CRISPR enzymes and systems

12110,490

16/063643

December 16, 2016

The invention provides for systems, methods, and compositions for targeting nucleic acids. In particular, the invention provides non-naturally occurring or engineered DNA or RNA-targeting systems comprising a novel DNA or RNA-targeting CRISPR effector protein and at least one targeting nucleic acid component like a guide RNA.

The Broad Institute, Inc. (Cambridge, MA, US); Massachusetts Institute of Technology (Cambridge, MA, US); President and Fellows of Harvard College (Cambridge, MA, US)

THE BROAD INSTITUTE, INC. (Cambridge, MA, US), MASSACHUSETTS INSTITUTE OF TECHNOLOGY (Cambridge, MA, US), PRESIDENT AND FELLOWS OF HARVARD COLLEGE (Cambridge, MA, US)

1. A composition comprising: a non-naturally occurring or engineered guide RNA (gRNA) comprising a guide sequence capable of hybridizing to a target sequence in a genomic locus of interest in a cell, wherein the gRNA is capable of forming a complex with a Cpf1 effector protein, wherein the gRNA comprises a loop comprising an aptamer sequence that is capable of binding to an adaptor protein; and a mutated Cpf1 effector protein, wherein the mutated Cpf1 effector protein comprises at least one mutation, such that the mutated Cpf1 effector protein has no more than 5% of the nuclease activity of a corresponding wild-type Cpf1 effector protein not having the at least one mutation, and wherein the mutated Cpf1 effector protein comprises one or more nuclear localization sequences.

2. The composition of claim 1 , wherein the composition further comprises a fusion protein comprising an adaptor protein fused to one or more heterologous functional domains.

3. The composition of claim 2 , wherein the mutated Cpf1 effector protein has a diminished nuclease activity of at least 97%, or 100% as compared with the corresponding wild-type Cpf1 effector protein not having the at least one mutation.

4. The composition of claim 2 , wherein the mutated Cpf1 effector protein comprises at least one mutation selected from D908A, E993A, or D1263A according to AsCpf1 protein or a corresponding mutation in an ortholog.

5. The composition of claim 2 , wherein the mutated Cpf1 effector protein comprises at least one mutation selected from D832A, E925A, D947A or D1180A according to LbCpf1 protein or a corresponding mutation in an ortholog.

6. The composition of claim 5 , wherein the mutated Cpf1 effector protein comprises two or more mutations.

7. The composition of claim 2 , wherein the mutated Cpf1 effector protein is fused to one or more heterologous functional domains.

8. The composition of claim 2 , wherein the fusion protein comprises a linker between the adaptor protein and the heterologous functional domain, the linker optionally comprising a GlySer linker.

9. The composition of claim 2 , wherein the one or more heterologous functional domains fused to the adaptor protein comprise a transcriptional activation domain.

10. The composition of claim 7 , wherein the one or more heterologous functional domains fused to the mutated Cpf1 effector protein comprise a transcriptional activation domain.

11. The composition of claim 9 , wherein the transcriptional activation domain is VP64, p65, MyoD1, HSF1, RTA or SET7/9.

12. The composition of claim 10 , wherein the transcriptional activation domain is VP64, p65, MyoD1, HSF1, RTA or SET7/9.

13. The composition of claim 2 , wherein the one or more heterologous functional domains fused to the adaptor protein comprise a transcriptional repressor domain.

14. The composition of claim 7 , wherein the one or more heterologous functional domains fused to the mutated Cpf1 effector protein comprise a transcriptional repressor domain.

15. The composition of claim 13 , wherein the transcriptional repressor domain is a KRAB domain.

16. The composition of claim 13 , wherein the transcriptional repressor domain is a NuE domain, NcoR domain, SID domain or a SID4X domain.

17. The composition of claim 2 , wherein at least one of the one or more heterologous functional domains fused to the adaptor protein has one or more activities comprising methylase activity, demethylase activity, transcription activation activity, transcription repression activity, transcription release factor activity, histone modification activity, DNA integration activity RNA cleavage activity, DNA cleavage activity or nucleic acid binding activity.

18. The composition of claim 7 , wherein at least one of the one or more heterologous functional domains fused to the mutated Cpf1 effector protein has one or more activities comprising methylase activity, demethylase activity, transcription activation activity, transcription repression activity, transcription release factor activity, histone modification activity, DNA integration activity RNA cleavage activity, DNA cleavage activity, nucleic acid binding activity, or molecular switch activity or chemical inducibility or light inducibility.

19. The composition of claim 2 , wherein the adaptor protein is a bacteriophage coat protein selected from the group consisting of MS2, PP7, Qβ, GA, JP501, M12, R17, BZ13, JP34, JP500, KU1, M11, MX1, TW18, VK, SP, FI, ID2, NL95, TW19, AP205, ϕCb5, ϕCb8r, ϕCb12r, ϕCb23r, 7s, and PRR1.

20. The composition of claim 2 , wherein the cell is a eukaryotic cell.

21. The composition of claim 20 , wherein the eukaryotic cell is a mammalian cell.

22. The composition of claim 21 , wherein the mammalian cell is a human cell.

23. The composition of claim 20 , wherein the eukaryotic cell is a plant cell.

24. A non-human transgenic cell or cell line which has been transformed with the composition according to claim 2 .

25. A non-human transgenic mammalian model, wherein the model has been transformed with the composition according to claim 2 .

26. An isolated host cell or cell line comprising the composition of claim 2 .

27. The isolated host cell or cell line according to claim 26 , wherein the cell is a eukaryotic cell.

28. The isolated host cell or cell line according to claim 26 , wherein the cell is an animal cell.

29. The isolated host cell or cell line according to claim 28 , wherein the cell is a human cell.

30. The isolated host cell or cell line according to claim 26 , comprising a stem cell or stem cell line.

31. The isolated host cell or cell line according to claim 26 , wherein the cell is a plant cell.

32. A vector system comprising one or more vector(s) comprising nucleic acid molecule(s) encoding: a guide RNA (gRNA) and a mutated Cpf1 effector protein, wherein the mutated Cpf1 effector protein comprises at least one mutation, such that the mutated Cpf1 effector protein has no more than 5% of the nuclease activity of a corresponding wild-type Cpf1 effector protein not having the at least one mutation, and wherein the mutated Cpf1 effector protein comprises at least one or more nuclear localization sequences, and wherein the gRNA is a non-naturally occurring or engineered gRNA comprising a guide sequence capable of hybridizing to a target sequence in a genomic locus of interest in a cell, wherein the gRNA is capable of forming a complex with a Cpf1 effector protein, wherein the gRNA comprises a loop comprising an aptamer sequence that is capable of binding to an adaptor protein.

33. The vector system of claim 32 , nucleic acid molecule(s) further encoding a fusion protein comprising an adaptor protein fused to one or more heterologous functional domains.

8361725 January 2013 Russell et al.
8697359 April 2014 Zhang
8889356 November 2014 Zhang
9790490 October 2017 Zhang et al.
10253365 April 2019 Doudna et al.
10648020 May 2020 Zhang et al.
10669540 June 2020 Zhang et al.
11091798 August 2021 Zhang et al.
11286478 March 2022 Zhang et al.
20140242699 August 2014 Zhang
20140356956 December 2014 Church et al.
20150079681 March 2015 Zhang
20160208243 July 2016 Zhang et al.
20170233756 August 2017 Begemann et al.
20180282713 October 2018 Van Der Oost
20190083656 March 2019 Khalili
20190218602 July 2019 Zhang et al.
20190233814 August 2019 Zhang et al.
20190256900 August 2019 Zhang et al.
20190264186 August 2019 Yamano et al.
20200080112 March 2020 Zhang et al.
20200181623 June 2020 Zhang
20200263190 August 2020 Zhang et al.
20200283755 September 2020 Zhang et al.
20200318172 October 2020 Zhang et al.
20200318173 October 2020 Zhang et al.
20210040546 February 2021 Zhang et al.
20210076366 March 2021 Jang et al.
20210155911 May 2021 Zhang et al.
20220162584 May 2022 Zhang et al.
20220195503 June 2022 Zhang et al.
103261213 August 2013
104017821 September 2014
105602993 May 2016
106536729 March 2017
3 009 511 April 2016
1506509.7 April 2016
2501850 April 2009
201425580 July 2014
WO-2014/093622 June 2014
WO-2014/093712 June 2014
WO-2014/118272 August 2014
WO-2014/191521 December 2014
WO-2014/197568 December 2014
WO-2014/197748 December 2014
WO-2014/204723 December 2014
WO-2014/204724 December 2014
WO-2015/035139 March 2015
WO-2015/089364 June 2015
WO-2015/089419 June 2015
WO-2015/089473 June 2015
WO-2015/089486 June 2015
WO-2016/049258 March 2016
WO-2016/094872 June 2016
WO-2016/166340 October 2016
WO-2016/201155 December 2016
WO-2016/205711 December 2016
WO-2016/205749 December 2016
WO-2016/205764 December 2016
WO-2017/064546 April 2017
WO-2017/106657 June 2017
WO-2017/127807 July 2017

Zetsche et al entitled “Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System” (Cell 2015, vol. 163, published Oct. 22, 2015, pp. 759-771. (Year: 2015). cited by examiner
Zetsche et al. (Cell vol. 163, pp. 759-771, Oct. 22, 2015; Available online Sep. 25, 2015; IDS ref.). (Year: 2015). cited by examiner
Leford (Nature vol. 526, Oct. 1, 2015, p. 17. (Year: 2015). cited by examiner
Konermann et al. (Nature, 2015, 517, pp. 583-588) . (Year: 2015). cited by examiner
3rd Party Citation D46 from EP Opposition Proceedings for EP Pat. No. 3009511—Barrangou, “Class 2 large effector protein architectures”, PowerPoint Presentation Slide, Jun. 20, 2015, 1 page. cited by applicant
3rd Party Citation D47 from EP Opposition Proceedings for EP Pat. No. 3009511—CRIPSR Conference 2015, Website Print-out of Event Announcement, New York, New York, Jun. 18-20, 2015, accessed at https://web.archive.org/web/20150708120205/https:/www.crispr2015.com/ on Jul. 30, 2019, 1 page. cited by applicant
3rd Party Citation D48 from EP Opposition Proceedings for EP Pat. No. 3009511—CRIPSR Conference 2015, Conference Program including Schedule of Events, New York, New York, Jun. 18-20, 2015, accessible at https://web.archive.org/web/20151109114832/http:/nebula.wsimg.com/f9aa9f29c2be9e03bc66d1da9e0f2634?AccessKeyId=377234A383373D636692&disposition=0&alloworigin=1, 8 pages. cited by applicant
3rd Party Citation D49 from EP Opposition Proceedings for EP Pat. No. 3009511—Barrangou, et al., “Class 2 large effector protein architectures”, Caribou Biosciences Mail—New Systems with PowerPoint Presentation Slide, Jun. 20, 2015, 2 pages. cited by applicant
3rd Party Citation D50 from EP Opposition Proceedings for EP Pat. No. 3009511—Declaration of Prof. Dr. Rodolophe Barrangou with Appendices, Aug. 13, 2019, 33 pages. cited by applicant
3rd Party Citation D51 from EP Opposition Proceedings for EP Pat. No. 3009511—Declaration of Andrew P. May DPhil with Appendices, Aug. 9, 2019, 24 pages. cited by applicant
3rd Party Citation D52 from EP Opposition Proceedings for EP Pat. No. 3009511—Declaration of Rachel E. Haurwitz, PH.D. with Appendices, Aug. 13, 2019, 8 pages. cited by applicant
Assignment from Bernd Zetsche to The Broad Institute Inc. for U.S. Appl. No. 14/975,085 dated Jan. 5, 2016, 2 pages. cited by applicant
Assignment from Feng Zhang to The Broad Institute Inc. for U.S. Appl. No. 14/975,085 dated Dec. 23, 2015, 2 pages. cited by applicant
Assignment from Ian Slaymaker to The Broad Institute Inc. for U.S. Appl. No. 14/975,085 dated Jan. 6, 2016, 2 pages. cited by applicant
Assignments from Inventors, Ian Slaymaker, Omar O. Abudayyeh, Feng Zhang, Jonathan Gootenberg, and Bernd Zetsche to The Broad Institute Inc. or Presidents and Fellows of Harvard College for U.S. Appl. No. 14/975,085 (annex to Summons to attend oral proceedings), Jan. 30, 2017, 15 pages. cited by applicant
Chen et al., “Targeted activation of diverse CRISPR-Cas systems for mammalian genome editing via proximal CRISPR targeting”, Nature Communications, vol. 8, Apr. 7, 2017, DOI: 10.1038/ncomms14958, pp. 1-12. cited by applicant
Cho, Seung Woo, et al., “Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease,” Nature Biotechnology, vol. 31 pp. 230-232, including Supplementary Information, 14 pages. cited by applicant
Daligault et al., GenBank Accession No. AJJ47668, Feb. 9, 2015, 2 pages. cited by applicant
D'Astolfo et al., “Efficient Intracellular Delivery of Native Proteins”, Cell, vol. 161, Apr. 23, 2015, http://dx.doi.org/10.1016/j.cell.2015.03.028, pp. 674-690. cited by applicant
Declaration of Steven R. Trybus in EPO opposition proceedings concerning European Patent No. 3 009 511 dated Sep. 14, 2018, 13 pages. cited by applicant
Expert Declaration of Dmitrij Frishman with Exhibits dated Aug. 12, 2019, 25 pages. cited by applicant
Fagerlund et al., “The Cpf1 CRISPR-Cas protein expands genome-editing tools”, Genome Biology, vol. 16, No. 251, Nov. 7, 2015, DOI 10.1186/s13059-015-0824-9, pp. 1-3. cited by applicant
Graham et al., “Resources for the design of CRISPR gene editing experiments”, Genome Biology, vol. 16, No. 260, Nov. 27, 2015, DOI 10.1186/s13059-015-0823-x, pp. 1-21. cited by applicant
Hsu, et al., “DNA targeting specificity of RNA-guided Cas9 nucleases,” Nature Biotechnology, vol. 31, 2013, pp. 827-834. cited by applicant
Hwang W., et al., “Efficient In Vivo Genome Editing Using RNA-Guided Nucleases,” Nature Biotechnology, vol. 31, No. 3, Mar. 2013, pp. 227-229 (12 pages). cited by applicant
Jiang et al., “Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis. tobacco, sorghum and rice”, Nucleic Acids Research, vol. 41, No. 20, e188, Sep. 2, 2013, pp. 1-12. cited by applicant
Kim et al., “Genome-wide analysis reveals specificities of Cpf1 endonucleases in human cells”, Nature Biotechnology, vol. 34, No. 8, Jun. 6, 2016 (corrected Jul. 18, 2016), pp. 863-888. cited by applicant
Liu et al., “C2c1-sgRNA Complex Structure Reveals RNA-Guided DNA Cleavage Mechanism”, Molecular Cell, vol. 65, Jan. 19, 2017, pp. 310-322. cited by applicant
Liu et al., “Two Distant Catalytic Sites are Responsible for C2c2 RNase Activities”, Cell, vol. 168, Jan. 12, 2017, pp. 121-134. cited by applicant
Lundgren et al., Methods in Molecular Biology, vol. 1311, Chapters 1 and 4, 2015, pp. 1-21 and 47-75. cited by applicant
Mastroianni, et al., “Group II Intron-Based Gene Targeting Reactions in Eukaryotes” Plos One, vol. 3, 2008, pp. 1-15, 15 pages. Doi:10.1371/journal.pone.0003121. cited by applicant
New England Biolabs, “NEBuffer 3 product information”, Feb. 26, 2018, 3 pages. cited by applicant
Nishimasu et al., “Crystal Structure of Cas9 in Complex with Guide RNA and Target RNA,” Cell, 156(5):935-49 (2014). cited by applicant
Nishimasu et al., “Crystal Structure of Staphylococcus aureus Cas9”, Cell, 2015, vol. 162, pp. 1113-1126, Supplemental Information. cited by applicant
Prakash et al., “Targeted delivery of antisense oligonucleotides to hepatocytes using triantennary N-acetylgalactosamine improves potency 10-fold in mice”, Nucleic Acids Research, vol. 42, No. 13, Jul. 3, 2014, doi: 10.1093/nar/gku531, pp. 8796-8807. cited by applicant
Request for Grant of a European patent for Appl. Ser. No. 16150428.7 dated Jan. 28, 2016, 6 pages. cited by applicant
Sadowski et al., “The sequence-structure relationship and protein function prediction”, Current Opinion in Structural Biology, vol. 19 pp. 2009, 357-362 (6 pages). cited by applicant
Sander, et al., “CRISPR-Cas systems for editing, regulating and targeting genomes,” Nature Biotechnology, vol. 32, 2014, pp. 347-355, 9 pages. cited by applicant
ScienceDirect Excerpt—D'Astolfo et al., “Efficient Intracellular Delivery of Native Proteins”, Cell, vol. 161, Issue 3, Apr. 23, 2015, pp. 674-690 (article provided separately—excerpt 1 page only). cited by applicant
Seffernick et al., “Melamine Deaminase and Atrazine Chlorohydrolase: 98 Percent Identical but Functionally Different”, Journal Bacteriology, vol. 183, 2001, 2405-2410, (6 pages). cited by applicant
Sequence listing filed for EP Application No. 16150428.7. cited by applicant
Slaymaker et al., “Rationally engineered Cas9 nucleases with improved specificity”, Science, vol. 351, No. 6268, Jan. 1, 2016, pp. 84-88. cited by applicant
Tang et al., “Identification of Dehalobacter reductive dehalogenases that catalyse dichlorination of chloroform, 1,1,1-trichloroethane and 1,2-dichloroethane”, Philosophical Transactions of the Royal Society B, vol. 368, 2013, pp. 1-10 (10 pages). cited by applicant
Witkowski et al., “Conversation of a β-Ketoacyl Synthase to a Malonyl Decarboxylase by Replacement of the Active-Site Cysteine with Glutamine”, Biochemistry, vol. 38, 1999, p. 11643-11650. cited by applicant
Xie, et al. “RNA-Guided Genome Editing in Plants Using a CRISPR-Cas System” Molecular Plant, vol. 6, Nov. 2013, 1975-1983, 9 pages. cited by applicant
Xie, K, et al., “Boosting CRISPR/Cas9 multiplex editing capability with the endogenous tRNA-processing system”, Proc. Natl. Acad. Sci. U.S.A., 2015, vol. 112. pp. 3570-3575. cited by applicant
Yang et al., “Making and Breaking Nucleic Acids: Two-Mg2-Ion Catalysis and Substrate Specificity”, Molecular Cell, vol. 22, Apr. 7, 2006, pp. 5-13. cited by applicant
Yang et al., “PAM-Development Target DNA Recognition and Cleavage by C2c1 CRISPR-Cas Endonuclease”, Cell, vol. 167, Dec. 15, 2016, pp. 1814-1828. cited by applicant
Takashi et al., “Crystal structure of Cpf1 in complex with guide RNA and target DNA”, Cell, Apr. 2016, vol. 165, No. 4, pp. 949-962. cited by applicant
Zetsche et al., “Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system”, Cell, Oct. 2015, vol. 163, No. 3, pp. 759-771. cited by applicant
International Search Report Issued in International Patent Application No. PCT/US2016/067201, dated May 16, 2017. cited by applicant
Guo, et al., “Protein Tolerance to Random Amino Acid Change”, The National Academy of Sciences, PNAS, Jun. 22, 2004, vol. 101, No. 25, pp. 9205-9210. cited by applicant
Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, Case PGR2018-00072, U.S. Pat. No. 9,790,490 B2, Patent Trial and Appeal Board Decision Denying Institution of Post-Grant Review, entered Jan. 22, 2019, 21 pages. cited by applicant
Charpentier et al., “Rewriting a genome”, Nature, Mar. 2013, vol. 495, 2 pages. cited by applicant
Dahlman et al., “Orthogonal gene knockout and activation with a catalytically active Cas9 nuclease”, Nature Biotechnology, vol. 33, No. 11, Oct. 5, 2015, pp. 1159-1161, XP055381172, US. cited by applicant
Database UniProt [Online] “SubName: Full=CRISPR-associated protein Cpf1, subtype Prefran {ECO:0000313 | EMBL: AJJ47668.1};”, XP002760659, retrieved from EBI accession No. Uniprot: A0AOB6KQP9, Database accession No. A0A0b6kqp9 sequence, Apr. 1, 2015. cited by applicant
Database UniProt [Online] Nov. 30, 2010, SubName: Full =Uncharacterized protein {EC0:0000313:EMBL:EFL46285.1}; XP002769441, retrieved from EBI accession No. Uniprot: E1KQG5, Database accession No. E1KQG5. cited by applicant
Dickey et al., “Moraxella bovoculi hypothetical protein”, Database ENA [Online] EMBL-EBI, Dec. 16, 2015, Database accession No. AKG14689, XP002772302, 3 pages. cited by applicant
Dickey et al., “Moraxella bovoculi hypothetical protein”, Database ENA [Online] EMBL-EBI, May 5, 2015, Database accession No. AKG12737, XP002772309, 2 pages. cited by applicant
Dong, et al. “The crystal structure of Cpf1 in complex with CRISPR RNA,” Nature, vol. 532, pp. 523-525, including Research Letter, dated 2016. cited by applicant
Exhibit 1001—U.S. Pat. No. 9,790,490—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1002—Prosecution History of the '490 patent—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1003—Declaration of Dr. Chase L. Beisel and accompanying Appendices A-C—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1004—Schunder et al., “First indication for a functional CRISPR/Cas system in Francisella tularensis,” International Journal of Medical Microbiology, 303:51-60 (2013)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1005—Zetsche et al., “Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System,” Cell, 163:759-71 (2015)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1006—Zetsche et al., “A Survey of Genome Editing Activity for 16 Cpf1 orthologs,” bioRxiv, doi: https://doi.org/10.1101/134015 (2017)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1007—Hsu et al., “Development and Applications of CRISPR-Cas9 for Genome Engineering,” Cell, 157:1262-78 (2014)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1008—Shmakov et al., “Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems,” Molecular Cell, 60:385-97 (2015)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1009—Koonin et al., “Diversity, classification and evolution of CRISPR-Cas systems,” Current Opinion in Microbiology, 37:67-78 (2017)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1010—Karvelis et al., “Rapid characterization of CRISPR-Cas9 protospacer adjacent motif sequence elements,” Genome Biology, 16:253, 1-13 (2015)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1011—Lowder et al., “Rapid Evolution of Manifold CRISPR Systems for Plant Genome Editing,” Frontiers in Plant Science, 7(1683):1-12 (2016)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1012—Leenay et al., “Identifying and visualizing functional PAM diversity across CRISPR-Cas systems,” Mol Cell, 62(1):137-47 (2016)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1013—Makarova & Koonin, “Annotation and Classification of CRISPRCas Systems,” Chapter 4 in CRISPR: Methods and Protocols, Methods in Molecular Biology, 1311:47-75 (2015)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1014—HMM Summary Page: TIGR04330 (http://tigrfams.jcvi.org/cgibin/HmmReportPage.cgi?acc=TIGR04330) last visited Jun. 27, 2018—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1015—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)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1016—Ran et al., “In vivo genome editing using Staphylococcus aureus Cas 9,” Nature, 520(7546):186-91 (2015)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1017—Kleinstiver et al., “Engineered CRISPR-Cas9 nucleases with altered PAM specificities,” Nature, 523(7561):481-85 (2015)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1018—Gao et al., “Engineered Cpf1 variants with altered PAM specificities increase genome targeting range,” Nature Biotechnology, 35(8):789-92 (2017)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1019—Stella et al., “Structure of the Cpf1 endonuclease R-loop complex after target DNA cleavage,” Nature, 546(7659):559-63 (2017)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1020—Hirano et al., “Structure and Engineering of Francisella novicida Cas9,” Cell, 164(5):950-61 (2016)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1021—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)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1022—U.S. Pat. No. 8,697,359—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1023—Chiu et al., “Engineered GFP as a vital reporter in plants,” Current Biology, 6(3):325-30 (1996)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1024—Mali et al., “RNA-Guided Human Genome Engineering via Cas9,” Science, 339(6121):823-26 (2013)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1025—Sandy et al., “Mammalian RNAi: a practical guide,” BioTechniques, 39:215-24 (2005)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1026—United States Patent Application Publication No. 2013/0302401—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1027—International Publication No. WO 2014/118272—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1028—Nair et al., “Multivalent N-Acetylgalactosamine-Conjugated siRNA Localizes in Hepatocytes and Elicits Robust RNAi-Mediated Gene Silencing,” JACS, 136:16958-63 (2014)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1029—Ludlum et al., “Alkylation of Synthetic Polynucleotides,” Science, 145(3630):397-99 (1964)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1030—Glen Research, The Glen Report, 19(1):1-16 (2007)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1031—El-Andaloussi et al., “Exosome-mediated delivery of siRNA in vitro and in vivo,” Nat Protoc, 7(12):2112-26 (2012)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1032—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 IoxP site,” J Virol., 70(3):1792-98 (1996)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1033—Bergemann et al., “Excision of specific DNA-sequences from integrated retroviral vectors via site-specific recombination,” Nucleic Acids Research, 23(21):4451-56 (1995)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1034—Dahlman et al., “In vivo endothelial siRNA delivery using polymeric nanoparticles with low molecular weight,” Nat Nanotechnol., 9(8):648-55 (2014)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1035—Senis et al., “CRISPR/Cas9-mediated genome engineering: an adeno-associated viral (AAV) vector toolbox,” Biotechnol J., 9(11):1402-12 (2014)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1036—Shukla et al., “Precise genome modification in the crop species Zea mays using zinc-finger nucleases,” Nature, 459(7245):437-41 (2009)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1037—Jinek et al., “A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity,” Science, 337(6069):816-21 (2012)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1038—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)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1039—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)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1040—Jansen et al., “Identification of genes that are associated with DNA repeats in prokaryotes,” Molecular Microbiology, 43(6):1565-75 (2002)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1041—Bolotin et al., “Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin,” Microbiology, 151(Pt 8):2551-61 (2005)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1042—Mojica et al., “Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements,” J Mol Evol, 60(2):174-82 (2005)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1043—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)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1044—Barrangou et al., “CRISPR provides acquired resistance against viruses in prokaryotes,” Science, 315(5819):1709-12 (2007)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1045—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)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1046—Brouns et al., “Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes,” Science, 321(5891):960-64 (2008)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1047—Garneau et al., “The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA,” Nature, 468(7320):67-71 (2010)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1048—Deveau et al., “Phage Response to CRISPR-Encoded Resistance in Streptococcus thermophilus,” Journal of Bacteriology, 190(4):1390-1400 (2008)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1049—Mojica et al., “Short motif sequences determine the targets of the prokaryotic CRISPR defence system,” Microbiology, 155(Pt3):733-40 (2009)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1050—Anders et al., “Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease,” Nature, 215(7219):569-73 (2014)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1051—Nishimasu et al., “Crystal Structure of Cas9 in Complex with Guide RNA and Target RNA,” Cell, 156(5):935-49 (2014)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1052—Deltcheva et al., “CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III,” Nature, 471(7341): 602-07 (2011)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1053—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)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1054—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)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1055—Haurwitz et al., “Sequence- and structure-specific RNA processing by a CRISPR endonuclease,” Science, 329(5997):1355-58 (2010)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1056—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)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1057—Rouillon et al., “Structure of the CRISPR Interference Complex CSM Reveals Key Similarities with Cascade,” Molecular Cell, 52:124-34 (2013)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1058—Hale et al., “RNA-Guided RNA Cleavage by a CRISPR RNACas Protein,” Cell, 139(5):945-56 (2009)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1059—Vestergaard et al., “CRISPR adaptive immune systems of Archaea,” RNA Biology, 11(2):156-67 (2014)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1060—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)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1061—Findlay et al., “A Digital PCR-Based Method for Efficient and Highly Specific Screening of Genome Edited Cells,” PLoS One, 11(4):e0153901 (2016)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1062—Kim et al., “Genotyping with CRISPR-Cas-derived RNA-guided endonucleases,” Nat Commun, 5:3157 (2014)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1063—Minton, “How can biochemical reactions within cells differ from those in test tubes?,” Journal of Cell Science, 119:2863-69 (2006)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1064—Ellis, “Macromolecular crowding: obvious but underappreciated,” Trends Biochem Sci, 26(10):597-604 (2001)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1065—Nishimasu et al., “Structural Basis for the Altered PAM Recognition by Engineered CRISPR-Cpf1,” Mol Cell, 67(1):139-47 (2017)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1066—Shmakov et al., “Diversity and evolution of class 2 CRISPR-Cas systems,” Nat Rev Microbiol., 15(3):169-82 (2017)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1067—Aravind et al., “Holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories,” Nucleic Acids Research, 28(18):3417-32 (2000)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1068—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)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1069—Leenay & Beisel, “Deciphering, communicating, and engineering the CRISPR PAM,” J Mol Biol., 429(2):177-91 (2017)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1070—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)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1071—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)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Jul. 17, 2018. cited by applicant
Exhibit 1072—Transcript of Teleconference with the Board, taken Nov. 27, 2018—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Dec. 4, 2018. cited by applicant
Exhibit 1073—Errata to Transcript of Teleconference with the Board, taken Nov. 27, 2018—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, U.S. Pat. No. 9,790,490, Petition for Post Grant Review, filed Dec. 4, 2018. cited by applicant
Exhibit 2001—Ledford, “Five big mysteries about CRISPR's origins,” Nature, 541, 7637, (2017) (last visited Oct. 5, 2018) https://www.nature.com/news/five-big-mysteries-about-crispr-sorigins-1.21294—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, Case PGR2018-00072, U.S. Pat. No. 9,790,490, Patent Owners' Preliminary Response, filed Oct. 24, 2018. cited by applicant
Exhibit 2002—Sapranauskas et al., “The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli,” Nucleic Acids Research, 39(21): 9275-9282, (2011)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, Case PGR2018-00072, U.S. Pat. No. 9,790,490, Patent Owners' Preliminary Response, filed Oct. 24, 2018. cited by applicant
Exhibit 2003—Gasiunas et al., “Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria,” PNAS, 10.1073, (2012)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, Case PGR2018-00072, U.S. Pat. No. 9,790,490, Patent Owners' Preliminary Response, filed Oct. 24, 2018. cited by applicant
Exhibit 2004—Marraffini and Sontheimer, “CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA,” Science, 322(5909): 1843-1845, (2008) (Author Manuscript—supplementary material available on-line)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, Case PGR2018-00072, U.S. Pat. No. 9,790,490, Patent Owners' Preliminary Response, filed Oct. 24, 2018. cited by applicant
Exhibit 2005—Sinkunas et al., “In vitro reconstruction of cascade-mediated CRISPR immunity in Streptococcus thermophilus,” The EMBO J, 32, 385-394 (2013) (Supplementary material available on-line)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, Case PGR2018-00072, U.S. Pat. No. 9,790,490, Patent Owners' Preliminary Response, filed Oct. 24, 2018. cited by applicant
Exhibit 2006—Jackson, et al., “Crystal structure of the CRISPR RNA-guided surveillance complex from Escherichia coli*,” Science, 345(6203): 1473-1479 (2014) (Author Manuscript—supplementary material available on-line)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, Case PGR2018-00072, U.S. Pat. No. 9,790,490, Patent Owners' Preliminary Response, filed Oct. 24, 2018. cited by applicant
Exhibit 2007—Mulepati et al., “Crystal structure of a CRISPR RNA-guided surveillance complex bound to a ssDNA target,” Science, 345(6203): 1479-1484, (2014) (Author Manuscript—supplementary material available on-line)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, Case PGR2018-00072, U.S. Pat. No. 9,790,490, Patent Owners' Preliminary Response, filed Oct. 24, 2018. cited by applicant
Exhibit 2008—Thabet et al., “Evolutionary trends of the transposase-encoding open reading frames A and B (orfA and orfB) of the mycobacterial IS6110 Insertion sequence,” PLOS One, 10(6): 1-5, (2015) (Supplementary material available on-line)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, Case PGR2018-00072, U.S. Pat. No. 9,790,490, Patent Owners' Preliminary Response, filed Oct. 24, 2018. cited by applicant
Exhibit 2009—Cong et al., “Multiple genome engineering using CRISPR/Cas system,” Science, 339(6121): 819-823 (2013) (Author Manuscript—supplementary material available on-line)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, Case PGR2018-00072, U.S. Pat. No. 9,790,490, Patent Owners' Preliminary Response, filed Oct. 24, 2018. cited by applicant
Exhibit 2010—Mali et al., “Cas9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering,” Nat Biotechnol, 31(9): 833-838, (2013) (Author Manuscript—supplementary material available on-line)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, Case PGR2018-00072, U.S. Pat. No. 9,790,490, Patent Owners' Preliminary Response, filed Oct. 24, 2018. cited by applicant
Exhibit 2011—Pennisi, “The CRISPR craze,” Science, 15-17, (2013)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, Case PGR2018-00072, U.S. Pat. No. 9,790,490, Patent Owners' Preliminary Response, filed Oct. 24, 2018. cited by applicant
Exhibit 2012—Qi et al., “Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression,” Cell 152, 1173-1183, (2013) (Supplementary material available on-line)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, Case PGR2018-00072, U.S. Pat. No. 9,790,490, Patent Owners' Preliminary Response, filed Oct. 24, 2018. cited by applicant
Exhibit 2013—Gilbert et al., “CRISPR-Mediated modular RNA-guided regulation of transcription in Eukaryotes,” Cell 154, 442-451, (2013) (Supplementary material available on-line)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, Case PGR2018-00072, U.S. Pat. No. 9,790,490, Patent Owners' Preliminary Response, filed Oct. 24, 2018. cited by applicant
Exhibit 2014—Wu et al., “Target specificity of the CRISPR-Cas9 system,” Quant Biol, 2(2): 59-70, (2014) (Author Manuscript—supplementary material available on-line)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, Case PGR2018-00072, U.S. Pat. No. 9,790,490, Patent Owners' Preliminary Response, filed Oct. 24, 2018. cited by applicant
Exhibit 2015—Doudna et al., “The new frontier of genome engineering with CRISPR-Cas9,” Science, 346(6213), 1077-1086 (2014)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, Case PGR2018-00072, U.S. Pat. No. 9,790,490, Patent Owners' Preliminary Response, filed Oct. 24, 2018. cited by applicant
Exhibit 2016—O'Geen et al., “How specific is CRISPR/Cas9 really?” Current Opinion in Chemical Biology, 29: 72-78-, (2015)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, Case PGR2018-00072, U.S. Pat. No. 9,790,490, Patent Owners' Preliminary Response, filed Oct. 24, 2018. cited by applicant
Exhibit 2017—Chen et al., “Engineering human stem cell lines with inducible gene knockout using CRISPR/Cas9,” Cell Stem Cell 17, 233-244 (2015) (Supplementary material available on-line)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, Case PGR2018-00072, U.S. Pat. No. 9,790,490, Patent Owners' Preliminary Response, filed Oct. 24, 2018. cited by applicant
Exhibit 2018—Dow et al., “Inducible in vivo genome editing with CRISPR/Cas9,” Nat Biotechnol, 33(4): 390-394, (2015) (Author Manuscript—supplementary material available on-line)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, Case PGR2018-00072, U.S. Pat. No. 9,790,490, Patent Owners' Preliminary Response, filed Oct. 24, 2018. cited by applicant
Exhibit 2019—Didovyk et al., “Transcriptional regulation with CRISPR-Cas9: principles, advances and applications,” Curr Opin Biotechnol, 40: 177-184, (2016) (Author Manuscript). cited by applicant
Exhibit 2020—Guilinger et al., “Fusion of catalytically inactive Cas9 to Fokl nuclease improves the specificity of genome modification,” Nat Biotechnol, 32(6): 577-582, (2014) (Author Manuscript—supplementary material available on-line)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, Case PGR2018-00072, U.S. Pat. No. 9,790,490, Patent Owners' Preliminary Response, filed Oct. 24, 2018. cited by applicant
Exhibit 2021—Horvath et al., “CRISPR/Cas, the immune system of bacteria and archaea,” Science 327, 167-170, (2010)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, Case PGR2018-00072, U.S. Pat. No. 9,790,490, Patent Owners' Preliminary Response, filed Oct. 24, 2018. cited by applicant
Exhibit 2022—Maggio et al., “Adenoviral vector delivery of RNA-guided CRISPR/Cas9 nuclease complexes induces targeted mutagenesis in a diverse array of human cells,” Scientific Reports, 4: 5105, 1-11, (2014) (Supplementary material available on-line)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, Case PGR2018-00072, U.S. Pat. No. 9,790,490, Patent Owners' Preliminary Response, filed Oct. 24, 2018. cited by applicant
Exhibit 2023—Kwon et al., “Locus-specific histone deacetylation using a synthetic CRISPR-Cas9-based HDAC,” NComms 15315, 1-8 (2017) (Supplementary material available on-line)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, Case PGR2018-00072, U.S. Pat. No. 9,790,490, Patent Owners' Preliminary Response, filed Oct. 24, 2018. cited by applicant
Exhibit 2024—U.S. Patent Application Publication No. 20180148735 (published May 31, 2018) (Benson Hill Biosystems, Inc., applicant)—Benson Hill Biosystems, Inc., Petitioner, v. The Broad Institute Inc., Presidents and Fellows of Harvard College & Massachusetts Institute of Technology, Patent Owners, Case PGR2018-00072, U.S. Pat. No. 9,790,490, Patent Owners' Preliminary Response, filed Oct. 24, 2018. cited by applicant
Flatman, “Magnesium Transport across Cell Membranes”, Journal of Membrane Biology, 80, 1984, pp. 1-14. cited by applicant
Gao, et al. “Engineered Cpf1 Enzymes with Altered PAM Specificities”, BioRxiv Preprint, XP-002769442, 2016, doi:http://dx.doi.org/10.1101/091611, 1-13, including Figure Legends. cited by applicant
Gao, et al. “Engineered Cpf1 variants with altered PAM specificities”, Nature Biotechnology, 2017, 1-4, doi:10.1038/nbt.3900, advanced online publication including Supplementary Information. cited by applicant
Guilinger et al., “Fusion of catalytically inactive Cas9 to Fokl nuclease improves the specificity of genome modification”, Nature Biotechnology, Jun. 2014, vol. 32, No. 6, pp. 577-581. cited by applicant
Haft, D.H., “HMM Summary Page: TIGR04330”, 2012, XP-002757584, http://jcvi.org/cgi-bin/tigrfams/HmmReportPage.cgi?acc=TIGR04330. cited by applicant
Kleinstiver, et al. “Engineered CRISPR-Cas9 nucleases with altered PAM specificities,” Nature, vol. 523, pp. 481-485, including Research Letter, dated 2015. cited by applicant
Leenay, et al. “Identifying and Visualizing Functional PAM Diversity across CRISPR-Cas Systems”, Molecular Cell, 2016, 62:137-147. cited by applicant
Makarova, et al. “An updated evolutionary classification of CRISPR-Cas systems” Nature Reviews-Microbiology, 2015, 13:722-736. cited by applicant
Mali et al., “CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering”, Nature Biotechnology, Sep. 2013, vol. 31, No. 9, pp. 833-837. cited by applicant
Naito et al., “CRISPRdirect: Software for designing CRISPR/Cas guide RNA with reduced off-target sites”, Bioinformatics, 2015, vol. 31, No. 7, pp. 1120-1123. cited by applicant
Pattanayak et al., “High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity”, Nature Biotechnology, Sep. 2013, vol. 31, No. 9, pp. 839-845. cited by applicant
Ran et al., “Double Nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity”, Cell, Sep. 2013, vol. 154, pp. 1380-1389. cited by applicant
Schunder et al., “First indication for a functional CRISPR/Cas system in Francisella tularensis”, International Journal of Medical Microbiology, 2013, vol. 303, pp. 51-60. cited by applicant
Shmakov et al., “Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems”, Molecular Cell, vol. 60, No. 3, Oct. 22, 2015. pp.385-397, XP055267512, US. cited by applicant
Type V CRISPR-associated protein Cpfi [Acidaminococcus sp. Bv3L6], 2017, NCBI Reference Sequence: WP_02173622.1, Non-redundant Protein Sequence. cited by applicant
Van Der Oost et al., “Unravelling the structural and mechanistic basis of CRISPR-Cas systems”, Nature Reviews, Microbiology, Jul. 2014, vol. 12, pp. 479-492. cited by applicant
Van Der Oost, “New tool for genome surgery”, Science, Feb. 2013, vol. 339, pp. 768-770. cited by applicant
Vestergaard et al., “CRISPR adaptive immune systems of Archaea”, RNA Biology, 2014, vol. 11, No. 2, pp. 156-167. cited by applicant
Wiedenfeft et al., “Structural Basis for DNase Activity of a Conserved Protein Implicated in CRISPR-Mediated Genome Defense”, Structure, 17, 2009, pp. 904-912. cited by applicant
Gao, L., et al., Engineered Cpf1 enzymes with altered PAM specificities. bioRxiv preprint doi: https://doi.org/10.1101/091611, Dec. 4, 2016, pp. 1/14-14/14, pp. 1/3-3/3 of Figs, and pp. S1-S8. cited by applicant
Gen Bank Accession No. WP _051666128.1, publicly available Aug. 16, 2015, printed as p. 1/1. cited by applicant
Bikard et al., “Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system,” Nucleic Acids Research, 2013, vol. 41, No. 15 (pp. 7429-7437). cited by applicant
Cai et al., “Targeted transgene integration in plant cells using designed zinc finger nucleases,” Plant Molecular Biology, 2009, vol. 69 (pp. 699-709). cited by applicant
Gen Bank Accession No. A0Q7Q2.1, RecName: Full=CRISPR-associated endonuclease Cpf1; AltName: Full=FnCpf1, publicly available Dec. 2015, printed as pp. 1/2-2/2. (Year: 2015). cited by applicant
Gen Bank Accession No. U2UMQ6.1, Rec Name: Full=CRISPR-associated endonuclease Cpf1; AltName: Full=AsCpf1, publicly available Dec. 2015, printed as pp. 1/2-2/2. (Year: 2015). cited by applicant
Lee et al., “Site-specific integration in CHO cells mediated by CRISPR/Cas9 and homology-directed DNA repair pathway,” Scientific Reports, Feb. 25, 2015, vol. 5 (pp. 1-11). cited by applicant
Leinonen et al., “The EMBL sequence version archive,” Bioinformatics, 2003 vol. 19, No. 14 (pp. 1861-1862). cited by applicant
Qi et al., “Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression,” Cell, Feb. 28, 2013, vol. 152 (pp. 1173-1183). cited by applicant
Wang et al., “Delivery of CRISPR/Cas9 by Novel Strategies for Gene Therapy,” ChemBioChem,2019 vol. 20 (pp. 634-643). cited by applicant
Wu et al., “Correction of a Genetic Disease in Mouse via Use of CRISPR-Cas9,” Cell Stem Cell, Brief Report, vol. 13, Dec. 5, 2013, pp. 659-662. cited by applicant
Yamano et al., “Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA,” Cell, vol. 165, May 5, 2016 (pp. 949-962). cited by applicant
Zhu et al., “A CRISPR/Cas-Mediated Selection-free Knockin Strategy in Human Embryonic Stem Cells,” Stem Cell Reports, Jun. 9, 2015, vol. 4, (pp. 1103-1111). cited by applicant
U.S. Appl. No. 14/975,085, filed Dec. 18, 2015. cited by applicant
U.S. Appl. No. 15/783,770, filed Oct. 13, 2017. cited by applicant
U.S. Appl. No. 15/844,608, filed Dec. 17, 2017. cited by applicant
U.S. Appl. No. 16/048,038, filed Jul. 27, 2018. cited by applicant
U.S. Appl. No. 16/071,896, filed Jul. 20, 2018. cited by applicant
U.S. Appl. No. 16/095,170, filed Oct. 19, 2018. cited by applicant
U.S. Appl. No. 16/095,207, filed Oct. 19, 2018. cited by applicant
U.S. Appl. No. 16/095,253, filed Oct. 19, 2018. cited by applicant
U.S. Appl. No. 16/400,026, filed Apr. 30, 2019. cited by applicant
U.S. Appl. No. 16/909,064, filed Jun. 23, 2020. cited by applicant
U.S. Appl. No. 16/909,101, filed Jun. 23, 2020. cited by applicant
U.S. Appl. No. 17/034,553, filed Sep. 28, 2020. cited by applicant
U.S. Appl. No. 17/554,314, filed Dec. 17, 2021. cited by applicant
U.S. Appl. No. 17/554,333, filed Dec. 17, 2021. cited by applicant
U.S. Appl. No. 17/666,248, filed Dec. 7, 2022. cited by applicant
Pougach, K.S., et al., “CRISPR Adaptive Immunity Systems of Prokaryotes,” Molecular Biology, 2012, vol. 46 (pp. 175-182). cited by applicant
Doudna et al., “The new frontier of genome engineering with CRISPR-Cas9,” Science, Nov. 28, 2014, vol. 346 (pp. 1077-1087). cited by applicant
Rohmer et al., Gen Bank accession No. AOQ7Q2, Dec. 9, 2015 (3 pages). cited by applicant
Singh et al., “Protein Engineering Approaches in the Post-Genomic Era,” Current Protein and Peptide Science, 2018, vol. 19, No. 1 (pp. 5-15). cited by applicant
Calero-Garcia et al., “Gene-ectomy: Gene Ablation with CRISPR/Cas9 in Human Hematopoietic Cells,” Cell Stem Cell, Nov. 6, 2014 (2 pages). cited by applicant
Long et al., “Prevention of muscular dystrophy in mice by CRISPR/Cas9 mediated editing of germline DNA,” Science, Sep. 5, 2014, vol. 345, No. 6201 (pp. 1184-1188). cited by applicant

edspgr.12110490