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  1. Viral Vectors 101: Systemic Capsids

    Type
    Blog Post
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    Oct. 12, 2023, 1:15 p.m.
    ...more information on reagents and protocols, visit https://clover.caltech.edu. Figure adapted from Challis... Review of Neuroscience. 2022 Jul 8;45:447-469. https://doi.org/10.1146/annurev-neuro-111020-100834 Challis...in rodents. Nature Protocols;14, 379–414 (2019). https://doi.org/10.1038/s41596-018-0097-3 More resources...Using AAV-PHP.S. eNeuro,9(3), ENEURO.0373-21.2022. https://doi.org/10.1523/ENEURO.0373-21.2022 Brown, D.,...Sequencing. Frontiers in immunology, 12, 730825. https://doi.org/10.3389/fimmu.2021.730825 Campos LJ, Arokiaraj...system. Current Research in Neurobiology, 4, 100086. https://doi.org/10.1016/j.crneur.2023.100086. Challis... Annual Review of Neuroscience, 45(1), 447–469. https://doi.org/10.1146/annurev-neuro-111020-100834 Chan...
  2. Typing CRISPR Systems

    Type
    Blog Post
    Published
    March 18, 2025, 1:15 p.m.
    ... with CRISPR–Cas13. Nature, 550(7675), 280–284. https://doi.org/10.1038/nature24049 Altae-Tran, H., Kannan... deep terascale clustering. Science, 382(6673). https://doi.org/10.1126/science.adi1910 Chylinski, K.,...systems. Nucleic Acids Research, 42(10), 6091–6105. https://doi.org/10.1093/nar/gku241 Cong, L., Ran, F. A...CRISPR/CAS systems. Science, 339(6121), 819–823. https://doi.org/10.1126/science.1231143 Cox, D. B. T.,...with CRISPR-Cas13. Science, 358(6366), 1019–1027. https://doi.org/10.1126/science.aaq0180 Harrington, L....CRISPR-Cas14 enzymes. Science, 362(6416), 839–842. https://doi.org/10.1126/science.aav4294 Hu, C., Myers,...applications. Molecular Cell, 84(3), 463-475.e5. https://doi.org/10.1016/j.molcel.2023.12.034 Kolesnik,...
  3. Viral Vectors 101: AAV Variables That Matter

    Type
    Blog Post
    Published
    June 1, 2023, 1:15 p.m.
    ... Gene Therapy: An Overview. Cells, 12(5), 1–41. https://doi.org/10.3390/cells12050785 Murlidharan, G.,...system. Frontiers in Molecular Neuroscience, 7. https://doi.org/10.3389/fnmol.2014.00076 References and...and 9 in the Mouse Brain. PLOS ONE, 8(9), e76310. https://doi.org/10.1371/journal.pone.0076310 Damdindorj...adeno-associated viral vectors. PLoS ONE, 9(8), 1–10. https://doi.org/10.1371/journal.pone.0106472 de Backer...Hypothalamus. Human Gene Therapy, 21(6), 673–682. https://doi.org/10.1089/hum.2009.169 Dudek, A. M., Pillay...Independent of AAV Receptor. Journal of Virology, 92(7). https://doi.org/10.1128/jvi.02213-17 Favre, D., Blouin...Virus. Journal of Virology, 76(22), 11605–11611. https://doi.org/10.1128/JVI.76.22.11605-11611.2002 Griffin...
  4. Quick Guide to Near-Infrared Fluorescent Proteins

    Type
    Blog Post
    Published
    Oct. 5, 2021, 1:15 p.m.
    ...miRFP703 https://www.addgene.org/79988/ 674 703 90,900 8.6 127 Monomer 394 4.5 37 miRFP709 https://www.addgene.org...mIFP https://www.addgene.org/54620/ 683 705 82,000 8.4 112 Monomer 54 4.5 15  15 miRFP https://www.addgene.org....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...iRFP682 https://www.addgene.org/45459/ 663 682 90,000 11.1 162 Dimer 490 4.5 105 iRFP702 https://www.addgene.org...iRFP713 https://www.addgene.org/31857/ 690 713 98,000 6.3 100 Dimer 960 4.5 100  19 iRFP720 https://www.addgene.org...emiRFP703 https://www.addgene.org/136558/ 674 703 90,900 8.6 127 Monomer 700 4.5 90 miRFP713 https://www.addgene.org...iRFP713, % d Ref BphP-based FPs miRFP670 https://www.addgene.org/79987/ 642 670 87,400 14.0 198...
  5. Plasmids 101: Modular Cloning Applications and Kits

    Type
    Blog Post
    Published
    May 14, 2024, 1:15 p.m.
    ...Science (PLoS), 18 Feb. 2011, p. e16765. Crossref, https://doi.org/10.1371/journal.pone.0016765. Moore, Simon...Society (ACS), 2 May 2016, pp. 1059–69. Crossref, https://doi.org/10.1021/acssynbio.6b00031. Iverson, Sonya...Society (ACS), 4 Nov. 2015, pp. 99–103. Crossref, https://doi.org/10.1021/acssynbio.5b00124. Obst, Ulrike...Society (ACS), 15 Mar. 2017, pp. 1016–25. Crossref, https://doi.org/10.1021/acssynbio.6b00337. Lee, Michael...Society (ACS), 1 May 2015, pp. 975–86. Crossref, https://doi.org/10.1021/sb500366v. Shaw, William M., et...Society (ACS), 6 Nov. 2023, pp. 3393–405. Crossref, https://doi.org/10.1021/acssynbio.3c00423. Pérez-González...and Business Media LLC, 13 Nov. 2017. Crossref, https://doi.org/10.1186/s12896-017-0393-y. Engler, Carola...
  6. Overcoming the AAV Size Limitation for CRISPR Delivery

    Type
    Blog Post
    Published
    Sept. 16, 2020, 1 p.m.
    ...and its host response. Nat Methods 13:868–874 . https://doi.org/10.1038/nmeth.3993  Cong L, Ran FA, Cox... Using CRISPR/Cas Systems. Science 339:819–823 .https://doi.org/10.1126/science.1231143  Cox DBT, Gootenberg...editing with CRISPR-Cas13. Science 358:1019–1027 . https://doi.org/10.1126/science.aaq0180  Fine EJ, Appleton...using compact expression cassettes. Sci Rep 5: . https://doi.org/10.1038/srep10777  Garneau JE, Dupuis ...bacteriophage and plasmid DNA. Nature 468:67–71 . https://doi.org/10.1038/nature09523  Ibraheim R, Song ...Neisseria meningitidis Cas9 in vivo. Genome Biol 19: . https://doi.org/10.1186/s13059-018-1515-0  Kim E, Koo ...derived from Campylobacter jejuni. Nat Commun 8: . https://doi.org/10.1038/ncomms14500  Levy JM, Yeh W-H,...
  7. Viral Vectors 101: AAV Serotypes and Tissue Tropism

    Type
    Blog Post
    Published
    Jan. 16, 2025, 3:42 p.m.
    ...and 9 in the mouse brain. PloS One, 8(9), e76310. https://doi.org/10.1371/journal.pone.0076310 Bish, L. ...and Rat. Human Gene Therapy, 19(12), 1359–1368. https://doi.org/10.1089/hum.2008.123 Dalkara, D., Byrne...Science Translational Medicine, 5(189), 189ra76. https://doi.org/10.1126/scitranslmed.3005708 Goertsen,...Therapy. Methods & Clinical Development, 26, 331–342. https://doi.org/10.1016/j.omtm.2022.07.010 Issa, S. S....in Gene Therapy: An Overview. Cells, 12(5), 785. https://doi.org/10.3390/cells12050785 Kaludov, N., Brown...Specificity. Journal of Virology, 75(15), 6884–6893. https://doi.org/10.1128/jvi.75.15.6884-6893.2001 Pillay...adeno-associated virus infection. Nature, 530(7588), 108–112. https://doi.org/10.1038/nature16465 Rubin, J. D., Nguyen...
  8. Getting to Know Expansion Microscopy

    Type
    Blog Post
    Published
    June 20, 2023, 1:15 p.m.
    ...conservation of a conoid. PLoS Biology 19:e3001020. https://doi.org/10.1371/journal.pbio.3001020  Chen F, ...2015) Expansion microscopy. Science 347:543–548. https://doi.org/10.1126/science.1260088 Damstra HG, Mohar...Robust Expansion Microscopy (TREx). Elife 11:e73775. https://doi.org/10.7554/elife.73775  Dani A, Huang B, ...Chemical Synapses in the Brain. Neuron 68:843–856. https://doi.org/10.1016/j.neuron.2010.11.021  Gambarotto...expansion microscopy (U-ExM). Nat Methods 16:71–74. https://doi.org/10.1038/s41592-018-0238-1  Klimas A, Gallagher... for expansion microscopy. Nat Biotechnol 1–12. https://doi.org/10.1038/s41587-022-01546-1  Mikhaylova...using anti-tubulin nanobodies. Nat Commun 6:7933. https://doi.org/10.1038/ncomms8933  M’Saad O, Bewersdorf...
  9. An “elegans” Approach to Better CRISPR/Cas9 Editing Efficiency

    Type
    Blog Post
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    Dec. 17, 2020, 1:30 p.m.
    ... Caenorhabditis elegans. Genetics 198:837–846 . https://doi.org/10.1534/genetics.114.169730 Bottcher R...Drosophila cells. Nucleic Acids Research 42:e89–e89 . https://doi.org/10.1093/nar/gku289 Chen C, Fenk LA, de...recombination. Nucleic Acids Research 41:e193–e193 . https://doi.org/10.1093/nar/gkt805 Dickinson DJ, Pani ...Drug Selection Cassette. Genetics 200:1035–1049 . https://doi.org/10.1534/genetics.115.178335 Dokshin GA... Caenorhabditis elegans. Genetics 210:781–787 . https://doi.org/10.1534/genetics.118.301532 Ebbing A, ...alternative gene editing system for AT-rich sequences https://doi.org/10.17912/W2237D Farboud B, Severson AF...Editing Using CRISPR-Cas9. Genetics 211:431–457 . https://doi.org/10.1534/genetics.118.301775 Ghanta KS,...
  10. CRISPR 101: Cytosine and Adenine Base Editors

    Type
    Blog Post
    Published
    Feb. 13, 2025, 2:15 p.m.
    ... editing. Nature Biotechnology, 41(5), 663–672. https://doi.org/10.1038/s41587-022-01532-7 Gaudelli, N...without DNA cleavage. Nature, 551(7681), 464–471. https://doi.org/10.1038/nature24644 Gaudelli, N. M., Lam...application. Nature Biotechnology, 38(7), 892–900. https://doi.org/10.1038/s41587-020-0491-6 Grünewald, J... editing. Nature Biotechnology, 38(7), 861–864. https://doi.org/10.1038/s41587-020-0535-y Kim, Y. B., ... fusions. Nature Biotechnology, 35(4), 371–376. https://doi.org/10.1038/nbt.3803 Koblan, L. W., Doman,...reconstruction. Nature Biotechnology, 36(9), 843–846. https://doi.org/10.1038/nbt.4172 Komor, A. C., Kim, Y....double-stranded DNA cleavage. Nature, 533(7603), 420–424. https://doi.org/10.1038/nature17946 Komor, A. C., Zhao...
  11. An Introduction to Adenovirus

    Type
    Blog Post
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    Oct. 3, 2023, 1:15 p.m.
    ...native viral promoters. Mol Ther, 7(4), 526–534. https:/doi.org/10.1016/S1525-0016(03)00023-6. PMID: 12727116...evidence. Emerg Microbes Infect, 8(1), 1679–1687. https://doi.org/10.1080/22221751.2019.1690953. PMID: 31749409...Reference Module in Biomedical Sciences. Elsevier. https://doi.org/10.1016/B978-0-12-801238-3.02523-X. Hofmann...Adenoviruses In Vivo. J Virol, 73(8), 6930–6936. https://doi.org/10.1128/JVI.73.8.6930-6936.1999. PMID:...therapy. Proc Natl Acad Sci U S A, 95(19), 11377. https://doi.org/10.1073/PNAS.95.19.11377. PMID: 9736744...Nuclear Pore Complex. PLoS Pathog, 11(6), e1004821. https://doi.org/10.1371/journal.ppat.1004821. PMID: 26042599...adenoviruses. J Clin Pathol Suppl (R Coll Pathol)., 6, 39. https://doi.org/10.1136/jcp.s3-6.1.39. PMID: 4376152. ...
  12. CRISPR 101: Engineering the Plant Genome Using CRISPR/Cas9

    Type
    Blog Post
    Published
    Oct. 11, 2016, 2:30 p.m.
    ...using the CRISPR/Cas system. Plant Methods 9:39 . https://doi.org/10.1186/1746-4811-9-39 Gao Q, Xu W, Yan...cereal genomic studies. New Phytol 223:2120–2133 . https://doi.org/10.1111/nph.15889 Gelvin SB (2003) Agrobacterium-Mediated...behind the “Gene-Jockeying” Tool. MMBR 67:16–37 . https://doi.org/10.1128/mmbr.67.1.16-37.2003 Khatodia ...Application in Improvement of Crops. Front Plant Sci 7: . https://doi.org/10.3389/fpls.2016.00506 Kwak S-Y, Lew ...nanotube carriers. Nat Nanotechnol 14:447–455 . https://doi.org/10.1038/s41565-019-0375-4 Lowder LG, Zhang...Transcriptional Regulation. Plant Physiol 169:971–985 . https://doi.org/10.1104/pp.15.00636 Ma X, Zhang X, Liu...virally delivered CRISPR–Cas9. Nat Plants 6:773–779 . https://doi.org/10.1038/s41477-020-0704-5 Santana I, Wu...
  13. Four Ways to Package Transgenes That Exceed the Size Limit of Adeno-associated Virus

    Type
    Blog Post
    Published
    Sept. 1, 2020, 1:15 p.m.
    ...delivery in mice. J Clin Invest 118:1955–1964 . https://doi.org/10.1172/jci34316 Bak RO, Porteus MH (2017...Using AAV Donor Vectors. Cell Reports 20:750–756 . https://doi.org/10.1016/j.celrep.2017.06.064  Carvalho...Approaches for Retinal Targeting. Front Neurosci 11: . https://doi.org/10.3389/fnins.2017.00503  Chamberlain ...Virus Capsids. Human Gene Therapy Methods 27:1–12 . https://doi.org/10.1089/hgtb.2015.140 Frischmeyer PA (...Lacking Termination Codons. Science 295:2258–2261 . https://doi.org/10.1126/science.1067338 Ghosh A, Yue Y...Transgene-independent Manner. Molecular Therapy 16:124–130 . https://doi.org/10.1038/sj.mt.6300322 Halbert CL, Allen...parts of a larger gene. Nat Biotechnol 20:697–701 . https://doi.org/10.1038/nbt0702-697 Hirsch ML, Agbandje-McKenna...
  14. Five Popular Model Organisms, Part 2

    Type
    Blog Post
    Published
    Sept. 29, 2020, 1:15 p.m.
    ...The unexhausted potential of E. coli. ELife, 4. https://doi.org/10.7554/elife.05826 Blum, M., & Ott, T...Disease. Cells Tissues Organs, 205(5–6), 303–313. https://doi.org/10.1159/000490898 Gibbs, R., Weinstock...mammalian evolution. Nature 428, 493–521 (2004). https://doi.org/10.1038/nature02426 Iannaccone, P. M.,...! Disease Models & Mechanisms, 2(5–6), 206–210. https://doi.org/10.1242/dmm.002733 Idalia, V.-M. N., &...Pathogenesis and Biotechnological Applications. InTech. https://doi.org/10.5772/67306 Koornneef, M., & Meinke,...model plant. The Plant Journal, 61(6), 909–921. https://doi.org/10.1111/j.1365-313x.2009.04086.x Krämer...ecological context with Arabidopsis thaliana. ELife, 4. https://doi.org/10.7554/elife.06100 Liu, L. S., Zhao, ...
  15. CRISPR 101: Epigenetics and Editing the Epigenome

    Type
    Blog Post
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    June 24, 2020, 5:45 p.m.
    ...epigenome editing. Nucleic Acids Research 47:e23–e23. https://doi.org/10.1093/nar/gky1286 Hilton IB, D’Ippolito...and enhancers. Nature Biotechnology 33:510–517 . https://doi.org/10.1038/nbt.3199 Find plasmids from this...human genome. Nature Biotechnology 35:561–568 . https://doi.org/10.1038/nbt.3853 Find plasmids from this...-MQ1 fusion protein. Nature Communications 8: . https://doi.org/10.1038/ncomms16026 Find plasmids from...in the Mammalian Genome. Cell 167:233–247.e17 . https://doi.org/10.1016/j.cell.2016.08.056 Find plasmids...fusion proteins. Nature Biotechnology 31:1137–1142 . https://doi.org/10.1038/nbt.2726 Find plasmids from this...site-specific DNA methylation. Biology Open 5:866–874 . https://doi.org/10.1242/bio.019067 Find plasmids from...
  16. Live and Let Dye: Self-Labeling Protein Tags

    Type
    Blog Post
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    April 16, 2024, 1:15 p.m.
    ...targets. Nature Communications, 7(1), Article 1. https://doi.org/10.1038/ncomms10778 Erdmann, R. S., Baguley...SNAP-tags. Cell Chemical Biology, 26(4), 584-592.e6. https://doi.org/10.1016/j.chembiol.2019.01.003 Gallagher...Reactivity. ACS Chemical Biology, 4(7), 547–556. https://doi.org/10.1021/cb900062k Gautier, A., Juillerat...Living Cells. Chemistry & Biology, 15(2), 128–136. https://doi.org/10.1016/j.chembiol.2008.01.007 Griffin...Inside Live Cells. Science, 281(5374), 269–272. https://doi.org/10.1126/science.281.5374.269 Jing, C.,... Accounts of Chemical Research, 44(9), 784–792. https://doi.org/10.1021/ar200099f Keppler, A., Gendreizig...in vivo. Nature Biotechnology, 21(1), Article 1. https://doi.org/10.1038/nbt765 Lavis, L. (2016, September...
  17. A History of Genome Engineering in Popular Culture

    Type
    Blog Post
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    Feb. 25, 2020, 2:15 p.m.
    ...double-strand breaks or donor DNA. Nature 576:149–157 . https://doi.org/10.1038/s41586-019-1711-4 Avery OT, MacLeod...The Journal of Experimental Medicine 79:137–158 . https://doi.org/10.1084/jem.79.2.137 Carroll D (2011) ...With Zinc-Finger Nucleases. Genetics 188:773–782 . https://doi.org/10.1534/genetics.111.131433 Doudna JA,...engineering with CRISPR-Cas9. Science 346:1258096 . https://doi.org/10.1126/science.1258096 Gaudelli NM, Komor...genomic DNA without DNA cleavage. Nature 559:E8–E8 . https://doi.org/10.1038/s41586-018-0070-x Griffith F (...Pneumococcal Types. Journal of Hygiene 27:113–159 . https://doi.org/10.1017/s0022172400031879 Hershey AD, ...BACTERIOPHAGE. The Journal of General Physiology 36:39–56 . https://doi.org/10.1085/jgp.36.1.39 Komor AC, Kim YB, ...
  18. To Codon Optimize or Not: That is the Question

    Type
    Blog Post
    Published
    Nov. 12, 2020, 2:15 p.m.
    ...for codon usage tables. BMC Bioinformatics 18: . https://doi.org/10.1186/s12859-017-1793-7 Dresios J, Chappell...initiation in eukaryotes. Nat Struct Mol Biol 13:30–34 . https://doi.org/10.1038/nsmb1031 Gustafsson C, Govindarajan...expression. Trends in Biotechnology 22:346–353 . https://doi.org/10.1016/j.tibtech.2004.04.006 Hausser ...inhibit translation. Genome Research 23:604–615 . https://doi.org/10.1101/gr.139758.112 Mauro VP, Chappell...therapeutics. Trends in Molecular Medicine 20:604–613  https://doi.org/10.1016/j.molmed.2014.09.003 Nakamura ... year 2000. Nucleic Acids Research 28:292–292 . https://doi.org/10.1093/nar/28.1.292 Sauna ZE, Kimchi-...mutations to human disease. Nat Rev Genet 12:683–691. https://doi.org/10.1038/nrg3051 Sharp PM, Li W-H (1987...
  19. CRISPR Activation: A Practical Guide

    Type
    Blog Post
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    Aug. 18, 2016, 2:30 p.m.
    ...using CRISPR–Cas9 screens. Nature 568:511–516 . https://doi.org/10.1038/s41586-019-1103-9 Bialek JK, Dunay...Transcriptional Activator Systems. PLoS ONE 11:e0158294 . https://doi.org/10.1371/journal.pone.0158294 Chari R, ...library-on-library approach. Nat Methods 12:823–826 . https://doi.org/10.1038/nmeth.3473 Chavez A, Scheiman ...transcriptional programming. Nat Methods 12:326–328 . https://doi.org/10.1038/nmeth.3312 Chavez A, Tuttle M,...activators in multiple species. Nat Methods 13:563–567 . https://doi.org/10.1038/nmeth.3871 Gilbert LA, Horlbeck...Gene Repression and Activation. Cell 159:647–661 . https://doi.org/10.1016/j.cell.2014.09.029 Konermann S...engineered CRISPR-Cas9 complex. Nature 517:583–588 . https://doi.org/10.1038/nature14136 Pan J, Meyers RM, ...
  20. Antibodies 101: Single Chain Fragment Variables (scFvs)

    Type
    Blog Post
    Published
    June 3, 2021, 1:15 p.m.
    ...Clinical and Developmental Immunology 2012:1–15 . https://doi.org/10.1155/2012/980250  Bates A, Power CA...Prospects of Antibody Fragments. Antibodies 8:28 . https://doi.org/10.3390/antib8020028  Bird R, Hardman ...antigen-binding proteins. Science 242:423–426 . https://doi.org/10.1126/science.3140379  Bradbury ARM,...display technologies. Nat Biotechnol 29:245–254 . https://doi.org/10.1038/nbt.1791  Deal CE, Balazs AB (...infection. Current Opinion in HIV and AIDS 10:190–197 . https://doi.org/10.1097/coh.0000000000000145  Gąciarz ...intrinsically stable scFv. PLoS ONE 12:e0189964 . https://doi.org/10.1371/journal.pone.0189964  Huston JS...the National Academy of Sciences 85:5879–5883 . https://doi.org/10.1073/pnas.85.16.5879  Leavy O (2016...
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