This website uses cookies to ensure you get the best experience. By continuing to use this site, you agree to the use of cookies.
Addgene will be closed November 22nd & 23rd for the Thanksgiving holiday. Order processing and shipping may be delayed the week of Nov 19th - 23rd. If you have any questions, please contact us at [email protected].

Please note: Your browser does not support the features used on Addgene's website. You may not be able to create an account or request plasmids through this website until you upgrade your browser. Learn more

Please note: Your browser does not fully support some of the features used on Addgene's website. If you run into any problems registering, depositing, or ordering please contact us at [email protected] Learn more

CRISPR Plasmids: Interfere


Catalytically dead dCas9, or dCas9 fused to a transcriptional repressor peptide like KRAB, can knock down gene expression by interfering with transcription. Design your gRNA to target your gene of interest’s promoter/enhancer or the beginning of the coding sequence. If the plasmid you’re using does not also express a gRNA, you will need to use a separate gRNA expression plasmid to target the dCas9-repressor to your specific locus.

CRISPR-repression-horizontal.png

Browse, sort, or search the tables below for CRISPR plasmids for transcriptional inhibition.
Plasmids are available for expression in mammalian systems, bacteria, plants, and yeast.


Mammalian

Plasmid Gene/Insert Promoter Selectable Marker PI Publication Hidden Extra Search Info
pdCas9-humanizeddead Cas9 with 3X NLS (Homo sapiens)MSCV LTR promoterPuromycin Qi Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression. Cell. 2013 Feb 28;152(5):1173-83. doi: 10.1016/j.cell.2013.02.022. Expression of a catalytically inactive, human codon-optimized Cas9 under the control of Murine Stem Cell retroVirus LTR promoter for mammalian gene knockdown pMSCVpuro
pdCas9::BFP-humanizeddCas9 fused to BFP (Homo sapiens)MSCV LTR promoterPuromycin Qi Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression. Cell. 2013 Feb 28;152(5):1173-83. doi: 10.1016/j.cell.2013.02.022. Expression of a catalytically inactive, human codon-optimized Cas9-BFP fusion under the control of Murine Stem Cell retroVirus LTR promoter for mammalian gene knockdown pMSCVpuro
pHR-SFFV-dCas9-BFPdCas9-BFP fusion (Homo sapiens)SFFV Weissman CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes. Cell. 2013 Jul 9. pii: S0092-8674(13)00826-X. doi: 10.1016/j.cell.2013.06.044. Human expression vector containing SFFV promoter, dCas9 that is fused to 2x NLS and tagBFP pHR
pHR-SFFV-dCas9-BFP-KRABdCas9-BFP-KRAB fusion (Homo sapiens)SFFV Weissman CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes. Cell. 2013 Jul 9. pii: S0092-8674(13)00826-X. doi: 10.1016/j.cell.2013.06.044. Human expression vector containing SFFV promoter, dCas9 that is fused to 2x NLS, tagBFP and a KRAB domain pHR
pcDNA-dCas9dCas9 (Other)CMV Gersbach RNA-guided gene activation by CRISPR-Cas9-based transcription factors. Nat Methods. 2013 Jul 25. doi: 10.1038/nmeth.2600. Expresses inactivated S. pyogenes dCas9 (D10A, H840A) in mammalian cells pcDNA3.1
Cas9m2Cas9m2 (Other) Church CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat Biotechnol. 2013 Aug 1. doi: 10.1038/nbt.2675. Cas9 D10A+H840A pcDNA3.3_TOPO
Cas9m3Cas9m3 (Other) Church CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat Biotechnol. 2013 Aug 1. doi: 10.1038/nbt.2675. Cas9 D10A+D839A+H840A pcDNA3.3_TOPO
Cas9m4Cas9m4 (Other) Church CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat Biotechnol. 2013 Aug 1. doi: 10.1038/nbt.2675. Cas9 D10A+D839A+H840A+N863A pcDNA3.3_TOPO
pHAGE TRE dCas9dCas9 (Other)TRENeomycin (select with G418) Wolfe Cas9 effector-mediated regulation of transcription and differentiation in human pluripotent stem cells. Development. 2014 Jan;141(1):219-23. doi: 10.1242/dev.103341. Tet-regulatable dCas9 lentiviral expression vector pHAGE
pHAGE TRE dCas9-KRABdCas9 (Other)TRENeomycin (select with G418) Wolfe Cas9 effector-mediated regulation of transcription and differentiation in human pluripotent stem cells. Development. 2014 Jan;141(1):219-23. doi: 10.1242/dev.103341. Tet-regulatable dCas9-KRAB lentiviral expression vector pHAGE
pHAGE EF1α dCas9-KRABdCas9 (Other)EF1alphaPuromycin Wolfe Cas9 effector-mediated regulation of transcription and differentiation in human pluripotent stem cells. Development. 2014 Jan;141(1):219-23. doi: 10.1242/dev.103341. Constitutive dCas9-KRAB lentiviral expression vector pHAGE
pSLQ1658-dCas9-EGFPdCas9 fuse to EGFP (Homo sapiens)MSCV LTR promoterPuromycin Qi Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System. Cell. 2013 Dec 19;155(7):1479-91. doi: 10.1016/j.cell.2013.12.001. Template for NLS-dCas9-NLS-EGFP fusion protein for CRISPR imaging (the recipient vector can be TetON 3G promoter system) pMSCVpuro
pLV hUbC-dCas9-T2A-GFPhumanized dead Cas9 T2A GFP (Other)hUbCZeo marker is outside the LTRs and will not be packaged into virus. Gersbach Multiplex CRISPR/Cas9-based genome engineering from a single lentiviral vector. Nucleic Acids Res. 2014 Aug 13. pii: gku749. Co-expresses human optimized S. pyogenes dCas9 and GFP FUGW
pcDNA3.1-CibN-dCas9CibN-dCas9 (Arabidopsis thaliana)CMVNeomycin (select with G418) Gersbach A light-inducible CRISPR-Cas9 system for control of endogenous gene activation. Nat Chem Biol. 2015 Feb 9. doi: 10.1038/nchembio.1753. Expresses CibN-dCas9 in mammalian cells pcDNA3.1
pcDNA3.1-dCas9-CibNdCas9-CibN (Arabidopsis thaliana)CMVNeomycin (select with G418) Gersbach A light-inducible CRISPR-Cas9 system for control of endogenous gene activation. Nat Chem Biol. 2015 Feb 9. doi: 10.1038/nchembio.1753. Expresses dCas9-CibN in mammalian cells pcDNA3.1
pcDNA3.1-CibN-dCas9-CibNdCas9-CibN (Arabidopsis thaliana)CMVNeomycin (select with G418) Gersbach A light-inducible CRISPR-Cas9 system for control of endogenous gene activation. Nat Chem Biol. 2015 Feb 9. doi: 10.1038/nchembio.1753. Expresses CibN-dCas9-CibN in mammalian cells pcDNA3.1
pHR-SFFV-KRAB-dCas9-P2A-mCherryKRAB-dCas9-P2A-mCherry fusion (Homo sapiens)SFFVmCherry Weissman Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation. Cell. 2014 Oct 23;159(3):647-61. doi: 10.1016/j.cell.2014.09.029. Epub 2014 Oct 9. 2nd Generation Lentiviral vector. Expresses an N-terminal KRAB-dCas9 fusion protein and mCherry pHR
pcDNA-dCas9-HAS.pyogenes dCas9 with c-terminal HA tag (Synthetic)CMV Gersbach Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nat Biotechnol. 2015 May;33(5):510-7. doi: 10.1038/nbt.3199. Epub 2015 Apr 6. encodes c-terminal HA-tagged S. pyogenes dCas9 driven by CMV promoter pcDNA3.1
pX330A_dCas9-1x2humanized S. pyogenes dCas9 (Other)CBh Yamamoto Production of knockout mice by DNA microinjection of various CRISPR/Cas9 vectors into freeze-thawed fertilized oocytes. BMC Biotechnol. 2015 May 22;15(1):33. Expresses dCas9 and gRNA pUC ori vector
pX330A_dCas9-1x3humanized S. pyogenes dCas9 (Other)CBh Yamamoto Production of knockout mice by DNA microinjection of various CRISPR/Cas9 vectors into freeze-thawed fertilized oocytes. BMC Biotechnol. 2015 May 22;15(1):33. Expresses dCas9 and gRNA pUC ori vector
pX330A_dCas9-1x5humanized S. pyogenes dCas9 (Other)CBh Yamamoto Production of knockout mice by DNA microinjection of various CRISPR/Cas9 vectors into freeze-thawed fertilized oocytes. BMC Biotechnol. 2015 May 22;15(1):33. Expresses dCas9 and gRNA pUC ori vector
pX330A_dCas9-1x6humanized S. pyogenes dCas9 (Other)CBh Yamamoto Production of knockout mice by DNA microinjection of various CRISPR/Cas9 vectors into freeze-thawed fertilized oocytes. BMC Biotechnol. 2015 May 22;15(1):33. Expresses dCas9 and gRNA pUC ori vector
pEF1a-CRY2PHR-SID4XSID4X-CYR2PHR (Synthetic)EF1alpha Kong Aspirin cooperates with p300 to activate the acetylation of H3K9 and promote FasL-mediated apoptosis of cancer stem-like cells in colorectal cancer Theranostics AAV expression of CRYS2PHR-SID4X pAAV
px330-CIB1-dCas9U6 and CMV Kong Aspirin cooperates with p300 to activate the acetylation of H3K9 and promote FasL-mediated apoptosis of cancer stem-like cells in colorectal cancer Theranostics Mammalian gRNA expression vector also expressing CIB1-dCas9 px330
pCCL-PGK-SPdCas9-BFP-DNMT1dCas9-BFP-DNMT1, catalytic domain Luo Genome-wide determination of on-target and off-target characteristics for RNA-guided DNA methylation by dCas9 methyltransferases. Gigascience. 2018 Mar 1;7(3):1-19. doi: 10.1093/gigascience/giy011. dCas9 fused to BFP and the human DNMT1 catalytic domain 3rd Generation lentiviral vector
pCCL-PGK-SPdCas9-BFP-DNMT3AdSpCas9-BFP-DNMT3A, catalytic domain of DNMT3A (Synthetic) Luo Genome-wide determination of on-target and off-target characteristics for RNA-guided DNA methylation by dCas9 methyltransferases. Gigascience. 2018 Mar 1;7(3):1-19. doi: 10.1093/gigascience/giy011. dCas9 fused to BFP and the human DNMT3A catalytic domain 3rd Generation lentiviral vector
pCCL-PGK-SPdCas9-BFP-DNMT3BdSpCas9-BFP-DNMT3B, catalytic domain of DNMT3B (Synthetic) Luo Genome-wide determination of on-target and off-target characteristics for RNA-guided DNA methylation by dCas9 methyltransferases. Gigascience. 2018 Mar 1;7(3):1-19. doi: 10.1093/gigascience/giy011. dCas9 fused to BFP and the human DNMT3B catalytic domain 3rd Generation lentiviral vector
pCCL-PGK-SPdCas9-BFP-EGFPdSpCas9-BFP-EGFP (Synthetic) Luo Genome-wide determination of on-target and off-target characteristics for RNA-guided DNA methylation by dCas9 methyltransferases. Gigascience. 2018 Mar 1;7(3):1-19. doi: 10.1093/gigascience/giy011. dCas9 fused to BFP and EGFP 3rd Generation lentiviral vector
pEF_dCas9dCas9 (Other)human EF1[alpha] Rinn Multiplexable, locus-specific targeting of long RNAs with CRISPR-Display. Nat Methods. 2015 Jul;12(7):664-70. doi: 10.1038/nmeth.3433. Epub 2015 Jun 1. Transient expression of Sp-dCas9 in mammalian cells, under an EF1-alpha promoter. pNEB193
  • Tag / Fusion Protein
    • 3xFLAG (C terminal on insert)
  • pCCL-PGK-SPdCas9-BFP-DNMT3A(E752A)dSpCas9-BFP-DNMT3A(E752A), DNMT3A catalytic domain with inactivation mutation E752A (Synthetic) Luo Genome-wide determination of on-target and off-target characteristics for RNA-guided DNA methylation by dCas9 methyltransferases. Gigascience. 2018 Mar 1;7(3):1-19. doi: 10.1093/gigascience/giy011. dCas9 fused to BFP and the human DNMT3A catalytically inactive domain 3rd Generation lentiviral vector
    pCCL-PGK-SPdCas9-BFP-DNMT3B(E697A)dSpCas9-BFP-DNMT3B(E697A), DNMT3B catalytic domain with inactivation mutation E697A (Other) Luo Genome-wide determination of on-target and off-target characteristics for RNA-guided DNA methylation by dCas9 methyltransferases. Gigascience. 2018 Mar 1;7(3):1-19. doi: 10.1093/gigascience/giy011. dCas9 fused to BFP and the human DNMT3B catalytically inactive domain 3rd Generation lentiviral vector
    pLenti-EF1a-SPdCas9-EGFP-2A-BlastdSpCas9-EGFP (Synthetic) Luo Genome-wide determination of on-target and off-target characteristics for RNA-guided DNA methylation by dCas9 methyltransferases. Gigascience. 2018 Mar 1;7(3):1-19. doi: 10.1093/gigascience/giy011. dCas9 fused to EGFP 3rd generation lentiviral vector
    pLenti-EF1a-SPdCas9-DNMT3A-2A-BlastdSpCas9-DNMT3A catalytic domain (Synthetic) Luo Genome-wide determination of on-target and off-target characteristics for RNA-guided DNA methylation by dCas9 methyltransferases. Gigascience. 2018 Mar 1;7(3):1-19. doi: 10.1093/gigascience/giy011. dCas9 fused to human DNMT3A catalytic domain 3rd generation lentiviral vector
    pLenti-EF1a-SPdCas9-DNMT3B-2A-BlastdSpCas9-DNMT3B catalytic domain (Synthetic) Luo Genome-wide determination of on-target and off-target characteristics for RNA-guided DNA methylation by dCas9 methyltransferases. Gigascience. 2018 Mar 1;7(3):1-19. doi: 10.1093/gigascience/giy011. dCas9 fused to human DNMT3B catalytic domain 3rd generation lentiviral vector
    pLenti-EF1a-SPdCas9-DNMT3A(E752A)-2A-BlastdSpCas9-DNMT3A(E752A) Luo Genome-wide determination of on-target and off-target characteristics for RNA-guided DNA methylation by dCas9 methyltransferases. Gigascience. 2018 Mar 1;7(3):1-19. doi: 10.1093/gigascience/giy011. dCas9 fused to the human DNMT3A catalytically inactive domain 3rd generation lentiviral vector
    pLenti-EF1a-SPdCas9-DNMT3B(E697A)-2A-BlastdSpCas9-DNMT3B(E697A), DNMT3B catalytic domain with inactivation mutation E697A (Other) Luo Genome-wide determination of on-target and off-target characteristics for RNA-guided DNA methylation by dCas9 methyltransferases. Gigascience. 2018 Mar 1;7(3):1-19. doi: 10.1093/gigascience/giy011. dCas9 fused to the human DNMT3B catalytically inactive domain 3rd Generation lentiviral vector
    pLV hU6-sgRNA hUbC-dCas9-KRAB-T2a-Purohumanized dCas9-KRAB T2A Puro (Other), sgRNAPuromycin Gersbach Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements. Nat Methods. 2015 Dec;12(12):1143-9. doi: 10.1038/nmeth.3630. Epub 2015 Oct 26. Express sgRNA and dCas9-KRAB from lentiviral vector FUGW
    pLV hU6-sgRNA hUbC-dCas9-KRAB-T2a-GFPhumanized dCas9-KRAB T2A GFP (Other), sgRNA Gersbach Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements. Nat Methods. 2015 Dec;12(12):1143-9. doi: 10.1038/nmeth.3630. Epub 2015 Oct 26. Express sgRNA and dCas9-KRAB from 3rd generation lentiviral vector FUGW
    pCR1003T7pr_10xHis-MBP-TEV-SPydCas9 (D10A, H840A) Corn Enhancing homology-directed genome editing by catalytically active and inactive CRISPR-Cas9 using asymmetric donor DNA. Nat Biotechnol. 2016 Jan 20. doi: 10.1038/nbt.3481. Express Streptococcus pyogenes dCas9 (D10A, H840A) SPynCas9
    pCR1056T7pr_6xHis-MBP-TEV-SPydCas9 (D10A,H840A)-2xNLS Corn Enhancing homology-directed genome editing by catalytically active and inactive CRISPR-Cas9 using asymmetric donor DNA. Nat Biotechnol. 2016 Jan 20. doi: 10.1038/nbt.3481. Express Streptococcus pyogenes dCas9 (D10A, H840A) carrying two C-terminal SV40 NLS SPynCas9
    pAC1445-pmax-dCas9dCas9 (Synthetic)CAGGS + chim intron Cheng pAC1445 (unpublished) dCas9 expressed in pmax vector pAC90-pmax-DEST
    pAAVS1-NDi-CRISPRi (Gen1)dCas9-KRAB-P2A-mCherry (Synthetic), rtTA (Synthetic)TRE3G, CAGNeomycin (select with G418) Conklin CRISPR Interference Efficiently Induces Specific and Reversible Gene Silencing in Human iPSCs. Cell Stem Cell. 2016 Apr 7;18(4):541-53. doi: 10.1016/j.stem.2016.01.022. Epub 2016 Mar 10. Dox-inducible CRISPR interference (CRISPRi) knock in construct into the AAVS1 locus with mCherry marker pAAVS1
    pAAVS1-NDi-CRISPRi (Gen2)dCas9-KRAB (Synthetic), rtTA (Synthetic)TRE3G, CAGNeomycin (select with G418) Conklin CRISPR Interference Efficiently Induces Specific and Reversible Gene Silencing in Human iPSCs. Cell Stem Cell. 2016 Apr 7;18(4):541-53. doi: 10.1016/j.stem.2016.01.022. Epub 2016 Mar 10. Dox-inducible CRISPR interference (CRISPRi) knock in construct into the AAVS1 locus pAAVS1
    pAAVS1-NC-CRISPRi (Gen3)dCas9-KRAB (Synthetic)CAGNeomycin (select with G418) Conklin CRISPR Interference Efficiently Induces Specific and Reversible Gene Silencing in Human iPSCs. Cell Stem Cell. 2016 Apr 7;18(4):541-53. doi: 10.1016/j.stem.2016.01.022. Epub 2016 Mar 10. Constitutive CRISPR interference (CRISPRi) knock in construct into the AAVS1 locus pAAVS1
    pHAGE-TO-dCas9Sp dCas9 (Synthetic)CMV-TO Pederson Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. Nat Biotechnol. 2016 Apr 18. doi: 10.1038/nbt.3526. dCas9 pHAGE-DEST
    WN10150dead (908A) AsCpf1Neomycin (select with G418) Welker Mb- and FnCpf1 nucleases are active in mammalian cells: activities and PAM preferences of four wild-type Cpf1 nucleases and of their altered PAM specificity variants. Nucleic Acids Res. 2018 Sep 20. pii: 5103950. doi: 10.1093/nar/gky815. Expresses dead (908A) AsCpf1 pcDNA3.1
    CSII-U6-gRNA-CBh-3xFLAG-PA-dCas9-P2A-PurosgRNA and dCas9 from pX330 (Other)U6 for sgRNA and CBh for dCas9Puromycin Kimura Dr. Sekita CRISPR/Cas9 (unpublished) Lentivirus vector to express guideRNA and dCas9 with puro resistant gene CSII
    pLV-dCas9-KRAB-PGK-HygRhumanized dead Cas9 KRAB (Other), aminoglycoside phosphotransferase from E. coli (Other)Human Ubiquitin C Promoter, mouse phosphoglycerate kinase 1 promoterHygromycin Gersbach CRISPR-Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome. Nat Biotechnol. 2017 Apr 3. doi: 10.1038/nbt.3853. Lentiviral Sp dCas9-KRAB fusion with Hygromycin B resistance cassette. FUGW
    pSLQ2818 pPB: CAG-PYL1-KRAB-IRES-Puro-WPRE-SV40PA PGK-ABI-tagBFP-SpdCas9ABI-tagBFP-Sp dCas9 (Arabidopsis thaliana), PYL1-KRAB (Arabidopsis thaliana)PGK, CAGPuromycin Qi Complex transcriptional modulation with orthogonal and inducible dCas9 regulators. Nat Methods. 2016 Oct 24. doi: 10.1038/nmeth.4042. Expresses ABA-inducible KRAB-Sp dCas9 PB
    pSLQ2813 pPB: CAG-GID1-KRAB-IRES-Puro-WPRE PGK-ABI-tagBFP-SpdCas9GAI-tagBFP-Sp dCas9 (Arabidopsis thaliana), GID1-KRAB (Arabidopsis thaliana)PGK, CAGPuromycin Qi Complex transcriptional modulation with orthogonal and inducible dCas9 regulators. Nat Methods. 2016 Oct 24. doi: 10.1038/nmeth.4042. Expresses GA-inducible KRAB-Sp dCas9 PB
    pSLQ2815 pPB: CAG-Puro-WPRE PGK-KRAB-tagBFP-SpdCas9KRAB-tagBFP-Sp dCas9 (Synthetic), PuroPGK, CAGPuromycin Qi Complex transcriptional modulation with orthogonal and inducible dCas9 regulators. Nat Methods. 2016 Oct 24. doi: 10.1038/nmeth.4042. Expresses direct fusion KRAB-Sp dCas9 PB
    pGH125_dCas9-BlastdCas9 and Blasticidin resistanceBlasticidin Bassik Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells. Nat Methods. 2016 Oct 31. doi: 10.1038/nmeth.4038. lentiviral expression vector for dCas9 with Blasticidin selectable marker Addgene #61425
    TRE-KRAB-dCas9-IRES-BFPKRAB-dCas9-IRES-BFP (Synthetic)TRE3GBFP Lander Systematic mapping of functional enhancer-promoter connections with CRISPR interference. Science. 2016 Sep 29. pii: aag2445. Lentiviral vector expressing a KRAB-dCas9 fusion protein and BFP pHR
    TRE-KRAB-dCas9-IRES-GFPKRAB-dCas9-IRES-GFP (Synthetic)TRE3GGFP Lander Systematic mapping of functional enhancer-promoter connections with CRISPR interference. Science. 2016 Sep 29. pii: aag2445. 2nd generation lentiviral vector expressing a KRAB-dCas9 fusion protein and GFP pHR
    pMH0001dCas9 (Other)SFFVBFP fluorescence Weissman A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response. Cell. 2016 Dec 15;167(7):1867-1882.e21. doi: 10.1016/j.cell.2016.11.048. UCOE-SFFV-dCas9-BFP-KRAB pHR-SFFV-dCas9-BFP-KRAB
    pTE4565hMbCpf1(D986A)CMVNeomycin (select with G418) Welker Mb- and FnCpf1 nucleases are active in mammalian cells: activities and PAM preferences of four wild-type Cpf1 nucleases and of their altered PAM specificity variants. Nucleic Acids Res. 2018 Sep 20. pii: 5103950. doi: 10.1093/nar/gky815. Expresses inactive/dead, humanized MbCpf1 nuclease pcDNA3.1
    pTE4889Fn crRNA, hFnCpf1(D917A)human U6, CMVNeomycin (select with G418) Welker Mb- and FnCpf1 nucleases are active in mammalian cells: activities and PAM preferences of four wild-type Cpf1 nucleases and of their altered PAM specificity variants. Nucleic Acids Res. 2018 Sep 20. pii: 5103950. doi: 10.1093/nar/gky815. Expresses FnCpf1 crRNA and inactive/dead, humanized FnCpf1 nuclease pcDNA3.1
    Lenti-dCas9-KRAB-blastdCas9 (Synthetic)Blasticidin Hon Multiplexed Engineering and Analysis of Combinatorial Enhancer Activity in Single Cells. Mol Cell. 2017 Apr 20;66(2):285-299.e5. doi: 10.1016/j.molcel.2017.03.007. Epub 2017 Apr 13. Plasmid expression dCas9 protein in fusion with KRAB domain plenti
    pX330-HA-dSpCas9dead/inactive SpCas9 (Other)Cbh Welker Crossing enhanced and high fidelity SpCas9 nucleases to optimize specificity and cleavage. Genome Biol. 2017 Oct 6;18(1):190. doi: 10.1186/s13059-017-1318-8. Expression plasmid for human codon-optimized dead/inactive SpCas9 (without U6-sgRNA coding sequence) pX330-like (without U6-sgRNA coding sequence)
    pX330-Flag-dSpCas9dead/inactive SpCas9 with FLAG tag (Other)Cbh Welker Crossing enhanced and high fidelity SpCas9 nucleases to optimize specificity and cleavage. Genome Biol. 2017 Oct 6;18(1):190. doi: 10.1186/s13059-017-1318-8. Expression plasmid for human codon-optimized dead/inactive SpCas9 (without U6-sgRNA coding sequence) pX330-like (without U6-sgRNA coding sequence)
    pX330-Flag-deSpCas9dead/inactive eSpCas9 with FLAG tag (Other)Cbh Welker Crossing enhanced and high fidelity SpCas9 nucleases to optimize specificity and cleavage. Genome Biol. 2017 Oct 6;18(1):190. doi: 10.1186/s13059-017-1318-8. Expression plasmid for human codon-optimized dead/inactive increased fidelity eSpCas9 (1.1) (without U6-sgRNA coding sequence) pX330-like (without U6-sgRNA coding sequence)
    pX330-Flag-dSpCas9-HF1dead/inactive SpCas9-HF1 with FLAG tag (Other)Cbh Welker Crossing enhanced and high fidelity SpCas9 nucleases to optimize specificity and cleavage. Genome Biol. 2017 Oct 6;18(1):190. doi: 10.1186/s13059-017-1318-8. Expression plasmid for human codon-optimized dead/inactive high-fidelity SpCas9-HF1 (without U6-sgRNA coding sequence) pX330-like (without U6-sgRNA coding sequence)
    pX330-Flag-dHeFSpCas9dead/inactive HeFSpCas9 with FLAG tag (Other)Cbh Welker Crossing enhanced and high fidelity SpCas9 nucleases to optimize specificity and cleavage. Genome Biol. 2017 Oct 6;18(1):190. doi: 10.1186/s13059-017-1318-8. Expression plasmid for human codon-optimized dead/inactive increased fidelity HeFSpCas9 (without U6-sgRNA coding sequence) pX330-like (without U6-sgRNA coding sequence)
    pLX_311-KRAB-dCas9dCas9 (Other)EF1aBlasticidin Hahn Complementary information derived from CRISPR Cas9 mediated gene deletion and suppression. Nat Commun. 2017 May 23;8:15403. doi: 10.1038/ncomms15403. for CRISPRi, lentiviral expression of KRAB-dCas9 and BlastR. Also called pXPR_121 pXPR
  • Tag / Fusion Protein
    • KRAB (N terminal on insert)
  • pXPR_123dCas9 (Other)EF1aBlasticidin Root Orthologous CRISPR-Cas9 enzymes for combinatorial genetic screens. Nat Biotechnol. 2018 Feb;36(2):179-189. doi: 10.1038/nbt.4048. Epub 2017 Dec 18. for CRISPRi, lentiviral expression of dCas9-p300 2A BlastR. pXPR
  • Tag / Fusion Protein
    • p300 (C terminal on insert)
  • lenti-EF1a-dCas9-KRAB-PurodCas9-KRAB-T2A-Puro (Other)EF-1aPuromycin, Zeocin Brennand Evaluating Synthetic Activation and Repression of Neuropsychiatric-Related Genes in hiPSC-Derived NPCs, Neurons, and Astrocytes. Stem Cell Reports. 2017 Aug 8;9(2):615-628. doi: 10.1016/j.stemcr.2017.06.012. Epub 2017 Jul 27. 3rd generation lenti vector encoding dCas9-KRAB with 2A puromycin resistance marker (EF1a-dCas9-KRAB-T2A-Puro-WPRE) pLenti
    pHR-EF1a-dCas9-HA-BFP-KRAB-NLSdCas9-HA-BFP-KRAB-NLS (Homo sapiens)EF1aTagBFP Corn Corn Lab Cas9 plasmids (unpublished) Lentiviral expression of dCas9-HA-BFP-KRAB-NLS for CRISPRi driven by a hEF1alpha promoter pHR
  • Tag / Fusion Protein
    • HA-TagBFP-KRAB-NLS (C terminal on insert)
  • pCXLE-dCas9GFP-shP53dCas9GFP-shP53 (Other)CAG Otonkoski Human pluripotent reprogramming with CRISPR activators. Nat Commun. 2018 Jul 6;9(1):2643. doi: 10.1038/s41467-018-05067-x. EBNA episome plasmid for CAG promoter constitutive expression of dCas9-GFP. Includes p53 shRNA expression cassette. pCXLE
    PB-tight-DDdCas9GFP-IRES-NeoDDdCas9GFP-IRES-Neo (Other)TRE-tightNeomycin (select with G418) Otonkoski Human pluripotent reprogramming with CRISPR activators. Nat Commun. 2018 Jul 6;9(1):2643. doi: 10.1038/s41467-018-05067-x. PiggyBac construct with doxycyline inducible TRE-tight promoter expression of dCas9-GFP followed by IRES-Neomycin selection cassette. PB-tight
    pAW91.dCas9dCas9Blasticidin Young YY1 Is a Structural Regulator of Enhancer-Promoter Loops. Cell. 2017 Dec 14;171(7):1573-1588.e28. doi: 10.1016/j.cell.2017.11.008. Epub 2017 Dec 7. Expresses dCas9 dcas9-vp64
    MMW1578: CAG-human dLbCpf1(D832A)-NLS-3xHAdLbCpf1 (D832A) (Other)CAG Joung Inducible and multiplex gene regulation using CRISPR-Cpf1-based transcription factors. Nat Methods. 2017 Oct 30. doi: 10.1038/nmeth.4483. Mammalian expression vector for catalytically inactive Cpf1 from Lachnospiraceae bacterium (dLbCpf1) pCAG-GFP
    AAV CMV-dSaCas9-KRAB-bGHpAdead S. aureus Cas9 KRAB (Other)CMV Gersbach RNA-guided transcriptional silencing in vivo with S. aureus CRISPR-Cas9 repressors. Nat Commun. 2018 Apr 26;9(1):1674. doi: 10.1038/s41467-018-04048-4. AAV expressing deactivated S. aureus Cas9 fused to a KRAB repressor pAAV
    pLV hUbC-dSaCas9-KRAB-T2A-PuroRdead S. aureus Cas9 KRAB T2A PuroR (Other)hUbCPuromycin Gersbach RNA-guided transcriptional silencing in vivo with S. aureus CRISPR-Cas9 repressors. Nat Commun. 2018 Apr 26;9(1):1674. doi: 10.1038/s41467-018-04048-4. Lentiviral vector with puro selection for expression of S. aureus dCas9-KRAB FUGW
    SID4x-dCas9-KRABSID4x (Homo sapiens), KRAB (Homo sapiens)Neomycin (select with G418) Gertz Multiplex Enhancer Interference Reveals Collaborative Control of Gene Regulation by Estrogen Receptor alpha-Bound Enhancers. Cell Syst. 2017 Oct 25;5(4):333-344.e5. doi: 10.1016/j.cels.2017.08.011. Epub 2017 Sep 27. Expresses catalytically inactive dCas9 with N-terminal fusion of Sin3a Interacting Domain (SID) and C-terminal fusion of repressive KRAB domain pAC95-pmax (Addgene: 48227)
    AAV-nEF-dCas9nEF-dCas9nEF Belmonte In Vivo Target Gene Activation via CRISPR/Cas9-Mediated Trans-epigenetic Modulation. Cell. 2017 Dec 14;171(7):1495-1507.e15. doi: 10.1016/j.cell.2017.10.025. Epub 2017 Dec 7. Expresses SpdCas9 from the nEF promoter in AAV backbone AAV
    pdCas9-NEDCMV Kiss Establishment of Cell Lines Stably Expressing dCas9-Fusions to Address Kinetics of Epigenetic Editing. Methods Mol Biol. 2018;1767:395-415. doi: 10.1007/978-1-4939-7774-1_22. Mammalian vector for expressing effector domains fused to dCas9. pMLM3705 (Addgene plasmid #47754).
  • Tag / Fusion Protein
    • dCas9, SV40 NLS, 3xFLAG (N terminal on backbone)
  • pHAGE EF1α dCas9-NEDEF-1αPuromycin Kiss Establishment of Cell Lines Stably Expressing dCas9-Fusions to Address Kinetics of Epigenetic Editing. Methods Mol Biol. 2018;1767:395-415. doi: 10.1007/978-1-4939-7774-1_22. Lentiviral vector for expressing effector domains fused to dCas9. pHAGE EF1α dCas9-VP64 (Addgene plasmid #50918)
  • Tag / Fusion Protein
    • 3xHA (N terminal on backbone)
  • dCas9-KRABdCas9-KRAB (Synthetic)CMV Church An enhanced CRISPR repressor for targeted mammalian gene regulation. Nat Methods. 2018 Jul 16. pii: 10.1038/s41592-018-0048-5. doi: 10.1038/s41592-018-0048-5. Conventional dCas9 repressor-dCas9-KRAB pcDNA3.3_TOPO
    dCas9-KRAB-MeCP2dCas9-KRAB-MeCP2 (Synthetic)CMV Church An enhanced CRISPR repressor for targeted mammalian gene regulation. Nat Methods. 2018 Jul 16. pii: 10.1038/s41592-018-0048-5. doi: 10.1038/s41592-018-0048-5. Improved dCas9 repressor-dCas9-KRAB-MeCP2 pcDNA3.3_TOPO
    pB-CAGGS-dCas9-KRABdCas9-KRAB (Synthetic)CAGGSBlasticidin Church An enhanced CRISPR repressor for targeted mammalian gene regulation. Nat Methods. 2018 Jul 16. pii: 10.1038/s41592-018-0048-5. doi: 10.1038/s41592-018-0048-5. PiggyBac compatible plasmid expressing dCas9-KRAB pB-CAGGS
    pB-CAGGS-dCas9dCas9 (Synthetic)CAGGSBlasticidin Church An enhanced CRISPR repressor for targeted mammalian gene regulation. Nat Methods. 2018 Jul 16. pii: 10.1038/s41592-018-0048-5. doi: 10.1038/s41592-018-0048-5. PiggyBac compatible plasmid expressing dCas9 pB-CAGGS
    pB-CAGGS-dCas9-KRAB-MeCP2dCas9-KRAB-MeCP2 (Synthetic)CAGGSBlasticidin Church An enhanced CRISPR repressor for targeted mammalian gene regulation. Nat Methods. 2018 Jul 16. pii: 10.1038/s41592-018-0048-5. doi: 10.1038/s41592-018-0048-5. PiggyBac compatible plasmid expressing dCas9-KRAB-MeCP2 pB-CAGGS
    pCR1063dCas9-KRAB (Homo sapiens) Corn CRISPR-Cas9 genome editing in human cells occurs via the Fanconi anemia pathway. Nat Genet. 2018 Aug;50(8):1132-1139. doi: 10.1038/s41588-018-0174-0. Epub 2018 Jul 27. Expresses dCas9-KRAB tagged with mCherry: pHR-hEF1a-dCas9-mcherry-KRAB-mPGK-Hyg pLentiXI
  • Tag / Fusion Protein
    • mCherry (C terminal on insert)
  • pLL7 lenti-dcas9-3xflag-blastdCas9(D10A, N863A)-T2A-Blast (Synthetic)EF1aBlasticidin Meng Intrinsic Nucleotide Preference of Diversifying Base Editors Guides Antibody Ex Vivo Affinity Maturation. Cell Rep. 2018 Oct 23;25(4):884-892.e3. doi: 10.1016/j.celrep.2018.09.090. lenti vector encoding dcas9-3xflag with T2A Blastcidin resistance marker (EF1a-NLS-dCas9-3Xflag-T2A-Blast-WPRE) lenti dCAS-VP64_Blast
    KRAB-dCas9KRAB (Homo sapiens)CMVNeomycin (select with G418) Segal dCas9-based epigenome editing suggests acquisition of histone methylation is not sufficient for target gene repression. Nucleic Acids Res. 2017 Sep 29;45(17):9901-9916. doi: 10.1093/nar/gkx578. KRAB fused to N-terminus of dCas9; pCDNA3 vector backbone, mammalian expression pcDNA3.3-TOPO
    lentiCRISPR v2-dCas9dCas9 (Synthetic), Porumycin resistance (Other)EFS-NS, EFS-NSPuromycin Gilmore lentiviral expression plasmid for gRNA, puromycin, and dCas9 (unpublished) Lentiviral plasmid for expression of gRNA and dCas9 in mammalian cells; derivative of lentiCRISPR v2 Custom
    pXPR_118dCas9 (Other)Hygromycin Doench Doench CRISPR plasmids (unpublished) Lentiviral vector expressing dCas9 pXPR_118

    Bacteria

    Plasmid Gene/Insert Promoter PI Publication Hidden Extra Search Info
    pMJ841Cas9 (Other)T7 Doudna A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity. Science. 2012 Jun 28. pEC-K-MBP
  • Tags / Fusion Proteins
    • MBP (N terminal on backbone)
    • His6 (N terminal on backbone)
  • pdCas9-bacteriadCas9 (bacteria) (Other)pLtetO-1 Qi Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression. Cell. 2013 Feb 28;152(5):1173-83. doi: 10.1016/j.cell.2013.02.022. aTc-inducible expression of a catalytically inactive bacterial Cas9 (S. pyogenes) for bacterial gene knockdown p15A vector
    pdCas9tracrRNA (Other), dcas9 (Other), CRISPR array Marraffini Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Res. 2013 Jun 12. Expresses the tracrRNA, the dCas9 catalytic site mutant and a CRISPR array designed for the easy cloning of new spacers. pACYC184
    DS-SPcasN-Cas9, nuclease-null (Other), tracrRNA precursor (Other)proC, tracdrRNA promoter Church Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nat Methods. 2013 Sep 29. doi: 10.1038/nmeth.2681. Bacterial nuclease-null SP Cas9 expression cloDF13-aadA
    10xHis-MBP-TEV-S. pyogenes dCas9 M1C D10A C80S H840A C574SdCas9 M1C D10A C80S H840A C574S (Other) Doudna Programmable RNA recognition and cleavage by CRISPR/Cas9. Nature. 2014 Sep 28. doi: 10.1038/nature13769. dCas9 with single cysteine residue (M1C) for site-specific labelling pHMGWA
    pAN-PTet-dCas9dCas9 (Other)Ptet Voigt Multi-input CRISPR/Cas genetic circuits that interface host regulatory networks. Mol Syst Biol. 2014 Nov 24;10:763. doi: 10.15252/msb.20145735. controls the expression of S. pyogenes dCas9 from a Tc‐inducible PTet promoter. unknown
    pCRISPathBrickConstitutive native promoters Koffas CRISPathBrick: Modular Combinatorial Assembly of Type II-A CRISPR Arrays for dCas9-Mediated Multiplex Transcriptional Repression in E. coli. ACS Synth Biol. 2015 Mar 30. E. coli vector for expression of S. pyogenes dCas9, tracrRNA, and nontargeting CRISPR array with BsaI site for inserting user-defined spacer-repeat bricks pdCas9-Marraffini (pACYC184)
    MSP712mammalian codon-optimized Streptococcus pyogenes dCas9 (D10A/H840A)-NLS-3XFlag, and SpCas9 gRNA (Other)T7 (x2) Joung Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature. 2015 Jun 22. doi: 10.1038/nature14592. Bacterial expression plasmid for Sp-dCas9 & sgRNA (need to clone in spacer into BsaI sites): T7-humanSpdCas9(D10A/H840A)-T7-BsaIcassette-Sp-sgRNA pACYCDuet-1
  • Tags / Fusion Proteins
    • NLS (C terminal on insert)
    • 3x FLAG (C terminal on insert)
  • pMM704dCas9, LacI, sgRNA Lu Programming a Human Commensal Bacterium, Bacteroides thetaiotaomicron, to Sense and Respond to Stimuli in the Murine Gut Microbiota Cell Systems, 2015 IPTG-inducible CRISPRi vector targeting BT1854, pNBU2 backbone, AmpR pExchange-tdk
    pET302-6His-dCas9-HaloHis6-dCas9-Halo (Synthetic) Lionnet CASFISH: CRISPR/Cas9-mediated in situ labeling of genomic loci in fixed cells. Proc Natl Acad Sci U S A. 2015 Sep 22;112(38):11870-5. doi: 10.1073/pnas.1515692112. Epub 2015 Aug 31. Encodes a Halo-labeled fusion of nuclease deficient Cas9 pET302
    pMD19T-psba1-Ppsba2-dCas9-SpRdCas9 from S. pyogenes (Other)PpsbA2 Hudson Multiple Gene Repression in Cyanobacteria Using CRISPRi. ACS Synth Biol. 2015 Dec 28. Contains dCas9 from S. pyogenes under constitutive promoter. Suicide vector inserts into psba1 site of Synechocystis. Carries spectinomycin resist. Recommend E. coli Copy cutter for propogation. pMD19T simple
    pMD19T-psba1-TetR-PL22-dCas9-SpRdCas9 from S. pyogenes (Other)PL22 Hudson Multiple Gene Repression in Cyanobacteria Using CRISPRi. ACS Synth Biol. 2015 Dec 28. Contains dCas9 from S. pyogenes under aTc inducible promoter. Suicide vector inserts into psba1 site of Synechocystis. Carries spectinomycin resist. Recommend E. coli Copy cutter for propogation. pMD19T simple
    pdCas9-M-C4Repressor C4 (orthogonal T7-lac repressor) (Synthetic)Constitutive wild-type S. pyogenes promoter Koffas Rapid generation of CRISPR/dCas9-regulated, orthogonally repressible hybrid T7-lac promoters for modular, tuneable control of metabolic pathway fluxes in Escherichia coli. Nucleic Acids Res. 2016 Apr 13. pii: gkw231. CRISPR synthetic transcription factor repressor plasmid encoding dCas9, tracrRNA, and a single spacer CRISPR array encoding crRNA for orthogonal repression of T7-lac promoter variant C4. pdCas9
    pdCas9-M-3F2Repressor C4 (orthogonal T7-lac repressor) (Synthetic)Constitutive wild-type S. pyogenes promoter Koffas Rapid generation of CRISPR/dCas9-regulated, orthogonally repressible hybrid T7-lac promoters for modular, tuneable control of metabolic pathway fluxes in Escherichia coli. Nucleic Acids Res. 2016 Apr 13. pii: gkw231. CRISPR synthetic transcription factor repressor plasmid encoding dCas9, tracrRNA, and a single spacer CRISPR array encoding crRNA for orthogonal repression of T7-lac promoter variant 3F2. pdCas9
    pdCas9-M-3H5Repressor 3H5 (orthogonal T7-lac repressor) (Synthetic)Constitutive wild-type S. pyogenes promoter Koffas Rapid generation of CRISPR/dCas9-regulated, orthogonally repressible hybrid T7-lac promoters for modular, tuneable control of metabolic pathway fluxes in Escherichia coli. Nucleic Acids Res. 2016 Apr 13. pii: gkw231. CRISPR synthetic transcription factor repressor plasmid encoding dCas9, tracrRNA, and a single spacer CRISPR array encoding crRNA for orthogonal repression of T7-lac promoter variant 3H5. pdCas9
    pdCas9-M-1B6Repressor 1B6 (orthogonal T7-lac repressor) (Synthetic)Constitutive wild-type S. pyogenes promoter Koffas Rapid generation of CRISPR/dCas9-regulated, orthogonally repressible hybrid T7-lac promoters for modular, tuneable control of metabolic pathway fluxes in Escherichia coli. Nucleic Acids Res. 2016 Apr 13. pii: gkw231. CRISPR synthetic transcription factor repressor plasmid encoding dCas9, tracrRNA, and a single spacer CRISPR array encoding crRNA for orthogonal repression of T7-lac promoter variant 1B6. pdCas9
    pdCas9-M-4F2Repressor 4F2 (orthogonal T7-lac repressor) (Synthetic)Constitutive wild-type S. pyogenes promoter Koffas Rapid generation of CRISPR/dCas9-regulated, orthogonally repressible hybrid T7-lac promoters for modular, tuneable control of metabolic pathway fluxes in Escherichia coli. Nucleic Acids Res. 2016 Apr 13. pii: gkw231. CRISPR synthetic transcription factor repressor plasmid encoding dCas9, tracrRNA, and a single spacer CRISPR array encoding crRNA for orthogonal repression of T7-lac promoter variant 4F2. pdCas9
    pdCas9-M-5F5Repressor 5F5 (orthogonal T7-lac repressor) (Synthetic)Constitutive wild-type S. pyogenes promoter Koffas Rapid generation of CRISPR/dCas9-regulated, orthogonally repressible hybrid T7-lac promoters for modular, tuneable control of metabolic pathway fluxes in Escherichia coli. Nucleic Acids Res. 2016 Apr 13. pii: gkw231. CRISPR synthetic transcription factor repressor plasmid encoding dCas9, tracrRNA, and a single spacer CRISPR array encoding crRNA for orthogonal repression of T7-lac promoter variant 5F5. pdCas9
    pdCas9-M-1D4Repressor 1D4 (orthogonal T7-lac repressor) (Synthetic)Constitutive wild-type S. pyogenes promoter Koffas Rapid generation of CRISPR/dCas9-regulated, orthogonally repressible hybrid T7-lac promoters for modular, tuneable control of metabolic pathway fluxes in Escherichia coli. Nucleic Acids Res. 2016 Apr 13. pii: gkw231. CRISPR synthetic transcription factor repressor plasmid encoding dCas9, tracrRNA, and a single spacer CRISPR array encoding crRNA for orthogonal repression of T7-lac promoter variant 1D4. pdCas9
    pdCas9-M-4A6Repressor 4A6 (orthogonal T7-lac repressor) (Synthetic)Constitutive wild-type S. pyogenes promoter Koffas Rapid generation of CRISPR/dCas9-regulated, orthogonally repressible hybrid T7-lac promoters for modular, tuneable control of metabolic pathway fluxes in Escherichia coli. Nucleic Acids Res. 2016 Apr 13. pii: gkw231. CRISPR synthetic transcription factor repressor plasmid encoding dCas9, tracrRNA, and a single spacer CRISPR array encoding crRNA for orthogonal repression of T7-lac promoter variant 4A6. pdCas9
    pdCas9-M-3A2Repressor 3A2 (orthogonal T7-lac repressor) (Synthetic)Constitutive wild-type S. pyogenes promoter Koffas Rapid generation of CRISPR/dCas9-regulated, orthogonally repressible hybrid T7-lac promoters for modular, tuneable control of metabolic pathway fluxes in Escherichia coli. Nucleic Acids Res. 2016 Apr 13. pii: gkw231. CRISPR synthetic transcription factor repressor plasmid encoding dCas9, tracrRNA, and a single spacer CRISPR array encoding crRNA for orthogonal repression of T7-lac promoter variant 3A2. pdCas9
    pdCas9-M-1E4Repressor 1E4 (orthogonal T7-lac repressor) (Synthetic)Constitutive wild-type S. pyogenes promoter Koffas Rapid generation of CRISPR/dCas9-regulated, orthogonally repressible hybrid T7-lac promoters for modular, tuneable control of metabolic pathway fluxes in Escherichia coli. Nucleic Acids Res. 2016 Apr 13. pii: gkw231. CRISPR synthetic transcription factor repressor plasmid encoding dCas9, tracrRNA, and a single spacer CRISPR array encoding crRNA for orthogonal repression of T7-lac promoter variant 1E4. pdCas9
    pdCas9-M-G6Repressor G6 (orthogonal T7-lac repressor) (Synthetic)Constitutive wild-type S. pyogenes promoter Koffas Rapid generation of CRISPR/dCas9-regulated, orthogonally repressible hybrid T7-lac promoters for modular, tuneable control of metabolic pathway fluxes in Escherichia coli. Nucleic Acids Res. 2016 Apr 13. pii: gkw231. CRISPR synthetic transcription factor repressor plasmid encoding dCas9, tracrRNA, and a single spacer CRISPR array encoding crRNA for orthogonal repression of T7-lac promoter variant G6. pdCas9
    pZ8-T_dCas9dcas9ptac Lu Corynebacterium glutamicum Metabolic Engineering with CRISPR Interference (CRISPRi). ACS Synth Biol. 2016 Feb 16. pZ8-1 plasmid carrying dcas9, driven by the IPTG-inducible Ptac promoter, KanR pZ8-1
    pZ8-P_dCas9dcas9Propionate inducible promoter (prp) Lu Corynebacterium glutamicum Metabolic Engineering with CRISPR Interference (CRISPRi). ACS Synth Biol. 2016 Feb 16. pZ8-1 plasmid carrying dcas9 driven by the propionate-inducible prpD2 promoter (PprpD2), KanR pZ8-Prp
    pJMP1dCas9 (Other)xylA Gross A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria. Cell. 2016 Jun 2;165(6):1493-506. doi: 10.1016/j.cell.2016.05.003. Epub 2016 May 26. Bacillus subtilis dCas9 expression vector; integrates into lacA/ganA pAX01
    pCas2AdCas9PEZ3 Pfleger CRISPR interference as a titratable, trans-acting regulatory tool for metabolic engineering in the cyanobacterium Synechococcus sp. strain PCC 7002. Metab Eng. 2016 Jul 29. pii: S1096-7176(16)30062-3. doi: 10.1016/j.ymben.2016.07.007. dCas9 expressed from aTc-inducible promoter in acsA, A RBS: AGGAGA pACSA
    pCas2BdCas9PEZ3 Pfleger CRISPR interference as a titratable, trans-acting regulatory tool for metabolic engineering in the cyanobacterium Synechococcus sp. strain PCC 7002. Metab Eng. 2016 Jul 29. pii: S1096-7176(16)30062-3. doi: 10.1016/j.ymben.2016.07.007. dCas9 expressed from aTc-inducible promoter in acsA, B RBS: TCGAGA pACSA
    pCas2CdCas9PEZ3 Pfleger CRISPR interference as a titratable, trans-acting regulatory tool for metabolic engineering in the cyanobacterium Synechococcus sp. strain PCC 7002. Metab Eng. 2016 Jul 29. pii: S1096-7176(16)30062-3. doi: 10.1016/j.ymben.2016.07.007. dCas9 expressed from aTc-inducible promoter in acsA, C RBS: TGGACA pACSA
    pCas2DdCas9PEZ3 Pfleger CRISPR interference as a titratable, trans-acting regulatory tool for metabolic engineering in the cyanobacterium Synechococcus sp. strain PCC 7002. Metab Eng. 2016 Jul 29. pii: S1096-7176(16)30062-3. doi: 10.1016/j.ymben.2016.07.007. dCas9 expressed from aTc-inducible promoter in acsA, D RBS: AGGACG pACSA
    pCas2EdCas9PEZ3 Pfleger CRISPR interference as a titratable, trans-acting regulatory tool for metabolic engineering in the cyanobacterium Synechococcus sp. strain PCC 7002. Metab Eng. 2016 Jul 29. pii: S1096-7176(16)30062-3. doi: 10.1016/j.ymben.2016.07.007. dCas9 expressed from aTc-inducible promoter in acsA, E RBS: AGGGCG pACSA
    pCas2FdCas9PEZ3 Pfleger CRISPR interference as a titratable, trans-acting regulatory tool for metabolic engineering in the cyanobacterium Synechococcus sp. strain PCC 7002. Metab Eng. 2016 Jul 29. pii: S1096-7176(16)30062-3. doi: 10.1016/j.ymben.2016.07.007. dCas9 expressed from aTc-inducible promoter in acsA, F RBS: TGGGCG pACSA
    pCas7dCas9c225 Pfleger CRISPR interference as a titratable, trans-acting regulatory tool for metabolic engineering in the cyanobacterium Synechococcus sp. strain PCC 7002. Metab Eng. 2016 Jul 29. pii: S1096-7176(16)30062-3. doi: 10.1016/j.ymben.2016.07.007. dCas9 expressed from low constituve promoter, c225, in acsA pACSA
    pCas8dCas9none Pfleger CRISPR interference as a titratable, trans-acting regulatory tool for metabolic engineering in the cyanobacterium Synechococcus sp. strain PCC 7002. Metab Eng. 2016 Jul 29. pii: S1096-7176(16)30062-3. doi: 10.1016/j.ymben.2016.07.007. dCas9 without a promoter in acsA pACSA
    pRH2502dcas9 (Other)uv15tetO Husson Investigating essential gene function in Mycobacterium tuberculosis using an efficient CRISPR interference system. Nucleic Acids Res. 2016 Jul 12. pii: gkw625. Expression of dcas9 D10A H840A from a TetR-regulated uvtetO promoter pTC-0X-1L
    pAW019-2dcas9 (Other)PxylA (B. megaterium) Chou Development of a CRISPR-Cas9 toolkit for comprehensive engineering of Bacillus subtilis. Appl Environ Microbiol. 2016 Jun 3. pii: AEM.01159-16. Inducible dCas9 integration vector for Bacillus subtilis pAX01 (ColE1)
    pUC18-mini-Tn7T-Lac-dCas9 (Ptac)S. pasteurianus dCas9 (Other) Prather A Robust CRISPR Interference Gene Repression System in Pseudomonas. J Bacteriol. 2018 Mar 12;200(7). pii: JB.00575-17. doi: 10.1128/JB.00575-17. Print 2018 Apr 1. Tn7 integrating plasmid with S. pasteurianus dCas9 expressed from the Ptac promoter for expression in P. putida and P. fluorescens pUC18
    pUC18-mini-Tn7T-Plac-dCas9 (Plac)S. pasteurianus dCas9 (Other) Prather A Robust CRISPR Interference Gene Repression System in Pseudomonas. J Bacteriol. 2018 Mar 12;200(7). pii: JB.00575-17. doi: 10.1128/JB.00575-17. Print 2018 Apr 1. Tn7 integrating plasmid with S. pasteurianus dCas9 expressed from the Plac promoter for expression in P. aeruginosa pUC18
    Biomolecular FeedBack (FB)pJ23100mut-dCas9-T- phtpG1-sgRNA (Other) Ellis Burden-driven feedback control of gene expression. Nat Methods. 2018 Mar 26. pii: nmeth.4635. doi: 10.1038/nmeth.4635. This construct encodes for two units. The first contains a constitutively expressed dCas9 protein. The second contains an sgRNA cassette under the control of the burden-responsive htpG1 promoter. pAZ16 ( Plasmid has got AmpR and p15A origin)
    pSET-dCas9dCas9 (Synthetic)ermE*p Lu CRISPR/dCas9-Mediated Multiplex Gene Repression in Streptomyces. Biotechnol J. 2018 Jun 3. doi: 10.1002/biot.201800121. Expression of the dCas9 gene in Streptomyces pSET152
    pSET-dCas9-actII-4-NT-S1dCas9 (Synthetic), sgRNAermE*p, J23119 Lu CRISPR/dCas9-Mediated Multiplex Gene Repression in Streptomyces. Biotechnol J. 2018 Jun 3. doi: 10.1002/biot.201800121. Repression of gene expression in Streptomyces by CRISPRi pSET152
    pCT310dCas9 (Other)T7 Tjian dCas9-targeted locus-specific protein isolation method identifies histone gene regulators. Proc Natl Acad Sci U S A. 2018 Mar 20;115(12):E2734-E2741. doi: 10.1073/pnas.1718844115. Epub 2018 Mar 5. Bacterial expression of 6His-dCas9-3XFlag pET302/NT-His
    pNS38-SadCas9-SNAPCas9 (Other) Schwank Covalent linkage of the DNA repair template to the CRISPR-Cas9 nuclease enhances homology-directed repair. Elife. 2018 May 29;7. pii: 33761. doi: 10.7554/eLife.33761. Bacterial vector for expression of Snap-tagged Staphylococcus aureus dCas9 pET His6 MBP N10 TEV LIC cloning vector (2C-T)
    PLJR962Sth1 sgRNA scaffold (Other), Sth1 dCas9 (Other), TetR (Other), L5 attP (Other), L5 Int (Other), KanR (Other) Fortune Programmable transcriptional repression in mycobacteria using an orthogonal CRISPR interference platform. Nat Microbiol. 2017 Feb 6;2:16274. doi: 10.1038/nmicrobiol.2016.274. Sth1 dCas9 TetR and KanR L5 Int attP for M. smegmatis custom design
    PLJR965Sth1 sgRNA scaffold (Other), Sth1 dCas9 (Other), TetR (deleted TetON) MtbCO (Other), L5 attP (Other), L5 Int (Other), KanR (Other) Fortune Programmable transcriptional repression in mycobacteria using an orthogonal CRISPR interference platform. Nat Microbiol. 2017 Feb 6;2:16274. doi: 10.1038/nmicrobiol.2016.274. Sth1 dCas9 TetR and KanR L5 Int attP for M. tuberculosis custom design

    Plant

    Plasmid Gene/Insert Promoter Selectable Marker PI Publication Hidden Extra Search Info
    pBUN6I11dCas9-KRAB (Synthetic), gRNA scaffold (Synthetic)Ubi1p, OsU3pBar Chen A CRISPR/Cas9 toolkit for multiplex genome editing in plants. BMC Plant Biol. 2014 Nov 29;14(1):327. CRISPR/Cas based plant genome editing and gene regulation; expresses dCas9-KRAB, gRNA scaffold for insertion of target sequence (OsU3 promoter), Bar resistance pGreen-like binary vector
    pHSN6I01dCas9-KRAB (Synthetic), gRNA scaffold (Synthetic)2×35Sp, AtU6-26pHygromycin Chen A CRISPR/Cas9 toolkit for multiplex genome editing in plants. BMC Plant Biol. 2014 Nov 29;14(1):327. CRISPR/Cas based plant genome editing and gene regulation; expresses dCas9-KRAB, gRNA scaffold for insertion of target sequence (AtU6-26 promoter), Hyg resistance pGreen-like binary vector
    pEGB 35S:dCas9:Tnos (GB1191)dCas9 (Other)35S Orzaez GoldenBraid 2.0: a comprehensive DNA assembly framework for plant synthetic biology. Plant Physiol. 2013 Jul;162(3):1618-31. Transcriptional unit for human codon optimized with mutated (D10A, H840A) and inactivated catalytic domains Cas9 protein plant expression driven by the 35S promoter pDGB3alpha2
    pYPQ153pco-dCas9-3X(SRDX) (Plant codon-optimized) (Other) Qi A CRISPR/Cas9 toolbox for multiplexed plant genome editing and transcriptional regulation. Plant Physiol. 2015 Aug 21. pii: pp.00636.2015. Gateway entry vector with pco-dCas9-3X(SRDX) pYPQ185-linker1
    pdCas9 (GB1079)Cas9 coding region with mutated (D10A, H840A) and inactivated catalytic domains (human codon optimised) (Other) Orzaez A modular toolbox for gRNA-Cas9 genome engineering in plants based on the GoldenBraid standard. Plant Methods. 2016 Feb 1;12:10. doi: 10.1186/s13007-016-0101-2. eCollection 2016. Provides the human codon optimized CDS of Cas9 protein with mutated (D10A, H840A) and inactivated catalytic domains as a level 0 GoldenBraid part for C-terminal fusions pUPD
    pEGB 35s:dCas:BRD:tNos (GB1172)dCas9:BRD (Synthetic)35S Orzaez A modular toolbox for gRNA-Cas9 genome engineering in plants based on the GoldenBraid standard. Plant Methods. 2016 Feb 1;12:10. doi: 10.1186/s13007-016-0101-2. eCollection 2016. Transcriptional unit of (human codon optimized) inactivated Cas9 fused to the BRD Transcriptional Repressor pDGB3alpha2
    pYPQ223 (dAsCpf1-SRDX)dAsCpf1-SRDX (Other) Qi A CRISPR-Cpf1 system for efficient genome editing and transcriptional repression in plants. Nat Plants. 2017 Feb 17;3:17018. doi: 10.1038/nplants.2017.18. Deactivated AsCpf1-SRDX repressor fusion; transcriptional repressor dCpf1 Gateway entry plasmid pYPQ221
    pYPQ233 (dLbCpf1-SRDX)LbCpf1-SRDX (Other) Qi A CRISPR-Cpf1 system for efficient genome editing and transcriptional repression in plants. Nat Plants. 2017 Feb 17;3:17018. doi: 10.1038/nplants.2017.18. Deactivated LbCpf1-SRDX repressor fusion; transcriptional repressor dCpf1 Gateway entry plasmid pYPQ221
    pMOD_A0402 AtCas9_dead (D10A + H840A) (Synthetic) AtUbi10 Voytas A multi-purpose toolkit to enable advanced genome engineering in plants. Plant Cell. 2017 May 18. pii: tpc.00922.2016. doi: 10.1105/tpc.16.00922. Module A, Promoter: AtUbi10, Gene: AtCas9_dead (D10A + H840A), Terminator: HSP pMOD_A1001
    pMOD_A0408 AtCas9_dead (D10A + H840A) (Synthetic) EC1.2 Voytas A multi-purpose toolkit to enable advanced genome engineering in plants. Plant Cell. 2017 May 18. pii: tpc.00922.2016. doi: 10.1105/tpc.16.00922. Module A, Promoter: EC1.2, Gene: AtCas9_dead (D10A + H840A), Terminator: HSP pMOD_A1001
    pMOD_A0801 Csy4-P2A-AtCas9_dead (D10A + H840A) (Synthetic) 35S Voytas A multi-purpose toolkit to enable advanced genome engineering in plants. Plant Cell. 2017 May 18. pii: tpc.00922.2016. doi: 10.1105/tpc.16.00922. Module A, Promoter: 35S, Gene: Csy4-P2A-AtCas9_dead (D10A + H840A), Terminator: HSP pMOD_A1001
    pMOD_A0802 Csy4-P2A-AtCas9_dead (D10A + H840A) (Synthetic) AtUbi10 Voytas A multi-purpose toolkit to enable advanced genome engineering in plants. Plant Cell. 2017 May 18. pii: tpc.00922.2016. doi: 10.1105/tpc.16.00922. Module A, Promoter: AtUbi10, Gene: Csy4-P2A-AtCas9_dead (D10A + H840A), Terminator: HSP pMOD_A1001
    pMOD_A0808 Csy4-P2A-AtCas9_dead (D10A + H840A) (Synthetic) EC1.2 Voytas A multi-purpose toolkit to enable advanced genome engineering in plants. Plant Cell. 2017 May 18. pii: tpc.00922.2016. doi: 10.1105/tpc.16.00922. Module A, Promoter: EC1.2, Gene: Csy4-P2A-AtCas9_dead (D10A + H840A), Terminator: HSP pMOD_A1001
    pMOD_A1410 TaCas9_dead (D10A + H840A) (Synthetic) ZmUbi Voytas A multi-purpose toolkit to enable advanced genome engineering in plants. Plant Cell. 2017 May 18. pii: tpc.00922.2016. doi: 10.1105/tpc.16.00922. Module A, Promoter: ZmUbi, Gene: TaCas9_dead (D10A + H840A), Terminator: HSP pMOD_A1001
    pMOD_A1810 Csy4-P2A-TaCas9_dead (D10A + H840A) (Synthetic) ZmUbi Voytas A multi-purpose toolkit to enable advanced genome engineering in plants. Plant Cell. 2017 May 18. pii: tpc.00922.2016. doi: 10.1105/tpc.16.00922. Module A, Promoter: ZmUbi, Gene: Csy4-P2A-TaCas9_dead (D10A + H840A), Terminator: HSP pMOD_A1001
    pDIRECT_21B Engineering Reagent: 35S:AtCas9_dead + AtU6:gRNA (Synthetic)Hygromycin Voytas A multi-purpose toolkit to enable advanced genome engineering in plants. Plant Cell. 2017 May 18. pii: tpc.00922.2016. doi: 10.1105/tpc.16.00922. Direct Cloning, Type: T-DNA, Engineering Reagent: 35S:AtCas9_dead + AtU6:gRNA, Plant Selection: 2x35S:hpt II pTRANS_210
    pDIRECT_25G Engineering Reagent: ZmUbi:TaCas9_dead + TaU6:gRNA (Synthetic)Hygromycin Voytas A multi-purpose toolkit to enable advanced genome engineering in plants. Plant Cell. 2017 May 18. pii: tpc.00922.2016. doi: 10.1105/tpc.16.00922. Direct Cloning, Type: T-DNA, Engineering Reagent: ZmUbi:TaCas9_dead + TaU6:gRNA , Plant Selection: PvUbi2:hpt II pTRANS_250d
    pDIRECT_26G Engineering Reagent: ZmUbi:TaCas9_dead + TaU6:gRNA (Synthetic)Basta Voytas A multi-purpose toolkit to enable advanced genome engineering in plants. Plant Cell. 2017 May 18. pii: tpc.00922.2016. doi: 10.1105/tpc.16.00922. Direct Cloning, Type: T-DNA, Engineering Reagent: ZmUbi:TaCas9_dead + TaU6:gRNA , Plant Selection: PvUbi2:bar pTRANS_260d
    pAtCas9-dead_1 AtCas9_D10A+H840A (dead) (Synthetic)Hygromycin Voytas A multi-purpose toolkit to enable advanced genome engineering in plants. Plant Cell. 2017 May 18. pii: tpc.00922.2016. doi: 10.1105/tpc.16.00922. Cas9 only expression, Cas9 Type: AtCas9_D10A+H840A (dead), Plant Selection: 2x35S:hpt II pCAMBIA
    pAtCas9-dead_2 AtCas9_D10A+H840A (dead) (Synthetic)Kanamycin Voytas A multi-purpose toolkit to enable advanced genome engineering in plants. Plant Cell. 2017 May 18. pii: tpc.00922.2016. doi: 10.1105/tpc.16.00922. Cas9 only expression, Cas9 Type: AtCas9_D10A+H840A (dead), Plant Selection: 2x35S:npt II pCAMBIA
    pAtCas9-dead_3 AtCas9_D10A+H840A (dead) (Synthetic)Basta Voytas A multi-purpose toolkit to enable advanced genome engineering in plants. Plant Cell. 2017 May 18. pii: tpc.00922.2016. doi: 10.1105/tpc.16.00922. Cas9 only expression, Cas9 Type: AtCas9_D10A+H840A (dead), Plant Selection: 2x35S:bar pCAMBIA
    pTaCas9-dead_5 TaCas9_D10A+H840A (dead) (Synthetic)Hygromycin Voytas A multi-purpose toolkit to enable advanced genome engineering in plants. Plant Cell. 2017 May 18. pii: tpc.00922.2016. doi: 10.1105/tpc.16.00922. Cas9 only expression, Cas9 Type: TaCas9_D10A+H840A (dead), Plant Selection: PvUbi2:hpt II pCAMBIA
    pTaCas9-dead_6 TaCas9_D10A+H840A (dead) (Synthetic)Basta Voytas A multi-purpose toolkit to enable advanced genome engineering in plants. Plant Cell. 2017 May 18. pii: tpc.00922.2016. doi: 10.1105/tpc.16.00922. Cas9 only expression, Cas9 Type: TaCas9_D10A+H840A (dead), Plant Selection: PvUbi2:bar pCAMBIA
    pHdzCas9-KRABCaMV35SHygromycin Ng CRISPRi mediated phosphoenolpyruvate carboxylase regulation to enhance the production of lipid in Chlamydomonas reinhardtii. Bioresour Technol. 2017 May 4. pii: S0960-8524(17)30619-3. doi: 10.1016/j.biortech.2017.04.111. Expression dzCas9-KRAB in microalgae. CRISPR/Cas based plant genome editing and gene regulation, Hyg resistance pHdzCas9-KRAB
  • Tag / Fusion Protein
    • KRAB (C terminal on insert)
  • pORFE0003AtDeadCAS9 D10A H840A (Other) Chevalier Chevalier Lab plasmids (unpublished) AtDeadCAS9 D10A H840A module CDS1 pICH41308
    pORFE0005AtDeadCAS9 D10A H840A without stop codon (Other) Chevalier Chevalier Lab plasmids (unpublished) AtDeadCAS9 D10A H840A without stop codon module CDS1ns pAGM1287

    Yeast

    Plasmid Gene/Insert Promoter Selectable Marker PI Publication Hidden Extra Search Info
    pTDH3-dCas9dCas9TDH3LEU2 Weissman CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes. Cell. 2013 Jul 9. pii: S0092-8674(13)00826-X. doi: 10.1016/j.cell.2013.06.044. Yeast CEN/ARS vector (Leu2) that contains dCas9 fused to NLS controlled by TDH3 promoter pJED103
    pTDH3-dCas9-Mxi1dCas9-Mxi1TDH3LEU2 Weissman CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes. Cell. 2013 Jul 9. pii: S0092-8674(13)00826-X. doi: 10.1016/j.cell.2013.06.044. Yeast CEN/ARS vector (Leu2) that contains dCas9 fused to NLS and Mxi1 domain controlled by TDH3 promoter pJED103
    pJZC518dCas9 (Other)pTdh3LEU2 Qi Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds. Cell. 2014 Dec 18. pii: S0092-8674(14)01570-0. doi: 10.1016/j.cell.2014.11.052. Yeast dCas9 expression plasmid pNH605
    pTPGI_dCas9Yeast-optimized dCas9 (Saccharomyces cerevisiae)pTPGITRP1 Lu Tunable and Multifunctional Eukaryotic Transcription Factors Based on CRISPR/Cas. ACS Synth Biol. 2013 Sep 11. encodes yeast-optimized dCas9 synthetic transcription factor pRS304
    pRS416-dCas9-Mxi1 + TetR + pRPR1(TetO)-NotI-gRNAdCas9-Mxi1 (Synthetic), Tet Repressor (Other), Structural gRNA for S pyogenes (Synthetic)pTef1, pGPM1, pRPR1(TetO)URA3 Davis Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design. Genome Biol. 2016 Mar 8;17(1):45. doi: 10.1186/s13059-016-0900-9. pRS416 Ura marked Cen/Ars plasmid with dCas9-Mxi1 under Tef1 promoter, and tet-incucibile RPR1 promoter with NotI cloning site adjacent to gRNA pRS416
    pCRISPRi_Mxi1_ylCodon optimized dCas9-Mxi1 (Synthetic), sgRNA expression cassette (Synthetic)UAS1B8-TEF(136), SCR1'-tRNALEU2 Wheeldon CRISPRi repression of nonhomologous end-joining for enhanced genome engineering via homologous recombination in Yarrowia lipolytica. Biotechnol Bioeng. 2017 Aug 19. doi: 10.1002/bit.26404. CRISPR-dCas9-Mxi1 vector for Yarrowia lipolytica, expressing dCas9-Mxi1 and AvrII site for sgRNA insertion pUC19
    pCRISPRi_Mxi1_yl_NHEJCodon optimized dCas9-Mxi1 (Synthetic), KU70 sgRNA expression cassette (Synthetic), KU80a sgRNA expression cassette (Synthetic), KU80b sgRNA expression cassette (Synthetic)UAS1B8-TEF(136), SCR1'-tRNA, SCR1'-tRNA, SCR1'-tRNALEU2 Wheeldon CRISPRi repression of nonhomologous end-joining for enhanced genome engineering via homologous recombination in Yarrowia lipolytica. Biotechnol Bioeng. 2017 Aug 19. doi: 10.1002/bit.26404. CRISPRi vector for Yarrowia lipolytica, repressing KU70 and KU80 for enhanced HR pUC19


    Addgene Blugene icon

    Do you have suggestions for other plasmids that should be added to this list?

    Fill out our Suggest a Plasmid form or e-mail [email protected] to help us improve this resource!