleic acids” (id. at 2,
¶ 0012).
Principles of Law
“A reference may be said to teach away when a person of ordinary
skill, upon reading the reference, would be discouraged from following the
path set out in the reference, or would be led in a direction divergent from
the path that was taken by the applicant. ” In re Gurley, 27 F.3d 551, 553
(Fed. Cir. 1994).
Analysis
Claim 1 is directed to a method of avoiding loss of a fluorescent label
during amplification of a target nucleic acid using a polymerase with
endonuclease or 5' exonuclease activity, comprising using a Scorpion primer
with the quencher at the 5' end of the probe region, separating the extension
product by electrophoresis, and detecting the extension product by detecting
the fluorophore of the Scorpion primer.
Whitcombe discloses a method of amplifying and detecting target
nucleic acid molecules in a sample using Scorpion primers having the
structure recited in claim 1 (FFs 2-8). Whitcombe discloses that its primers
are “particularly suited to real time assays” (FF 9). Slepnev discloses
methods of monitoring the amplification of target nucleic acid sequences in
real time using fluorescently labeled primers and electrophoretic separation
of amplification products (FFs 11-14). Slepnev discloses that the separation
of the fluorescently labeled products allows for the determination of the
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abundance of the target nucleic acid(s) (FF 15). In view of these disclosures,
it would have been obvious to one of ordinary skill in the art to separate and
detect the fluorescently labeled reaction products of Whitcombe using the
method of Slepnev in order to monitor target abundance during
amplification, because Whitcombe discloses that its primers are “particularly
suited to real time assays” (FF 9), like the one taught by Slepnev.
Appellant argues that Whitcombe teaches away from combining its
Scorpion primer amplification method with Slepnev’s separation and
detection methods because it says that its method is generally “the last
(detection) step in the above methods” (Appeal Br. 7-8, quoting Whitcombe,
col. 5, ll. 63-64).
This argument is not persuasive. Although Whitcombe states that its
method is “[i]n general” used as the detection step in amplification reactions
(see Whitcombe, col. 5, ll. 63-64), it does not suggest that its method would
not function unless it were the last step in an amplification process.
Whitcombe therefore does not teach away from combining its method with
Slepnev’s electrophoretic separation method. As discussed above, a skilled
worker would have considered it obvious to combine Whitcombe’s
amplification process with Slepnev’s separation and detection because
Slepnev discloses that its methods “permit improved determination of the
abundance of one or more target nucleic acids” (FF 15).
Appellant also argues that Slepnev teaches away from using primers
that are double-labeled since Slepnev disparages the use of “Taqman and
Molecular Beacons [which] are primers/probes that are double-labeled with
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both a quencher and a fluorophore” (Appeal Br. 9, citing Slepnev at 1,
¶¶ 0005-0007).
This argument is not persuasive. The cited portion of Slepnev
discusses the limitations of quencher/fluorophore-based techniques, in that
they require a different probe for each species to be analyzed in a multiplex
reaction. However, Slepnev’s discussion of the background art would not
suggest to one of skill in the art that Whitcombe’s Scorpion probes would be
unsuccessful if used as the fluorescently labeled probe in Slepnev’s
separation and detection method. In addition, Slepnev does not require that
its method be used to detect multiple targets in the same amplification
reaction, and describes its method as providing “improved determination of
the abundance of one or more target nucleic acids” (FF 15, emphasis added).
Thus, Slepnev does not teach away from combining its method with
Whitcombe’s Scorpion probes.
Appellant argues that an evaluation of the invention as a whole shows
that the invention would not have been obvious because “Appellant
identified that when the quencher was 5' to the fluorophore in a Scorpion
primer, the extension product retains the fluorescent label from the Scorpion
primer” (Appeal Br. 8).
This argument is not persuasive. We agree with Appellant that
considering the problem solved is part of the consideration of the invention
as a whole. However, “the law does not require that the references be
combined for the reasons contemplated by the inventor.” In re Beattie, 974
F.2d 1309, 1312 (Fed. Cir. 1992). Here, Whitcombe suggests that primers
that have the quencher in the 5' position are preferable because having the
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fluorophore in the middle of the molecule allows for better quenching of the
fluorophore. Appellants’ asserted identification of an additional benefit to
this configuration does not distinguish the claimed method from the method
made obvious by the cited references.
Conclusion of Law
The evidence of record supports the Examiner’s conclusion that claim
1 would have been obvious in view of the cited references.
SUMMARY
We affirm the rejection claims 1-14 under 35 U.S.C. § 103(a).
TIME PERIOD FOR RESPONSE
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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