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  1. Plasmids 101: Codon usage bias

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    Blog Post
    ...genetic code is used by most organisms on Earth, but different organisms have different preferences for...codons are used preferentially in which organisms - organisms have codon usage bias. You can find many...peptide of interest and produce that peptide in your organism of choice. Unfortunately, codon preferences make...and expect your sequence to express well in any organism. So what are the evolutionary constraints that... do about them? Read on to find out!   Why do organisms have different codon usage biases? The reasons...reasons for varied codon preferences among organisms aren’t completely understood, but some possible reasons... tRNAs with the appropriate amino acids. If an organism uses only a subset of codons, it only needs to...

  2. RNA Interference in Plant Biology: New Tools for an Old Favorite

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    ...many organisms. When supplemented with adenine analogs such as 2-fluoroadenine (2-FA), organisms with ...Zurich. He is fascinated by how organisms exquisitely and robustly self-organize at the cellular and multicellular...Plant Cell 25:1507–1522 . https://doi.org/10.1105/tpc.113.112235 Morgens DW, Deans RM, Li A, Bassik MC (...Fortunately, researchers studying plants and other organisms lacking this innate immunity need not worry and...different genes known to be required for viability (Morgens et al., 2016). Only upon combining the data generated...plants Once you’ve introduced your RNAi into your organism, how do you identify the actively silenced ones... of APT and any gene target of interest, only organisms that are actively silencing to a sufficient degree...

  3. Live and Let Dye: Self-Labeling Protein Tags

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    ... fluorescent protein somebody made because they forgot it was already in the freezer… you get the idea...Various Many Complicated   Applications Organic dyes are typically both brighter and more photostable...imaging of ER and mitochondria reveals dynamic organelle interactions. a) Labeling scheme. b) COS-7 cell...at a price, though. Purchasing lots and lots of organic dyes or specialized ligands is more expensive than...ligands brings up bad memories of undergraduate organic chemistry lab, don’t worry – many SNAP-tag and ...Nature Communications, 7(1), Article 1. https://doi.org/10.1038/ncomms10778 Erdmann, R. S., Baguley, S....Cell Chemical Biology, 26(4), 584-592.e6. https://doi.org/10.1016/j.chembiol.2019.01.003 Gallagher, S. S....

  4. Quick Guide to Near-Infrared Fluorescent Proteins

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    ... Ref BphP-based FPs miRFP670 https://www.addgene.org/79987/ 642 670 87,400 14.0 198 Monomer  155...155 4.5 72 5 miRFP703 https://www.addgene.org/79988/ 674 703 90,900 8.6 127 Monomer 394 4.5 37 ... miRFP709 https://www.addgene.org/79989/ 683 709 78,400 5.4 69 Monomer 192 4.5 30 mIFP https://www.addgene.org...112 Monomer 54 4.5 15  15 miRFP https://www.addgene.org/108409/ 674 703 92,400 9.7 145 Monomer ND ...ND 4.3 ND 16 IFP2.0 e https://www.addgene.org/54785/ 688 709 98,000 8.1 128 Dimer 108 4.5 8  17 ... iRFP670 https://www.addgene.org/45457/ 643 670 114,000 12.2 225 Dimer 290 4.0 119 18 iRFP682 https...https://www.addgene.org/45459/ 663 682 90,000 11.1 162 Dimer 490 4.5 105 iRFP702 https://www.addgene.org...

  5. Deep Dive: Fixing and Permeabilizing for Immunofluorescence

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    ...reagents to use - organic solvents and detergents.  Organic Solvents  As mentioned above, organic solvents can... for use with this type of fixation*. Organic Solvents Organic solvents, generally acetone, methanol,...types of fixatives - chemical cross-linkers and organic solvents.  Chemical Cross-Linkers Chemical cross-linkers...quite as well as a cross-linker. This is because organic solvents can be quite harsh - lipids and soluble...disrupt your target epitope (Fig. 1). So, while organic solvents may improve antibody binding for some ...targets, they can destroy it for others. That said, organic solvents’ impact on lipids means that they are ...and permeabilize a sample. But you can also use organic solvents after fixing your sample with a cross-...

  6. Overcoming the AAV Size Limitation for CRISPR Delivery

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    ...host response. Nat Methods 13:868–874 . https://doi.org/10.1038/nmeth.3993  Cong L, Ran FA, Cox D, Lin ...CRISPR/Cas Systems. Science 339:819–823 .https://doi.org/10.1126/science.1231143  Cox DBT, Gootenberg JS... CRISPR-Cas13. Science 358:1019–1027 . https://doi.org/10.1126/science.aaq0180  Fine EJ, Appleton CM, ...compact expression cassettes. Sci Rep 5: . https://doi.org/10.1038/srep10777  Garneau JE, Dupuis M-È, Villion...bacteriophage and plasmid DNA. Nature 468:67–71 . https://doi.org/10.1038/nature09523  Ibraheim R, Song C-Q, Mir ...meningitidis Cas9 in vivo. Genome Biol 19: . https://doi.org/10.1186/s13059-018-1515-0  Kim E, Koo T, Park SW... Campylobacter jejuni. Nat Commun 8: . https://doi.org/10.1038/ncomms14500  Levy JM, Yeh W-H, Pendse N...

  7. Summer SciComm: Preprints

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    ...and biomedical scientists (see: bioRxiv.org or medRxiv.org) in the past few years.   Figure 1: Stand...fields like math and physics for decades (see: arXiv.org), but have been only adopted by biological and...their CV or grant applications. A number of organizations (such as ASAPbio) advocate for preprints, and...manuscript to a journal for formal peer review. Some organizations, including some journals, also support open ...general public (say, policymakers or community organizations) to use your work but don’t think they’ll have...here at Addgene! Along with other open-science organizations, we support scientists in sharing their results...out there and finish that experiment (and don’t forget the controls!). And when you’re ready to write ...

  8. Viral Vectors 101: AAV Serotypes and Tissue Tropism

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    ...which allow AAVs to broadly spread throughout an organism, including difficult-to-target tissues like the...vector cargo designs and administration doses. Don't forget to submit your validation data after your experiment...serotypes. Scientific Reports, 15(1), 20927. https://doi.org/10.1038/s41598-025-05518-8 Bish, L. T., Morine,...Human Gene Therapy, 19(12), 1359–1368. https://doi.org/10.1089/hum.2008.123 Dhungel, B. P., Xu, H., Nagarajah... viruses. Cell, S0092-8674(25)00692-0. https://doi.org/10.1016/j.cell.2025.06.026 Halbert, C. L., Allen...Journal of Virology, 75(14), 6615–6624. https://doi.org/10.1128/jvi.75.14.6615-6624.2001 Han, Z., Luo, ...transduction. Nature Communications, 14(1), 3792. https://doi.org/10.1038/s41467-023-39554-7 Issa, S. S., Shaimardanova...

  9. CRISPR Activation: A Practical Guide

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    ...over-express coding sequences from a given cell type or organism, have been used in a similar manner to Cas9 activators...lines (HEK293T, MCF7, U2-OS, Hela, N2A, 3T3) and organisms (Chavez et al., 2016). To learn more about the...CRISPR–Cas9 screens. Nature 568:511–516 . https://doi.org/10.1038/s41586-019-1103-9 Bialek JK, Dunay GA, ...Activator Systems. PLoS ONE 11:e0158294 . https://doi.org/10.1371/journal.pone.0158294 Chari R, Mali P, Moosburner...library-on-library approach. Nat Methods 12:823–826 . https://doi.org/10.1038/nmeth.3473 Chavez A, Scheiman J, Vora S... programming. Nat Methods 12:326–328 . https://doi.org/10.1038/nmeth.3312 Chavez A, Tuttle M, Pruitt BW...multiple species. Nat Methods 13:563–567 . https://doi.org/10.1038/nmeth.3871 Gilbert LA, Horlbeck MA, Adamson...

  10. A History of Genome Engineering in Popular Culture

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    ...capability of transforming the genetic code of living organisms and its societal implications even before the ...pneumoniae bacteria could be transformed from one organism to the other. This is now famed as the Griffith...about other genome editing methods Resources on Addgene.org Visit our CRISPR guide Find CRISPR plasmids ...breaks or donor DNA. Nature 576:149–157 . https://doi.org/10.1038/s41586-019-1711-4 Avery OT, MacLeod CM,... of Experimental Medicine 79:137–158 . https://doi.org/10.1084/jem.79.2.137 Carroll D (2011) Genome Engineering...Zinc-Finger Nucleases. Genetics 188:773–782 . https://doi.org/10.1534/genetics.111.131433 Doudna JA, Charpentier...with CRISPR-Cas9. Science 346:1258096 . https://doi.org/10.1126/science.1258096 Gaudelli NM, Komor AC, ...

  11. Plasmids 101: Expressing shRNAs for RNA Interference

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    ...https://www.addgene.org/collections/mammalianrnai/","href_with_scheme":"https://www.addgene.org/collections...2004). MicroRNAs. Cell, 116(2), 281–297. https://doi.org/10.1016/s0092-8674(04)00045-5 De Rie, D., Abugessaisa... Nature Biotechnology, 35(9), 872–878. https://doi.org/10.1038/nbt.3947 Fire, A., Xu, S., Montgomery, ...Caenorhabditis elegans. Nature, 391(6669), 806–811. https://doi.org/10.1038/35888  Iwakawa, H., & Tomari, Y. (2021)...complex. Molecular Cell, 82(1), 30–43. https://doi.org/10.1016/j.molcel.2021.11.026 Kilikevicius, A., ...Nucleic Acids Research, 50(2), 617–634. https://doi.org/10.1093/nar/gkab1256 Lee, Y., Kim, M., Han, J.,.... The EMBO Journal, 23(20), 4051–4060. https://doi.org/10.1038/sj.emboj.7600385 McIntyre, G. J., & Fanning...

  12. An Introduction to Adenovirus

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    ...6936. https://doi.org/10.1128/JVI.73.8.6930-6936.1999. PMID: 10400791. Kafri, T., Morgan, D., Krahl, T...viral promoters. Mol Ther, 7(4), 526–534. https:/doi.org/10.1016/S1525-0016(03)00023-6. PMID: 12727116. ...Emerg Microbes Infect, 8(1), 1679–1687. https://doi.org/10.1080/22221751.2019.1690953. PMID: 31749409. ...Module in Biomedical Sciences. Elsevier. https://doi.org/10.1016/B978-0-12-801238-3.02523-X. Hofmann, C....Proc Natl Acad Sci U S A, 95(19), 11377. https://doi.org/10.1073/PNAS.95.19.11377. PMID: 9736744. Kremer...Complex. PLoS Pathog, 11(6), e1004821. https://doi.org/10.1371/journal.ppat.1004821. PMID: 26042599. Pereira... Pathol Suppl (R Coll Pathol)., 6, 39. https://doi.org/10.1136/jcp.s3-6.1.39. PMID: 4376152. Rowe, W. ...

  13. Getting to Know Expansion Microscopy

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    ...of a conoid. PLoS Biology 19:e3001020. https://doi.org/10.1371/journal.pbio.3001020  Chen F, Tillberg ...Expansion microscopy. Science 347:543–548. https://doi.org/10.1126/science.1260088 Damstra HG, Mohar B, Eddison...Expansion Microscopy (TREx). Elife 11:e73775. https://doi.org/10.7554/elife.73775  Dani A, Huang B, Bergan J,...Synapses in the Brain. Neuron 68:843–856. https://doi.org/10.1016/j.neuron.2010.11.021  Gambarotto D, Zwettler...microscopy (U-ExM). Nat Methods 16:71–74. https://doi.org/10.1038/s41592-018-0238-1  Klimas A, Gallagher ...expansion microscopy. Nat Biotechnol 1–12. https://doi.org/10.1038/s41587-022-01546-1  Mikhaylova M, Cloin...anti-tubulin nanobodies. Nat Commun 6:7933. https://doi.org/10.1038/ncomms8933  M’Saad O, Bewersdorf J (2020...

  14. CRISPR 101: Cytosine and Adenine Base Editors

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    ... Nature Biotechnology, 41(5), 663–672. https://doi.org/10.1038/s41587-022-01532-7 Gaudelli, N. M., Komor... cleavage. Nature, 551(7681), 464–471. https://doi.org/10.1038/nature24644 Gaudelli, N. M., Lam, D. K.... Nature Biotechnology, 38(7), 892–900. https://doi.org/10.1038/s41587-020-0491-6 Grünewald, J., Zhou, ... Nature Biotechnology, 38(7), 861–864. https://doi.org/10.1038/s41587-020-0535-y Kim, Y. B., Komor, A.... Nature Biotechnology, 35(4), 371–376. https://doi.org/10.1038/nbt.3803 Koblan, L. W., Doman, J. L., Wilson... Nature Biotechnology, 36(9), 843–846. https://doi.org/10.1038/nbt.4172 Komor, A. C., Kim, Y. B., Packer... cleavage. Nature, 533(7603), 420–424. https://doi.org/10.1038/nature17946 Komor, A. C., Zhao, K. T., ...

  15. Four Ways to Package Transgenes That Exceed the Size Limit of Adeno-associated Virus

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    ...in mice. J Clin Invest 118:1955–1964 . https://doi.org/10.1172/jci34316 Bak RO, Porteus MH (2017) CRISPR-Mediated...Donor Vectors. Cell Reports 20:750–756 . https://doi.org/10.1016/j.celrep.2017.06.064  Carvalho LS, Turunen...Retinal Targeting. Front Neurosci 11: . https://doi.org/10.3389/fnins.2017.00503  Chamberlain K, Riyad .... Human Gene Therapy Methods 27:1–12 . https://doi.org/10.1089/hgtb.2015.140 Frischmeyer PA (2002) An ...Termination Codons. Science 295:2258–2261 . https://doi.org/10.1126/science.1067338 Ghosh A, Yue Y, Lai Y, ...Manner. Molecular Therapy 16:124–130 . https://doi.org/10.1038/sj.mt.6300322 Halbert CL, Allen JM, Miller...larger gene. Nat Biotechnol 20:697–701 . https://doi.org/10.1038/nbt0702-697 Hirsch ML, Agbandje-McKenna...

  16. Plasmids 101: The Wide World of Natural Plasmids

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    ... a variety of functions that allow their host organisms to thrive in competitive environments. The genes...the competition, and Penicillium isn’t the only organism that knows it. Some bacteria possess plasmid-borne...encode genes that allow the host to infect other organisms. If you’ve ever wondered why E. coli is safe to...means to deliver DNA and other molecules to host organisms. For instance, vectors derived from the Agrobacterium...like by living where no one else wants to. Some organisms manage this with plasmids that allow them to eat... eat unusual substrates that other organisms can’t use. Other plasmids offer resistance to toxic substances... which protect the host from attacks by other organisms. To conserve energy, these specialized degradative...

  17. CRISPR 101: Epigenetics and Editing the Epigenome

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    ...editing. Nucleic Acids Research 47:e23–e23. https://doi.org/10.1093/nar/gky1286 Hilton IB, D’Ippolito AM, Vockley...enhancers. Nature Biotechnology 33:510–517 . https://doi.org/10.1038/nbt.3199 Find plasmids from this publication...genome. Nature Biotechnology 35:561–568 . https://doi.org/10.1038/nbt.3853 Find plasmids from this publication...fusion protein. Nature Communications 8: . https://doi.org/10.1038/ncomms16026 Find plasmids from this publication...Mammalian Genome. Cell 167:233–247.e17 . https://doi.org/10.1016/j.cell.2016.08.056 Find plasmids from ...proteins. Nature Biotechnology 31:1137–1142 . https://doi.org/10.1038/nbt.2726 Find plasmids from this publication... methylation. Biology Open 5:866–874 . https://doi.org/10.1242/bio.019067 Find plasmids from this publication...

  18. Using CRISPR/Cas9 to Edit Disease Out of the Genome

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    ... post was originally written in 2014 by Kendall Morgan and updated in 2022 by Lucie Wilson. Lucie is an...used to generate mutations in a wide range of organisms, but its potential to efficiently correct disease...functional correction of the gene in clonally expanded organoids. “CRISPR in adult stem cells has huge potential...potential, because the genomes of adult stem cells in organoid cultures are stable,” said Gerald Schwank, first..., however, because the disease affects multiple organ systems. Nevertheless, the findings are proof-of-principle...therapy.” Journal of cellular physiology.  https://doi.org/10.1002/jcp.30064 2. Barman et al. 2020. “A glance...CRISPR-Cas9 technology.” Current genetics. https://doi.org/10.1007/s00294-019-01040-3 3. Khatibi et al. 2021...

  19. Antibodies 101: Single Chain Fragment Variables (scFvs)

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    ...and Developmental Immunology 2012:1–15 . https://doi.org/10.1155/2012/980250  Bates A, Power CA (2019) David... Antibody Fragments. Antibodies 8:28 . https://doi.org/10.3390/antib8020028  Bird R, Hardman K, Jacobson...antigen-binding proteins. Science 242:423–426 . https://doi.org/10.1126/science.3140379  Bradbury ARM, Sidhu S,...technologies. Nat Biotechnol 29:245–254 . https://doi.org/10.1038/nbt.1791  Deal CE, Balazs AB (2015) Vectored...Current Opinion in HIV and AIDS 10:190–197 . https://doi.org/10.1097/coh.0000000000000145  Gąciarz A, Ruddock...intrinsically stable scFv. PLoS ONE 12:e0189964 . https://doi.org/10.1371/journal.pone.0189964  Huston JS, Levinson...National Academy of Sciences 85:5879–5883 . https://doi.org/10.1073/pnas.85.16.5879  Leavy O (2016) The birth...

  20. New Optogenetic Tools for Cytoskeleton and Membrane Control

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    ...zebrafish left-right organizer development. PLoS Genetics, 19(5), e1010765. https://doi.org/10.1371/journal.pgen...7), 7. https://doi.org/10.1038/s41557-023-01214-0. Preprint on bioRxiv: https://doi.org/10.1101/2022.09.26.509516...Optogenetics gives you the power to control cells or organisms with the flip of a switch. You may be familiar...chromosomes during mitosis, support transport of organelles and vesicles, and more. Although several strategies...family proteins support vesicle trafficking and organelle dynamics, but with dozens of family members and...forming the cilia that help establish left-right organization of the embryo (Aljiboury et al., 2023). It’s...Vectors 101: Optogenetics Additional resources on Addgene.org Optogenetics Guide Optogenetics Plasmids References...
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