Ex Parte 6,410,278 et al

Board of Patent Appeals and Interferences

Mar 23, 2012

90010702 (B.P.A.I. Mar. 23, 2012)

UNITED STATES PATENT AND TRADEMARKOFFICE
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.
90/010,702 10/01/2009 6,410,278 59046.001005 2407
30734 7590 03/26/2012
BAKER & HOSTETLER LLP
WASHINGTON SQUARE, SUITE 1100
1050 CONNECTICUT AVE. N.W.
WASHINGTON, DC 20036-5304
EXAMINER
CAMPELL, BRUCE R
ART UNIT PAPER NUMBER
3991
MAIL DATE DELIVERY MODE
03/26/2012 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 EIKEN KAGAKU KABUSHIKI KAISHA
Patent Owner and Appellant
____________

Appeal 2011-011866
Reexamination Control 90/010,702
Patent 6,410,278 B1
Technology Center 3900
____________

Before RICHARD E.SCHAFER, ROMULO H. DELMENDO, and
RICHARD M. LEBOVITZ, Administrative Patent Judges.

LEBOVITZ, Administrative Patent Judge.

DECISION ON APPEAL
This is a decision on the appeal by the Patent Owner of U.S. Patent
No. 6,410,278 from the Patent Examiner’s rejections of claims 1-26 in an ex
parte reexamination proceeding. The Board’s jurisdiction for this appeal is
under 35 U.S.C. §§ 6(b), 134(b), and 306. We reverse.
Appeal 2011-011866
Reexamination Control 90/010,702
Patent 6,410,278 B1

2
STATEMENT OF CASE
U.S. Patent No. 6,410,278 (hereinafter, the ‘278 patent) issued June
25, 2002. A “Request for Ex Parte Reexamination” of the issued claims of
the ‘278 patent was filed October 1, 2009, pursuant to 35 U.S.C. §§ 302-307
and 37 C.F.R § 1.510. Reexamination was ordered.
The claims of the ‘278 patent are directed to a method of amplifying a
nucleic acid. Claim 1 is representative of the appealed subject matter and
reads as follows:
1. A method of amplifying a nucleic acid comprising:

A) providing a template having (i) a 3' end portion comprising a
first region located 3' terminal and a first complementary region
which, under suitable conditions, anneal to one another to form
a first loop, (ii) a 5' end portion comprising a second region
located 5' terminal and a second complementary region which,
under suitable conditions, anneal to one another to form a
second loop, and (iii) a region connecting the 3' end portion and
the 5' end portion;

B) extending the 3' terminal of the template to the 5' end of the
template by means of a polymerase having strand displacement
activity, when the first region and first complementary region
are annealed to one another to form the first loop, to form a
template extension which includes a third region located 3'
terminal and a third complementary region which are
substantially the same as the second complementary region and
second region, respectively, and which, under suitable
conditions, anneal to one another to form a third loop;

C) annealing to the first loop of the extended template an
oligonucleotide primer comprising at the 3' terminal a
nucleotide sequence complementary to at least part of the first
Appeal 2011-011866
Reexamination Control 90/010,702
Patent 6,410,278 B1

3
loop and at the 5' terminal a nucleotide sequence
complementary to the first region of the template;

D) extending the oligonucleotide primer along the extended
template, by means of a polymerase having strand displacement
activity, to form a new template complementary to the template,
thereby displacing the template extension formed during said
extending in step B);

E) Further extending the 3' terminal of the extended template to
the 5' end of the extended template by means of a polymerase
having strand displacement activity, when the third region and
the third complementary region are annealed to one another to
form the third loop, thereby displacing the new template from
the extended template; and

F) repeating steps A)-E) using the new template as the template
in step A), thereby amplifying the nucleic acid.

The claims stand rejected by the Examiner as follows:
1. Claims 1, 2, 5-8, 10-17 and 20-26 under 35 U.S.C. § 102(e) as
anticipated by Rabbanias evidenced by the Backman declaration (dated
January 27, 2009); 1
2. Claims 3, 4, 18 and 19 under 35 U.S.C. § 103(a) as obvious over
Rabbani in view of Chamberlin;2 and
3. Claim 9 under 35 U.S.C. § 103(a) as obvious over Rabbani in view
of Abbott.3

1 Rabbani et al., US 6,743,650 B1 (issued June 1, 2004).
2 Chamberlin et al. US 6,270,962 B1 (issued August 7, 2001).
3 Abbott et al. US 5,104,791 (issued April 14, 1992).
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Appeal 2011-011866
Reexamination Control 90/010,702
Patent 6,410,278 B1

5
forms an unpaired “loop” structure. The entire structure is also known as a
“hairpin,” because it resembles a hairpin used to hold hair in place.
The key issue in this appeal is whether Rabbani describes the
extension of a nucleic acid molecule with two loop structures at each end to
form a nucleic acid molecule with three loop structures. It is undisputed that
Rabbani does not expressly describe a nucleic acid molecule with three
loops, but the Examiner takes the position that a three-looped nucleic acid
molecule would inherently be formed during Rabbani’s amplification
process.

Legal Principles
“To anticipate a claim, a prior art reference must disclose every
limitation of the claimed invention, either explicitly or inherently.” In re
Schreiber, 128 F.3d 1473, 1477 (Fed. Cir. 1997). When the limitations of a
claim are not expressly described in the prior art, the PTO must show “sound
basis for believing” that despite the failure of the prior art to describe them,
the limitations are inherently there and “the products of the applicant and the
prior art are the same.” In re Spada, 911 F.2d 705, 708 (Fed. Cir. 1990).
“Inherency, however, may not be established by probabilities or
possibilities. The mere fact that a certain thing may result from a given set
of circumstances is not sufficient. If, however, the disclosure is sufficient to
show that the natural result flowing from the operation as taught would
result in the performance of the questioned function, it seems to be well
settled that the disclosure should be regarded as sufficient.” In re Oelrich,
666 F.2d 578, 581 (CCPA 1981).
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Patent 6,410,278 B1

7
extended displaced primer creates a template with secondary
structure that should allow multiple binding, extension and
displacement events under isostatic or limited cycle conditions.
A product can be formed that has secondary structure [first
loop] at one end derived from sequences contributed from the
first novel primer and its complement and secondary structure
[second loop] at the other end derived from sequences
contributed by the second novel primer and its complement.
Since this structure has a loop structure on each strand that
regenerates a single-stranded segment capable of being used as
a primer binding site, further binding and extension of novel
primers or nucleic acid constructs can be initiated on either
strand under isostatic or limited cycle conditions.
(Rabbani, col. 21, ll. 37-52; emphasis added.)
[FF6] Example 1 of Rabbani describes a process of nucleic acid
amplification using two novel primers (Rabbani, col. 32, l. 43).
[FF7] Rabbani describe analyzing the amplification product (“PCR
Product”) by gel electrophoresis:
Under UV illumination, three bands appeared that as judged by
DNA size markers were approximately 210, 180 and 170 bp in
length. The band corresponding to 210 bp is the linear PCR
product that had been anticipated and presumably the other two
bands correspond to the same size amplicons where secondary
structures are formed on either one or both ends thereby
changing their effective mobilities.
(Rabbani, col. 33, ll. 13-19.)
[FF8] The PCR amplification product was subjected to isothermal
amplification using the two novel primers:
The product of these reactions is a series of bands that form a
discrete pattern. This is in contrast to a single discrete band that
is usually seen in PCR or the two or three bands seen
previously with the LC and RC primers after PCR
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Appeal 2011-011866
Reexamination Control 90/010,702
Patent 6,410,278 B1

9
structures as required in step B) of claims 1 and 11, but determined that
Rabbani’s method utilized the same starting materials and reaction
conditions as required by the claims, and thus would have been reasonably
believed to produce the same nucleic acid (Answer 3).
In concluding that claim 1 was anticipated by Rabbani, the Examiner
relied on a declaration by Dr. Keith C. Backman, an expert with 30 years of
experience in genetic engineering and biotechnology (Backman Decl. ¶ 3).
Dr. Backman is the Third Party Requester’s expert. Dr. Backman testified
that the bottom-most strand in step (4) of Figure 3 of Rabbani (FF4), having
loops on each end, would “necessarily” self-prime to produce a nucleic acid
with the claimed three-loop structure. Normally, an exogenous primer
hybridizes to primer binding site on a target nucleic acid, and the primer is
extended, using the target nucleic acid as a template. “Self-priming” means
that the nucleic acid uses the loop structure to extend itself, without needing
an exogenous primer.
Dr. Backman testified in his written declaration that the bottom-most
nucleic acid strand depicted Figure 3, step (4) (FF4), of Rabbani represented
a molecule with all the properties required of the template of step A) of
claim 1 of the ‘278 patent (Backman Decl. ¶ 45).
Dr. Backman further testified that this bottom-most strand would self-
prime and extend under the conditions disclosed by Rabbani (Backman
Decl. ¶ 47). Dr. Backman stated:
As discussed . . . , the 3’ end of a nucleic acid molecule is
subject to extension by a nucleic acid polymerase, whether
depicted by an arrowhead or not. Therefore, when the template
is combined with a strand-displacing polymerase (e.g., Bst
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Appeal 2011-011866
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Patent 6,410,278 B1

11
not appear in the Rabbani patent, but was created by Dr. Backman to
represent what he believed occurred.
The Patent Owner provided a declaration by its expert, Dr. Gerald F.
Joyce, who testified that Rabbani did not disclose that the bottom-most
strand with loops at each end was further amplified in Rabbani’s process
(Joyce Decl. ¶ 31, dated May 14, 2010; Exhibit 1 of Appeal Brief). Dr.
Joyce is a scientist with more 20 years of experience in nucleic acid
amplification (Joyce Decl. ¶ 4). Dr. Joyce also questioned the evidence that
double-stranded nucleic acid molecule with loop structures at both the 5’ and
3’ ends had been obtained by Rabbani (Joyce Decl. ¶¶ 34 & 40).
Dr. Joyce noted the following disclosure in Rabbani that led him to
doubt that the double-stranded loop structure depicted in Figure 3, step (4)
(FF4), had been produced in Example 1 of Rabbani:
• Lack of a photograph showing a gel with the band said to be the
nucleic acid with loop structures (Joyce Decl. ¶ 38);
• Alternative explanations for the appearance of bands in the gel
described by Rabbani to be the nucleic acid with loop structures at each end
(Joyce Decl. ¶ 39); and
• Inconsistencies in Rabbani’s description of gel bands (Joyce Decl. ¶
40)
Dr. Joyce’s arguments are not persuasive. As pointed out by the
Examiner, even if other processes occurred and additional products were
made in the Example 1 experiments, this does not preclude a process in
which a single-stranded nucleic acid molecule with loops at both ends was
made. While Dr. Joyce may be correct that Rabbani did not prove the step
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Patent 6,410,278 B1

12
(4) molecule was produced in Example 1, Rabbani described it (FF3, FF5, &
FF7) and drew it (FF4), giving the Examiner reasonable basis to believe that
such nucleic acid had, in fact, been made, shifting the burden to Patent
Owner to show that it did not. Spada, 911 F.2d at 708. This burden was not
met.
On the other hand, the data that the step (4) molecule (FF4) self-
primed to form a three-loop nucleic acid structure as asserted by Dr.
Backman, is more doubtful. Dr. Backman stated that when all the needed
ingredients for DNA synthesis were present, “the template will necessarily
self-prime and be extended” to form the structure capable forming the three-
looped nucleic acid (Backman Dec. ¶ 47), the same molecule recited in
claim 1. Dr. Backman referred to Figure 10 and Examples 1-3 of Rabbani as
support for his opinion. Figure 10 shows self-priming of a hairpin structure
(FF10), the same kind of loop structure recited in claim 1. It is undisputed
that self-priming is known to occur on loop or hairpin structures. However,
the issue is whether it necessarily occurred in Example 1 and thus met the
corresponding limitation of claim 1. Oelrich, 666 F.2d at 581. As explained
in more detail below, we conclude that the preponderance of the evidence is
insufficient to establish that a three loop nucleic acid molecule was
necessarily produced in Rabbani.
In Example 1 of Rabbani, a PCR product was subjected to isothermal
amplification using the two novel primers (FF8). This PCR product was
characterized by Rabbani as containing a nucleic acid with loops at both
ends (FF7), the nucleic acid of step (4) (FF4). Rabbani states that this
product can serve as a template for further amplification, but not via self-
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13
priming as required by claim 1, but rather by priming using a primer that
anneals to a primer binding site on the step (4) nucleic acid (“Since this
structure has a loop structure on each strand that regenerates a single-
stranded segment capable of being used as a primer binding site, further
binding and extension of novel primers or nucleic acid constructs can be
initiated” (FF5)).
In actual experiments, when this product was subjected to
amplification, Rabbani states that multiple bands were observed which “may
possibly be due to the presence of the secondary structures allowing the
amplicons to function as primers as well as templates or it may be an
indication of strand switching.” (FF8.) Thus, Rabbani suggested that that
two loop structure (FF4) might “possibly” self-prime (“function as
primers”), but Rabbani did not conclude that it necessarily did. Thus, Dr.
Joyce’s opinion that self-priming and extension “were not necessarily
observed” (Joyce Decl. ¶ 42) is supported by Rabbani’s own description of
the process.
In addition to this, Dr. Joyce testified that the results obtained by
Rabbani were “unreliable” because even the control showed product when
no target template DNA was present (Joyce Decl. ¶ 43; FF9). When no
template DNA is present, no amplification would occur because there is
nothing to be amplified and no product should be observed. That a product
was observed, casts doubt on the reliability of the experiment. Thus, we
agree with Dr. Joyce, that this discrepancy, coupled with Rabbani’s own
statement that the extra band might “possibly” be due to self-priming,
militates against the conclusion that self-priming necessarily occurred.
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14
Dr. Backman cited Examples 2 and 3 as support for his position that
self-priming and extension necessarily occurred, but Dr. Backman did not
provide an explanation or analysis of the examples (Backman Decl. ¶ 47).
Dr. Joyce, on the other hand, analyzed the experiments performed in
Examples 2 and 3, and identified problems with non-specific binding,
inconsistencies in assay results, and high background, that he concluded
made it “impossible to tell” whether a DNA product with loops at both ends
was made or that such product was self-extended (Joyce Decl. ¶¶ 45-53).
Thus, Dr. Joyce’s opinion that self-priming did not occur is supported by
factual evidence and credible scientific reasoning.
The Examiner concluded that since Rabbani “discloses a process
which utilizes the same starting materials (template nucleic acid, primers,
nucleotides, polymerase enzyme, etc.) and reaction conditions as the ‘278
patent claims, and [it] therefore will inherently yield the same products.”
(Answer 13.) The Examiner found these similarities sufficient scientific
reasoning to establish inherency (Answer 13). The Examiner relied on Dr.
Backman’s explanation “that Rabbani uses oligonucleotides of the same
design, the same polymerase, and the same reaction conditions as the ‘278
patent - and therefore the same reactions will occur.” (Answer 13).
Dr. Joyce, in his second declaration (“Second Joyce Decl.”),
specifically identified differences in the starting materials and conditions
utilized in the ‘278 patent as compared to Rabbani. For example, Dr. Joyce
identified specific difference in the reaction conditions (Second Joyce Decl.
¶¶ 20 & 21) and primers (Second Joyce Decl. ¶ 21) that would explain why
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15
the hairpin structure was self-priming in the ‘278 patent, but not in Rabbani,
and why different results were produced (Second Joyce Decl. ¶¶ 22-25).
The Examiner responded:
Dr. Joyce’s response is essentially, “Notomi’s reaction worked,
Rabbani’s did not, therefore the methods are different” (second
Joyce declaration, ¶ 28).
(Answer 14).
We do not agree. Dr. Joyce in his second declaration mentioned
specific conditions that would account for the different results, including the
design of the primers and ion concentrations (Second Joyce Dec. ¶ 21). The
requirement in claim 1 that reaction be performed under “suitable
conditions” would exclude other conditions, such as those disclosed in
Rabbani, that do not work. Dr. Joyce also established, as discussed above,
that certain results obtained by Rabbani were “unreliable” because even the
control showed a product when no template target DNA was present in the
amplification mixture (Joyce Decl. ¶ 43; FF9). The Examiner faulted Dr.
Joyce for not providing experimental evidence. However, we see no reason
why Dr. Joyce’s scientific reasoning, backed by factual evidence, should be
discounted simply because no experimental data was presented.
For the foregoing reasons, we conclude that there was insufficient
basis to believe the nucleic acid molecule of Figure 3, step (3), of Rabbani
self-primed and extended to form a nucleic acid with three loops as required
by claims 1 and 11. We thus reverse the anticipation rejection of
independent claims 1 and 11, and claims 1, 2, 5-8, 10, 12-17 and 20-26
which depend on the independent claims.

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16
OBVIOUSNESS REJECTIONS
Claims 3, 4, 18 and 19 stand rejected under 35 U.S.C. § 103(a) as
obvious over Rabbani in view of Chamberlin. Claim 9 stands rejected under
35 U.S.C. § 103(a) as obvious over Rabbani in view of Abbott.
Chamberlin and Abbott were relied upon by the Examiner to teach
additional limitations recited in the dependent claims. As these publications
were not found by the Examiner to address any of the alleged deficiencies in
Rabbani as to claims 1 and 11, we reverse the rejection of these claims, as
well.
REVERSED

ack/rvb

Patent Owner:

BAKER & HOSTETLER, LLP
Washington Square, Suite 1100
1050 Connecticut Ave., N.W.
Washington, DC 20036-5304

Third Party Requester:

Hunton & Williams, LLP
Intellectual Property Department
1900 K Street, N.W.
Suite 1200 Washington, DC 20006-1109