Ex Parte Petrovykh et al

Patent Trial and Appeal Board

Feb 8, 2017

11457713 (P.T.A.B. Feb. 8, 2017)

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.
11/457,713 07/14/2006 Dmitri Y. Petrovykh 97607-US2 7597
26384 7590 02/09/2017
NAVAL RESEARCH LABORATORY
ASSOCIATE COUNSEL (PATENTS)
CODE 1008.2
4555 OVERLOOK AVENUE, S.W.
WASHINGTON, DC 20375-5320
EXAMINER
PRIEST, AARON A
ART UNIT PAPER NUMBER
1637
MAIL DATE DELIVERY MODE
02/09/2017 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 PATENT TRIAL AND APPEAL BOARD
__________

Ex parte DMITRI Y. PETROVYKH, LLOYD J. WHITMAN,
MICHAEL J. TARLOV, ARIC M. OPDAHL, and
HIROMI KIMURA-SUDA1
__________

Appeal 2016-002966
Application 11/457,713
Technology Center 1600
__________

Before ROBERT A. POLLOCK, TAWEN CHANG, and
RACHEL H. TOWNSEND, Administrative Patent Judges.

POLLOCK, Administrative Patent Judge.

DECISION ON APPEAL
Appellants appeal under 35 U.S.C. § 134(a) from the final rejection of
claims 1–8, 10–23, 25, 27–39, 41–51, 53–65, and 67–69. We have
jurisdiction under 35 U.S.C. § 6(b).
We affirm.
STATEMENT OF THE CASE
Appellants’ invention relates to methods for immobilizing nucleic
acids to a metal surface.

1 Appellants identify the real party-in-interest as The Government of the
United States of America, as represented by the Secretary of the Navy. App.
Br. 2.
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Claims 1, 16, 33, 45, and 57 are independent. For the purpose of this
appeal, claim 1 is representative (emphasis added):
1. A method for attaching nucleic acids or nucleic acid
analogs to a metal surface in a controlled conformation
comprising:
providing a metal surface;
providing an immobilization solution comprising at least
one nucleic acid or nucleic acid analog, said nucleic acid or
nucleic acid analog comprising a functional sequence and at
least one block of adenine nucleotides or adenine nucleotide
analogs having a length of about 5 to about 25;
identifying solute and temperature conditions tending to
cause a configuration wherein the at least one block of
adenine nucleotides or adenine nucleotide analogs attaches
directly to and substantially flat along said metal surface and
the functional sequence extends away from the metal surface;
and
contacting said immobilization solution with said metal
surface under the solute and temperature conditions.
Claims 1–5, 8, 10–20, 23, 25, 27–32, 57–62, and 67–69 stand rejected
under 35 U.S.C. § 103(a) as obvious over the combination of Demers,2
Kimura-Suda,3 and Petrovykh.4

2 Demers et al., A Fluorescence-Based Method for Determining the Surface
Coverage and Hybridization Efficiency of Thiol-Capped Oligonucleotides
Bound to Gold Thin Films and Nanoparticles, 72 Anal. Chem. 5535–41
(2000) (“Demers”).
3 Kimura-Suda et al., Base-Dependent Competitive Adsorption of Single-
Stranded DNA on Gold, 125 J. Am. Chem. Soc. 9014–15 (2003) (“Kimura-
Suda”).
4 Petrovykh et al., Quantitative Analysis and Characterization of DNA
Immobilized on Gold, 125 J. Am. Chem. Soc. 5219–26 (2003)
(“Petrovykh”).
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Claims 6, 7, 21, 22, 33–39, 41–44, 63, and 64 stand rejected under
35 U.S.C. § 103(a) as obvious over the combination of Demers, Kimura-
Suda, Petrovykh, and Zhao.5
Claims 45–51 and 54–56 stand rejected under 35 U.S.C. § 103(a) as
obvious over the combination of Demers, Kimura-Suda, Petrovykh, and
Kumar.6
Claim 53 stands rejected under 35 U.S.C. § 103(a) as obvious over the
combination of Demers, Kimura-Suda, Petrovykh, Kumar, and Lizardi.7
Claim 65 stands rejected under 35 U.S.C. § 103(a) as obvious over the
combination of Demers, Kimura-Suda, Petrovykh, and Mergny.8
ANALYSIS
We have reviewed Appellants’ contentions that the Examiner erred in
rejecting claims 1–8, 10–23, 25, 27–39, 41–51, 53–65, and 67–69 as
unpatentable over the cited art. App. Br. 1–9; Reply Br. 2–5.9 We disagree
with Appellants’ contentions and, to the extent not otherwise clarified
below, adopt the findings regarding the scope and content of the prior art set
forth in the Examiner’s Answer, as well as the Examiner’s reasoned analysis

5 Zhao et al., Immobilization of oligodeoxyribonucleotides with
multiple anchors to microchips, 29(4) Nucl. Acids Res. 955–59 (2001)
(“Zhao”).
6 Kumar, US 5,912,124, issued June 15, 1999.
7 Lizardi, US 5,854,033, issued Dec. 29, 1998.
8 Mergny et al., Fluorescence energy transfer as a probe for nucleic acid
structures and sequences, 22(6) Nucl. Acids Res. 920–28 (1994)
(“Mergny”).
9 Appellants did not argue the rejections separately. Rather, they focused on
an alleged lack of teaching or suggestion of the configuration recited by the
independent claims.
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with respect to secondary considerations. For emphasis, we highlight and
address the following:
Findings of Fact
FF1. In discussing the solute and temperature conditions for the
immobilization of nucleic acids or nucleic acid analogs to a metal
surface, the Specification provides that “[t]he immobilization solution
temperature ranges from about 20 °C to about 35 °C. The salt added to
immobilization solution can be NaCl, KCl, K2HPO4, KH2PO4, CaCl2, or
MgCl2. The salt concentration ranges from about 1 to about 3 M.” Spec.
¶ 70; see Ans. 20–21.
FF2. Demers explores conditions for binding single-strand oligonucleotides
to gold nanoparticle and films. Demers, Abstract. Demers discloses
thio-derivatized oligonucleotides SA20N12f and S3’X20N12f (where X may
be A or T), comprising a functional sequence of 12 DNA monomer units
and a block of 20 adenine nucleotides. Id. at 5539 & Table 2, 5540 &
Table 4. Demers teaches that a “salt aging step was crucial in obtaining
stable oligonucleotides-modified nanoparticles. . . . [which] resisted
aggregation when centrifuged, even in high ionic strength solutions (up
to 1 M NaCl).” Id. at 5539. According to Demers,
Using the SA20N12f modified particles, we examined the
effect of electrolyte conditions on oligonucleotide surface
loading. As shown in Table 3, final surface coverages for Au
nanoparticles that were exposed to oligonucleotides in water
for 48 h are much lower ( 7.9 ± 0.2 pmoV cm2) as compared
with those that were “aged” in salt or prepared by increasing
the salt concentration gradually over the course of the final
24 h of the deposition experiment.
Id. at 5539–5540, Table 3 (employing buffer containing 1.0 M NaCl).
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FF3. Kimura-Suda “examine[d] room-temperature adsorption of homo-
oligonucleotides onto polycrystalline [gold] films . . . by soaking clean
Au substrates in 1 μM solutions of unmodified homo-oligonucleotides (1
M NaCL–TE buffer) for 20 h.” Kimura-Suda 9014. Kimura-Suda
disclose that “the homo-oligonucleotides adsorb on Au with relative
affinity A > C ≥ G > T.” Id. at 9014. Kimura-Suda further state:
To examine the relevance of our results to applications that
use thiol-modified ssDNA on Au, unmodified (dA)25 was
mixed with thiolated (dT)25. Thiolated (dT)25 probes adsorb
on Au as randomly coiled molecules each anchored via the
thiol group. Thus, one would expect this mixture to result in
(dA)25·(dT)25 duplexes adsorbed via the thiolated 5’ end of
the (dT)25. However, the extraordinary affinity of oligo(dA)
for Au again produces a film composed largely of adsorbed
(dA)25 (Figure 2, bottom).
Id. at 9015.
FF4. Petrovykh “describe[s] the complementary use of X-ray photoelectron
spectroscopy (XPS) and Fourier transform infrared (FTIR) spectroscopy
to quantitatively characterize the immobilization of thiolated (dT)25
single-stranded DNA (ssDNA) on gold.” Petrovykh, Abstract. These
studies show “that at lower coverages much of the DNA lies flat on the
surface, with a substantial fraction of the thymine bases chemisorbed. At
higher immobilization densities, the (dT)25 film consists of randomly
coiled ssDNA molecules each anchored via the thiol group and at
possibly one or two other bases.” Id.; see id. at 5224. Petrovykh reports
“strong effects of different buffer salts on the immobilization efficiency”
and that “cation valence has a larger effect on immobilization than its
concentration.” Id. at 5224–25. In particular, “[b]uffers with divalent
salts dramatically increase the efficiency of immobilization and result in
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very high surface densities (>5 x 1013/ cm2), densities that may only be
possible if the divalent counterions induce strong attractive
intermolecular interactions.” Id. at Abstract; see also id. at 5220 (studies
conducted at room temperature). In Figure 7, Petrovykh states that
maximum coverage is “obtained with 2 M CaCl2 and 0.1 M MgCl2.”
Analysis
During prosecution, an application’s claims are given their broadest
reasonable scope consistent with the specification. In re Am. Acad. of Sci.
Tech. Ctr., 367 F.3d 1359, 1364 (Fed. Cir. 2004). “[T]he specification ‘is
always highly relevant to the claim construction analysis. Usually it is
dispositive; it is the single best guide to the meaning of a disputed term.’” In
re Abbott Diabetes Care Inc., 696 F.3d 1142, 1149 (Fed. Cir. 2012) (quoting
Phillips v. AWH Corp., 415 F.3d 1303, 1315 (Fed. Cir. 2005) (en banc)).
Our reviewing court cautions, however, that “[t]here is a fine line between
construing the claims in light of the specification and improperly importing a
limitation from the specification into the claims.” Retractable Techs., Inc. v.
Becton, Dickinson, and Co., 653 F.3d 1296, 1305 (Fed. Cir. 2011), reh’g
and reh’g en banc denied, 659 F.3d 1369 (Fed. Cir. 2011), cert. denied, 133
S. Ct. 833 (2013). Any special definition for a claim term must be set forth
in the specification with reasonable clarity, deliberateness, and precision. In
re Paulsen, 30 F.3d 1475, 1480 (Fed. Cir. 1994).
Our analysis focuses on whether the prior art teaches or suggests the
claim term, “identifying solute and temperature conditions tending to cause a
configuration wherein the at least one block of adenine nucleotides or
adenine nucleotide analogs attaches directly to and substantially flat along
said metal surface and the functional sequence extends away from the metal
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surface” as set forth in each of the independent claims. As an initial matter,
the Examiner interprets the words “tending to cause . . .” in this phrase to
mean “leaning toward but not necessarily causing.” Ans. 21. As Appellants
do not object to this definition, we adopt the Examiner’s definition as within
the common and ordinary meaning consistent with the Specification. See
Reply 1–5.
The Examiner and Appellants generally refer to the “configuration
wherein the at least one block of adenine nucleotides or adenine nucleotide
analogs attaches directly to and substantially flat along said metal surface
and the functional sequence extends away from the metal surface,” set forth
in claim 1 as an “L-shaped” configuration. See Ans. 21; Reply 2–3.
However, the Examiner interprets the referenced claim language as not
limited to a strict L-shape configuration, whereas Appellants contend that
the claim language should be read to exclude configurations in which the
functional sequence exhibits a random coil configuration. Id. Appellants do
not convince us that the claim is so limited.
Figure 2 of the Specification is reproduced below.

Figure 2 “is an idealized schematic of d(Tm-An) oligonucleotides adsorbed
on gold” (Spec. ¶ 10) and illustrates “an absorption model (L-shape model)
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where d(A) blocks preferentially adsorb on the gold substrate and the d(T)
blocks extend away from the substrate” (id. ¶ 58). With reference to Figure
2, the Specification states:
Films obtained using oligos with long d(T) blocks, such as
d(T25-A5) and d(T25-A10) display the same trend of
decreasing grafting density with increasing length of the d(A)
block, but overall have lower grafting densities than short
block oligos—an effect attributed to steric and electrostatic
repulsion between the longer d(T25) brush strands, which can
no longer be approximated as [] extended chains, but instead
behave as anchored random coils.
Id. ¶ 59. Accordingly, the Specification draws a distinction between
“extended chains” in the first two rows of Figure 2, and “anchored random
coils” in the third row of the figure. Notably, the claim phrase at issue does
not use the terms “L-shaped,” “extended chains,” or “anchored random
coils.” Nevertheless, because “the longer d(T25) brush strands,” of Figure 2,
that “behave as anchored random coils,” generally extend away from the
substrate, they comprise “functional sequence [that] extends away from the
metal surface,” as set forth in claim 1. Accordingly, we do not read the
instant claims as excluding random coils.
Our opinion as to the meaning of this claim phrase is further informed
by Figure 12, reproduced below.
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“FIG. 12 shows FTIR spectra and XPS oligonucleotide coverages
before and after denaturing.” Id. ¶ 21. With reference to the inset in the
lower right hand portion of Figure 12, the Specification further states:
Because of the complementary nature of the d(Tm-An)
oligos, films of oligos with both long d(T) and long d(A)
blocks, such as d(T25-A15) and d(T25-A20), contain stable
hybrids. Exposing these films to denaturing conditions
recovers the d(T25) brush structure, i.e, the structure with
d(T) blocks extending away from the surface, as shown in
FIG. 12.
Id. ¶ 59 (italics added). The inset of Figure 12 depicts a d(T25-A15)
oligonucleotide hybridized to a gold film via its poly-A block, before and
after urea treatment. See id. ¶ 90. Although paragraph 59 of the
Specification state that, after the urea treatment, “d(T) blocks extend[s] away
from the surface,” Figure 12 does not show the d(T25-A15) oligonucleotide
as forming the strict L-configuration depicted in the top two rows of Figure
2. To the contrary, the “brush structure” of “d(T) blocks extending away
from the surface,” in the inset of Figure 12, is not substantially different
from the “random coils” shown in the bottom row of Figure 2. See also
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Whitman Declaration ¶ 6 (implying that Fig. 4B of the Specification
represents the “L-shaped configuration”).10 This underscores our
determination that the claimed “configuration wherein . . . the functional
sequence extends away from the metal surface,” may encompass random
coils.
In setting forth the rejection, the Examiner relies on
Demers as teaching a method for attaching nucleic acids to a
surface at a controlled surface density comprising: (a)
providing a gold surface . . . (b) providing a solution
comprising at least one chemical functional unit attached at one
of its ends to at least one block of 20 adenine nucleotides . . .
(c) providing at least one separate lateral spacer block of 20
adenine nucleotides . . . (d) contacting the immobilization
solution and the lateral spacer block with the surface for a
period of time sufficient to directly attach the adenine
nucleotide block and the lateral spacer block to the gold
surface.
Ans. 5–6 (citations omitted). The Examiner relies on Kimura-Suda as
teaching the high affinity of poly-adenine for gold surfaces in 1 M NaCl at
room temperature. See id. at 6–7. The Examiner further relies on Petrovykh
as describing the immobilization of thiolated poly-T oligonucleotides on a
gold surface, where the salt concentration of the immobilization solution in
both Petrovykh and Demers is a results-effective variable influencing
immobilization density and orientation. Id. at 7.
In short, the Examiner further finds that
both Petrovykh and Demers explicitly teach L-shaped poly-A
anchors and their benefits; and all of Petrovykh, Demers and
Kimura-Suda teach the same conditions as described in the

10 See App. Br. 5 (incorporating by reference the Declaration under 37
C.F.R. § 1.132 of Lloyd J. Whitman.
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instant Specification which cause L-shaped anchors. Thus,
both Petrovykh and Demers teach the claimed limitations of
“solute and temperature conditions tending to cause a
configuration wherein the at least one block of adenine
nucleotides or adenine nucleotide analogs attaches directly to
and substantially flat along said metal surface and the
functional sequence extends away from the metal surface.”
Id. at 22. Accordingly, the Examiner concludes that in view of Demers and
Petrovykh,
the ordinary artisan would have been motivated to conduct
routine experimentation to determine the optimal
immobilization conditions for achieving the desired result of
immobilization of the oligonucleotides at the desired density
and with the desired orientation, i.e., with direct (horizontal)
attachment of the lateral spacer block as taught by Demers
and also with direct (horizontal) attachment of the adenine
block in the oligonucleotide of Demers additionally
containing the functional sequence as suggested by the
teachings of Kimura-Suda describing the very strong affinity
of adenine nucleotides for gold surfaces.
Id. at 7–8.
Appellants respond that the Examiner has failed to establish that the
cited references teach or suggest the claimed “configuration wherein the at
least one block of adenine nucleotides or adenine nucleotide analogs
attaches directly to and substantially flat along said metal surface and the
functional sequence extends away from the metal surface,” and, thus, the
desirability of identifying solute and temperature conditions tending to cause
that configuration. See Ans. 5–9; Reply Br. 2–9.
With respect to Petrovykh, Appellants argue that “Petrovykh
describes a structure going from nearly flat to randomly coiled. At no point
is an L shape expected.” Reply Br. 3–4. As noted above, however, we do
not read the claim as excluding a random coil configuration. Petrovykh
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teaches that immobilization efficiency and, thus, density, is a results-
effective variable dependent on cation valence and salt concentration. See
FF 4. “At higher immobilization densities, the (dT)25 film consists of
randomly coiled ssDNA molecules each anchored via the thiol group and at
possibly one or two other bases.” Appellants point to the following Figure
from Petrovykh as evidencing a random coil configuration.

See Reply Br. 3. The above figure depicts the absorption of (dT)25 to gold
film at high and low density. As depicted here, under high-density
conditions (upper panel) a substantial portion of the poly-T tails extend away
from the gold substrate. Petrovykh further teaches that maximum density is
obtained at room temperature in 2 M CaCl2—conditions with the scope of
those disclosed in Appellants’ Specification. See FF 1, 4. Accordingly, and
contrary to the Whitman Declaration upon which Appellants rely, we agree
with the Examiner that Petrovykh teaches “identifying solute and
temperature conditions tending to cause a configuration wherein the at least
one block of adenine nucleotides or adenine nucleotide analogs attaches
directly to and substantially flat along said metal surface and the functional
sequence extends away from the metal surface,” as required by the rejected
claims. Moreover, even if one or more of the cited references do not
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expressly disclose the recited conformation, because they identify the same
solute and temperature conditions set forth in the Specification, we agree
with the Examiner that the disclosed conditions would at least “tend to
cause” the configuration as claimed. See Ans. 22, 24–27, 31, 40 (concluding
that “the combination of the prior art of record clearly teaches to use the
same ‘solute and temperature conditions’ of the claimed invention which
tend to yield L-shaped poly-A anchors, if not explicitly teaches the L-shape
poly-A anchors”).
Appellants argue that Demers “fails to even hint at the L-shaped
configuration” because rather than employing a block of poly-A nucleotides
to attach the oligonucleotide to the substrate, Demers Scheme 3 relies on
chemical modification at the end of the oligonucleotide to achieve a vertical
orientation and, thus, “teaches away from having any part of the nucleotides
in flat contact with a surface.” App. Br. 6–9. Demers, however, is not
limited to the experiments set forth in Scheme 3. “It is well settled that a
prior art reference is relevant for all that it teaches to those of ordinary skill
in the art.” In re Fritch, 972 F.2d 1260, 1265 (Fed. Cir. 1992).
Demers teaches the adsorption of SA20N12f oligonucleotides to gold particles
and “aging” the adsorbed complex under solute and temperature conditions
taught by Appellants’ Specification. See Ans. 26–28; FF 2.
The Examiner has the burden of providing reasonable proof that a
claim limitation is an inherent characteristic of the prior art. In re Best, 562
F.2d 1252, 1254–55 (CCPA 1977); see also Crown Operations Int’l, Ltd. v.
Solutia Inc., 289 F.3d 1367, 1377 (Fed. Cir. 2002). The Examiner meets this
“burden of production by ‘adequately explain[ing] the shortcomings it
perceives so that the applicant is properly notified and able to respond.’” In
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re Jung, 637 F.3d 1356, 1362 (Fed. Cir. 2011) (quoting Hyatt v. Dudas, 492
F.3d 1365, 1370 (Fed. Cir. 2007)). The burden of proof then shifts to the
applicant “to prove that the subject matter shown to be in the prior art does
not possess the characteristic relied on.” In re Best, 562 F.2d at 1254–55; In
re Schreiber, 128 F.3d 1473, 1478 (Fed. Cir. 1997) (holding that once the
Examiner established a prima facie case of anticipation, the burden of proof
was properly shifted to the inventor to rebut the finding of inherency).
In re Mousa, 479 F. App’x 348, 352 (Fed. Cir. 2012).
In the present case, Appellants rely on the Whitman declaration,
which asserts that “under condition analogous to those of Demers et al., the
claimed L-shaped configuration was not achieved (see the present
Specification, FIG. 4A as compared to FIG. 4 B, explained in ¶[0064].”
Whitman Decl. ¶ 6. Appellants do not explain, however, why the cited
portions of the Specification represent “analogous” conditions, nor address
the relevance of any differences—such as the significance of the length of
the poly-A blocks (20 in Demers vs. 5 in Figure 4) and differences in
adsorption conditions (e.g., oligonucleotide concentration of 1 μM used in
Figure 4A as compared to the 3 μM used in Figure 4B and Demers). See
Demers, at e.g., 5536. Accordingly, we do not find Appellants’ argument
persuasive.
In sum, we agree with the Examiner that
Petrovykh, Demers and Kimura-Suda explain the benefits of
poly-A anchors/attachments (optimized high-density and L-
oriented nucleic acid attachments in the presence of high-salt
solutions to allow higher throughput and sensitivity of detection
and analysis . . . [such that] a skilled artisan would have been
motivated to apply the poly-A anchors/attachments of
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Petrovykh, Demers and Kimura-Suda in order to take
advantages of such benefits.
Ans. 21–22. Moreover, “[t]he teachings of Petrovykh, Demers, and Kimura-
Suda concerning immobilization conditions and the factors influencing the
interaction with the surface would have provided the ordinary artisan with
the required reasonable expectation of success.” Id. at 13.
SUMMARY
I. We affirm the rejection of claims 1–5, 8, 10–20, 23, 25, 27–32, 57–
62, and 67–69 under 35 U.S.C. § 103(a) as obvious over the
combination of Demers, Kimura-Suda, and Petrovykh.
II. We affirm the rejection of claims 6, 7, 21, 22, 33–39, 41–44, 63, and
64 under 35 U.S.C. § 103(a) as obvious over the combination of
Demers, Kimura-Suda, Petrovykh, and Zhao.
III. We affirm the rejection of claims 45–51 and 54–56 under 35 U.S.C.
§ 103(a) as obvious over the combination of Demers, Kimura-Suda,
Petrovykh, and Kumar.
IV. We affirm the rejection of claim 53 under 35 U.S.C. § 103(a) as
obvious over the combination of Demers, Kimura-Suda, Petrovykh,
Kumar, and Lizardi.
V. We affirm the rejection of claim 65 under 35 U.S.C. § 103(a) as
obvious over the combination of Demers, Kimura-Suda, Petrovykh,
and Mergny.

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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