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  1. Plan Your Experiment

    Type
    Collection
    ...designed your gRNA(s), the next step is to choose how to express your Cas enzyme and gRNA(s) in your target...., Adamson, B., Norman, T. M., Lander, E. S., Weissman, J. S., Friedman, N., & Regev, A. (2016). Perturb-Seq...Ploegh, H. L., Bassik, M. C., Qi, L. S., Kampmann, M., & Weissman, J. S. (2014). Genome-Scale CRISPR-Mediated...References CRISPR ( C lustered R egularly I nterspaced S hort P alindromic R epeats) is a powerful system that...generally only compatible with smaller Cas enzymes, like S. aureus Cas9. For more information, see our blog post...

  2. Fluorescent Proteins: FRET

    Type
    Collection
    ...BRET assays. References Bajar, B. T., Wang, E. S., Zhang, S., Lin, M. Z., & Chu, J. (2016). A Guide to Fluorescent...new window) Algar, W. R., Hildebrandt, N., Vogel, S. S., & Medintz, I. L. (2019). FRET as a biomolecular...

  5. Typing CRISPR Systems

    Type
    Blog Post
    ....2017.05.008 Makarova, K. S., Wolf, Y. I., Alkhnbashi, O. S., Costa, F., Shah, S. A., Saunders, S. J., Barrangou,... Makarova, K. S., Wolf, Y. I., Iranzo, J., Shmakov, S. A., Alkhnbashi, O. S., Brouns, S. J. J., Charpentier...H., Kannan, S., Suberski, A. J., Mears, K. S., Demircioglu, F. E., Moeller, L., Kocalar, S., Oshiro, R...Keston-Smith, E., Sothiselvam, S., Garrity, A. J., Chong, S., Makarova, K. S., Koonin, E. V., Cheng, D. R...References Abudayyeh, O. O., Gootenberg, J. S., Essletzbichler, P., Han, S., Joung, J., Belanto, J. J., Verdine...Barrangou, R., Brouns, S. J. J., Charpentier, E., Haft, D. H., Horvath, P., Moineau, S., Mojica, F. J. M., Terns..., D. H., Horvath, P., Moineau, S., Mojica, F. J. M., Scott, D., Shah, S. A., Siksnys, V., Terns, M. P....

  6. Empty Backbones - Choosing Your Perfect Plasmid Backbone

    Type
    Collection
    ...expression empty vector pFA6a vectors - Epitope tagging in S. pombe Insect/Baculovirus UAS, MT, Polyhedrin Targeted...expression pFA6a vectors - PCR-based C-terminal tagging in S. cerevisiae pCS2FLAG - N- or C-terminal ...display of proteins on the extracellular surface of S. cerevisiae cells His-tagged versions of pFastBac ... Plasmids page pBF3060 - Metabolic engineering in S. cerevisiae TALENs Gene targeting TALEN kits - Construct...capture and expression of bacterial gene clusters S. cerevisiae plasmids for multiple marker selection...

  7. K. phaffii: Rising to the Occasion

    Type
    Blog Post
    ...it grows fast to boot. The yeast strains S. cerevisiae and S. pombe have dominated the research scene....the most frequently used yeast strains: S. pombe (fission) and S. cerevisiae (budding). Yeast make for ...probably wondering if the “biotech yeast” is S. pombe or S. cerevisiae. Actually, it’s neither. The most...phaffii and other yeast strains.     S. cerevisiae S. pombe K. phaffii Growth properties ...glycerol). K. phaffii is only distantly related to S. pombe and S. cerevisiae; evolutionarily it evolved much... K. phaffii to work   The yeast giants - S. cerevisiae and S. pombe - aren’t going anywhere anytime soon...Amenable to genetic manipulation The first eukaryote (S. cerevisiae) to have its genome fully sequenced There...

  8. Mammalian RNAi Tools

    Type
    Collection
    ... Marmari, V., Ebrahimi, M., Rashno, M. M., Abadi, S. J., & Gharagouzlo, E. (2017). Molecular mechanisms... opens in a new window) . Rao, D. D., Vorhies, J. S., Senzer, N., & Nemunaitis, J. (2009). siRNA vs. shRNA...

  9. Degrading DNA with Cascade-Cas3

    Type
    Blog Post
    ...0 Makarova, K. S., Wolf, Y. I., Alkhnbashi, O. S., Costa, F., Shah, S. A., Saunders, S. J., Barrangou,...Toh, M. S., Irby, M. J., Edwards, L. S., Lin, C., Owen, A. L. G., Künne, T., . . . Sternberg, S. H. (2019...Cas3’s degradative power in the future! References and Resources References Loeff, L., Brouns, S. J.,... H., Sasakawa, N., Naito, Y., Nakada, S., Yamamoto, T., Sano, S., Hotta, A., Takeda, J., & Mashimo, T....x Cameron, P., Coons, M. M., Klompe, S. E., Lied, A. M., Smith, S. C., Vidal, B., Donohoue, P. D., Rotstein...Barrangou, R., Brouns, S. J. J., Charpentier, E., Haft, D. H., Horvath, P., Moineau, S., Mojica, F. J. M., Terns...through the Cas3. This mechanism is important for Cas3’s biggest trick. Cas3 likes to bluff, making you into...

  10. Plasmids 101: Yeast Vectors

    Type
    Blog Post
    ...source. S. cerevisiae  no no   LEU2 L-leucine no S. cerevisiae yes - This can complement leu1- S. pombe...L-hisitidine no S. cerevisiae  no yes   URA3 pyrimidine (uracil) yes - Grow with 5-FOA. S. cerevisiae yes... ura4+. leu1+ L-leucine   S. pombe  no no   ade6+ purine (adenine)   S. pombe  no no   Considerations...are included (reviewed here). Plasmids for use in S. pombe, on the other hand, do not require a well defined...sequence) dictate the replication of these vectors. S. pombe plasmids oftentimes utilize an ARS to aid in... yes - This can complement ura4- S. pombe, but the complementation is weak. yes   LYS2 L-lysine yes ... yes   TRP1 L-tryptophan yes - Grow with 5-FAA. S. cerevisiae no  no TRP1 alters some yeast phenotypes...

  11. AAV for Neuronal Tracing

    Type
    Collection
    ... Neuronal Tracing References Wickersham IR, Finke S, Conzelmann KK, Callaway EM. 2007a. Retrograde neuronal...Wickersham IR, Lyon DC, Barnard RJ, Mori T, Finke S, Conzelmann KK, Young JA, Callaway EM. 2007b. Monosynaptic...

  12. CASTing Off for New Shores in Human Genome Editing

    Type
    Blog Post
    ...s41596-023-00927-3 Klompe, S. E., Vo, P. L. H., Halpin-Healy, T. S., & Sternberg, S. H. (2019). Transposon-encoded.... R., Vo, P. L. H., Klompe, S. E., Ronda, C., Wang, H. H., & Sternberg, S. H. (2024). Bacterial genome...s41586-019-1323-z Peters, J. E., Makarova, K. S., Shmakov, S., & Koonin, E. V. (2017). Recruitment of CRISPR-Cas....1709035114 Witte, I. P., Lampe, G. D., Eitzinger, S., Miller, S. M., Berríos, K. N., McElroy, A. N., King, R...Chen, A. T., Tolar, J., Osborn, M. J., Sternberg, S. H., & Liu, D. R. (2025). Programmable gene insertion...

  13. A Needle in a Base-Stack: Cas9 Structural Biology

    Type
    Blog Post
    ...Osuka, S., Isomura, K., Kajimoto, S., Komori, T., Nishimasu, H., Shima, T., Nureki, O., & Uemura, S. (2018... J. P. K., Liu, M.-S., Hibshman, G. N., Dangerfield, T. L., Jung, K., McCool, R. S., Johnson, K. A., &...Nishimasu, H., Ran, F. A., Hsu, P. D., Konermann, S., Shehata, S. I., Dohmae, N., Ishitani, R., Zhang, F., &...://doi.org/10.1038/nature15544 Sternberg, S. H., Redding, S., Jinek, M., Greene, E. C., & Doudna, J. A....   Figure 1: A cartoon depiction of Cas9’s two major lobes, REC and NUC, and their subdomains...pyogenes.   Figure 2:  Crystal structure of S. pyogenes Cas9 in the apo state (PDB ID 4CMP) with...can offer more information on these regions.   Cas9’s transition from weak, random binding to precision ...

  14. Pathways Over Time Plasmids Engage Students in Functional Genomics Research

    Type
    Blog Post
    ...rearrangements in the S. cerevisiae lineage (7). In our class research project, students transform S. cerevisiae...plasmids carrying MET/Met genes from either S. pombe or S. cerevisiae. Students then determine if expression...shown that most, but not all, S. pombe Met genes complement the corresponding S. cerevisiae met deficiencies...strains is available (6). Methionine synthesis in S. cerevisiae (Figure 1) occurs through a well-characterized..., have the same function as their counterparts in S. cerevisiae. The two yeasts are thought to have diverged... the plasmids in either E. coli (ori and ampR) or S. cerevisiae (2µm ori and URA3). The presence of the...successfully transformed with the plasmids, because the S. cerevisiae deletion strains are ∆ura3 mutants and...

  15. The PAM Requirement and Expanding CRISPR Beyond SpCas9

    Type
    Blog Post
    ...Addgene. Kim D, Kim J, Hur JK, Been KW, Yoon S, Kim J-S (2016) Genome-wide analysis reveals specificities...Cho H-Y, Song DW, Lee KJ, Jung MH, Kim S, Kim JH, Kim JH, Kim J-S (2017) In vivo genome editing with a ...sequences While PAM sequences for the commonly used S. pyogenes Cas9 (3'-NGG) are abundant throughout the...to circumvent this limitation: 1) the use of novel S. pyogenes Cas9 variants with varying PAM sequences... of Cas9 homologs derived from species other than S. pyogenes, and 3) the use of non-Cas9 enzymes. (For...site, check out this video from IGI!) Synthetic S. pyogenes Cas9s with novel PAM recognition In 2015...selection screens in bacteria to identify mutants of S. pyogenes Cas9 that were able to cleave target DNA...

  16. Viral Vectors 101: AAV Serotypes and Tissue Tropism

    Type
    Blog Post
    ...B.-Y., Viswanathan, S., Gaj, T., Lavzin, M., Ritola, K. D., Lindo, S., Michael, S., Kuleshova, E., Ojala...resources References Ahuja, V., Jeyabalan, S., & Tzanakakis, E. S. (2025). Evaluation of transduction efficiency...https://doi.org/10.1038/s41467-023-39554-7 Issa, S. S., Shaimardanova, A. A., Solovyeva, V. V., & Rizvanov... L., Marhic, A., Chapart, M., Vasseur, S., Benkhelifa-Ziyyat, S., Bigot, A., Butler-Browne, G., Mouly,...doi.org/10.1089/hum.2019.173 Pillay, S., Meyer, N. L., Puschnik, A. S., Davulcu, O., Diep, J., Ishikawa,...j.neuron.2016.09.021 Walters, R. W., Yi, S. M., Keshavjee, S., Brown, K. E., Welsh, M. J., Chiorini, J...., Wong, A. C. H., Gokal, D., Feng, Y., Tabar, M. S., Metierre, C., Parsania, C., Song, X., Wang, G., ...

  17. Viral Vectors 101: AAV Variables That Matter

    Type
    Blog Post
    ...and happy optimizing!  Recommended Reading Issa, S. S., Shaimardanova, A. A., Solovyeva, V. V., & Rizvanov...Resources References Aschauer, D. F., Kreuz, S., & Rumpel, S. (2013). Analysis of Transduction Efficiency...10.1089/hum.2009.169 Dudek, A. M., Pillay, S., Puschnik, A. S., Nagamine, C. M., Cheng, F., Qiu, J., Carette... https://doi.org/10.1038/s41434-019-0075-6 Issa, S. S., Shaimardanova, A. A., Solovyeva, V. V., & Rizvanov...10.1371/journal.pone.0076310 Damdindorj, L., Karnan, S., Ota, A., Hossain, E., Konishi, Y., Hosokawa, Y.,...Fong, D. M., Mouravlev, A., Young, D., & O’Carroll, S. J. (2019). Astrocyte-selective AAV gene therapy through...cells12050785 Kanaan, N. M., Sellnow, R. C., Boye, S. L., Coberly, B., Bennett, A., Agbandje-McKenna, M...

  18. The Advances Behind The World's First Personalized CRISPR Treatment

    Type
    Blog Post
    ..., J. C., McCague, S., Burke, S. M., Wright, C. M., Bick, S., Indurthi, V., Sharma, S., … Ahrens-Nicklas...Edwards, A., Gehrke, J. M., Lee, S.-J., Liquori, A. J., Murray, R., Packer, M. S., Rinaldi, C., Slaymaker, I...Benjamin Kleinstiver’s lab engineered new variants of S. pyogenes Cas9. While the wild-type enzyme requires...Resources References Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P. D., Wu, X., Jiang...Gaudelli, N. M., Komor, A. C., Rees, H. A., Packer, M. S., Badran, A. H., Bryson, D. I., & Liu, D. R. (2017...-020-0491-6  Komor, A. C., Kim, Y. B., Packer, M. S., Zuris, J. A., & Liu, D. R. (2016). Programmable .... https://doi.org/10.1038/nature17946  Lander, E. S. (2016). The Heroes of CRISPR. Cell, 164(1), 18–28...

  19. Cpf1: A New Tool for CRISPR Genome Editing

    Type
    Blog Post
    ...depletion assay to discover FnCpf1’s PAM sequence requirements. Cpf1’s preferred PAM is 5’-TTN, differing...RuvC-like endonuclease domain, but they lack Cas9’s second HNH endonuclease domain. Cpf1 cleaves DNA in... RuvC-like endonuclease domain, but it lacks Cas9’s other HNH endonuclease domain, indicating that Cpf1... nuclease could potentially overcome some of Cas9’s shortcomings - namely its blunt double stranded cleavage...nucleotides in length, about the same size as Cas9’s, but with the direct repeat preceding the spacer rather...crRNA is also much simpler in structure than Cas9’s; only a short stem-loop structure in the direct repeat... added another option to the CRISPR toolbox. Cpf1’s staggered cleavage pattern opens up the possibility...

  20. Plasmids for Stem Cell Research

    Type
    Collection
    ...induced pluripotent stem cells. Proc Natl Acad Sci U S A. 2014 Jul 22;111(29):10678-83. Capecchi Replicating...single polycistronic vector. Proc Natl Acad Sci U S A. 2009 Jan 6. 106(1):157-62. Jaenisch Lentivirus ... of canonical Wnt signaling. Proc Natl Acad Sci U S A. 2012 May 29. Palecek Fibroblasts Cardiomyocytes...fibroblasts to dopaminergic neurons. Proc Natl Acad Sci U S A. 2011 Jun 21;108(25):10343-8. Parmar Fibroblasts...tripotent neural precursor cells. Proc Natl Acad Sci U S A. 2012 Feb 14;109(7):2527-32. Wernig Fibroblasts ...
Showing: 21 - 40 of 431 results