Ex Parte Baker et al

Patent Trial and Appeal Board

Feb 17, 2015

10701265 (P.T.A.B. Feb. 17, 2015)

UNITED STATES PATENT AND TRADEMARK OFFICE
____________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
____________

Ex parte BRENDA F. BAKER, ANNE B. ELDRUP,
MUTHIAH MANOHARAN, BALKRISHEN BHAT,
RICHARD H. GRIFFEY, ERIC E. SWAYZE, and
STANLEY T. CROOKE
____________

Appeal 2012-0112791
Application 10/701,265
Technology Center 1600
____________

Before DONALD E. ADAMS, ULRIKE W. JENKS, and
CHRISTOPHER G. PAULRAJ, Administrative Patent Judges.

JENKS, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 involving claims directed to a
composition comprising oligonucleotide RNA-gapmer duplexes containing
2’-sugar modification on both strands. The Examiner rejects the claims as
obvious. We have jurisdiction under 35 U.S.C. § 6(b).
We reverse.

1 Appellants state that the Real Party in Interest is Isis Pharmaceuticals, Inc.
(App. Br. 1.)
Appeal 2012-011279
Application 10/701,265

2
STATEMENT OF THE CASE
Claims 120, 121, 124, 127, and 136–138 are on appeal, 2 and can be
found in the Claims Appendix of the Appeal Brief (App. Br. 13–14). Claim
120 is representative of the claims on appeal, and reads as follows (emphasis
added):
120. A composition comprising a duplex consisting of a first
chemically synthesized oligonucleotide and a second
chemically synthesized oligonucleotide, wherein:
each of the first chemically synthesized oligonucleotide
and the second chemically synthesized oligonucleotide
independently consists of 17 to 25 linked nucleosides, each
nucleoside comprising a nucleobase and a sugar;
the first chemically synthesized oligonucleotide is 100%
complementary to the second chemically synthesized
oligonucleotide and to a target mRNA;
the first chemically synthesized oligonucleotide and the
second chemically synthesized oligonucleotide are not
covalently linked to each other; and
the first chemically synthesized oligonucleotide is a
gapmer, wherein the gap comprises at least 4 nucleosides, each
comprising a 2’-hydroxy-pentofuranosyl sugar moiety, and
wherein each nucleoside of each wing comprises a 2’ -sugar
modification; and

2 Claims 120, 121, 124, 127, and 136–138 are also provisionally rejected on
the ground of nonstatutory obviousness type double patenting as being
unpatentable over claims 1 and 130–156 of copending Application
No.10/859,825 in view of Wyatt, Manche, Monia, and Shibahara (Final Rej.
9). Claims 120, 121, 124, 127, and 136–138 are also provisionally rejected
on the ground of nonstatutory obviousness type double patenting as being
unpatentable over claims 86–123 of copending Application No. 10/701,264
in view of Wyatt, Manche, Monia, and Shibahara (Final Rej. 9–10).
Appellants in a prior response request that these rejections be held in
abeyance until allowable subject matter is indicated (Response Dec. 14,
2010, p. 10).
Appeal 2012-011279
Application 10/701,265

3
the second chemically synthesized oligonucleotide
comprises at least one nucleoside that comprises a 2’ -sugar
modification.
The Examiner rejected claims 120, 121, 124, 127, and 136–138 under
35 U.S.C. § 103(a) as unpatentable over Wyatt,3 Manche,4 Monia,5 and
Shibahara.6 (Ans. 5–9.)

The Examiner takes the position that Wyatt, Monia, and Manche
“demonstrate that [the] production of short RNA-containing duplexes was
routine in the art for the purpose of studying” activity and structural
requirements of different enzymes. (Ans. 7; see also FF 2–9, infra.) The
Examiner, however, recognizes that “these references do not explicitly teach
duplexes wherein a first oligonucleotide is an RNA gapmer and the
references do not explicitly teach duplexes wherein both strands of the
duplex are RNA gapmers.” (Ans. 7.) The Examiner looks to Shibahara for
teaching the inclusion of 2’-O-methylribooligonucleotides because they “are
resistant to various nucleases, including RNase H and DNases.” (Ans. 7.)
The Examiner concludes
It would have been obvious to one of ordinary skill in the art at
the time the invention was made to make synthetic ribonuclease
substrates wherein the substrate is an artificial duplex of a target

3 Jacqueline R. Wyatt & G. Terrance Walker, Deoxynucleotide-containing
oligoribonucleotide duplexes: stability and susceptibility to RNase V1 and
RNase H, 17 Nucleic Acids Research 7833 (1989).
4 Manche et al., Interactions between Double-Stranded RNA Regulators and
the Protein Kinase DAI, 12 Mol. & Cell. Bio. 5238–5248 (1992).
5 Monia et al., Evaluation of 2’-Modified Oligonucleotides Containing 2’-
Deoxy Gaps as Antisense Inhibitors of Gene Expression, 268 J. Bio. Chem.
14514 (1993).
6 Shibahara et al., EP 0 339 842 A2, published Nov. 2, 1989.
Appeal 2012-011279
Application 10/701,265

4
RNA and a 2’-OMe-nucleotide-containing oligonucleotide
because it was well known by those of skill in the art to study
enzymes with such artificial substrates.
(Ans. 8.)
Does the preponderance of the evidence of record support the
Examiner’s conclusion that the combination of references disclosed:
(I.) oligonucleotide duplexes comprising 17–25 linked nucleosides,
(II.) incorporation of at least one 2’-sugar modification on both strands, and
(III.) a gap comprising “at least 4 nucleosides, each comprising a 2’hydroxy-
pentofuranosyl sugar moiety”?

Findings of Fact
1. The Specification provides that a “blockmer is an
oligonucleotide having a block of at least two consecutive nucleotides of a
first type located immediately adjacent at least one nucleotide of a second
type and where said nucleotides of said first type are different from said
nucleotides of said second type.” (Spec. 9: ¶ 29.) “Chimeric oligomeric
compounds of the invention may be formed as composite structures of two
or more oligonucleotides, oligonucleotide analogs, oligonucleosides and/or
oligonucleotide mimetics as described herein. Such oligomeric compounds
have also been referred to in the art as hybrids, hemimers, gapmers or
inverted gapmers.” (Spec. 14: ¶ 50.) “In gapmers, a block or segment of
one type of nucleotides or nucleosides is interspaced between first and
second blocks of the second type.” (Spec. 15: ¶ 53.)
2. Table 1 of Wyatt, reproduced below, disclosed
oligoribonucleoside duplexes containing deoxynucleoside residues for
studying RNase V and RNase H.
App
App

Tabl
dupl
oligo
5’GC
deox
sequ
eal 2012-0
lication 10
e 1 shows
exes are 14
ribonucle
GCGGAU
ynucleotid
3. Th
ence comp
4. W
O
residues
cleavage
site-spec
problem
11279
/701,265
the meltin
nucleoba
otide duple
CCGGCC
e substitu
e Examin
lementary
yatt disclo
ligoribonu
used in co
of large R
ificity of c
s often enc
g tempera
ses in leng
x, 5’GGCC
3’, was co
tions.” (W
er finds th
to the AD
sed that
cleotides c
njunction
NA mole
leavage an
ountered w
5
tures of va
th. “The
GGAUC
mpared to
yatt 7837
at “[t]hese
CK2 gene
ontaining
with RNas
cules. The
d minimi
ith RNas
rious dupl
melting be
CGCGC3’
those of d
.)
duplexes
.” (Ans. 6
two to fou
e H will a
probes w
ze seconda
e H fragm
exes. The
havior of
·
uplexes w
[of Wyatt]
.)
r deoxy
llow direc
ill increase
ry structu
entation u
disclosed
the fully
ith
contain a
ted

re
sing

Appeal 2012-011279
Application 10/701,265

6
oligodeoxynucleotides. Probe sequences are limited by the
method of synthesis; some sequence flexibility can be gained
by incorporating deoxynucleotides outside the cleavage site
since a single hybrid base pair is not recognized by RNase H.
While chemically synthesized probes containing
deoxynucleotides and either ribonucleotides or 2’-O-
methylribonucleotides would allow more sequence variability
and will ultimately be the method of choice, the techniques for
enzymatic synthesis are more generally available.
Oligoribonucleotides containing one or more deoxy
residues may be useful in structural studies of splice sites or
ribonuclease cleavage sites since the substitutions, while
presumably altering structure very little, would be resistant to
2’OH mediated cleavage. Deoxy residues within
oligoribonucleotides can be used for NMR studies; the change
at the 2’ position would aid in assignment.
(Wyatt 7841 (emphasis added).)
5. Manche disclosed:
Synthesis and characterization of RNA duplexes. (A)
Schematic of short dsRNAs produced by transcription of pBSII
KS+ polylinker sequences. The several transcripts of 15 to 104
nt synthesized by T3 RNA polymerase . . . were annealed to the
complementary 358-nt transcript. . . . After RNase digestion,
the duplexes were purified by electrophoresis in nondenaturing
gels.
(Manche, 5239, Fig. 1; see also Ans. 6.)
6. Manche disclosed that the data
[S]uggest that DAI interacts with as little as 11 bp (one helical
turn) of dsRNA, but activation is associated with the formation
of a stable DAI-dsRNA complex. The formation of such a
complex requires at least 30 bp of duplex (about three turns)
and probably takes place when both of the enzyme’s RNA
binding motifs are engaged with the ligand.
(Manche, 5246.) Manche disclosed that RNA “[d]uplexes with sizes of 15
and 23 bp did not bind detectably” to DAI. (Manche, 5241.) “[H]igh
App
App

conc
reov
shor
inhib
oligo
form
repro
(Mon
oligo
eal 2012-0
lication 10
entration a
irus dsRNA
ter than 30
it activati
7. M
nucleotide
ing a gap
duced bel
Fig. 1. 2
design.
Ha-ras c
that cont
otherwis
Sequenc
deoxy nu
centered
ia 14516,
8. M
nucleotide
11279
/701,265
flush-end
.” (Man
to 40 bp b
on” of DA
onia discl
s containi
between u
ow, shows
’ -O-Met
Phosphoro
odon 12 s
ain betwe
e uniform
es contain
mber refe
“gap” wit
Fig. 1; se
onia discl
s that form
ed 23-bp d
che, 5241
ind weakl
I. (Manch
osed chim
ng betwee
niform 2’-
chimeric
hyl chime
thiate olig
equences (
en 1 and 9
ly modifie
ing 2’-O-m
rs to the nu
hin the oli
e also Ans
osed 17-m
a duplex
7
sRNA inh
(emphasis
y and cann
e, 5243 (e
eric phosp
n 1 and 9
O-methyl
oligonucle
ric, antise
onucleoti
GGC → G
centered d
d 2’-O-me
ethyl mod
mber of d
gonucleoti
. 6.)
er phospho
with a 25
ibited the
added).)
ot activat
mphasis a
horothioat
centered 2
molecules
otides:
nse oligon
des, target
TC), wer
eoxy resid
thyl oligon
ifications
eoxy resid
de.
rothioate
-mer fragm
activation
Thus, [d]u
e although
dded).)
e 2’ -O-me
’ -deoxy r
. Fig. 1 of
ucleotide
ed to muta
e synthesiz
ues in a[n
ucleotide
are boxed
ues formi
chimeric
ent of RN
of DAI by
plexes
they
thyl
esidues,
Monia,

nt
ed
]
.
;
ng a
A

Appeal 2012-011279
Application 10/701,265

8
corresponding to residues from Ha-ras mRNA. (Monia 14516, Fig. 2.) The
inclusion of 2’-O-methyl modifications increased duplex formation. “[T]he
full deoxy 17-mer formed the least stable duplex whereas the full 2’-O-
methyl 17-mer formed the most stable duplex. Furthermore as 2’-O-methyl
content was decreased, a concomitant reduction in binding affinity to the
structured target was observed.” (Monia 14517.)
9. Monia disclosed making 2’sugar modifications, and these
modifications include “2’-O-methyl, 2’ -O-propyl, 2’ -O-pentyl, and 2’ -
fluoro.” (Monia Abstract; see also 14521, Fig. 9 emphasis omitted.) A
benefit of these modifications includes “[i]ncreased cell penetration by
oligonucleotides containing lipophilic 2’ sugar modifications. . . . [Also]
methylphosphonate chimeras have been reported to increase antisense
specificity by reducing nonspecific RNase H cleavage of partially
complementary RNA-oligonucleotide duplexes in vitro.” (Monia 14522.)
10. Shibahara disclosed “2’-O-methylribooligonucleotide forms a
stable duplex with RNA having its complementary nucleotide sequence and
shows resistance various enzymes (nucleases) for decomposing DNA or
RNA. . . . In addition, 2’-O-methylribooligonucleotide can be prepared as in
oligoribonucleotide using less expensive raw materials than in
deoxyoligonucleotide.” (Shibahara p. 14, ll. 4–10; see also Ans. 7–8.)

Principle of Law
“In proceedings before the Patent and Trademark Office, the
Examiner bears the burden of establishing a prima facie case of obviousness
based upon the prior art.” In re Fritch, 972 F.2d 1260, 1265 (Fed. Cir.
1992).
Appeal 2012-011279
Application 10/701,265

9
Analysis
Appellants contend “the Wyatt article provides no teaching or
suggestion that would have prompted those skilled in the art to produce
oligonucleotide duplexes in which the first oligonucleotide is a gapmer
having 2’-modified wings and the second oligonucleotide comprises at least
one 2’-sugar modification.” (App. Br. 6.) Appellants contend that Manche
provides “experiments involved binding DAI to RNA duplexes of 15, 23,
34, 40, 55, 67, 85, or 104 nucleotides in vitro. The RNA duplexes were not
chemically modified.” (App. Br. 6). Additionally, Appellants contend that
the “Monia article contains no teaching or description that would have
prompted those of ordinary skill in the art to incorporate at least one
modified sugar into both strands of an oligomeric compound duplex.” (App.
Br. 7.)
Appellants err in attacking the references individually, as the rejection
is based on a combination of references. See In re Merck & Co., 800 F.2d
1091, 1097 (Fed. Cir. 1986). The Examiner explains that it is the
combination of references that renders the claims obvious. “As indicated in
the rejection, Wyatt is relied upon, among other references, to demonstrate
the state of the art at the time of the instant invention.” (Ans. 10.)
(I.) Oligonucleotide duplexes comprising 17–25 linked nucleosides
The Examiner looks to Wyatt for teaching a gapmer made of an
oligoribonucleotide sequence (RNA) that is interspaced with a
deoxynucleotide sequence (DNA) (FF 2). Wyatt “teach[es] duplexes of
complementary 14-mer oligoribonucleotides in which
2’-deoxyribonucleotides were site-specifically incorporated to allow study of
duplexes containing covalently linked deoxy and ribo-nucleotides.” (Final
Appeal 2012-011279
Application 10/701,265

10
Rej. 5.) Wyatt’s duplexes contain strands that are 100% complementary to
each other (FF 2). Wyatt also teaches that the deoxynucleotide gap can
consist of 2–4 deoxy residues and thereby would be resistant to 2’OH
mediated cleavage (FF 4). Thus, “Wyatt, like others at the time, made small
RNA duplexes and incorporated 2’-H modifications into both strands to
study RNase activity. Likewise, Manche, et al. and Monia, et al. also made
oligonucleotide duplexes for studying nucleic-acid-dependent enzymes.”
(Ans. 10; see also FF 5–7.) The Examiner finds that Monia “[t]he first
oligonucleotide is a 17-mer gapmer having phosphorothioate linkages, at
least 4 deoxyribonucleosides (DNA) in the gap, and each wing comprising
2’-OMe-modified nucleotides.” (Ans. 7; see also FF 7–9.) Manche made
RNA duplexes ranging in size from 15-104 nucleotides for studying DAI
interactions with ds-RNA complexes (Ans. 6; FF 5–6).
The Examiner’s concludes that arriving at duplex structures that fall
within the claimed size range would be obvious because the combination of
Wyatt, Monia, and Manche. Wyatt “made small RNA duplexes and
incorporated 2’-H modifications into both strands to study RNase activity.
Likewise, Manche, et al. and Monia, et al. also made oligonucleotide
duplexes for studying nucleic-acid-dependent enzymes.” (Ans. 10.)
“[W]here the general conditions of a claim are disclosed in the prior art, it is
not inventive to discover the optimum or workable ranges by routine
experimentation.” In re Aller, 220 F.2d 454, 456 (CCPA 1955).
We agree with the Examiner that the combination of references
disclosed oligonucleotides duplexes comprising 17–25 linked nucleosides
that are useful for studying enzyme activities.
Appeal 2012-011279
Application 10/701,265

11
(II.) Incorporation of at least one 2’-sugar modification on both strands
of an oligonucleotide duplex
Appellants contend that the combination of references does not
provide a reason to introduce sugar-modified nucleosides into both strands
of an oligonucleotide complex. (App. Br. 6.) “Shibahara application does
not describe or suggest any reason to introduce chemical modifications into
oligonucleotide duplexes.” (Reply Br. 2.)
We have considered, but are not persuaded, Appellants contentions
that the Examiner has erred with respect to incorporating sugar
modifications onto both strands of a duplex molecule.
The Examiner looks to Shibahara that teaches “that 2’-O-
methylribooligonucleotides are resistant to various nucleases, including
RNase H and DNases, and they form duplexes with complementary RNAs
that are more stable than DNA-RNA duplexes. . . . [These] 2’-O-methylribo
oligonucleotides are less expensive to prepare than are
deoxyoligonucleotides.” (Ans. 7–8.) The Examiner concludes that
It would have been obvious to one of ordinary skill in the art at
the time the invention was made to make synthetic ribonuclease
substrates wherein the substrate is an artificial duplex of a target
RNA and a 2’-OMe-nucleotide-containing oligonucleotide
because it was well known by those of skill in the art to study
enzymes with such artificial substrates.
(Ans. 8.)
We agree with the Examiner, that the combination of references
would have prompted the ordinary artisan to make 2’sugar modifications on
one or both strands of a double stranded complex in order prevent
oligonucleotide decomposition (see FF 9–10). Although we recognize that
Wyatt did not exemplify duplexes containing sugar modifications,
Appeal 2012-011279
Application 10/701,265

12
nevertheless, we find that Wyatt suggests “chemically synthesized probes
containing deoxynucleotides and either ribonucleotides or 2’-O-
methylribonucleotides would allow more sequence variability and will
ultimately be the method of choice.” (FF 4.) Thus, Wyatt provides
motivation to incorporate modified 2’-O-methylribonucleotides into a
duplex molecule because it generally desirable to provide for sequence
variability in these enzyme studies. (FF 2.) It is also recognized that 2’-
sugar modifications also have the added recognized benefit of increasing cell
penetration by the composition (FF 9–10).
We find no error with the Examiner’s position that the incorporation
of modified sugars into both stands of an oligonucleotide complex would
generically afford protection to nucleases. The Examiner finds that “[t]hose
of skill in the art are well apprised of the pervasiveness of RNase enzymes in
cellular extracts and, therefore, would know that the target RNA would
require protection from undesired nuclease activity, including exonuclease
activity, and that such protection could be afforded by incorporating
modifications in the target RNA as instantly claimed, at the end(s) of the
target RNA.” (Ans. 12–13.) Although, the Examiner does not rely on Wyatt
for teaching 2’ -sugar modifications, we note that Wyatt disclosed that the
incorporation of 2’-O-methylribonucleotides would be desirable as it would
allow for sequence variability (FF 4). There is nothing in Wyatt that would
suggest that the contemplated inclusion of 2’ modified sugars is limited to
only one strand of the oligonucleotide duplex (FF 4). We agree with the
Examiner’s conclusion that the totality of the references teach that the
incorporation of 2’sugar modifications would afford protection against
Appeal 2012-011279
Application 10/701,265

13
nucleases (FF 4, 10), thus, the inclusion of such modification into both
strands of a complex is obvious.
Because it was known that the inclusion of sugar modifications in the
oligonucleotide sequence improves the stability of a single strand, it would
be obvious to incorporate this same modification onto the opposite stand and
expect that this modification would have the same effect. (FF 7–10.) We
find no evidence in the record that incorporating the modified sugar into the
opposite strand of a duplex molecule is beyond the skill of the ordinary
artisan. See KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 417 (2007).
Accordingly, we agree with the Examiner’s position that incorporating 2’-
sugar modification into both strands of an oligonucleotide duplex is obvious.
(III.) A gap comprising “at least 4 nucleosides, each comprising a
2’-hydroxy-pentofuranosyl sugar moiety”
The Examiner recognizes that the Wyatt, Monia, and Manche do not
teach “duplexes wherein both strands of the duplex are RNA gapmers.”
(Ans. 7.) The Examiner finds “[o]ne of skill could substitute RNA for DNA
in the gapmer of Monia, et al.” (Ans. 8.) “One of skill would also recognize
that maintaining an unmodified RNA gap in the target strand would best
simulate the in vivo condition of the target.” (Ans. 8–9.)
Appellants contend that the Examiner has not provided sufficient
factual support for substituting DNA for RNA in the gapmers as disclosed in
Monia and Wyatt. (App. Br. 11.)
In response, the Examiner points to Shibahara as teaching “that the
antisense 2’-OCH3-modified RNAs appear to function better than DNA-
based antisense 2’-OCH3-modified oligonucleotides, such that one of
ordinary skill would be motivated to substitute RNA for DNA in the Monia
Appeal 2012-011279
Application 10/701,265

14
gapmer,” and concludes that “Shibahara provides a motivation to the skilled
artisan to use RNA in place of DNA.” (Ans. 14.)
According to the Specification, a gapmer is a construct that has a
sequence of one type of nucleotide flanked with sequences of another type
of nucleotide (FF1). Although the Specification is flexible with respect to
interspacing an oligonucleotide sequence with either DNA or RNA the
claims require that the “gap comprises at least 4 nucleosides, each
comprising a 2’-hydroxy-pentofuranosyl sugar moiety,” in other words the
gap as claimed encompasses ribose sugar moieties.
Based on the evidence presented, we find that Appellants have the
better position. We agree with Appellants that the Examiner has not
provided sufficient factual support to arrive at a conclusion that it would
have been obvious to swap the DNA in the gaps of Wyatt or Monia for
RNA. Shibahara suggests swapping a modified 2’-OCH3- oligonucleotides
for RNA (FF 10). The claims, however, are directed at compositions
comprising a gapmer, i.e., a structure having a gap that is flanked by another
type of sequence. Substituting modified 2’-OCH3- oligonucleotides into the
gap of Monia’s structures, as suggested by the Examiner, would not result in
compounds having “one type of nucleotides or nucleosides is interspaced
between first and second blocks of the second type.” (FF 1.) The Examiner
has not explained why it would be desirable to not only change the structures
in the gap but also change the surrounding structures in order to maintain a
gapmer construct.
Furthermore, we note that Wyatt explains that the inclusion of “one or
more deoxy residues [in the gap] may be useful in structural studies of splice
sites or ribonuclease cleavage sites since the substitutions, while presumably
Appeal 2012-011279
Application 10/701,265

15
altering structure very little, would be resistant to 2’OH mediated cleavage.”
(FF 4.) Even, if we agree with the Examiner’s position that maintaining
unmodified RNA target would be desirable, substituting the RNA for DNA
in Wyatt’s duplexes also would not result in structures that are gapmers, as
required by the claims. Additionally, Wyatt directs against the use of RNA
in the gap as they are more susceptible to 2’OH mediated cleavage. We find
that the Examiner has not provided a sufficient articulated rationale to
modify the structures to arrive at compositions comprising an RNA gap
interspaced between first and second blocks of the second type oligomer.
We conclude that the rejection of Appellants’ claims 120, 121, 124,
127, and 136–138 is not supported by sufficient evidence to make out a
prima facie case of obviousness. We therefore reverse the rejection.

SUMMARY
We reverse the rejection of claims 120, 121, 124, 127, and 136–138
under 35 U.S.C. § 103(a) as unpatentable over Wyatt, Manche, Monia, and
Shibahara.

REVERSED

cdc