`Paper No.
`Filed: December 4, 2018
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`
`
`UNITED STATES PATENT AND TRADEMARK OFFICE
`
`
`
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
`
`
`
`BENSON HILL BIOSYSTEMS, INC.,
`Petitioner
`v.
`THE BROAD INSTITUTE, INC., PRESIDENTS AND FELLOWS OF
`HARVARD COLLEGE, AND MASSACHUSETTS INSTITUTE OF
`TECHNOLOGY
`Patent Owner
`______________________
`
`Case PGR2018-00072
`Patent No. 9,790,490
`______________________
`
`PETITIONER’S UPDATED EXHIBIT LIST, SUBMISSION OF
`NOVEMBER 27, 2018 TRANSCRIPT, AND ERRATA
`
`
`
`
`
`

`

`Case PGR2018-00072
`Patent No. 9,790,490
`Further to 37 C.F.R. § 42.63(e), Petitioner hereby submits a current listing of
`
`its exhibits to counsel for Patent Owner. Exhibits 1072 (Transcript of Teleconference
`
`with the Board, taken November 27, 2018) and 1073 (Errata to Transcript of
`
`Teleconference with the Board, taken November 27, 2018) were filed on PTAB E2E
`
`and served via email to counsel of record for the Patent Owner.
`
`Filed
`Exhibits
`1001
`1002
`1003
`
`1004
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`1005
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`1006
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`1007
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`1008
`
`1009
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`1010
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`1011
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`Description
`
`
`
`United States Patent No. 9,790,490
`Prosecution History of the ’490 patent
`Declaration of Dr. Chase L. Beisel and accompanying Appendices
`A-C
`Schunder et al., “First indication for a functional CRISPR/Cas
`system in Francisella tularensis,” International Journal of Medical
`Microbiology, 303:51-60 (2013)
`Zetsche et al., “Cpf1 Is a Single RNA-Guided Endonuclease of a
`Class 2 CRISPR-Cas System,” Cell, 163:759-71 (2015)
`Zetsche et al., “A Survey of Genome Editing Activity for 16 Cpf1
`orthologs,” bioRxiv, doi: https://doi.org/10.1101/134015 (2017)
`Hsu et al., “Development and Applications of CRISPR-Cas9 for
`Genome Engineering,” Cell, 157:1262-78 (2014)
`Shmakov et al., “Discovery and Functional Characterization of
`Diverse Class 2 CRISPR-Cas Systems,” Molecular Cell, 60:385-97
`(2015)
`Koonin et al., “Diversity, classification and evolution of CRISPR-
`Cas systems,” Current Opinion in Microbiology, 37:67-78 (2017)
`Karvelis et al., “Rapid characterization of CRISPR-Cas9
`protospacer adjacent motif sequence elements,” Genome Biology,
`16:253, 1-13 (2015)
`Lowder et al., “Rapid Evolution of Manifold CRISPR Systems for
`Plant Genome Editing,” Frontiers in Plant Science, 7(1683):1-12
`(2016)
`
`2
`
`

`

`Filed
`Exhibits
`
`Description
`
`Case PGR2018-00072
`Patent No. 9,790,490
`
`1012
`
`1013
`
`1014
`
`1015
`
`1016
`
`1017
`
`1018
`
`1019
`
`1020
`
`1021
`
`1022
`1023
`
`1024
`
`1025
`1026
`1027
`
`Leenay et al., “Identifying and visualizing functional PAM
`diversity across CRISPR-Cas systems,” Mol Cell, 62(1):137-47
`(2016)
`Makarova & Koonin, “Annotation and Classification of CRISPR-
`Cas Systems,” Chapter 4 in CRISPR: Methods and Protocols,
`Methods in Molecular Biology, 1311:47-75 (2015)
`HMM Summary Page: TIGR04330 (http://tigrfams.jcvi.org/cgi-
`bin/HmmReportPage.cgi?acc=TIGR04330) last visited June 27,
`2018
`Begemann et al., “Characterization and Validation of a Novel
`Group of Type V, Class 2 Nucleases for in vivo Genome Editing,”
`bioRxiv, doi: http://dx.doi.org/10.1101/192799 (2017)
`Ran et al., “In vivo genome editing using Staphylococcus aureus
`Cas 9,” Nature, 520(7546):186-91 (2015)
`Kleinstiver et al., “Engineered CRISPR-Cas9 nucleases with
`altered PAM specificities,” Nature, 523(7561):481-85 (2015)
`Gao et al., “Engineered Cpf1 variants with altered PAM
`specificities increase genome targeting range,” Nature
`Biotechnology, 35(8):789-92 (2017)
`Stella et al., “Structure of the Cpf1 endonuclease R-loop complex
`after target DNA cleavage,” Nature, 546(7659):559-63 (2017)
`Hirano et al., “Structure and Engineering of Francisella novicida
`Cas9,” Cell, 164(5):950-61 (2016)
`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,” Nucleic Acids
`Research, 20(7):1785-91 (1992)
`United States Patent No. 8,697,359
`Chiu et al., “Engineered GFP as a vital reporter in plants,” Current
`Biology, 6(3):325-30 (1996)
`Mali et al., “RNA-Guided Human Genome Engineering via Cas9,”
`Science, 339(6121):823-26 (2013)
`Sandy et al., “Mammalian RNAi: a practical guide,”
`BioTechniques, 39:215-24 (2005)
`United States Patent Application Publication No. 2013/0302401
`International Publication No. WO 2014/118272
`
`3
`
`

`

`Filed
`Exhibits
`
`Description
`
`Case PGR2018-00072
`Patent No. 9,790,490
`
`1028
`
`1029
`1030
`1031
`
`1032
`
`1033
`
`1034
`
`1035
`
`1036
`
`1037
`
`1038
`
`1039
`
`1040
`
`Nair et al., “Multivalent N-Acetylgalactosamine-Conjugated siRNA
`Localizes in Hepatocytes and Elicits Robust RNAi-Mediated Gene
`Silencing,” JACS, 136:16958-63 (2014)
`Ludlum et al., “Alkylation of Synthetic Polynucleotides,” Science,
`145(3630):397-99 (1964).
`Glen Research, The Glen Report, 19(1):1-16 (2007)
`El-Andaloussi et al., “Exosome-mediated delivery of siRNA in
`vitro and in vivo,” Nat Protoc, 7(12):2112-26 (2012)
`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,” J Virol., 70(3):1792-98
`(1996)
`Bergemann et al., “Excision of specific DNA-sequences from
`integrated retroviral vectors via site-specific recombination,”
`Nucleic Acids Research, 23(21):4451-56 (1995)
`Dahlman et al., “In vivo endothelial siRNA delivery using
`polymeric nanoparticles with low molecular weight,” Nat
`Nanotechnol., 9(8):648-55 (2014)
`Senís et al., “CRISPR/Cas9-mediated genome engineering: an
`adeno-associated viral (AAV) vector toolbox,” Biotechnol J.,
`9(11):1402-12 (2014)
`Shukla et al., “Precise genome modification in the crop species Zea
`mays using zinc-finger nucleases,” Nature, 459(7245):437-41
`(2009)
`Jinek et al., “A programmable dual-RNA-guided DNA
`endonuclease in adaptive bacterial immunity,” Science,
`337(6069):816-21 (2012).
`Mojica et al., “Biological significance of a family of regularly
`spaced repeats in the genomes of Archaea, Bacteria and
`mitochondria,” Mol Microbiol, 36(1):244-46 (2000)
`Ishino et al., “Nucleotide Sequence of the iap Gene, Responsible
`for Alkaline Phosphatase Isozyme Conversion in Escherichia coli,
`and Identification of the Gene Product,” Journal of Bacteriology,
`169(12):5429-33 (1987)
`Jansen et al., “Identification of genes that are associated with DNA
`repeats in prokaryotes,” Molecular Microbiology, 43(6):1565-75
`(2002)
`
`4
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`

`

`Filed
`Exhibits
`1041
`
`1042
`
`1043
`
`1044
`
`1045
`
`1046
`
`1047
`
`1048
`
`1049
`
`1050
`
`1051
`
`1052
`
`1053
`
`Case PGR2018-00072
`Patent No. 9,790,490
`
`Description
`
`Bolotin et al., “Clustered regularly interspaced short palindrome
`repeats (CRISPRs) have spacers of extrachromosomal origin,”
`Microbiology, 151(Pt 8):2551-61 (2005)
`Mojica et al., “Intervening sequences of regularly spaced
`prokaryotic repeats derive from foreign genetic elements,” J Mol
`Evol, 60(2):174-82 (2005)
`Pourcel, “CRISPR elements in Yersinia pestis acquire new repeats
`by preferential uptake of bacteriophage DNA, and provide
`additional tools for evolutionary studies,” Microbiology, 151(Pt
`3):653-3 (2005)
`Barrangou et al., “CRISPR provides acquired resistance against
`viruses in prokaryotes,” Science, 315(5819):1709-12 (2007)
`Haft et al., “A Guild of 45 CRISPR-Associated (Cas) Protein
`Families and Multiple CRISPR/Cas Subtypes Exist in Prokaryotic
`Genomes,” PLOS Computational Biology, 1(6):474-83 (2005)
`Brouns et al., “Small CRISPR RNAs Guide Antiviral Defense in
`Prokaryotes,” Science, 321(5891):960-64 (2008)
`Garneau et al., “The CRISPR/Cas bacterial immune system cleaves
`bacteriophage and plasmid DNA,” Nature, 468(7320):67-71 (2010)
`Deveau et al., “Phage Response to CRISPR-Encoded Resistance in
`Streptococcus thermophilus,” Journal of Bacteriology,
`190(4):1390-1400 (2008)
`Mojica et al., “Short motif sequences determine the targets of the
`prokaryotic CRISPR defence system,” Microbiology, 155(Pt
`3):733-40 (2009)
`Anders et al., “Structural basis of PAM-dependent target DNA
`recognition by the Cas9 endonuclease,” Nature, 215(7219):569-73
`(2014)
`Nishimasu et al., “Crystal Structure of Cas9 in Complex with
`Guide RNA and Target RNA,” Cell, 156(5):935-49 (2014)
`Deltcheva et al., “CRISPR RNA maturation by trans-encoded
`small RNA and host factor RNase III,” Nature, 471(7341):602-07
`(2011)
`Makarova et al., “Unification of Cas protein families and a simple
`scenario for the origin and evolution of CRISPR-Cas systems,”
`Biology Direct, 6:38, pp. 1-27 (2011)
`
`5
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`

`

`Filed
`Exhibits
`1054
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`1055
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`1056
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`1057
`
`1058
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`1059
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`1060
`
`1061
`
`1062
`
`1063
`
`1064
`
`1065
`
`1066
`
`1067
`
`Case PGR2018-00072
`Patent No. 9,790,490
`
`Description
`
`Nam et al., “Cas5d protein process pre-crRNA and assembles into a
`Cascade-like interference complex in Subtype I-C/Dvulg CRISPR-
`Cas system,” Structure, 20(9):1574-84 (2012)
`Haurwitz et al., “Sequence- and structure-specific RNA processing
`by a CRISPR endonuclease,” Science, 329(5997):1355-58 (2010)
`Hatoum-Aslan et al., “Mature clustered, regularly interspaced, short
`palindromic repeats RNA (crRNA) length is measured by a ruler
`mechanism anchored at the precursor processing site,” PNAS,
`108(52):21218-222 (2011)
`Rouillon et al., “Structure of the CRISPR Interference Complex
`CSM Reveals Key Similarities with Cascade,” Molecular Cell,
`52:124-34 (2013)
`Hale et al., “RNA-Guided RNA Cleavage by a CRISPR RNA-Cas
`Protein,” Cell, 139(5):945-56 (2009)
`Vestergaard et al., “CRISPR adaptive immune systems of
`Archaea,” RNA Biology, 11(2):156-67 (2014)
`Voskarides & Deltas, “Screening for Mutations in Kidney-Related
`Genes Using SURVEYOR Nuclease for Cleavage at Heteroduplex
`Mismatches,” Journal of Molecular Diagnostics, 11(4):311-18
`(2009)
`Findlay et al., “A Digital PCR-Based Method for Efficient and
`Highly Specific Screening of Genome Edited Cells,” PLoS One,
`11(4):e0153901 (2016)
`Kim et al., “Genotyping with CRISPR-Cas-derived RNA-guided
`endonucleases,” Nat Commun, 5:3157 (2014)
`Minton, “How can biochemical reactions within cells differ from
`those in test tubes?,” Journal of Cell Science, 119:2863-69 (2006)
`Ellis, “Macromolecular crowding: obvious but underappreciated,”
`Trends Biochem Sci, 26(10):597-604 (2001)
`Nishimasu et al., “Structural Basis for the Altered PAM
`Recognition by Engineered CRISPR-Cpf1,” Mol Cell, 67(1):139-
`47 (2017)
`Shmakov et al., “Diversity and evolution of class 2 CRISPR-Cas
`systems,” Nat Rev Microbiol., 15(3):169-82 (2017)
`Aravind et al., “Holliday junction resolvases and related nucleases:
`identification of new families, phyletic distribution and
`
`6
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`

`

`Filed
`Exhibits
`
`Description
`
`Case PGR2018-00072
`Patent No. 9,790,490
`
`1068
`
`1069
`
`1070
`
`1071
`
`1072
`
`1073
`
`evolutionary trajectories,” Nucleic Acids Research, 28(18):3417-32
`(2000)
`Chen et al., “Structural asymmetry in the Thermus thermophilus
`RuvC dimer suggests a basis for sequential strand cleavages during
`Holiday junction resolution,” Nucleic Acids Research, 41(1):648-
`59 (2013)
`Leenay & Beisel, “Deciphering, communicating, and engineering
`the CRISPR PAM,” J Mol Biol., 429(2):177-91 (2017)
`Pul et al., “Identification and characterization of E. coli CRISPR-
`cas promoters and their silencing by H-NS,” Mol Microbiol,
`75(6):1495-512 (2010)
`Kim et al., “Highly efficient RNA-guided genome editing in human
`cells via delivery of purified Cas9 ribonucleoproteins,” Genome
`Res., 24(6):1012-9 (2014)
`Transcript of Teleconference with the Board, taken November 27,
`2018
`Errata to Transcript of Teleconference with the Board, taken
`November 27, 2018
`
`
`
`
`Dated: December 4, 2018
`
`By:/Howard W. Levine/
`Howard W. Levine, Lead Counsel
`Reg. No. 41,453
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`CERTIFICATE OF SERVICE
`The undersigned hereby certifies that a copy of the foregoing Petitioner’s
`
`Case PGR2018-00072
`Patent No. 9,790,490
`
`Updated Exhibit List and Exhibits 1072-1073 were served on December 4, 2018,
`
`via email directed to counsel of record for the Patent Owner at the following:
`
`Steven R. Trybus
`strybus@jenner.com
`
`Stephen B. Maebius
`smaebius@foley.com
`
`Raymond N. Nimrod
`raynimrod@quinnemanuel.com
`
`Sandra L. Haberny
`sandrahaberny@quinnemanuel.com
`
`DL_PGR2018-00072@jenner.com
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`
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`
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`Dated: December 4, 2018
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`By: /Lisa C. Hines/
`Lisa C. Hines
`Litigation Legal Assistant
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`FINNEGAN, HENDERSON, FARABOW,
`GARRETT & DUNNER, LLP
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