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Gootenberg, Jonathan

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Gootenberg

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Jonathan

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Gootenberg, Jonathan

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2015 - 20205

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Author's Publications: search.filters.isAuthorOfPublication.3a31d596-4caf-4879-995c-3a4034628ff9

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Now showing 1 - 6 of 6
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    In vivo genome editing using Staphylococcus aureus Cas9
    (2015) Ran, F. Ann; Cong, Le; Yan, Winston; Scott, David A.; Gootenberg, Jonathan; Kriz, Andrea J.; Zetsche, Bernd; Shalem, Ophir; Wu, Xuebing; Makarova, Kira S.; Koonin, Eugene; Sharp, Phillip A.; Zhang, Feng
    The RNA-guided endonuclease Cas9 has emerged as a versatile genome-editing platform. However, the size of the commonly used Cas9 from Streptococcus pyogenes (SpCas9) limits its utility for basic research and therapeutic applications that employ the highly versatile adeno-associated virus (AAV) delivery vehicle. Here, we characterize six smaller Cas9 orthologs and show that Cas9 from Staphylococcus aureus (SaCas9) can edit the genome with efficiencies similar to those of SpCas9, while being >1kb shorter. We packaged SaCas9 and its sgRNA expression cassette into a single AAV vector and targeted the cholesterol regulatory gene Pcsk9 in the mouse liver. Within one week of injection, we observed >40% gene modification, accompanied by significant reductions in serum Pcsk9 and total cholesterol levels. We further demonstrate the power of using BLESS to assess the genome-wide targeting specificity of SaCas9 and SpCas9, and show that SaCas9 can mediate genome editing in vivo with high specificity.
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    Field-deployable viral diagnostics using CRISPR-Cas13
    Yozwiak, Nathan; Michael, Scott; Isern, Sharon; Nogueira, Mauricio; Barnes, Kayle; Freije, Catherine; Sabeti, Pardis; Abudayyeh, Omar; Gehrke, Lee; Myhrvold, Cameron; Bosch, Irene; Durbin, Ann; Gootenberg, Jonathan; Kellner, Max; Zhang, Feng; Metsky, Hayden; Tan, Amanda; Parham, Leda; Garcia, Kimberly; Lorenzana, Ivette; Chak, Bridget; Mondini, Adriano; Macinnis, Bronwyn; Paul, Lauren
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    Barcode extension for analysis and reconstruction of structures
    (Nature Publishing Group, 2017) Myhrvold, Cameron; Baym, Michael; Hanikel, Nikita; Ong, Luvena L; Gootenberg, Jonathan; Yin, Peng
    Collections of DNA sequences can be rationally designed to self-assemble into predictable three-dimensional structures. The geometric and functional diversity of DNA nanostructures created to date has been enhanced by improvements in DNA synthesis and computational design. However, existing methods for structure characterization typically image the final product or laboriously determine the presence of individual, labelled strands using gel electrophoresis. Here we introduce a new method of structure characterization that uses barcode extension and next-generation DNA sequencing to quantitatively measure the incorporation of every strand into a DNA nanostructure. By quantifying the relative abundances of distinct DNA species in product and monomer bands, we can study the influence of geometry and sequence on assembly. We have tested our method using 2D and 3D DNA brick and DNA origami structures. Our method is general and should be extensible to a wide variety of DNA nanostructures.
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    Multiplex gene editing by CRISPR-Cpf1 through autonomous processing of a single crRNA array
    (2016) Zetsche, Bernd; Heidenreich, Matthias; Mohanraju, Prarthana; Fedorova, Iana; Kneppers, Jeroen; DeGennaro, Ellen M.; Winblad, Nerges; Choudhury, Sourav R.; Abudayyeh, Omar O.; Gootenberg, Jonathan; Wu, Wen Y.; Scott, David A.; Severinov, Konstantin; van der Oost, John; Zhang, Feng
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    Orthogonal gene knock out and activation with a catalytically active Cas9 nuclease
    (2015) Dahlman, James E.; Abudayyeh, Omar O.; Joung, Julia; Gootenberg, Jonathan; Zhang, Feng; Konermann, Silvana
    We have developed a CRISPR-based method that uses catalytically active Cas9 and distinct sgRNA constructs to knock out and activate different genes in the same cell. These sgRNAs, with 14 15 bp target sequences and MS2 binding loops, can activate gene expression using an active Cas9 nuclease, without inducing DSBs. We use these ‘dead RNAs’ to perform orthogonal gene knockout and transcriptional activation in human cells.
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    Clinical Validation of a Cas13-Based Assay for the Detection of SARS-CoV-2 RNA
    (2020-08-26) Petchsung, Maturada; Jantarug, Krittapas; Pattama, Archiraya; Aphicho, Kanokpol; Suraritdechachai, Surased; Meesawat, Piyachat; Sappakhaw, Khomkrit; Leelahakorn, Nattawat; Ruenkam, Theerawat; Wongsatit, Thanakrit; Athipanyasilp, Niracha; Eiamthong, Bhumrapee; Lakkanasirorat, Benya; Phoodokmai, Thitima; Niljianskul, Nootaree; Pakotiprapha, Danaya; Chanarat, Sittinan; Homchan, Aimorn; Tinikul, Ruchanok; Kamutira, Philaiwarong; Phiwkaow, Kochakorn; Soithongcharoen, Sahachat; Kantiwiriyawanitch, Chadaporn; Pongsupasa, Vinutsada; Trisrivirat, Duangthip; Jaroensuk, Juthamas; Wongnate, Thanyaporn; Maenpuen, Somchart; Chaiyen, Pimchai; Kamnerdnakta, Sirichai; Swangsri, Jirawat; Chuthapisith, Suebwong; Sirivatanauksorn, Yongyut; Chaimayo, Chutikarn; Sutthent, Ruengpung; Kantakamalakul, Wannee; Joung, Julia; Ladha, Alim; Jin, Xin; Gootenberg, Jonathan; Abudayyeh, Omar; Zhang, Feng; Horthongkham, Navin; Uttamapinant, Chayasith; Uttamapinant