RNA-guided DNA insertion with CRISPR-associated transposases by Strecker, Jonathan, Ladha, Alim, Gardner, Zachary, Schmid-Burgk, Jonathan L., Makarova, Kira S., Koonin, Eugene V., Zhang, Feng

“…ShCAST catalyzes RNA-guided DNA transposition by unidirectionally inserting segments of DNA 60 to 66 base pairs downstream of the protospacer. …”
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DNA targeting specificity of RNA-guided Cas9 nucleases by Hsu, Patrick, Scott, David Arthur, Weinstein, Joshua, Ran, F. Ann, Konermann, Silvana M., Agarwala, Vineeta, Li, Yinqing, Fine, Eli J., Wu, Xavier, Shalem, Ophir, Cradick, Thomas J., Marraffini, Luciano A., Bao, Gang, Zhang, Feng

“…The Streptococcus pyogenes Cas9 (SpCas9) nuclease can be efficiently targeted to genomic loci by means of single-guide RNAs (sgRNAs) to enable genome editing1, 2, 3, 4, 5, 6, 7, 8, 9, 10. …”
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The Transposon-Encoded Protein TnpB is an RNA-Guided Nuclease by Nety, Suchita P.

“…We investigate the biogenesis of the guide RNA, finding that TnpB can process its own mRNA to yield the guide RNA. …”
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RNA-guided editing of bacterial genomes using CRISPR-Cas systems by Jiang, Wenyan, Bikard, David, Cox, David Daniel, Zhang, Feng, Marraffini, Luciano A.

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Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA by Nishimasu, Hiroshi, Dohmae, Naoshi, Ishitani, Ryuichiro, Nureki, Osamu, Ran, Fei, Hsu, Patrick, Konermann, Silvana M, Shehata, Soraya I., Zhang, Feng

“…The CRISPR-associated endonuclease Cas9 can be targeted to specific genomic loci by single guide RNAs (sgRNAs). Here, we report the crystal structure of Streptococcus pyogenes Cas9 in complex with sgRNA and its target DNA at 2.5 Å resolution. …”
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Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA by Nishimasu, Hiroshi, Dohmae, Naoshi, Ishitani, Ryuichiro, Nureki, Osamu, Ran, Fei, Hsu, Patrick, Konermann, Silvana M, Shehata, Soraya I., Zhang, Feng

“…The CRISPR-associated endonuclease Cas9 can be targeted to specific genomic loci by single guide RNAs (sgRNAs). Here, we report the crystal structure of Streptococcus pyogenes Cas9 in complex with sgRNA and its target DNA at 2.5 Å resolution. …”
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Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity by Ran, F. Ann, Hsu, Patrick D., Lin, Chie Yu, Gootenberg, Jonathan S., Konermann, Silvana M., Trevino, Alexandro E., Scott, David A., Inoue, Azusa, Matoba, Shogo, Zhang, Yi, Zhang, Feng, Ran, F. Ann, Scott, David Arthur, Hsu, Patrick D.

“…Here, we describe an approach that combines a Cas9 nickase mutant with paired guide RNAs to introduce targeted double-strand breaks. …”
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The widespread IS200/IS605 transposon family encodes diverse programmable RNA-guided endonucleases by Altae-Tran, Han, Kannan, Soumya, Demircioglu, F Esra, Oshiro, Rachel, Nety, Suchita P, McKay, Luke J, Dlakić, Mensur, Inskeep, William P, Makarova, Kira S, Macrae, Rhiannon K, Koonin, Eugene V, Zhang, Feng

“…This work reveals a widespread class of transposon-encoded RNA-guided nucleases, which we name OMEGA (obligate mobile element–guided activity), with strong potential for developing as biotechnologies.…”
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Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System by Makarova, Kira S., van der Oost, John, Koonin, Eugene V., Zetsche, Bernd, Gootenberg, Jonathan S, Abudayyeh, Omar Osama, Slaymaker, Ian, Essletzbichler, Patrick, Volz, Sara E., Joung, Julia, Regev, Aviv, Zhang, Feng

“…Cpf1 is a single RNA-guided endonuclease lacking tracrRNA, and it utilizes a T-rich protospacer adjacent motif. …”
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C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector by Shmakov, S., Makarova, K. S., Semenova, E., Minakhin, L., Severinov, K., Koonin, E. V., Regev, Aviv, Gootenberg, Jonathan S, Konermann, Silvana M, Joung, Julia, Slaymaker, Ian, Cox, David Benjamin Turitz, Lander, Eric Steven, Zhang, Feng, Abudayyeh, Omar O.

“…In vitro biochemical analysis shows that C2c2 is guided by a single CRISPR RNA and can be programmed to cleave single-stranded RNA targets carrying complementary protospacers. …”
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Cas13b Is a Type VI-B CRISPR-Associated RNA-Guided RNase Differentially Regulated by Accessory Proteins Csx27 and Csx28 by Shmakov, Sergey, Makarova, Kira S., Koonin, Eugene V., Smargon, Aaron Andrew, Cox, David Benjamin Turitz, Pyzocha, Neena, Zheng, Kaijie, Slaymaker, Ian, Gootenberg, Jonathan S, Essletzbichler, Patrick, Zhang, Feng, Abudayyeh, Omar O.

“…CRISPR-Cas adaptive immune systems defend microbes against foreign nucleic acids via RNA-guided endonucleases. Using a computational sequence database mining approach, we identify two class 2 CRISPR-Cas systems (subtype VI-B) that lack Cas1 and Cas2 and encompass a single large effector protein, Cas13b, along with one of two previously uncharacterized associated proteins, Csx27 and Csx28. …”
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Structural basis for the promiscuous PAM recognition by Corynebacterium diphtheriae Cas9 by Hirano, Seiichi, Abudayyeh, Omar O., Gootenberg, Jonathan S, Horii, Takuro, Ishitani, Ryuichiro, Hatada, Izuho, Zhang, Feng, Nishimasu, Hiroshi, Nureki, Osamu

“…The RNA-guided DNA endonuclease Cas9 cleaves double-stranded DNA targets bearing a protospacer adjacent motif (PAM) and complementarity to an RNA guide. …”
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Structure and engineering of the minimal type VI CRISPR-Cas13bt3 by Nakagawa, Ryoya, Kannan, Soumya, Altae-Tran, Han, Takeda, Satoru N, Tomita, Atsuhiro, Hirano, Hisato, Kusakizako, Tsukasa, Nishizawa, Tomohiro, Yamashita, Keitaro, Zhang, Feng, Nishimasu, Hiroshi, Nureki, Osamu

“…Here, we report the structures of the Cas13bt3-guide RNA complex and the Cas13bt3-guide RNA-target RNA complex. …”
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Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells by Hartenian, E., Shi, X., Mikkelsen, T. S., Heckl, D., Ebert, B. L., Root, D. E., Doench, J. G., Shalem, Ophir, Sanjana, Neville E, Scott, David Arthur, Zhang, Feng

“…We show that lentiviral delivery of a genome-scale CRISPR-Cas9 knockout (GeCKO) library targeting 18,080 genes with 64,751 unique guide sequences enables both negative and positive selection screening in human cells. …”
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Structure and Engineering of Francisella novicida Cas9 by Hirano, Hisato, Horii, Takuro, Kimura, Mika, Nakane, Takanori, Ishitani, Ryuichiro, Hatada, Izuho, Nishimasu, Hiroshi, Nureki, Osamu, Gootenberg, Jonathan S, Abudayyeh, Omar Osama, Hsu, Patrick, Zhang, Feng

“…Summary The RNA-guided endonuclease Cas9 cleaves double-stranded DNA targets complementary to the guide RNA and has been applied to programmable genome editing. …”
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Crystal Structure of Staphylococcus aureus Cas9 by Nishimasu, Hiroshi, Ran, F. Ann, Kurabayashi, Arisa, Ishitani, Ryuichiro, Nureki, Osamu, Cong, Le, Yan, Winston Xia, Zetsche, Bernd, Li, Yinqing, Zhang, Feng

“…Summary The RNA-guided DNA endonuclease Cas9 cleaves double-stranded DNA targets with a protospacer adjacent mot if (PAM) and complementarity to the guide RNA. …”
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Implications of human genetic variation in CRISPR-based therapeutic genome editing by Scott, David A, Zhang, Feng

“…We find that this genetic variation confounds the target sites of certain Cas endonucleases more than others, and we provide a compendium of guide RNAs predicted to have high efficacy in diverse patient populations. …”
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Structure of the IscB–ωRNA ribonucleoprotein complex, the likely ancestor of CRISPR-Cas9 by Kato, Kazuki, Okazaki, Sae, Kannan, Soumya, Altae-Tran, Han, Esra Demircioglu, F, Isayama, Yukari, Ishikawa, Junichiro, Fukuda, Masahiro, Macrae, Rhiannon K, Nishizawa, Tomohiro, Makarova, Kira S, Koonin, Eugene V, Zhang, Feng, Nishimasu, Hiroshi

“…<jats:title>Abstract</jats:title><jats:p>Transposon-encoded IscB family proteins are RNA-guided nucleases in the OMEGA (obligate mobile element-guided activity) system, and likely ancestors of the RNA-guided nuclease Cas9 in the type II CRISPR-Cas adaptive immune system. …”
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Genome engineering using the CRISPR-Cas9 system by Ran, F. Ann, Hsu, Patrick, Wright, Jason, Agarwala, Vineeta, Scott, David Arthur, Zhang, Feng

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Improved vectors and genome-wide libraries for CRISPR screening by Sanjana, Neville E, Shalem, Ophir, Zhang, Feng

“…We sought to improve both the lentiviral packaging and choice of guide sequences in our original GeCKO library1, where a pooled library of synthesized oligonucleotides was cloned into a lentiviral backbone containing both the Streptococcus pyogenes Cas9 nuclease and the single guide RNA (sgRNA) scaffold. …”
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