UC Et Al. REPLY 3

Filed on behalf of Senior Party
THE REGENTS OF THE UNIVERSITY OF CALIFORNIA,

UNIVERSITY OF VIENNA, AND EMMANUELLE CHARPENTIER
By:
Todd R. Walters, Esq.

Erin M. Dunston, Esq.
Travis W. Bliss, Ph.D., Esq.
Christopher L. North, Ph.D., Esq.
BUCHANAN INGERSOLL & ROONEY PC
1737 King Street, Suite 500
Alexandria, Virginia 22314-2727
Telephone (703) 836-6620
Facsimile (703) 836-2021
todd.walters@bipc.com
erin.dunston@bipc.com
travis.bliss@bipc.com
christopher.north@bipc.com
By: Li-Hsien Rin-Laures, M.D., Esq.

Sandip H. Patel, Esq.
Greta Noland
MARSHALL GERSTEIN & BORUN LLP
6300 Willis Tower
233 South Wacker Drive
Chicago, Illinois 60606
Telephone (312) 474-6300
Facsimile (312) 474-0448
lrinlaures@marshallip.com
spatel@marshallip.com
gnoland@marshallip.com
UNITED STATES PATENT AND TRADEMARK OFFICE

____________________
BEFORE THE PATENT TRIAL AND APPEAL BOARD
____________________
THE BROAD INSTITUTE, INC., MASSACHUSETTS INSTITUTE OF
TECHNOLOGY, and PRESIDENT AND FELLOWS OF HARVARD COLLEGE
Patents 8,697,359; 8,771,945; 8,795,965; 8,865,406; 8,871,445; 8,889,356;
8,895,308; 8,906,616; 8,932,814; 8,945,839; 8,993,233; 8,999,641; and Application 14/704,551,
Junior Party,
v.
THE REGENTS OF THE UNIVERSITY OF CALIFORNIA, UNIVERSITY
OF VIENNA, AND EMMANUELLE CHARPENTIER,
Application 13/842,859,
Senior Party.
____________________
Patent Interference 106,048 (DK)
____________________
UC et al. REPLY 3
(To Substitute Count 1 with Proposed Count 2)
Interference No. 106,048

TABLE OF CONTENTS
Page
I.
INTRODUCTION ...............................................................................................................1
II.
THE EVIDENCE .................................................................................................................1
III.
STATEMENT OF MATERIAL FACTS.............................................................................1
IV.
ARGUMENT .......................................................................................................................1
A.
B.
V.
Count 1 is Improper .................................................................................................2

1.
Using the Type II CRISPR-Cas System in Eukaryotic Cells Is Not a

Separately Patentable Invention .................................................................. 2
2.
Count 1 is Defective Because it Explicitly Encompasses Inoperative

Methods....................................................................................................... 7
Proposed Count 2 is Proper Because it is Directed to Separately-Patentable

Commonly-Claimed Subject Matter and is Fair to Both Parties .............................7
1.
Methods of Using a Single-Molecule DNA-Targeting RNA are

Commonly Claimed and Properly Define the Interfering Subject Matter .. 7
2.
The Single-Molecule DNA-Targeting RNA of Proposed Count 2 is

Patentable Over the Prior Art, at Least to Senior Party .............................. 9
C.
Broad Will Not Be Prejudiced by Proposed Count 2 ............................................12
D.
Each of UCs Provisional Applications Described and Enabled an

Embodiment of Proposed Count 2 .........................................................................15
E.
All of Broads Claims Should Be Designated to Correspond to Proposed

Count 2 ...................................................................................................................15
CONCLUSION ..................................................................................................................16
APPENDIX 1 - LIST OF EXHIBITS

APPENDIX 2 STATEMENT OF FACTS
-i-

TABLE OF AUTHORITIES
Cases
Page(s)
Advanced Fiber Techs. (AFT) Trust v. J & L Fiber Servs., Inc.,

674 F.3d 1365 (Fed. Cir. 2012)............................................................................................9
Antos v. Juguin,
220 U.S.P.Q. 722 (B.P.A.I. 1981)........................................................................................2
Bard Peripheral Vascular, Inc. v. W.L. Gore & Assocs.,
776 F.3d 837 (Fed. Cir. 2015)................................................................................12, 13, 14
Concrete Appliances Co. v. Gomery,
269 U.S. 177 (1925) .............................................................................................................4
In re Droge,
695 F.3d 1334 (Fed. Cir. 2012)............................................................................................5
Ecolochem, Inc. v. S. Calif. Edison Co.,
227 F.3d 1361 (Fed. Cir. 2000)............................................................................................4
GPNE Corp. v. Apple Inc.,
119 U.S.P.Q.2d 1646 (Fed. Cir. 2016).................................................................................8
Howmedica Osteonics Corp. v. Zimmer, Inc.,
822 F.3d 1312 (Fed. Cir. 2016)............................................................................................8
Lee v. McIntyre,
55 U.S.P.Q.2d 1406 (B.P.A.I. 2000)....................................................................................2
In re Longi,
759 F.2d 887 (Fed. Cir. 1985)..............................................................................................5
Par Pharm., Inc. v. TWi Pharm., Inc.,
773 F.3d 1186 (Fed. Cir. 2014)........................................................................................5, 6
Univ. of S. Calif. v. DePuy Spine Inc.,
473 Fed.Appx. 893 (Fed. Cir. 2012). .............................................................................2, 15
- ii -

1
I.
INTRODUCTION
In UC Motion 3, Senior Party (UC) demonstrated that Count 1 should be substituted
with Proposed Count 2 for at least the following reasons. Count 1 is improperly limited to
eukaryotic cells. None of UCs involved claims are limited to eukaryotic cells and this limitation
excludes UCs best proofs. Only Broads claims recite this limitation. If there is an interference-
in-fact, then the method in eukaryotic cells cannot be separately patentable. UC has shown that
using the method in eukaryotic cells is not separately patentable. Thus, there is no basis for so
limiting the Count. Proposed Count 2 corrects Count 1 by removing the eukaryotic cell
limitation and directing the proceeding to subject matter that is both commonly claimed and
10
patentable to UC, wherein the DNA-targeting RNA is a single molecule. Unlike Count 1, the
11
claims of both parties are directed to the methods recited in Proposed Count 2. Broad is not
12
prejudiced by Proposed Count 2. Broad has not proffered any proofs that would be excluded by
13
Proposed Count 2 and that could possibly demonstrate either conception or reduction to practice
14
of Count 1 prior to UCs filing date. Accordingly, Proposed Count 2 appropriately recites the
15
commonly claimed subject matter and is fair to both parties.
16
II.
17
18
THE EVIDENCE
A list of exhibits upon which this Reply relies is set forth in Appendix 1.
III.
19
STATEMENT OF MATERIAL FACTS

Material Facts 1-78 in support of UC Motion 3, additional Material Facts 79-164 alleged
20
in Broad Opposition 3 (BO3), and the corresponding responses, are presented in Appendix 2.
21
IV.
22
23
ARGUMENT
Count 1 should be substituted with Proposed Count 2 for the reasons set forth in UC
Motion 3. BO3 fails to rebut any of the reasons for substituting Count 1.
-1-

1
A.
Count 1 is narrower than UCs involved claims because it limits the recited method to
Count 1 is Improper
being performed in eukaryotic cells. MF 1. None of UCs claims is limited to eukaryotic cells.
MF 2. Limiting Count 1 to eukaryotic cells improperly excludes UCs best proofs. MFs 3-11;
see Ex. 1507; Ex. 1024, 157-167; Ex. 1022, 165-175; Univ. of S. Calif. v. DePuy Spine
Inc., 473 Fed.Appx. 893, 895 (Fed. Cir. 2012). Count 1 is also improper because it encompasses
a separately patentable invention claimed by both parties, and is technically defective. MFs 1-
46, 63-70. Proposed Count 2 fairly addresses these problems.
9
10
1. Using the Type II CRISPR-Cas System in Eukaryotic Cells Is Not a

Separately Patentable Invention
11
The eukaryotic cell limitation of Count 1 would have been obvious from the Count
12
without that limitation. MFs 12-29. Because the method in eukaryotic cells is not separately
13
patentable, the Count should not be so limited. See, e.g., Lee v. McIntyre, 55 U.S.P.Q.2d 1406,
14
1411-12 (B.P.A.I. 2000); Antos v. Juguin, 220 U.S.P.Q. 722, 726 (B.P.A.I. 1981). At page 9,
15
lines 18-24 and page 10, line, 15 to page 11, line 3, of BO3, it is argued that using the method of
16
Count 1 in eukaryotic cells would not have been obvious from in vitro use because a person of
17
ordinary skill in the art would not have had a reasonable expectation of success. The response is
18
that overwhelming objective evidence demonstrates that use of the system in eukaryotic cells
19
was obvious from a disclosure of using the system in vitro. MFs 13-29; see Ex. 1024, 22,
20
118-156; Ex. 1022, 28, 124-164; Ex. 1535, 6-10; 18-109; 1534, 6-10, 18-109. The
21
motivation of a person of ordinary skill in the art to use the Type-II CRISPR-Cas system in
22
eukaryotic cells is not in dispute. See Ex. 1555, 100:17-102:6, 176:18-177:14; Ex. 1024,
23
122-125; Ex. 1022, 128-132; Ex. 1535, 33-38; Ex.1534, 33-38. Objective evidence of
24
a reasonable expectation of successfully doing so is found in both the art and contemporaneous
-2-

1
comments of those in the art. MFs 12-29; see Ex. 1024, 122-126; 135-139; Ex. 1022,
128-147; Ex. 1535, 52-61; Ex. 1534, 52-61. The prior art included a decades-long history
of successfully using prokaryotic DNA-targeting proteins, like Cas9, in eukaryotic cells. MFs
17-28; see Ex. 1024, 126; 135-139; Ex. 1022, 133, 143-147; Ex. 1535, 52-61; Ex.
1534, 52-61. As confirmed by Broads witnesses and described in its involved patents, all of
the techniques that one might use to employ a Type II CRISPR-Cas system in eukaryotic cells
(once the necessary and sufficient components of the system were defined by UC), including
expression vectors, codon-optimization, and nuclear localization signals, were well known and
routinely used in the art. MFs 19-25; see Ex. 1555, 131:22-132:10, 134:5-8; 134:14-20, 139:12-
10
140:15, 143:10-22, 147:10-152:10, 152:19-153:21; Ex. 2101, [0044], [0074]; Ex. 1024,
11
128-142; Ex. 1022, 135-150; Ex. 1535, 39-51; Ex. 1534, 39-51; Ex. 1638, 179:21-
12
180:2.
13
All of this explains why several independent research groups confirmed that the Type-II
14
CRISPR-Cas system worked in eukaryotic cells before, or at about the same time as, Broad. See
15
Ex. 1024, 143-154; Ex. 1022, 151-162; Ex. 1535, 62-74; Ex. 1534, 62-74; Ex.
16
1603, Ex. 1545; Ex. 1056; Ex. 1057; Ex. 1058; Ex. 1554; Ex. 1059. Shortly after UCs June
17
28, 2012, public disclosure of the complete and functional system (Ex. 1155) as recited in Count
18
1 and Proposed Count 2, Kim filed a patent application (Ex. 1545) on October 23, 2012,
19
reporting successful use of the system in eukaryotic cells, prior to Broads earliest possible filing
20
date of December 12, 2012. Manuscripts reporting success in eukaryotic cells were submitted to
21
peer-reviewed journals by Mali (Ex. 1056), Cho (Ex. 1059), Jinek (Ex. 1057), and Hwang (Exs.
22
1058, 1554), on October 25, November 20, December 15, and December 18, 2012,
23
respectivelyall before, or contemporaneous with, Broads earliest filing date. These groups,
-3-

1
including Broads inventors, credited UCs disclosure of an in vitro Type-II CRISPR-Cas system
as inspiration for their work. See Exs. 1558-1560, and 1620. It has long been recognized that
independent achievement of the same subject matter within a comparatively short space of time
is persuasive evidence that the achievement was merely the product of ordinary skill. See, e.g.,
Concrete Appliances Co. v. Gomery, 269 U.S. 177, 184 (1925); Ecolochem, Inc. v. S. Calif.
Edison Co., 227 F.3d 1361, 1379 (Fed. Cir. 2000. Broad has failed to provide evidence that
these different groups were not independent.
8
9
At page 13, line 20, to page 14, line 2 of BO3, it is argued that although predicted uses of
the system in eukaryotic cells by commentators in the art were suggestive of using Jinek 2012s
10
single-molecule DNA-targeting RNA (Chimera A), some researchers experienced failures or
11
poor results, and other researchers used unconventional techniques or modified versions. The
12
response is that at least seven different research groups reported success in eukaryotic cells
13
within a year after Jinek 2012 defined the necessary and sufficient components of the Type II
14
CRISPR-Cas system. See Ex. 1024, 143-154; Ex. 1022, 151-162; Ex. 1535, 62-74;
15
Ex. 1534, 62-74. A further response is that, as acknowledged by Broads witness, Dr.
16
Simons: (1) all of the cited references disclose successfully using a single-molecule DNA-
17
targeting RNA based on Jinek 2012s Chimera A in eukaryotic cells; and (2) the Cho paper (Ex.
18
1059) in fact reported using conventional techniques according to the manufacturers protocol.
19
For example, Dr. Simons, acknowledged that Cong (Ex. 1055), Cho (Ex. 1059), and Shen (Ex.
20
1060) reported using a single-molecule DNA-targeting RNA substantially identical to Jinek
21
2012s Chimera A, apart from targeting different DNA sequences, to successfully cleave DNA in
22
a eukaryotic cell. Ex. 1639, at 124:24125:8, 129:2-9, 138:8141:3. Dr. Simons initially
23
criticized the results of Cho (Ex. 1059) as allegedly employing unconventional techniques.
-4-

1
See Ex. 2009, 11.132-133. However, Dr. Simons acknowledged during cross-examination that
Cho reported using conventional techniques according to the manufacturers protocol and that
Dr. Simons had no evidence to the contrary. Ex. 1639, at 131:218, 134:4-13, 134:23-135:23.
Furthermore, Cho used substantially the same delivery method that they had previously used for
zinc finger nucleases (ZFNs) in eukaryotic cells. Ex. 1639, at 141:20-142:5. Dr. Simons also
acknowledged that Chen (Ex. 2125) showed clear success in using a two-molecule DNA-
targeting RNA in a Type II CRISPR-Cas system in eukaryotic cells, which was also disclosed in
Jinek 2012. Ex. 2009, 11.125 (Lane A shows that the conditions of treatment A generate
positive results.). In fact, all of Chens chimeric single-molecule DNA-targeting RNA were
10
11
shown to produce positive results. Ex. 2007, at 183:1-11.

At page 11, lines 4-9 of BO3, it is argued that the statement [i]t was immediately
12
obvious that [the Type II CRISPR-Cas] system might be repurposed for genome engineering,
13
similar to ZFNs and TALENs was made in October 2013 and is not relevant to obviousness.
14
The response is that the statement was made by a person in the field, who is not affiliated with
15
either party and objectively described what was immediately obvious when UC disclosed the
16
Type II CRISPR-Cas system in Jinek 2012. See Exs. 1473, at 304; 1024, 124; 1022, 130;
17
1535, 36; 1534, 36. The statement is entirely consistent with other objective comments that
18
were made by those in the art when UC first disclosed the system. MF 14; Ex. 1471.
19
At page 12, line 11, to page 13, line 6, of BO3, it is argued that Dr. Carroll wrote that
20
there is no guarantee that Cas9 will work effectively in eukaryotes. The response is twofold.
21
First, [o]bviousness does not require absolute predictability of success. In re Droge, 695 F.3d
22
1334, 1338-39 (Fed. Cir. 2012); see also In re Longi, 759 F.2d 887, 897 (Fed. Cir. 1985) (only a
23
reasonable expectation of success is required); Par Pharm., Inc. v. TWi Pharm., Inc., 773 F.3d
-5-

1
1186, 1198 (Fed. Cir. 2014). Second, Dr. Carroll expressed his expectation at that time that
those in the field would try, and be successful when he concluded his article with it is clearly
well worth a try. Stay tuned. Ex. 1024, 123; see also Ex.1535, 34; Ex. 1534, 34. Dr.
Carroll testified on cross-examination that, at that time, he saw no reason to think that a Type II
CRISPR-Cas system would not function in eukaryotic cells:
6
7
8
9
10
Based on the precedents, I think people would have expected that Cas9 would operate
effectively in eukaryotic cells. . . . I dont think there was any reason to think ahead of
time that there were unique properties of Cas9 that would have caused it to fail.
Ex. 2012, at 46:6-14.
At page 11, line 10, to page 12, line 6, and page 14, lines 3-16, of BO3, it is argued that
11
statements in patent applications filed before UCs invention disclosing the use of other CRISPR
12
systems in eukaryotic cells were mere expressions of hope that did not produce successful results
13
(citing Ex. 1435, at 101; Ex. 1161, at 8). The response is that the statements in these patent
14
applications confirm that there was motivation to use other CRISPR systems, and that the
15
applicants expected that techniques well known in art would permit those CRISPR systems to be
16
used, in eukaryotic cells. See Ex. 1161, at [0009], [0042], [0054], [0058], [0060]; Ex. 1555,
17
at p. 119, ll. 11-14; Ex. 1024, 125; Ex. 1022, 132; Ex. 1535, 22; Ex. 1534, 22. Broad
18
has not provided any evidence that the applicants of Ex. 1435 and Ex. 1161 failed in using those
19
other CRISPR systems in eukaryotic cells. Its unsupported argument therefore lacks merit.
20
At page 14, lines 9-16 of BO3, it is argued that Group II introns (or targetrons) are
21
analogous to Cas9 and have not been readily adapted for use and function in eukaryotic cells.
22
The response is twofold. First, persons of ordinary skill in the art in 2012 would not have looked
23
to Group II introns to predict the success of using Cas9 because Group II introns, which
24
comprise catalytic RNA, are not analogous to Cas9, which is a catalytic protein (Ex. 1535, at
25
89-92; Ex. 1534, at 89-92). Second, even if they did consider Group II introns, they would
-6-

1
have found many successful uses in eukaryotic cells by 2012, as confirmed by Broads own
evidence and testimony. Ex. 1024, 394; Ex. 1022, 403; Ex. 1556, at 219:21222:18; Ex.
1535, at 83-84; Ex. 1534, at 83-84; Ex. 1582; Ex. 1583.
4
5
6
2. Count 1 is Defective Because it Explicitly Encompasses Inoperative

Methods
At page 9, lines 6-15 of BO3, it is argued that Count 1 is not deficient in reciting the
language targeter RNA or guide sequence in element (a)(i) because Count 1 does not require
that the guide sequence hybridize with the activator. The response is that Broads argument
admits that Count 1 recites a non-operative alternative. MF 43; see Ex. 1022, 80-86; Ex.
10
1024, 73-79. The recitation of or guide sequence in element (a)(i) of Count 1 explicitly
11
encompasses systems that cannot perform all of the required elements of the method. Id. If
12
element (a)(i) comprises only the guide sequence and not the tracr mate, there will be no
13
sequence to hybridize with the tracrRNA, which is required for target cleavage by the system.
14
Id. The phrase or guide sequence should be removed to provide a Count that does not
15
encompass inoperable embodiments lacking utility.
16
17
B.
18
Proposed Count 2 does not limit the method to being performed in eukaryotic cells and
19
requires the DNA-targeting RNA to be a single molecule. Proposed Count 2 is proper because
20
both parties claims are directed to the single-molecule DNA-targeting RNA subject matter,
21
which UC Motion 3 shows is separately patentable, in contrast to the eukaryotic limitation of
22
Broads claims, which is not separately patentable and is only recited in Broads claims.
23
24
25
Proposed Count 2 is Proper Because it is Directed to Separately-Patentable

Commonly-Claimed Subject Matter and is Fair to Both Parties
1.
Methods of Using a Single-Molecule DNA-Targeting RNA are Commonly

Claimed and Properly Define the Interfering Subject Matter
Every involved claim of both parties is directed to the use of a single-molecule DNA-
-7-

1
targeting RNA. MFs 63, 77. At page 14, lines 18-23 of BO3, it is argued that only 55 of
Broads involved claims require a single-molecule DNA-targeting RNA. At page 15, line 5, it is
argued that the term guide RNA in Broads claims includes both two-molecule and single-
molecule DNA-targeting RNA. The response is twofold. First, Broad acknowledges that at least
55 of its involved claims and all of UCs claims require a single-molecule DNA-targeting RNA.
However, second, all of Broads claims, each of which recites a guide RNA, should be
construed as directed to this species. MFs 63-70; see Ex. 1024, 86-88; Ex. 1022, 92-94.
The intrinsic evidence of Broads specifications clearly shows that the term guide RNA
is interchangeable with single guide RNA in Broads patents. Id., see, also e.g., Ex. 1007 at
10
col. 12, ll. 6-10. Broad argues that claim differentiation requires a construction contrary to the
11
definition in its specifications. However, claim differentiation is a guide, not a rigid rule when
12
the specification or prosecution history dictates a contrary construction. Howmedica Osteonics
13
Corp. v. Zimmer, Inc., 822 F.3d 1312, 1323 (Fed. Cir. 2016); GPNE Corp. v. Apple Inc., 119
14
U.S.P.Q.2d 1646, 1651 (Fed. Cir. 2016). Broads citations to its specification do not support its
15
arguments. Broad cites the 359 Patent at col. 21, lines 41-45, but has not pointed to any
16
description that refers to a guide RNA wherein the tracr sequence and tracr mate sequence are
17
not contained within a single transcript. Ex. 1007, col. 21, ll. 41-45. Broad cites Example 1 of
18
the 359 Patent, but that section does not describe a two-molecule DNA-targeting RNA as a
19
guide RNA, instead referring to a crRNA:tracrRNA duplex. See, e.g. Ex. 1007, col. 44, ll. 3-
20
11. Broad also points to the 308 Patent at col 38, lines 33-43, but there, a chimeric guide RNA
21
is clearly distinguished from a duplex of separate tracrRNA and crRNA molecules. Ex. 1015,
22
col 38, ll. 33-34. Thus, when Broads patents refer to a two-molecule DNA targeting RNA, they
23
do not use the term guide RNA, but rather, explicitly use a different description.
-8-

1
At page 17, line 8, to page 19, line 2, of BO3, it is argued that extrinsic usage of guide
RNA was not synonymous with single guide RNA. The response is that extrinsic evidence
should be given no weight where, as here, the meaning of a claim term is clearly shown by
intrinsic evidence. See, e.g., Advanced Fiber Techs. (AFT) Trust v. J & L Fiber Servs., Inc., 674
F.3d 1365, 1375 (Fed. Cir. 2012).
6
7
2.
The Single-Molecule DNA-Targeting RNA of Proposed Count 2 is

Patentable Over the Prior Art, at Least to Senior Party
At page 13, lines 7-19, of BO3, it is argued that prior to May of 2012, it was known that
tracrRNA, crRNA, and Cas9 were necessary for the maturation and cleavage steps of CRISPR-
10
Cas9-mediated bacterial immunity. At page 20, line 2, to page 22, line 16, it is argued that the
11
skilled person would have thought it highly likely that a Cas9:crRNA:tracrRNA complex was
12
involved in cleavage because it was unlikely that the tracrRNA:crRNA duplex of the crRNA
13
maturation process disclosed in Deltcheva (Ex. 1032) would dissociate.
14
The response is that Broads hindsight-based revision of history mischaracterizes the
15
state of the art, which is clearly shown in contemporaneous documents. As admitted by Broads
16
witness, Deltcheva only taught that tracrRNA, crRNA, Cas9, and RNase III were required for
17
maturation of the crRNA, and that without maturation of the crRNA, cleavage could not occur in
18
the natural system. Ex. 1032, at Fig. 4 and Ex. 1638, at 62:2366:9. Deltcheva stated, and Dr.
19
Breaker conceded, that the components of the subsequent DNA cleavage step were unknown.
20
Ex. 1638, at 65:15-66:9. Dr. Breaker stated on cross-examination that UCs Jinek 2012
21
publication was the first public disclosure of the necessary and sufficient components (crRNA,
22
tracrRNA, and Cas9) for CRISPR-Cas9-mediated DNA cleavage. Ex. 1638, at 89:6-18. Thus,
23
after Deltcheva, the necessary and sufficient components of the Type II CRISPR-Cas system
24
DNA cleavage complex remained unknown until UCs First Provisional. This is objectively
-9-

1
shown in the subsequent review article by Makarova, in which a world-wide panel of experts in
the field compiled what was understood about CRISPR systems
at the time. Ex. 1156. In the figure excerpted at right,
Makarova showed tracr RNA present only in the first crRNA
maturation step (top of excerpt), not in a second maturation step
(second line of excerpt), and not in the cleavage of target DNA
(bottom of excerpt). Id., at Fig. 1. The enzyme(s) involved in
the second maturation step and the DNA cleavage step were
only hypothetically identified as Cas9, because the identity of
10
the enzyme(s) had not been demonstrated. Id., at Fig. 1, legend.
11
Likewise, Wiedenheft (Ex. 1159), recognized Cas9s role in the DNA cleavage complex as
12
merely hypothetical while explicitly proposing Type II CRISPR-Cas DNA cleavage complexes
13
that lacked tracrRNA. See Ex. 1159 at Fig. 2; Ex. 1638, at 80:2481:8 and 83:7-18. Thus,
14
historical evidence objectively demonstrates that it was not obvious to persons of ordinary skill
15
in the art from Deltcheva that, inter alia, tracrRNA would be a component of the Type II
16
CRISPR-Cas DNA cleavage complex. Furthermore, as acknowledged by Dr. Breaker, Broads
17
arguments relying upon thermodynamics of double-stranded RNAs did not consider the
18
interaction of RNA molecules with proteins, and, therefore, are not applicable to the
19
crRNA:tracrRNA duplex bound to proteins during the maturation process shown by Deltcheva.
20
Ex. 1638, at 98:21-99:3 and 100:23101:13. Broads analysis also did not take into
21
consideration the presence of other proteins, such as helicases, that, as their witness
22
acknowledged, were known to separate RNA duplexes in cells. Ex. 1638, at 101:14102:15.
23
Broad also failed to address the known example of RNAi, which, as admitted by Dr. Breaker,
- 10 -

1
had been analogized to CRISPR-Cas9 by Deltcheva and in which RNA duplexes similar in size
to the crRNA:tracrRNA duplex are specifically separated by helicases prior to acting on a target
nucleotide. Ex. 1638, at 59:8-21; 71:1-12 and 102:16-103:8.
At page 22, line 17, to page 24, line 12 of BO3, it is argued that it would have been
obvious to covalently link crRNA and tracrRNA and test whether Cas9 and covalently linked
crRNA-tracrRNA single-molecule DNA-targeting RNA would successfully cleave a DNA
target. At page 10, lines 6-12 of BO3, it is argued that concerns about whether a covalent
linkage between crRNA and tracrRNA would prevent the required binding to Cas9 could be
simply tested. The response is that prior to May 25, 2012, a person of ordinary skill in the art
10
would not have been motivated to combine, or have a reasonable expectation of success in
11
combining, crRNA and tracr RNA using a covalent linkage, a configuration that provided
12
unexpected results. MFs 32-41; see also Ex. 1024, 102-116; Ex. 1022, 111-121. It was
13
known that RNA binding proteins are highly sensitive to the structure of DNA. Id. As admitted
14
by Dr. Breaker, you cannot look at the sequence of an RNA or DNA and predict its fine
15
structure . . . . And even if you had that three dimensional structure, its hard to predict what the
16
function of that architecture might be. Ex. 1638, 14:20-115:2. Furthermore, Dr. Breaker
17
highlighted the unpredictability of altering the structure of RNA molecules, stating:
18
19
20
21
22
[Y]ou have functional groups in three dimensional space and that is to form a
catalytically active site or a binding site for a ligand. The movement of even -the movement at even a sub-angstrom level, if you displace one of those atoms by
an angstrom or sub-angstrom amount, it could greatly adversely affect the
function of the molecule.
23
Id. at 15:9-16. Thus, as acknowledged by Broads own witness, use of a single-molecule DNA-
24
targeting RNA in a Type II CRISPR-Cas system, even in view of Count 1, would have been
25
highly unpredictable. Further, Dr. Breaker admitted that Broads arguments regarding the use of
26
linkers in crystallography studies are irrelevant and inapplicable to the single-molecule DNA- 11 -

1
targeting RNA method of Proposed Count 2 because a crystallized form of the RNAs would not
be used in a method for cleaving DNA. Ex. 1638, at 103:20-104:17. During cross-examination,
he also admitted that none of Broads arguments regarding the study of RNA structure involved
using linkers to combine two separate RNA molecules into a single molecule, let alone maintain
the function of two separate RNA molecules that duplex in order to bind to a catalytic protein.
Ex. 1638, at 90:16-91:18.
Thus, Broads arguments carry no weight. The evidence of record clearly demonstrates
that a person of ordinary skill in the art would not have been motivated with a reasonable
expectation of success in using a Type II CRISPR-Cas system with the single-molecule DNA-
10
targeting RNA of Proposed Count 2.
11
C.
12
At page 5, line 12, to page 7, line 2 of BO3, it is argued that Proposed Count 2 would
Broad Will Not Be Prejudiced by Proposed Count 2
13
unfairly exclude Broads best proofs using a two-molecule DNA targeting RNA. The response
14
is that Broad failed to proffer any proof that shows either conception or reduction to practice of
15
Count 1 and that would be excluded by Proposed Count 2.
16
At page 5, line 22 to page 6, line 8, of BO3, it is argued that laboratory work from 2011
17
(Ex. 2412, at Z-5 to Z-23) that was submitted during prosecution and referenced in Paper No. 53
18
is excluded from the scope of Proposed Count 2. The response is that Ex. 2412 could not
19
possibly demonstrate either a conception or a reduction to practice of all of the elements of either
20
Count 1 or Proposed Count 2. As acknowledged by Dr. Simons, no page in this purported
21
notebook shows, or even implies, a tracrRNA, which is a required element of the system recited
22
in both Count 1 and Proposed Count 2. Ex. 1639, at 54: 24-55:2. Proof of conception exists
23
only when a definite and permanent idea of an operative invention, including every feature of
24
the subject matter sought to be patented, is known, which this document does not show. Bard
- 12 -

1
Peripheral Vascular, Inc. v. W.L. Gore & Assocs., 776 F.3d 837, 845 (Fed. Cir. 2015)(Bard).
At page 6, lines 9-17 of BO3, it is argued that an NIH grant application shows the design
of a mammalian CRISPR expression system. The response is that the grant application fails to
show appreciation of all of the elements of Count 1 (or Proposed Count 2). Ex. 2411 fails to
demonstrate any appreciation of the requirement of both Counts that crRNA and tracrRNA form
a complex with Cas9 to act on target DNA. Indeed, in the portion of the figure omitted in
Broads excerpt, only the crRNA (and not the tracrRNA) is illustrated as being complexed with
Cas9 during cleavage. Ex. 2411, at 16, Fig. 4A. The grant application states only that the
tracrRNA is to facilitate the processing of the crRNA and that it remains necessary to identify
10
the genes and RNA elements that will reconstitute a functional CRISPR system in mammalian
11
cells. Ex. 2411, at 16. Thus, Ex. 2411 shows that Broad did not conceive of all the required
12
elements of Count 1 and Proposed Count 2. As Dr. Breaker stated on cross-examination, those
13
elements were first publically disclosed by UC in Jinek 2012. Ex. 1638, at 89:16-18 (Q. What
14
is the first article that youre aware of that describes such a complex? A. That would be Jinek, et
15
al. 2012). Broad has proffered no evidence that the construct illustrated in Ex. 2411 was ever
16
successfully made and used. A part of the grant application omitted by Broad shows that the
17
authors didnt intend to work on the mammalian CRISPR expression system until months
18
later, long after UCs filing date. Ex. 1619, at 82; Ex. 1639, at 94:18-95:5. As acknowledged
19
by Dr. Simons, the construct in the grant application does not appear in Broads patent
20
applications or Cong 2013 (Ex. 1055). Ex. 1639, at 50:10-23. However, Dr. Simons
21
acknowledged that the construct from this grant application was included in Broads own
22
submission of PowerPoint slides from Shuailiang Lin, a student in Dr. Zhangs lab. Ex. 1639, at
23
75:376:1; 78:1779:4 and 97:6-11, and Ex. 1614, at 4, 10, 11, 19, 20. Broads own
- 13 -

1
PowerPoint slides show that the Zhang lab could not get CRISPR-Cas9-mediated DNA cleavage
in eukaryotic cells prior to June 2012. Id. The failure of the Zhang lab to successfully reduce to
practice an embodiment within the scope of Count 1 or Proposed Count 2 prior to June 2012 is
confirmed by the lab notebook of Shuailiang Lin, also submitted by Broad during ex parte
prosecution, and by his email to Dr. Doudna admitting that the Zhangs lab failure process
amounted to a joke. Ex. 1616, at 000035, 000044; Ex. 1475. Broads inventors, along with
others, were only able to use a Type II CRISPR-Cas system in eukaryotic cells after being
inspired by UCs Jinek 2012 disclosure. Exs. 1558-1560 and 1620. Thus, the grant
application cannot have represented a permanent idea of an operative invention. See Bard, 776
10
11
F.3d at 845.
At page 5, lines 18-20, of BO3 it is argued that Broads Cong publication indicates that
12
their work on non-covalently linked DNA-targeting RNA preceded their work on single-
13
molecule DNA-targeting RNA (citing Ex. 1055, at 819-820). The response is that the Cong
14
manuscript shows that it was submitted on October 5, 2012, after the filing date of UCs first
15
provisional application, and cannot be relied upon to prove any event preceding UCs filing date.
16
Ex. 1055, at 823. Broad did not proffer any evidence that any experiments described in Cong
17
were performed prior to UCs filing date. Consequently, Broads arguments about experiments
18
described in Cong should be given no weight and disregarded.
19
At page 7, line 3 to page 9, line 4 of BO3, it is argued that Count 1 is not unfair to UC.
20
The response is that UC proffered evidence of an actual reduction to practice of Proposed Count
21
2 prior to the filing dates of both parties that would be excluded by Count 1. MFs. 3-11; Ex.
22
1507; Ex. 1022, 166-175; Ex. 1024, 157-167. This is a long recognized basis rooted in
23
basic fairness for substitution of a count. See, e.g., Univ. of S. Calif, 473 Fed.Appx. at 895.
- 14 -

1
At page 7, lines 7 to 12, of BO3, it is argued that UC has attempted to game the system
by disagreeing with Broad as to whether eukaryotic CRISPR is a separately patentable
invention. At page 8, line 16, to page 9, line 4, of BO3, it is argued that UC should have moved
to undesignate its claims. The response is twofold. First, UC requested a contingent motion to
undesignate all of its claims from Count 1. See Paper No. 27, at 13. Second, undesignation of
all of UCs claims, by itself, would not resolve the issues between the parties. UCs position has
been consistent. Count 1 does not reflect the separately patentable subject matter claimed by
both Parties, and an interference between the claims of the parties is still necessary because
Broads claims are not separately patentable from UCs claims. Substitution of Proposed Count
10
2 for Count 1 would correct the deficiencies of Count 1 and provide for a proceeding that is fair
11
to both parties and directed to common patentable subject matter.
12
13
D.
14
At page 25, lines 8-23 of BO3, it is argued that UC has not provided sufficient evidence
Each of UCs Provisional Applications Described and Enabled an

Embodiment of Proposed Count 2
15
that it should be entitled to benefit of its provisional applications for Proposed Count 2. Broad
16
argues that the example of the First Provisional was conducted in a test tube on a natural target
17
and does not refer to a protospacer adjacent motif (PAM). The response is that none of Broads
18
arguments address elements of Proposed Count 2. As acknowledged by Dr. Simons, Proposed
19
Count 2 does not recite, let alone require, a PAM. Ex. 1639, at 21:5-8. The working example of
20
UCs First Provisional, and associated figures, which are carried forward to all of UCs
21
applications, demonstrate possession and enablement of an embodiment having all the elements
22
of Proposed Count 2. MFs 48-57; Ex. 1022, 332-454; Ex. 1024, 320-445.
23
24
E.
25
At page 26, line 3, to page 29, line 15 of BO3, it is argued that certain of Broads claims
All of Broads Claims Should Be Designated to Correspond to Proposed

Count 2
- 15 -

1
should not be designated as corresponding to Proposed Count 2. The response is that none of the
elements cited by Broad is separately patentable. Staphylococcus aureus Cas9 (SaCas9) was
known in the art at the time of Broads earliest possible filing date. See, e.g., Ex. 1038; Ex.
1563; Ex. 1022, 273-276; Ex. 1024, 264-267; Ex. 1535, 113-129. It would have been
expected that SaCas9 would work in a Type II CRISPR-Cas system. Id. Likewise, it would
have been obvious to use oneor moreNLS sequences to target a protein to a eukaryotic cell
nucleus, because it was known that the majority of genomic DNA is found in the nucleus of
eukaryotic cells, and NLSs had previously been used for this purpose. Ex. 1022, 269-272;
Ex. 1024, 260-263. Furthermore, by the time Broad filed its first provisional application, it
10
would have been obvious to use any tracrRNA length between the natural length and the
11
truncated length of Chimera A demonstrated in Jinek 2012. Ex. 1022, 302-305; Ex. 1024,
12
293-296.
13
V.
14
15
CONCLUSION
For at least the foregoing reasons, UCs Motion 3 should be granted.
Respectfully submitted,
By /Todd R. Walters/
Todd R. Walters, Esq. (Reg. No. 34,040)
Alexandria, Virginia 22314
Telephone (703) 836-6620
Facsimile (703) 836-2021
Counsel for UC and Vienna
By: / Sandip H. Patel /

Sandip H. Patel, Esq. (Reg. No. 43,848)
MARSHALL GERSTEIN & BORUN LLP
6300 Willis Tower, 233 South Wacker Dr.
Telephone (312) 474-6300
Facsimile (312) 474-0448
spatel@marshallip.com
Counsel for EC
Date: September 28, 2016
- 16 -

APPENDIX 1 LIST OF EXHIBITS
EXHIBIT NO.
1001
DESCRIPTION
U.S. Patent Application No. 13/842,859, filed on March 15, 2013, to
Jennifer Doudna et al. (the 859 Application)
1003
U.S. Provisional Application No. 61/652,086, filed on May 25, 2012, to

Martin Jinek et al. (the 086 Provisional or the First Provisional)
1004
U.S. Provisional Application No. 61/716,256, filed on October 19, 2012, to

Martin Jinek et al. (the 256 Provisional or the Second Provisional)
1005
U.S. Provisional Application No. 61/757,640, filed on January 28, 2013, to

Martin Jinek et al. (the 640 Provisional or the Third Provisional)
1007
U.S. Patent No. 8,697,359, issued on April 15, 2014, to Feng Zhang (the
359 Patent)
1008
U.S. Patent No. 8,771,945, issued on July 8, 2014, to Feng Zhang (the
945 Patent)
1009
U.S. Patent No. 8,945,839, issued on February 3, 2015, to Feng Zhang (the
839 Patent)
1010
U.S. Patent No. 8,889,356, issued on November 18, 2014, to Feng Zhang
(the 356 Patent)
1011
U.S. Patent No. 8,932,814, issued on January 13, 2015, to Le Cong and
Feng Zhang (the 814 Patent)
1012
U.S. Patent No. 8,795,965, issued on August 5, 2014, to Feng Zhang (the
965 Patent)
1-1

EXHIBIT NO.
1013
DESCRIPTION
U.S. Patent No. 8,871,445, issued on October 28, 2014, to Le Cong and
Feng Zhang (the 445 Patent)
1014
U.S. Patent No. 8,865,406, issued on October 21, 2014, to Feng Zhang and
Fei Ran (the 406 Patent)
1015
U.S. Patent No. 8,895,308, issued on November 25, 2014, to Feng Zhang
and Fei Ran (the 308 Patent)
1016
U.S. Patent No. 8,906,616, issued on December 9, 2014, to Feng Zhang et

al. (the 616 Patent)
1017
U.S. Patent No. 8,993,233, issued on March 31, 2015 to Feng Zhang et al.
(the 233 Patent)
1018
U.S. Patent No. 8,999,641, issued on April 7, 2015 to Feng Zhang et al.
(the 641 Patent)
1019
U.S. Patent Application No. 14/704,551, filed on May 5, 2015 to Feng

Zhang et al. (the 551 Application)
1022
Declaration of Carol Greider, Ph.D.
1023
Curriculum Vitae of Carol Greider, Ph.D.
1024
Declaration of Dana Carroll, Ph.D.
1025
Curriculum Vitae of Dana Carroll, Ph.D.
1029
Dai et al., The Transcription Factors GATA4 and dHAND Physically

Interact to Synergistically Activate Cardiac Gene Expression Through a
p300-dependent Mechanism, 277(27) J. BIOL. CHEM. 24390-24398 (2002)
(Dai)
1-2

EXHIBIT NO.
DESCRIPTION
1030
Gustafsson et al., Codon Bias and Heterologous Protein Expression, 22(7)

TRENDS BIOTECHNOL. 346-353 (2004) (Gustafsson)
1031
43 METHODS IN CELL BIOLOGY, Protein Expression In Animal Cells,

Chapters 2, 3, 6, 9 (Michael G. Roth ed., 1994) (Roth)
1032
Deltcheva et al., CRISPR RNA maturation by trans-encoded small RNA and

host factor RNase III, 471 NATURE 602-607 (2011) with Supplementary
Materials (Deltcheva)
1033
Sapranauskas et al., The Streptococcus thermophilus CRISPR/Cas system

provides immunity in Escherichia coli, 39(21) NUCL. ACIDS RES. 9275-9282
(2011) (Sapranauskas)
1038
National Center for Biotechnology Information

http://www.ncbi.nlm.nih.gov/protein/403411236?sat=16&satkey=13804560
(downloaded on Jan. 21, 2015) (NCBI)
1039
Boden et al., Efficient Gene Transfer of HIV-1-Specific Short Hairpin RNA

into Human Lymphocytic Cells Using Recombinant Adeno-associated Virus
Vectors, 9(3) MOL. THER. 396-402 (2004) (Boden)
1040
MOLECULAR CLONING: A LABORATORY MANUAL, Chpt. 16 (J. Sambrook &

D. Russell, 3rd ed. 2001) (Sambrook)
1055
Cong et al., Multiplex Genome Engineering Using CRISPR/Cas Systems,

339(6121) SCIENCE 819-823 (2013) with Supplemental Material (Cong)
1056
Mali et al., RNA-Guided Human Genome Engineering via Cas9, 339(6121)

SCIENCE 823-826 (2013) with Supplemental Materials (Mali)
1-3

EXHIBIT NO.
1057
DESCRIPTION
Jinek et al., RNA-Programmed Genome Editing in Human Cells, 2 ELIFE
e00471 (2013) (Jinek 2013)
1058
Hwang et al., Efficient In Vivo Genome Editing Using RNA-Guided

Nucleases, 31(3) NAT. BIOTECHNOL. 227-229 (2013) (Hwang)
1059
Cho et al., Targeted Genome Engineering in Human Cells With the Cas9
RNA-Guided Endonuclease, 31(3) NAT. BIOTECHNOL. 230-232 (2013) with
Supplemental Information (Cho)
1060
Shen et al., Generation of gene-modified mice via Cas9/RNA-mediated

gene targeting, 23(5) CELL RES. 720-723 (2013) (Shen)
1152
Carroll, A CRISPR approach to gene targeting, 20(9) MOLECULAR

THERAPY 1658-60 (2012)
1153
Garneau et al., The CRISPR/Cas bacterial immune system cleaves

bacteriophage and plasmid DNA, 468(7320) NATURE 67-71 (2010)
1155
Jinek et al., A programmable dual-RNA-guided DNA endonuclease in

adaptive bacterial immunity, 337(6096) SCIENCE 816-821 (2012) (Jinek
2012)
1156
Makarova et al., Evolution and classification of the CRISPR-Cas systems,

9(6) NAT. REV. MICROBIOL. 467-477 (2011)
1159
Wiedenheft et al., RNA-guided genetic silencing systems in bacteria and

archaea, 482(7385) NATURE 331-8 (2012) (Wiedenheft)
1161
U.S. Patent Publication No. 2010/0076057, published on March 25, 2010 to

Sontheimer et al.
1-4

EXHIBIT NO.
1194
DESCRIPTION
Anderson et al., A simple method for the rapid generation of recombinant
adenovirus vectors, 7 GENE THERAPY 1034-1038 (2000)
1200
Behr et al., Efficient gene transfer into mammalian primary endocrine cells
with lipopolyamine-coated DNA, 86 PNAS 6982-6986 (1989)
1203
Bergemann et al., Excision of specific DNA-sequences from integrated

retroviral vectors via site-specific recombination, 23(21) NUCL. ACIDS RES.
4451-4456 (1995)
1204
Bhaya et al., CRISPR-Cas Systems in Bacteria and Archaea: Versatile

Small RNAs for Adaptive Defense and Regulation, 45 ANNUAL REVIEW OF
GENETICS 273-297 (2011)
1213
Carney and Morgan, Induction of DNA Double-Strand Breaks by

Electroporation of Restriction Enzymes into Mammalian Cells, 113
METHODS IN MOL. BIOL. 465-471 (1999)
1215
Carte et al., Cas6 is an endoribonuclease that generates guide RNAs for

invader defense in prokaryotes, 22(24) GENES DEV. 3489-3496 (2008)
1217
Chiu et al., Engineered GFP as a vital reporter in plants, 6(3) CURR. BIO.
325-330 (1996)
1218
Choulika, et al., Transfer of single gene-containing long terminal repeats

into the genome of mammalian cells by a retroviral vector carrying the cre
gene and the loxP site, 70(3) J. VIROL. 1792-1798 (1996)
1229
Dykxhoorn et al., Killing the Messenger: Short RNAs That Silence Gene
Expression, 4 NATURE REV. 457-467 (2003)
1-5

EXHIBIT NO.
1233
DESCRIPTION
Fechheimer et al., Transfection of mammalian cells with plasmid DNA by
scrape loading and sonication loading, 84 PNAS 8463-8467 (1987)
1235
Fieck et al., Modifications of the E.coli Lac repressor for expression in

eukaryotic cells: effects of nuclear signal sequences on protein activity and
nuclear accumulation, 20(7) NUCL. ACIDS RES. 1785-1791 (1992)
1236
Fischer-Fantuzzi and Vesco, Cell-Dependent Efficiency of Reiterated

Nuclear Signals in a Mutant Simian Virus 40 Oncoprotein Targeted to the
Nucleus, 8(12) MOL. CELL BIOL. 5495-5503 (1988)
1248
Gorman et al., High efficiency gene transfer into mammalian cells, B307
PHIL. TRANS. R. SEC. LAND. 343-346 (1984)
1257
Hale et al., Prokaryotic silencing (psi)RNAs in Pyrococcus furiosus, 14(12)

RNA 2572-2579 (2008) (Hale 2008)
1260
Hashimoto et al., A novel method for transformation of intact yeast cells by

electroinjection of plasmid DNA, 21 APPLIED MICROBIOL. BIOTECHNOL.
336-339 (1985)
1262
Haurwitz et al., Sequence- and structure-specific RNA processing by a

CRISPR endonuclease, 329 SCIENCE 1355-1358 (2010)
1283
Li et al., In vivo genome editing restores haemostasis in a mouse model of

haemophilia, 475 NATURE 217-223 (2011)
1285
Lombardo et al., Gene editing in human stem cells using zinc finger
nucleases and integrase-defective lentiviral vector delivery, 25(11) NAT.
BIOTECHNOL. 1298-1306 (2007)
1-6

EXHIBIT NO.
1293
DESCRIPTION
Mastroianni et al., Group II intron-based gene targeting reactions in
eukaryotes, 3(9) PLOS ONE. e3121 (2008)
1302
Morgan et al., Inducible Expression and Cytogenetic Effects of the EcoRI

Restriction Endonuclease in Chinese Hamster Ovary Cells, 8(10) MOL.
CELL. BIOL. 4204-4211 (1988)
1307
Neumann et al., Gene transfer into mouse lyoma cells by electroporation in

high electric fields, 1(7) EMBO JOURNAL 841-845 (1982)
1319
Planey et al., Inhibition of Glucocorticoid-induced Apoptosis in 697 Pre-B

Lymphocytes by the Mineralocorticoid Receptor N-terminal Domain,
277(44) J. BIOL. CHEM. 42188-42196 (2002)
1327
Raymond and Soriano, High-efficiency FLP and C31 site-specific

recombination in mammalian cells, 2(1) PLOS ONE. e162 (2007)
1329
Reiss et al., RecA protein stimulates homologous recombination in plants,

93 PROC. NATL. ACAD. SCI. USA 3094-3098 (1996)
1332
Sandy et al., Mammalian RNAi: a practical guide, 39 BIOTECHNIOUES 215224 (2005)
1335
Sauer, Functional expression of the cre-lox site-specific recombination

system in the yeast saccharomyces cerevisiae, 7(6) MOL. CELL. BIOL. 20872096 (1987) (Sauer 1987)
1336
Sauer and Henderson, Site-specific DNA recombination in mammalian cells

by the Cre recombinase of bacteriophage P1, 85 PROC. NATL. ACAD. SCI.
USA 5166-5170 (1988)
1-7

EXHIBIT NO.
1337
DESCRIPTION
Schramm and Hernandez, Recruitment of RNA polymerase III to its target
promoters, 16(20) GENES DEV. 2593-2620 (2002)
1371
Gratz et al., Genome Engineering of Drosophila with the CRISPR RNAGuided Cas9 Nuclease, 194 GENETICS 1029-1035 (2013) (Gratz)
1372
DiCarlo et al., Genome engineering in Saccharomyces cerevisiae using

CRISPR-Cas systems, 41(7) NUCL. ACIDS RES. 4336-4343 (2013)
(DiCarlo)
1374
Heintze et al., A CRISPR CASe for high-throughput silencing, 4(193)

FRONTIERS IN GENETICS 1-6 (2013)
1375
Xu, The next generation biotechnology for Apple improvement and beyond:
The CRISPR/Cas9 Story, 21(4) NEW YORK FRUIT QUARTERLY 19-22 (2013)
1376
Chen et al., A critical stem-loop structure in the CR4-CR5 domain of

mammalian telomerase, 30(2) NUCL. ACIDS RES. 592-597 (2002)
1377
MacRae et al., Structural basis for double-stranded RNA processing by

dicer, 311 SCIENCE 195-198 (2006)
1379
Sternberg et al., Mechanism of substrate selection by a highly specific

CRISPR endoribonuclease, 18 RNA 661-672 (2012)
1380
List of Cited References
1435
International PCT Publication No. WO 2008/108989 A2, published on

September 12, 2008
1-8

EXHIBIT NO.
1455
DESCRIPTION
National Center for Biotechnology Information,
http://www.ncbi.nlm.nih.gov/protein/Q03LF7.1 (downloaded on Mar. 24,
2015)
1471
Brouns, A Swiss Army Knife of Immunity, 337 SCIENCE 808-809 (2012)
1473
Golic, RNA-Guided Nucleases: A New Era for Engineering the Genomes of

Model and Nonmodel Organisms, 195 GENETICS 303-308 (2013)
1507
[REDACTED] Martin Jinek notebook, pages 84-86
1511
Interview Summary with Draft Claim Amendments in U.S. Patent

Application No. 14/463,253, dated November 3, 2015
1534
Second Declaration of Carol Greider, Ph.D.
1535
Second Declaration of Dana Carroll, Ph.D.
1545
U.S. Provisional Application No. 61/717,324, filed October 23, 2012 to

Seung Woo Kim et al. (Toolgen Provisional)
1554
Hwang et al., Efficient genome editing in zebrafish using a CRISPR-Cas

system, 31(3) NATURE BIOTECHNOLOGY 227-229 (2013) with
Supplementary Materials
1555
Simons Deposition Transcript, July 18, 2016 with errata
1556
Simons Deposition Transcript, July 19, 2016 with errata
1558
[REDACTED] Email from Jin-Soo Kim to Jennifer Doudna, dated October

3, 2012 with attachment
1559
Email from George Church to Jennifer Doudna, dated November 14, 2012
1-9

EXHIBIT NO.
1560
DESCRIPTION
[REDACTED] Email from George Church to Jennifer Doudna, dated
December 8, 2012 with attachments
1563
Kinnevey et al., Emergence of Sequence Type 779 Methicillin-Resistant

Staphylococcus aureus Harboring a Novel Pseudo Staphylococcal Cassette
Chromosome mec (SCCmec)-SCC-SCCCRISPR Composite Element in Irish
Hospitals, 57(1) ANTIMICROB. AGENTS CHEMOTHER. 524-531 (2013)
1582
Truong et al., Retrohoming of a Mobile Group II Intron in Human Cells

Suggests How Eukaryotes Limit Group II Intron Proliferation, 11(8) PLOS
GENET. e1005422 (2015)
1583
Serganov and Patel, Ribozymes, riboswitches and beyond: regulation of

gene expression without proteins, 8 NATURE REVIEWS 776-790 (2007)
1603
Timeline of Reports of CRISPR-Cas9 in Eukaryotes Rapidly Submitted

Following Senior Partys Disclosure
1614
Summary of CRISPR work during Oct. 2011-Jun. 2012 presented by

Shuailiang Lin (Exhibit 14 to Neville Sanjana Declaration, dated July 23,
2015)
1616
Shuailiang Lin notebook pages (Exhibit 3 to Neville Sanjana Declaration,

dated July 23, 2015)
1619
Grant Application for Isogenic human pluripotent stem cell-based models

of human disease mutations submitted to National Institutes of Health on
January 12, 2012
1620
Email from Feng Zhang to Jennifer Doudna dated January 2, 2013
1-10

EXHIBIT NO.
DESCRIPTION
1638
Deposition Transcript of Ronald Breaker, Ph.D., September 13, 2016, with

errata
1639
Deposition Transcript of Paul Simons, Ph.D., September 15, 2016, with

errata
1-11

APPENDIX 2 - STATEMENT OF MATERIAL FACTS
UCs Material Facts 1-78 with Broads Responses
1.
Count 1 is limited to contacting in a eukaryotic cell a target DNA with a CRISPR-Cas
system. Redeclaration, Paper No. 32, at 10.

Answer: Admitted.
2.
None of Senior Partys claims are limited to eukaryotes. See Ex. 1022, 90; Ex. 1024,
84; Senior Party Clean Copy of Claims, filed January 25, 2016.
Answer: Admitted.
3.
Senior Party has proffered proofs that are excluded by Count 1, but would be evidence of
an actual reduction to practice of Proposed Count 2. Ex. 1507; Ex. 1022, 166-176; Ex. 1024,
157-167.
Answer: Denied.
4.
Ex. 1507 is a copy of pages from co-inventor Martin Jineks laboratory notebook that are
dated prior to the filing date of Senior Partys First Provisional Application. Ex. 1507.
Answer: Junior Party can neither admit nor deny.
5.
Ex. 1507 is evidence of an actual reduction to practice of Proposed Count 2 that would be
excluded by the eukaryotic cell limitation of Count 1. Ex. 1507; Ex. 1022, 166-176; Ex.
1024, 157-167.
Answer: Denied.
6.
Jinek set out to test chimeric RNA to see whether crRNA and tracrRNA can be fused to
generate a single RNA with which Csn1/Cas9 can be programmed. Ex. 1507, at 84.
2-1

7.
The experimental details recorded on pages 84-85 of the notebook show how target DNA
was contacted with a CRISPR-Cas system. See Ex. 1022, 173; Ex. 1024, 164.
Answer: Denied.
8.
The system was engineered and non-naturally occurring at least because, as illustrated on
page 86, the chimera A reactions contained crRNA and tracrRNA segments covalently linked to
form one molecule. See Ex. 1022, 173-174; Ex. 1024, 164-165.
Answer: Denied.
9.
In the natural system, the crRNA and tracrRNA are separate RNA molecules. Id.; see
also, e.g., Exs. 1032; 1033; Ex. 1022, 110; Ex. 1024, 103.
Answer: Admitted.
10.
The reaction details on pages 84-85, and the lane labels on page 86, show that Csn1/Cas9
protein was present in the system used in the chimera A reactions. Id.
Answer: Denied.
11.
The results recorded on page 86 of the notebook show that the target DNA was cleaved
when Csn1/Cas9 was complexed with a single-molecule DNA targeting RNA (i.e., chimera A).
See Ex. 1022, 175; Ex. 1024, 166.
Answer: Denied.
12.
On June 28, 2012, approximately one month after Senior Partys First Provisional was
filed, the Jinek Science Paper (Ex. 1155) (Jinek 2012), co-authored by Senior Partys
inventors, was published online, disclosing the necessary and sufficient components for cleavage
of target DNA by a Type II CRISPR-Cas system, demonstrating successful DNA cleavage using
the system outside of its natural environment in a prokaryotic cell, and describing use of a single
2-2

molecule DNA-targeting RNA. See Ex. 1022, 152-158; Ex. 1024, 143-149.
Answer: Denied.
13.
At the time of, and immediately following, the publication of Jinek 2012, commenters
predicted application of the Type II CRISPR-Cas system to eukaryotic cells. See Ex. 1022,
129-133; Ex. 1024, 122-125.
Answer: Denied.
14.
In the same issue of Science as Jinek 2012, Brouns wrote [b]ased on the 20-nucleotide
guide section of the crRNA, the enzyme could theoretically introduce breaks at unique sites in
any eukaryotic genome. Ex. 1471; Ex. 1022, 132; Ex. 1024, 124.
Answer: Admitted.
15.
Before any reports of the Type II CRISPR-Cas system being applied in eukaryotes had
been published, Dr. Dana Carroll wrote in a peer reviewed article that doing so was clearly well
worth a try, and he discussed methods that could be used to do so. See Ex. 1152; Ex. 1024,
123.
Answer: Denied.
16.
In reference to Jinek 2012, a researcher in the art stated that [i]t was immediately
obvious that [the CRISPR-Cas9] system might be repurposed for genome engineering, similar to
ZFNs and TALENs. See Ex. 1473, at 306; Ex. 1022, 131; Ex. 1024, 124.
Answer: Admitted.
17.
Before the Type II CRISPR-Cas system was fully elucidated, it had been suggested that
analogous CRISPR proteins could be used in eukaryotic cells. See Ex. 1161 (Sontheimer), at
0007; Ex. 1022, 133; Ex. 1024, 125.
Answer: Admitted.
2-3

18.
Sontheimer demonstrates that at least by September 23, 2009, researchers in the art were
motivated to adapt prokaryotic CRISPR systems to eukaryotic cells, were aware of routinely
used techniques available to do so (including the use of expression vectors, nuclear localization
signals, and codon optimization), and had an expectation of success in doing so. See Ex. 1161,
at 0009, 0042, 0054, 0058, 0060; Ex. 1022, 133; Ex. 1024, 125.
Answer: Denied.
19.
Techniques that one might use to practice the method of Count 1, or Proposed Count 2, in
eukaryotic cells were well-known and routinely used in the art prior to Senior Partys First
Provisional. See Ex. 1022, 134, 136-151; Ex. 1024, 126, 128-142.
Answer: Denied.
20.
Methods for introducing a nucleic acid into a eukaryotic cell had been well-known for
over 30 years. See, e.g., Exs. 1040; 1200; 1248; 1233; 1260; 1307; Ex. 1022, 143; Ex. 1024,
134.
Answer: Denied.
21.
It was well-known that a protein or nucleic acid, including prokaryotic polynucleotides,
can be expressed in a eukaryotic cell using an expression vector, including viral vectors. See,
e.g., Exs. 1031; 1039; 1194; 1203; 1218; 1229; 1332; 1337; 1353; Ex. 1022, 136-137; Ex.
1024, 128-129.
Answer: Denied.
22.
Well-known viral vectors had been used to express gene editing proteins in eukaryotic
cells. See, e.g., Exs. 1285; 1283; Ex. 1022, 138; Ex. 1024, 130.
Answer: Denied.
2-4

23.
It was well-understood that proteins could be targeted to the nucleus, where genomic
DNA is located in eukaryotes, and nuclear localization sequences (NLSs) had been routinely
used for decades. See, e.g., Exs. 1029; 1235; 1236; 1319; Ex. 1022, 140; Ex. 1024, 130.
Answer: Denied.
24.
One of ordinary skill in the art understood how to increase expression of prokaryotic
proteins in eukaryotic cells by codon optimization. See, e.g., Ex. 1030; Ex. 1022, 142; Ex.
1024, 133.
Answer: Denied.
25.
It was routine to combine use of an NLS with codon optimization. See, e.g., Ex. 1217;
Ex. 1022, 142; Ex. 1024, 133.

Answer: Denied.
26.
Neither an NLS nor codon optimization is actually necessary to achieve cleavage of
target DNA in a eukaryotic cell. See Exs. 1058; 1060, Ex. 1022, 141; Ex. 1024, 131.
Answer: Denied.
27.
Researchers had directly injected a pre-assembled prokaryotic protein/RNA complex
(ribonucleoprotein particles) into eukaryotic cells to cause genome modification in those cells.
Ex. 1293, at 12; Ex. 1022, 139; Ex. 1024, 131.
Answer: Denied.
28.
Analogous methods of manipulating DNA in eukaryotic cells using prokaryotic proteins
that had been demonstrated included the prokaryotic cre-lox site-specific recombination system,
prokaryotic RecA protein, the C31 recombinase, and bacterial restriction endonucleases. See,
e.g., Exs. 1335; 1336; Ex. 1329, at 3094-95, Fig. 1; Exs. 1327; 1213; 1302; Ex. 1022, 144-
2-5

150; Ex. 1024, 135-141.
Answer: Denied.
29.
In less than a year after Senior Partys disclosure of an in vitro method in Jinek 2012,
researchers completed and published uses of the CRISPR-Cas9 system in multiple types of
eukaryotic cells and organisms and specifically cited the Jinek 2012 paper as a basis of their
work. See Ex. 1022, 163; Ex. 1024, 154; see also Exs. 1055; 1056; 1058; 1059; 1060;
1371, and 1372.
Answer: Denied.
30.
Count 1 identifies the necessary components of the Type II CRISPR-Cas9 system without
specifying whether the RNA components are comprised in a single molecule. See Ex. 1022,
108; Ex. 1024, 102; Redeclaration, Paper No. 32, at 10.
Answer: Admitted.
31.
All of both parties claims are directed to use of a single-molecule DNA-targeting RNA.
See Ex. 1022, 87-108; Ex. 1024, 80-101.

Answer: Denied.
32.
Proposed Count 2 is directed to a single-molecule DNA-targeting RNA. See Ex. 1022,
110; Ex. 1024, 103.

Answer: Admitted.
33.
Given the generic subject matter of Count 1, it would not have been obvious at the time
Senior Partys First Provisional Application was filed that the crRNA and tracrRNA components
could be covalently linked to form a single-molecule DNA-targeting RNA while maintaining a
functioning CRISPR-Cas9 system. See Ex. 1022, 109-124; Ex. 1024, 102-117.
Answer: Denied.
2-6

34.
The natural type II CRISPR-Cas system uses two separate RNA molecules, a crRNA
molecule and a tracrRNA molecule, for DNA cleavage. See, e.g., Exs. 1032; 1033; Ex. 1022,
110; Ex. 1024, 103.
Answer: Admitted.
35.
The creation of a single-molecule DNA-targeting RNA requires covalently linking the
targeter-RNA (crRNA) and activator-RNA (tracrRNA). Ex. 1022, 112-113; Ex. 1024,
105-106; see also Ex.1155, at Fig 5A.
Answer: Denied.
36.
Prior to Senior Partys First Provisional Application and the teachings of Jinek 2012,
persons of ordinary skill in the art would have had good reason to doubt that the DNA-targeting
RNA could be combined into a single molecule and still function with Cas9 to cleave DNA. See
Ex. 1022, 114-122; Ex. 1024, 105-115.
Answer: Denied.
37.
Enzymes that interact with, and functionally rely on, nucleic acids were known to be very
sensitive to structural changes in the nucleic acids. Ex. 1022, 114-117; Ex. 1024, 107-110.
Answer: Denied.
38.
A key enzyme in another CRISPR system, Csy4, which, like Cas9, is a nuclease enzyme
that interacts with a crispr-RNA (crRNA) molecule via an RNA duplex region, was known to be
sensitive to even a relatively minor structural change to the RNA duplex region, such that even
small changes in the RNA resulted in a 1,600 to 49,000 fold decrease in RNA binding. See Ex.
1022, 114; Ex. 1024, 107; Ex. 1262, at 1355 and Fig. 2; Ex. 1379 at Figs. 3, 5A.
Answer: Denied.
2-7

39.
Argonaute, an RNA binding protein, is extremely sensitive to even small changes in
the ends of a double-stranded RNA duplex that it recognizes, such that even small changes
resulted in a 100 to 10,000 fold decrease in RNA binding and enzymatic activity. See Ex. 1022,
114; Ex. 1024, 107; Ex. 1377, at 196; Ex. 1378, at 318-320.
Answer: Denied.
40.
Telomerase is an enzyme that must bind to RNA having a specific structure, including a
stem and loop, to which the TERT protein is highly sensitive, to carry out its enzymatic activity,
such that mutations that extend the RNA duplex or merely change two residues in the loop
sequence resulted in a non-functional protein-RNA complex. See Ex. 1022, 117; Ex. 1024,
110; Ex. 1376, at 592, 595-597, Fig. 3.
Answer: Denied.
41.
Researchers in the art specifically noted the innovativeness of the single-molecule DNA-
targeting RNA. See, e.g., Ex. 1375 (The most innovative modification was to create a singleguide RNA (sgRNA) that is of the combined functions of crRNA and tracrRNA and is capable of
accurately guiding Cas9 to a predetermined site in the host genome (Jinek et al. 2012).); Ex.
1374 (Significant advances for the use of this technique have been promoted by the generation
of a single-guide RNA (sgRNA) that combines the function of the tracrRNA and crRNA in a
chimeric molecule).
Answer: Denied.
42.
As defined by Junior Party, a guide sequence does not include the tracr-mate portion
that is required for hybridization with the activator-RNA (tracrRNA) to form the necessary
protein binding segment. See Ex. 1022, 80-86; Ex. 1024, 73-79.
Answer: Admitted.
2-8

43.
The recitation of guide sequence in Count 1 encompasses non-functional systems. See
Ex. 1022, 80-86; Ex. 1024, 73-79.

Answer: Denied.
44.
Proposed Count 2 does not include the guide sequence recitation of Count 1.
Answer: Admitted.
45.
Junior Partys involved applications state that the term guide RNA can be used
interchangeably to refer to the single-molecule DNA-targeting RNA. Id.

Answer: Denied.
46.
Proposed Count 2 includes a guide RNA recitation.
Answer: Admitted.
47.
Each of Senior Partys Provisional Applications describes embodiments within the scope
of Proposed Count 2. See Ex. 1022, 341-454; Ex. 1024, 323-445.

Answer: Denied.
48.
Example 1 of Senior Partys First Provisional Application describes and enables a
working example of a method meeting all of the limitations of Proposed Count 2. See Ex. 1022,
449-454; Ex. 1024, 440-445; Ex. 1003, at 248-252, Fig. 3.
Answer: Denied.
49.
Examples, performed in the same, or substantially the same manner, as Example 1 of
Senior Partys First Provisional Application are presented, along with additional data and
description, in each of Senior Partys Second Provisional, Third Provisional, and the 859
Application. See Ex. 1022, 449; Ex. 1024, 440; compare Ex. 1003 at 00248-00252, Figs.
1, 3, 5; Ex. 1004, at 0006, 00312-00318, 00353-00358, Figs. 1, 3, 5, 17;31, 32; Ex. 1005, at
0031, 00234, 00360-00370, 00401-00406, Figs. 1, 3, 5, 13-17, 31, 32; Ex. 1001, at 0035,
2-9

0042-0046, 0049, 00504-00524, 00555-00560, Figs, 1, 10-14, 17, 18, 21, 23, 24, 26-31.
Answer: Denied.
50.
Example 1 of the First Provisional discloses an example in which DNA cleavage was
performed. See Ex. 1022, 450; Ex. 1024, 441; Ex. 1003, at 0249.
Answer: Denied.
51.
Sequences of the Cas9 and chimeraA single-molecule DNA-targeting RNA are shown in
the figures of the application and the method by which they were made are described. See Ex.
1022, 454; Ex. 1024, 445; Ex. 1003, at 00248, Figs. 2, 12A, 3B.
Answer: Admitted.
52.
The single-molecule DNA-targeting chimera A RNAs comprised a targeter-RNA that
hybridizes with the target sequence, and ii) an activator-RNA that are covalently linked as shown
in Figs. 1 and 3B. Ex. 1003, at Figs. 1, 3B.
Answer: Denied.
53.
The system of Example 1 was engineered and non-naturally occurring at least because a
single-molecule DNA-targeting RNA is not found in the naturally occurring system. See Ex.
1022, 452; Ex. 1024, 443; Ex. 1003, at 0012, Figs. 1, 3B, 9.
Answer: Admitted.
54.
Example 1 describes contacting an engineered and non-naturally occurring CRISPR-Cas9
system with a target DNA in that [t]he DNA-targeting RNA/polypeptide complexes were
assembled by incubation in the cleavage buffer and then the assembled complex was added to
target DNA and incubated. See Ex. 1022, 452; Ex. 1024, 443; Ex. 1003, at 249.
Answer: Denied.
2-10

55.
Targeting of the target DNA by the complex is illustrated in Fig. 1 of the First
Provisional. See Ex. 1022, 453; Ex. 1024, 444; Ex. 1003, at Fig. 1.
Answer: Denied.
56.
The results of Example 1, shown in Fig. 3A of the First Provisional, demonstrate that
reactions containing the Cas9/Chimera A complex cleaved target DNA. See Ex. 1022, 453;
Ex. 1024, 444; Ex. 1003, at Fig. 3A.
Answer: Denied.
57.
Each of Senior Partys Provisionals shares at least one inventor with the 859 Application
and the 859 Application contains the required reference to each of the Senior Partys
Provisionals. Ex. 1003, cover, Ex. 1004, at 264-269 (ADS); Ex. 1005, at 348-353 (ADS); Ex.
1001, at [0001] and 345-352 (ADS).
Answer: Admitted.
58.
Junior Party has not been accorded any benefit. See Redeclaration, Paper No. 32, at 13.
Answer: Admitted.
59.
References that have been cited in the parties applications are listed in Ex. 1380.

60.
Drs. Dana Carroll and Carol Greider have reviewed all the references previously
identified to the USPTO during prosecution of the Involved Patents or during the present
interference dated prior to Senior Partys First Provisional Application, filed May 25, 2012. Ex.
1022, 177-183, 242; Ex. 1023; Ex. 1024, 168-175, 234; Ex. 1025.
Answer: Denied.
61.
None of the references known to Senior Party that are dated prior to May 25, 2012,
together or separately, disclose, nor would have rendered obvious, a CRISPR-Cas9 method using
2-11

a single-molecule DNA-targeting RNA as required by Proposed Count 2. Id.
Answer: Denied.
62.
None of the references that have been applied to any involved patent or application or
specifically cited in this proceeding, alone or in combination, disclose or suggest a method of

using a single-molecule DNA-targeting RNA in a CRISPR-Cas9 system as required by Proposed
Count 2. See Ex. 1022, 242; Ex. 1024, 234.
Answer: Denied.
63.
All of Junior Partys involved claims should be construed as directed to use of a single-
molecule DNA-targeting RNA. Ex. 1022, 91-107; Ex. 1024, 85-101.

Answer: Denied.
64.
All of Junior Partys involved claims recite a CRISPR-Cas system that includes a Cas9
protein and a guide RNA. See, e.g., Second Replacement Broad Clean Copy of Claims, filed
April 22, 2016.
Answer: Admitted.
65.
Persons of ordinary skill in the art would have understood Junior Partys use of guide
RNA in the claims of its involved patents and application to mean a single-molecule DNAtargeting RNA. Ex. 1022, 91-107; Ex. 1024, 85-101.
Answer: Denied.
66.
The only definition of the term guide RNA in Junior Partys Involved Patents and
Application describes the guide RNA as a single-guide system:

In aspects of the invention the terms chimeric RNA, chimeric guide RNA,
guide RNA, single guide RNA and synthetic guide RNA are used
interchangeably and refer to the polynucleotide sequence comprising the guide
sequence, the tracr sequence and the tracr mate sequence.
2-12

See, e.g., Ex. 1007 at col. 12, ll. 6-10; Ex. 1022, 93; Ex. 1024, 87.
Answer: Denied.
67.
There is nothing in Junior Partys claims or specifications that is contrary to this
definition. See Ex. 1022, 95-97; Ex. 1024, 89-91.

Answer: Denied.
68.
The term guide RNA is used throughout Junior Partys specifications, including all of
the working examples, only in reference to a single-molecule DNA-targeting RNA. Id.

Answer: Denied.
69.
Junior Party has told the USPTO during prosecution that a guide RNA comprises not
only a guide sequence but also a tracrRNA sequence as well as other necessary sequence(s) for
the guide DNA [sic] to be fully functional in targeting a genomic locus of interest. See
Examiners Interview Summary in U.S. Pat. App. No. 14/463,253, dated Nov. 3, 2015 (Ex.
1511).
Answer: Denied.
70.
Many of Junior Partys involved claims contain limitations that explicitly specify that the
guide RNA is a single-molecule DNA targeting RNA. See Ex. 1022, 100-106; Ex. 1024,
94-100.
Answer: Admitted.
71.
A single-molecule DNA-targeting RNA of Proposed Count 2 would anticipate a
generically-construed guide RNA.

Answer: Denied.
72.
Both Senior Partys and Junior Partys involved claims contain limitations that are not
specifically recited in Proposed Count 2, however, each of these additional limitations would
2-13

have been obvious to one of ordinary skill in the art at the time these applications were filed,
whether taken alone or in combination. See Ex. 1022, 255; Ex. 1024, 246.
Answer: Denied.
73.
Where some claims of the parties recite systems, and not methods, Proposed Count 2
includes the same elements of the CRISPR-Cas9 system that are recited in those system claims.
See Ex. 1022, 255; Ex. 1024, 246.
Answer: Denied.
74.
None of the limitations in Junior Partys claims that are not explicitly recited in Proposed
Count 2 render any of Junior Partys claims separately patentable from the method recited in
Proposed Count 2. See Ex. 1022, 255-328; Ex. 1024, 246-319.
Answer: Denied.
75.
Proposed Count 2 recites all of the elements of Junior Partys claims except for certain
obvious variations. Ex. 1022, 250-254, Tables 1-13 of Appendices 1 and 2; Ex. 1024,
242-245, Tables 1-13 of Appendices 1 and 2.
Answer: Denied.
76.
Drs. Carol Greider and Dana Carroll, who are experts in the field, have considered each
of Junior Partys involved claims and explain, element-by-element, why the claims would have
been obvious in view of Proposed Count 2. Id.; see also Exs. 1023; 1025.
Answer: Denied.
77.
All of Senior Partys involved claims are directed to methods of using a single-molecule
DNA-targeting RNA in a Type II CRISPR-Cas system. Ex. 1022, 246-248, Appendices 1

and 2; Ex. 1024, 238-240; Appendices 1 and 2.
Answer: Admitted.
2-14

78.
Drs. Carol Greider and Dana Carroll, who are experts in the field, have considered each
of Senior Partys involved claims and explain, element-by-element, why the claims would have
been obvious in view of Proposed Count 2. Id.
Answer: Denied.
2-15

Broads Alleged Facts 79-164 with UCs Responses
79.
This interference concerns methods of using CRISPR to cleave or edit target DNA or
modulate its transcription. Ex. 2001, Simons 1st Dec 4.2. Response: Admitted.
80.
CRISPR occurs naturally in prokaryotic cells and is programmed in nature to target
specific phage or plasmid DNA targets. Ex. 2001, Simons 1st Dec 2.1. Response: Admitted
81.
Junior Party argued that the limitation to eukaryotic methods and systems made its claims
patentable over prior art CRISPR methods in other environments and then obtained their claims.
See, e.g. Ex. 2424. Response: Admitted only that this is a position that Junior Party has argued,
otherwise denied.
82.
UCs application in interference is related to eukaryotic CRISPR methods. Ex. 1001.
Response: Admitted that Senior Partys Applications described and enabled methods of using
Type-II CRISPR-Cas systems in eukaryotic cells.
83.
Guide RNA where the two RNA components that guide the Cas9 complex to the target
DNA are covalently linked together into a single molecule is sometimes called single guide
RNA or chimeric guide RNA. Ex. 2009, Simons 3rd Dec 12.20. Response: Insufficient
information, therefore unable to admit or deny.
84.
Guide RNA consisting of two separate molecules is called dual guide by UCs experts
and attorneys. Paper 45 at 19:6-15; Ex. 1022, Greider 374, 425; Ex. 1024, Carroll 365, 416.
Response: Denied as incomplete.
85.
UC filed its Motion 3 knowing Junior Partys best proofs used two-molecule guide RNA.
See Paper No. 27 at 30:12-31:12. Response: Denied.

86.
Junior Partys publication in Cong et al. shows that Junior Partys earlier work used dual-
molecule RNA systems. Ex. 1055 at 819-820. Response: Denied.
2-16

87.
In ex parte prosecution, Junior Party submitted numerous declarations describing its
laboratory work in 2011 and 2012 that was performed on dual guide RNA. Ex. 2009, Simons 3rd
Dec 12.5. Response: Denied.
88.
Junior Partys early work is shown in Junior Party inventors NIH grant application
discussed in Junior Partys 2015 submission to the PTO. Ex. 2411. Response: Denied.
89.
This NIH application, dated January 12, 2012, shows the design of an entire mammalian
CRISPR expression system, that does not include single molecule guide RNA. Id. at 16 (Figure
4). Response: Denied.
90.
Most of UCs involved specifications examples are in a eukaryotic environment. See,
generally, Ex. 1001 at 562-662. Response: Admitted.

91.
UC previously filed, but canceled, CRISPR claims require a eukaryotic environment. Ex.
2424. Response: Admitted that Senior Party has previously filed claims directed to use of
Type-II CRISPR-Cas systems in eukaryotic cells, otherwise denied.
92.
All of Junior Partys involved claims at issue require a eukaryotic environment. Ex.
1007-1019. Response: Admitted.

93.
Count 1 does not require that the activator-RNA hybridizes to the guide sequence. Ex.
2005, Greider Dep. at 30:7-10. Response: Denied.

94.
The activator-RNA hybridizes with some part of the targeter-RNA and the targeter-RNA
includes both the guide sequence and the tracrmate sequence. Ex. 2009, Simons 3d Dec. 12.9.
Response: Insufficient information, therefore unable to admit or deny.
95.
A person of skill in May 2012 would know that tests can be performed to determine
whether a tetraloop would or would not interfere with protein binding. Ex. 2009, Simons 3rd Dec
12.49. Response: Denied.
2-17

96.
In February 2008, a group of inventors disclosed that it was contemplated that the
CRISPR system be transferred into eukaryotic cells utilizing any suitable method known in the
art, including, but not limited to transformation via plasmids. Ex. 1435, 714 Application, p.
101, ll. 22-23. Response: Admitted.
97.
These inventors did not publish any results showing any CRISPR system in eukaryotic
cells before the Junior Partys inventors early 2013 publication. Ex. 2009, Simons 3d Dec.
12.14. Response: Insufficient information, therefore unable to admit or deny.
98.
In 2009, another group of inventors filed a patent application claiming a method of using
CRISPR in a eukaryotic cell. Ex. 1161, 589 Application, Claim 1. Response: Admitted.
99.
These inventors disclosed a representative of each type of CRISPR as model system: E.
coli (Type I), S. thermophilus (Type II) and S. epidermis (Type III). Ex. 1156 at 8 0054; Ex.
2009. Simons 3d Dec. 12.14. Response: Denied.
100.
These inventors never published working eukaryotic CRISPR methods. Simons 3d Dec.
12.14. Response: Unable to admit or deny.

101.
After receiving enablement rejections from the PTO, Sontheimer et al. abandoned their
patent application. Ex. 2413; Ex. 2009, Simons 3d Dec. 12.14. Response: Insufficient
102.
Dr. Carroll stated that because CRISPR originated in prokaryotic, not eukaryotic systems,
there is no guarantee that Cas9 will work effectively on a chromatin target or that the required
DNA-RNA hybrid can be stabilized in that context. Ex. 1152, Carroll 2012 at 660. Response:
Denied.
2-18

103.
Dr. Carroll asserted that a key CRISPR component might be disassembled by
endogenous eukaryotic enzymes, warning that eukaryotic DNA processing systems might cause
a potential side effect of extraneous DNA cuts. Id. Response: Denied.
104.
Carroll stated, gene editing through base pairing has been attempted many times. Id.
Response: Denied.
105.
Carroll referred to some prior attempts to obtain a CRISPR system that functions in
eukaryotes and described them as having efficiencies that were discouragingly low, having
limited range and less efficiency than other techniques. Id. Response: Denied.
106.
Carroll stated, Whether the CRISPR system will provide the next-next generation of
targetable cleavage reagents remains to be seen, but it is clearly well worth a try. Stay tuned. Id.
Response: Admitted.
107.
There are hundreds of CRISPR loci in the bacterial world, including many different Type
II systems. Ex. 2009, Simons 3d Dec. 12.16. Response: Insufficient information, therefore
unable to admit or deny.
108.
Most bacteria that have any Type II locus include multiple, different Type II loci in their
genomes. Id. Response: Insufficient information, therefore unable to admit or deny.

109.
It was known by May 2012 that tracrRNA, crRNA and Cas9 were necessary for the
combination of the maturation and cleavage steps. Ex. 2009, Simons 3d Dec. 12.43; see also
Ex. 2010, Breaker Dec. 1.11-1.26. Response: Denied.
110.
In May 2012 it was known that no other Cas protein was necessary for bacterial
immunity. Ex. 2009, Simons 3rd Dec 12.37. Response: Denied
2-19

111.
Group II introns, which are closely analogous to the CRISPR system and which involve
both RNA and protein from bacteria have not been readily adapted for use and function in
eukaryotic cells. Ex. 2010, Breaker Dec 1.50. Response: Denied
112.
The term guide RNA includes both two-molecule and single-molecule guide RNA. Ex.
2009, Simons 3d Dec. 12.1712.26. Response: Denied

113.
Junior Partys patents and application use the term guide RNA to refer to the RNA that
guides the Cas9:RNA complex to its DNA target. Ex. 2009, Simons 3d Dec. 12.1812.20.
Response: Denied
114.
The 359 Patent claim 1 requires a nucleotide sequence that encodes a guide RNA,
with no limitation on the number of molecules it contains. Ex. 1007 Claim 1. Response: Denied
115.
Dependent claim 4 of the 359 patent adds a single limitation wherein the guide RNAs
comprise a guide sequence fused to a trans-activating cr (tracr) sequence. Ex. 1007 Claim 4.
Response: Admitted.
116.
Example 6 of the 356 patent uses the term guide RNA to encompass both single guide
RNA and dual guide RNA. Ex. 1010 col. 105 lines 3-8. Response: Denied
117.
The 359 patent expressly states that in some embodiments the tracr sequence and the
tracr mate sequence are contained within a single transcript. Ex. 1007, 359 patent, col. 21, l.
41-45. Response: Admitted.
118.
Example 1 of the 359 patent includes several embodiments that use two-molecule guide
RNA. Id. at col. 43-50. Response: Denied.

119.
UC in its publications, UCs attorneys in this interference, and prior art authors have all
used the term guide RNA to mean whatever RNA guides the interference complex to the
target. Ex. 2009, Simons 3d Dec. 12.2712.31. Response: Denied.
2-20

120.
In Jinek 2012 the UC inventors wrote, In this ternary complex, the dual
tracrRNA:crRNA structure acts as guide RNA that directs the endonuclease Cas9 to the cognate
target DNA. Ex. 1155, Jinek 2012, Figure S1 caption. Response: Admitted.
121.
The ternary complex in Jinek 2012 refers to the three part complex consisting of (1)
Cas9, (2) a mature crRNA molecule and (3) a tracrRNA molecule. Ex. 2009, Simons 3d Dec.
12.27. Response: Admitted.
122.
The dual tracrRNA:crRNA structure of Jinek 2012 is a two component complex. Id.
Response: Admitted.
123.
In Jinek 2012, UC used the term guide RNA to refer to a dual guide complex
consisting of separate strands of tracrRNA and crRNA. Ex. 2009, Simons 3d Dec. 12.27.
Response: Denied.
124.
UCs 859 application defines the term DNA-targeting RNA as being synonymous
with guide RNA and as including two molecule guide RNA. Ex. 1001, 859 application at 130;
see also Ex. 2005, Greider Dep. at p. 291, l. 20 p. 292, l. 21. Response: Denied.
125.
UCs experts refer to the use of a composition that includes purified recombinant S.
pyogenes Cas9 protein and either a single-guide or dual-guide DNA targeting RNA, i.e., the
complex of Count 1 and Proposed Count 2 (single-guide DNA-targeting RNA complex.) Ex.
1022, Greider 374; Ex. 1024, Carroll 365 (emphasis added). Response: Admitted.
126.
UCs counsel represented to the Board that UC planned to propose a count that was
generic as to guide RNA, meaning that it covers both the dual guide and the single guide
embodiments. Paper 45, May 6, 2016 Conf. Call Tr. 19:8-11; Tr. p. 22, l. 12 p. 23, l. 7.
Response: Admitted.
2-21

127.
A 2011 paper explained, [t]he crRNA serves as a guide (hence the term guide RNA has
also been used) to allow for specific base paring between the exposed crRNA within the
ribonucleoprotein interference complex and the corresponding protospacer on the foreign DNA.
Ex. 1204, Bhaya at 286. Response: Admitted.
128.
The same paper explained, CRISPR RNA (crRNA): small noncoding RNA ... (also
known as psiRNAs or guide RNA) Based on their function, these small RNAs have also
been referred to as ... guide RNAs. Ex. 1204 at 276 (side bar citation omitted). Response:
Admitted.
129.
Many other papers used the term guide RNA in the same way. Ex. 1215, Carte et al. at
3490; Ex. 1257, Hale et al., at 2577; Ex. 2227, Jore at 529. Response: Insufficient information,
therefore unable to admit or deny.
130.
The rest of Junior Partys claims cover CRISPR methods that use dual guide RNA. Ex.
1007-1019. Response: Denied.

131.
Junior Partys statement in its 359 Patent that [i]n aspects of the invention, the terms
guide RNA along with single guide RNA and chimeric RNA are used interchangeably and
refer to the polynucleotide sequence comprising the guide sequence, the tracr sequence and the
tracr mate sequence is not a definition. Ex. 2009, Simons 3rd Dec 12.19. Response: Denied.
132.
The Deltcheva article, published in March 2011, disclosed that Cas9 and the precursors to
crRNA and tracrRNA complexed together as part of the maturation process of the crRNA and
the tracrRNA. Ex. 1032, Deltcheva at 603-605. Response: Admitted.
133.
Deltcheva showed that tracrRNA was involved in the maturation of crRNA, i.e., the
processing of the long pre-crRNA (repeat-spacer-repeat-spacer-repeat-etc. (possibly hundreds of
2-22

repeat-spacer units)) to the crRNA (a single repeat-spacer unit.) Ex. 1032, Deltcheva at 603.
Response: Admitted.
134.
Deltcheva showed that tracrRNA formed a complex with both crRNA and Cas9 during
this process, and described the third step of the CRISPR system as (3) interference with
invading cognate foreign genomes by mechanisms that are yet to be fully understood. Ex. 1032,
Deltcheva at 602. Response: Insufficient information, therefore unable to admit or deny.
135.
Deltcheva also states that [Cas9] may also be involved in the silencing of invading
sequences. Ex. 1032, Deltcheva at 605 (Fig 4. caption). Response: Admitted.

136.
The Garneau 2010 publication, cited by Deltcheva, states that the endonuclease activity
[of S. thermophilus CRISPR] seems to require [Cas9]. Ex. 1153, Garneau at 70. Response:
Admitted.
137.
It was known by 2012 that Cas9 was the only Cas protein necessary for cleavage. Ex.
2009, Ex. 2009, Simons 3rd Dec 12.37. Response: Denied.

138.
It was known by May 2012 that crRNA was involved in the interference step. . See Ex.
1033, Sapranauskas at 9275. Response: Admitted.

139.
Deltcheva showed that the precursors for the tracrRNA:crRNA duplex and Cas9 are
complexed together just before the formation of the mature crRNA. Ex. 1032, Deltcheva at 605.
Response: Denied.
140.
Deltcheva showed that the tracrRNA and crRNA form a hybridized duplex resulting from
a significant degree of Watson-Crick base pairing. Ex. 1032, Deltcheva at 603. Response:
Denied.
2-23

141.
Since the 1970s, techniques had been developed on the thermodynamics of disassociation
of double stranded RNA. Ex. 2009, Simons 3d Dec. 12.41. Response: Insufficient information,
therefore unable to admit or deny.
142.
Before May 2012, the widely-used algorithm mfold was available to provide an estimate
of the free energy of dissociation, G, for any RNA duplex. Ex. 2010, Breaker Dec. 1.15
1.16. Response: Denied.
143.
The mfold algorithm predicts a G value of -20.4 kcal/mole for an RNA duplex having
the base pairing shown in Deltcheva Figure 1. Id at 1.18. Response: Denied.

144.
A G value of 20.4 kcal/mole corresponds to a kinetic rate constant for dissociation that
is so small that no appreciable separation would be predicted to occur under biologically relevant
conditions. Ex. 2010, Breaker Dec. 1.171.18. Response: Denied.
145.
Based on the number of base pairs disclosed in the Deltcheva duplex, its melting
temperature would be much greater than 37C. Ex. 2010, Breaker Dec. 1.211.22; Ex. 1032 at
608. Response: Insufficient information, therefore unable to admit or deny.
146.
To ensure double stranded RNA properly forms in vitro it has been routine since the
1990s to connect the two strands by covalent linkers of four nucleotidescalled tetraloops.
Ex. 2010, Breaker Dec. 1.38. Response: Denied.
147.
Tetraloops ensure the desired folding of RNA. Ex. 2280, Molinaro at 3063. Response:
Denied.
148.
A common example of a well-known tetraloop used for this purpose was the sequence
GAAA, which was used in Jinek 2012. Ex. 2010, Breaker Dec. 1.301.33. Response:
Denied.
2-24

149.
RNA, especially double-stranded RNA, is notoriously badly behaved in crystal
structures, frequently resulting in neighboring molecules packing subtly out of register. Ex. 2272,
Ferr-DAmer at 625. Response: Insufficient information, therefore unable to admit or deny.
150.
It was disclosed in the 1990s that tetraloopsespecially the GAAA tetraloopare useful
for restoring the proper well-registered array of crystals. Ex. 2272, Ferr-DAmer at 625; Ex.
2010, Breaker Dec. 1.39. Response: Insufficient information, therefore unable to admit or
deny.
151.
Csy4, which like Cas9 was known to process pre-crRNA to tracrRNA in a different
CRISPR system, bound RNA most effectively when a GNRA-tetraloop structure (which include
GAAA) was used. Ex. 1379 at 665; see also Ex. 1262 at 1357. Response: Insufficient
152.
UC is not entitled to benefit of P1, P2 or P3 for Count 2. Ex. 2009, Simons 3d Dec.
11.16711.169. Response: Denied.

153.
The claims of the 406 and 308 patents require the use of a Staphylococcus aureus Cas9
(SaCas9) protein or a nucleotide sequence encoding such a protein, and are not anticipated or
rendered obvious by the prior art. Ex. 1014, 406 patent; Ex. 1015, 308 patent; Ex. 2009,
Simons 3d Dec. 12.5312.60. Response: Denied.
154.
CRISPR systems using SaCas9 have a surprising combination of high efficacy in
eukaryotes and small size. Ex. 2001, Simons 1st Dec. 7.6, 1 7.9; Ex. 1014. Response:
Denied.
155.
Knowing the domain structure provides no information about the potential for success or
failure of the Cas9 protein. Ex. 2001, Simons 1st Dec 7.8. Response: Denied.
2-25

156.
The Broad inventors discovered that, among the hundreds of other known Cas9 varieties,
SaCas9 works much better than StCas9 and as good as, if not better than the best prior art
Cas9SpCas9. Ex. 2001, Simons 1st Dec 7.8. Response: Denied.
157.
StCas9 was known to be inferior to the S. pyogenes Cas9 (SpCas9) in terms of cleavage
efficience, and SaCas9 shares only 17% sequence identity with SpCas9, teaching away from its
use. Ex. 2009, Simons.3d Dec 12.60. Response: Denied.
158.
There are significant structural differences between SaCas9 and SpCas9. Ex. 2227;
Nishimasu 2014; see e.g. Ex. 2008, Carroll Dep. at 233:5-234. Response: Denied.
159.
The size of the Cas9 would not have been relevant in adapting the CRISPR-Cas system to
eukaryotic cells. Ex. 2001, Simons 1st Dec 7.7. Response: Denied.
160.
The size of the Cas9 orthologue would be only one factor among many considered after
the CRISPR-Cas system had been successfully adapted to eukaryotic cells. Ex. 2001, Simons 1st
Dec 7.7-7.9. Response: Denied.
161.
Count 2 does not recite the use of any NLS. Paper 32, p. 10. Response: Admitted.
162.
Jinek 2012 did not disclose the use of NLSs and the only two UC applications which pre-
date Broads filing do not include any embodiment which uses an NLS. JINEK 2012 Response:
Denied.
163.
A person of ordinary skill in the art would have understood that adding amino acids to a
protein could alter the proteins folding and affect its structures and functions. Ex. 2001,
Simmons 7.18. Response: Insufficient information, therefore unable to admit or deny.
164.
Only 55 of Junior Partys approximately 400 involved claimsless than 15% of them
require single molecule guide RNA. Ex. 2009, Simons 3d Dec. 12.21. Response: Denied.
2-26

CERTIFICATE OF FILING AND SERVICE
I hereby certify that on this 28th day of September, 2016, the foregoing UC et al.
REPLY 3 is being filed, via the Interference Web Portal, by 5:00 PM Eastern Time. Pursuant to
agreement by the parties, service copies are being sent, via electronic mail by 8:00 PM Eastern
Time today, to Junior Partys counsel as follows:
Steven R. Trybus, Esq.
Harry J. Roper, Esq.
Paul D. Margolis, Esq.
JENNER & BLOCK LLP
353 North Clark Street
(312) 222-9350
strybus@jenner.com
hroper@jenner.com
pmargolis@jenner.com
Raymond N. Nimrod, Esq.
Quinn Emanuel Urquhart & Sullivan, LLP
51 Madison Avenue, 22nd Floor
New York, NY 10010
(212) 849-7000
raynimrod@quinnemanuel.com
/Todd R. Walters/
Todd R. Walters, Esq.
Registration No. 34,040
Alexandria, Virginia 22314
Telephone (703) 836-6620
Facsimile (703) 836-2021
Counsel for UC and Vienna

UC Et Al. REPLY 3

Загружено:

Сведения о документе

Оригинальное название

Авторское право

Доступные форматы

Поделиться этим документом

Поделиться или встроить документ

Параметры публикации

Этот документ был вам полезен?

Это неприемлемый материал?

Авторское право:

Доступные форматы

UC Et Al. REPLY 3

Загружено:

Авторское право:

Доступные форматы

Filed on behalf of Senior Party

THE REGENTS OF THE UNIVERSITY OF CALIFORNIA,

Todd R. Walters, Esq.

By: Li-Hsien Rin-Laures, M.D., Esq.

UNITED STATES PATENT AND TRADEMARK OFFICE

Interference No. 106,048

THE EVIDENCE .................................................................................................................1

STATEMENT OF MATERIAL FACTS.............................................................................1

Count 1 is Improper .................................................................................................2

Using the Type II CRISPR-Cas System in Eukaryotic Cells Is Not a

Count 1 is Defective Because it Explicitly Encompasses Inoperative

Proposed Count 2 is Proper Because it is Directed to Separately-Patentable

Methods of Using a Single-Molecule DNA-Targeting RNA are

The Single-Molecule DNA-Targeting RNA of Proposed Count 2 is

Broad Will Not Be Prejudiced by Proposed Count 2 ............................................12

Each of UCs Provisional Applications Described and Enabled an

All of Broads Claims Should Be Designated to Correspond to Proposed

APPENDIX 1 - LIST OF EXHIBITS

Interference No. 106,048

Advanced Fiber Techs. (AFT) Trust v. J & L Fiber Servs., Inc.,

Interference No. 106,048

commonly claimed subject matter and is fair to both parties.

STATEMENT OF MATERIAL FACTS

Interference No. 106,048

46, 63-70. Proposed Count 2 fairly addresses these problems.

1. Using the Type II CRISPR-Cas System in Eukaryotic Cells Is Not a

Interference No. 106,048

Interference No. 106,048

these different groups were not independent.

single-molecule DNA-targeting RNA (Chimera A), some researchers experienced failures or

1060) reported using a single-molecule DNA-targeting RNA substantially identical to Jinek

Interference No. 106,048

shown to produce positive results. Ex. 2007, at 183:1-11.

Interference No. 106,048

CRISPR-Cas system would not function in eukaryotic cells:

Interference No. 106,048

1535, at 83-84; Ex. 1534, at 83-84; Ex. 1582; Ex. 1583.

2. Count 1 is Defective Because it Explicitly Encompasses Inoperative

encompass inoperable embodiments lacking utility.

which UC Motion 3 shows is separately patentable, in contrast to the eukaryotic limitation of

Proposed Count 2 is Proper Because it is Directed to Separately-Patentable

Methods of Using a Single-Molecule DNA-Targeting RNA are Commonly

Interference No. 106,048

the specification or prosecution history dictates a contrary construction. Howmedica Osteonics

Interference No. 106,048

F.3d 1365, 1375 (Fed. Cir. 2012).

The Single-Molecule DNA-Targeting RNA of Proposed Count 2 is

maturation process disclosed in Deltcheva (Ex. 1032) would dissociate.

The response is that Broads hindsight-based revision of history mischaracterizes the

Interference No. 106,048

the field compiled what was understood about CRISPR systems

at the time. Ex. 1156. In the figure excerpted at right,

Makarova showed tracr RNA present only in the first crRNA

maturation step (top of excerpt), not in a second maturation step

(second line of excerpt), and not in the cleavage of target DNA

(bottom of excerpt). Id., at Fig. 1. The enzyme(s) involved in

only hypothetically identified as Cas9, because the identity of

the enzyme(s) had not been demonstrated. Id., at Fig. 1, legend.

CRISPR-Cas DNA cleavage complex. Furthermore, as acknowledged by Dr. Breaker, Broads

Interference No. 106,048

nucleotide. Ex. 1638, at 59:8-21; 71:1-12 and 102:16-103:8.

crRNA-tracrRNA single-molecule DNA-targeting RNA would successfully cleave a DNA

highlighted the unpredictability of altering the structure of RNA molecules, stating: