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Richard Murray Lab: CIDAR MoClo Extension

Unpublished

Plasmids from Article

ID Plasmid Purpose
120934P1mMoClo golden gate assembly AB part plasmid for J23101 (strength 1791x Anderson promoter; see http://parts.igem.org/Promoters/Catalog/Anderson); AB overhangs.
120935p3mMoClo golden gate assembly AB part for J23150 (strength ~400x Anderson promoter; see http://parts.igem.org/Promoters/Catalog/Anderson) - Please see Supplemental Documents for annotated Genbank file
120936p4mMoClo golden gate assembly AB part for J23151 (strength ~900x Anderson promoter; see http://parts.igem.org/Promoters/Catalog/Anderson) - Please see Supplemental Documents for annotated Genbank file
120937P9mMoClo golden gate assembly AB part for pOR1-OR2 (lambda cI-repressable strong promoter) - Please see Supplemental Documents for annotated Genbank file
120938P12mMoClo golden gate assembly AB part for pLas-TetO (Promoter activated by LasR and repressed by TetR; encodes <3OC12 AHL AND aTc> logic). Please see Supplemental Documents for annotated Genbank file.
120939P15mMoClo golden gate assembly AB part for pCin-TetO (Promoter activated by CinR and repressed by TetR; encodes <3OC14 AHL AND aTc> logic). Please see Supplemental Documents for annotated Genbank file.
120940P16mMoClo golden gate assembly AB part for pCin-LacO (Promoter activated by CinR and repressed by LacI; encodes <3OC14 AHL AND IPTG> logic). Please see Supplemental Documents for annotated Genbank file.
120941P18mMoClo golden gate assembly AB part for T7 promoter (strong, T7 polymerase-dependent constitutive promoter; use with C95m). Please see Supplemental Documents for annotated Genbank file.
120942P30mMoClo golden gate assembly AB part for pL-lacO1 (LacI-repressed promoter, as used in DOI:10.1038/35002125). Please see Supplemental Documents for annotated Genbank file.
120943P32mMoClo golden gate assembly AB part for PlacO (common LacI-repressed promoter; see DOI: 10.1126/science.1256272). Please see Supplemental Documents for annotated Genbank file.
120944P33mMoClo golden gate assembly AB part (medium-strength Mutalik library promoter; see DOI: 10.1038/nmeth.2404). Please see Supplemental Documents for annotated Genbank file.
120945P34mMoClo golden gate assembly AB part (low-strength Mutalik library promoter; see DOI: 10.1038/nmeth.2404). Please see Supplemental Documents for annotated Genbank file.
120946P35mMoClo golden gate assembly AB part for pLbda-CasRQi (strong lambda promoter with downstream dCas binding site for Qi-lab gRNA (UC16m); gRNA sequence taken from DOI: 10.1016/j.cell.2013.02.022).
120947P37mMoClo golden gate assembly AB part for pRpa* (improved pRpa from DOI: 10.1021/acssynbio.5b00286). Please see Supplemental Documents for annotated Genbank file.
120948P38mMoClo golden gate assembly AB part for pTra* (improved pTra from DOI: 10.1021/acssynbio.5b00286). Please see Supplemental Documents for annotated Genbank file.
120949P57mMoClo golden gate assembly AB part for pCin* (Adam Meyer's improved pCin promoter from https://doi.org/10.1101/285866, selected for dynamic range and less cross-sensitivity).
120950P58mMoClo golden gate assembly AB for pLas-A-10b (Adam Meyer's improved pLas promoter from https://doi.org/10.1101/285866, selected for dynamic range and less cross-sensitivity).
120951P59mMoClo golden gate assembly AB part for pLux76B (Adam Meyer's improved pLux promoter from https://doi.org/10.1101/285866, selected for dynamic range and less cross-sensitivity).
120952P60mMoClo golden gate assembly AB for pSalTTTC (Adam Meyer's improved pSal promoter from https://doi.org/10.1101/285866, selected for dynamic range and less cross-sensitivity).
120953P61mMoClo golden gate assembly AB part for pTac (Adam Meyer's improved pTac promoter selected for dynamic range and low cross-sensitivity; unpublished, using strategy from https://doi.org/10.1101/285866).
120954P66mMoClo golden gate assembly AB part for pRpa-AM (Adam Meyer's improved pRPA promoter from https://doi.org/10.1101/285866, selected for dynamic range and low cross-sensitivity).
120955C1mMoClo golden gate assembly CD part for deGFP (deGFP3 with 4aa N-truncation, 9aa C-truncation, F64L, and C203T (numbered with original sequence); see https://www.fpbase.org/protein/degfp3/)
120956C3mMoClo golden gate assembly CD part for sfGFP (Superfolder green fluorescent protein from DOI: 10.1038/nbt1172; slight variant on https://www.fpbase.org/protein/superfolder-gfp/)
120957C5mMoClo golden gate assembly CD part for mRFP (monomeric red fluorescent protein; see https://doi.org/10.1073/pnas.082243699 and https://www.fpbase.org/protein/mrfp1/).
120958C9mMoClo golden gate assembly CD part for deCFP (cyan fluorescent protein) - Please see Supplemental Documents for annotated Genbank file
120959C11mMoClo golden gate assembly CD part for Citrine (modified YFP; variant of https://www.fpbase.org/protein/citrine/) - Please see Supplemental Documents for annotated Genbank file
120960C13mMoClo golden gate assembly CD part for Cerulean (modified CFP; variant of https://www.fpbase.org/protein/cerulean/) - Please see Supplemental Documents for annotated Genbank file
120961C20mMoClo golden gate assembly CD part with sfYFP-ssrA (superfolder YFP with ssrA degradation tag; variant of https://www.fpbase.org/protein/yfp/)
120962C21mMoClo golden gate assembly CD part for MG-aptamer (fluorescent RNA aptamer of malachite green; see DOI: 10.1021/ja0529788) - Please see Supplemental Documents for annotated Genbank file
120963C22mMoClo golden gate assembly CD part for mSpinach (fluorescent RNA aptamer for DFHBI, suitable for in vivo use; see DOI: 10.1021/sb400089c). Please see Supplemental Documents for annotated Genbank file.
120964C24mMoClo golden gate assembly CD part for lambda cI (repressor of pL or pOR1-OR2; use C64m for temperature-sensitive version). Please see Supplemental Documents for annotated Genbank file.
120965C27mMoClo golden gate assembly CD part for TetR (tet repressor; identical to C2d but without ssrA degradation tag). Please see Supplemental Documents for annotated Genbank file.
120966C31mMoClo golden gate assembly CD part for Bxb1 integrase. See DOI: 10.1007/s00438-006-0129-5. Please see Supplemental Documents for annotated Genbank file.
120967C32mMoClo golden gate assembly CD part for CinR (Quorum-sensing receptor for 3OC14). Please see Supplemental Documents for annotated Genbank file.
120968C33mMoClo golden gate assembly CD part for AiiA (AHL degradase; see doi: [10.1126/science.aaa3794]). Please see Supplemental Documents for annotated Genbank file.
120969C35mMoClo golden gate assembly CD part for RhlR (Rhl quorum-sensing receptor for C4-HSL, synonymously modified to remove internal BbsI and BsaI cut sites).
120970C36mMoClo golden gate assembly CD part for RhlI (quorum-sensing synthase for 3OC14). Please see Supplemental Documents for annotated Genbank file.
120971C38mMoClo golden gate assembly CD for sigma38/RpoS (RNA polymerase active at transition from exponential phase to stationary phase). Please see Supplemental Documents for annotated Genbank file.
120972C39mMoClo golden gate assembly CD part for ccdB (DNA gyrase toxin, modified synonymously to remove BsaI cut site; ccdA/C79m is antitoxin). Please see Supplemental Documents for annotated Genbank file.
120973C40mMoClo golden gate assembly CD part for blank part (random 50bp sequence) - Please see Supplemental Documents for annotated Genbank file
120974C41mMoClo golden gate assembly CD part for dCas9 (Catalytically-inactive S. pyogenes Cas9, for gRNA-targeted repression). Please see Supplemental Documents for annotated Genbank file.
120975C51mMoClo golden gate assembly CD part for sfYFP (superfolder YFP; variant of https://www.fpbase.org/protein/yfp/ - Please see Supplemental Documents for annotated Genbank file
120976C59mMoClo golden gate assembly CD part for mScarlet (RFP variant; see https://www.fpbase.org/protein/mscarlet/). Please see Supplemental Documents for annotated Genbank file.
120977C61mMoClo golden gate assembly CD part for RpaR* (improved RpaR quorum-sensing activator from DOI: 10.1021/acssynbio.5b00286). Please see Supplemental Documents for annotated Genbank file.
120978C62mMoClo golden gate assembly CD part for TraR(W) (improved TraR quorum-sensing activator from DOI: 10.1021/acssynbio.5b00286). Please see Supplemental Documents for annotated Genbank file.
120979C63mMoClo golden gate assembly CD part for LacI (Lac repressor; identical to C1d but without ssrA degradation tag). Please see Supplemental Documents for annotated Genbank file.
120980C64mMoClo golden gate assembly CD part for cI857 (temperature-sensitive lambda repressor that represses at 30C but not at 37C; see https://doi.org/10.1016/S0022-2836(66)80269-3. Use with P9m).
120981C67mMoClo golden gate assembly CD part for Bxb1-mScarleti-LAA (Bxb1 integrase tagged with an mScarlet-I reporter and an LAA degradation tag). Please see Supplemental Documents for annotated Genbank file.
120982C70mMoClo golden gate assembly CD part for RpaR-TYQEVV (Adam Meyer's improved RpaR activator selected for dynamic range and low cross-sensitivity using methods from https://doi.org/10.1101/285866,).
120983C71mMoClo golden gate assembly CD part for CinR-CIDDHYRTC n-2 (Adam Meyer's improved CinR activator from https://doi.org/10.1101/285866, selected for dynamic range and less cross-sensitivity).
120984C72mMoClo golden gate assembly CD part for LacI-MVY (Adam Meyer's improved LacI repressor from https://doi.org/10.1101/285866, selected for dynamic range and low cross-sensitivity).
120985C73mMoClo golden gate assembly CD part for LasR-LSTPLVMI (Adam Meyer's improved LasR activator, selected for dynamic range and low cross-sensitivity with methods from https://doi.org/10.1101/285866).
120986C74mMoClo golden gate assembly CD part for LuxRQ-FMY (Adam Meyer's improved LuxR activator from https://doi.org/10.1101/285866, selected for dynamic range and low cross-sensitivity).
120987C75mMoClo golden gate assembly CD part for NahRQ-VHAC (Adam Meyer's improved NahR activator from https://doi.org/10.1101/285866, selected for dynamic range and low cross-sensitivity).
120988C76mMoClo golden gate assembly CD part for KanR (kanamycin resistance protein). Please see Supplemental Documents for annotated Genbank file.
120989C77mMoClo golden gate assembly CD partfor AmpR (ampicillin/carbenicillin resistance protein). Please see Supplemental Documents for annotated Genbank file.
120990C78mMoClo golden gate assembly CD cloning part for ChlorR (chloramphenicol resistance protein). Please see Supplemental Documents for annotated Genbank file.
120991C79mMoClo golden gate assembly CD part for ccdA (Antitoxin to ccdB/C39m. Sequence taken from pMAR7 plasmid sequence). Please see Supplemental Documents for annotated Genbank file.
120992C80mMoClo golden gate assembly CD part for mfLon protease (see doi: [10.1038/nbt.3053]). Please see Supplemental Documents for annotated Genbank file.
120993C82mMoClo golden gate assembly CD part for RpaI (synthase for Rpa-detected quorum sensing molecule 4-coumaroyl-homoserine lactone). Please see Supplemental Documents for annotated Genbank file.
120994C83mMoClo golden gate assembly CD part for pir (Initiation factor required for replication of R6K origin plasmids). Please see Supplemental Documents for annotated Genbank file.
120995C84mMoClo golden gate assembly CD part for sigma28/RpoF (RNA polymerase required for flagellar formation in E. coli). Please see Supplemental Documents for annotated Genbank file.
120996C85mMoClo golden gate assembly CD part for sigmaX (Bacillus subtilis RNA polymerase involved in heat response and biofilm formation). Please see Supplemental Documents for annotated Genbank file.
120997C86mMoClo golden gate assembly CD part (phage lysis protein; lethal to host when expressed). Please see Supplemental Documents for annotated Genbank file.
120998C90mMoClo golden gate assembly CD part for NahR-sfGFP fusion (Adam Meyer improved NahR (C75m) fused to superfolder GFP (C3m)). Please see Supplemental Documents for annotated Genbank file.
120999C91mMoClo golden gate assembly CD part for sfCFP (superfolder CFP developed by Ye Chen in Matthew Bennet's lab) - Please see Supplemental Documents for annotated Genbank file
121000C92mMoClo golden gate assembly CD part for sfCFP-pdt3 (superfolder CFP developed by Ye Chen in Matthew Bennet's lab, with a pdt3 tag for mfLon protease).
121001C95mMoClo golden gate assembly CD part for T7 RNA polymerase (use with P18m). Please see Supplemental Documents for annotated Genbank file.
121002C98mMoClo golden gate assembly CD part for Gp2 (RNA polymerase inhibitor from T7 phage; lethal to host when expressed). Please see Supplemental Documents for annotated Genbank file.
121003C99mMoClo golden gate assembly CD part for codon-optimized mScarlet-I (fast-folding mScarlet variant, codon-optimized for E. coli; see https://www.fpbase.org/protein/mscarlet-i/).
121004C100mMoClo golden gate assembly CD part sfYFP-ptd3 (superfolder YFP with pdt3 degradation tag for mfLon). Please see Supplemental Documents for annotated Genbank file.
121005C101mMoClo golden gate assembly CD part sfCFP-LAA (superfolder CFP developed by Ye Chen in Matthew Bennet's lab, with LAA degradation tag for ssrA).
121006C102mMoClo golden gate assembly CD part treRT-LAA (synthetic Lac-family repressor chimera with LAA degradation tag for ssrA; see DOI: 10.1021/sb500262f).
121007C103mMoClo golden gate assembly CD part for mScarlet-I-LAA (fast-folding mScarlet variant, codon-optimized for E. col, with LAA degradation tag; see https://www.fpbase.org/protein/mscarlet-i/).
121008C105mMoClo golden gate assembly CD part for sfYFP-AAV (superfolder YFP with AAV degradation tag for ssrA). Please see Supplemental Documents for annotated Genbank file.
121009C106mMoClo golden gate assembly CD part for sfYFP-DAS (superfolder YFP with DAS degradation tag for ssrA). Please see Supplemental Documents for annotated Genbank file.
121010C108mMoClo golden gate assembly CD part for mScarlet-I-pdt3 (fast-folding mScarlet variant, codon-optimized for E. col, with pdt3 degradation tag; see https://www.fpbase.org/protein/mscarlet-i/).
121011C109mMoClo golden gate assembly CD part for mfLon-pdt3 (mfLon protease with self-targeting degradation tag pdt3). Please see Supplemental Documents for annotated Genbank file.
121012C113mMoClo golden gate assembly CD part for Cas9 (S. pyogenes gRNA-targeted endonuclease Cas9). Please see Supplemental Documents for annotated Genbank file.
121013C114mMoClo golden gate assembly CD part for Cas9 (S. pyogenes gRNA-targeted endonuclease Cas9, with bbsI cut sites removed synonymously). Please see Supplemental Documents for annotated Genbank file.
121014C115mMoClo golden gate assembly CD part for TP901 integrase (Integrase from lactococcal phage TP901). Please see Supplemental Documents for annotated Genbank file.
121015U2mMoClo golden gate assembly BC part for BCD11 (Medium-high expression bi-cistronic RBS, engineered for downstream context-independence; see https://doi.org/10.1038/nmeth.2404).
121016U3mMoClo golden gate assembly BC part for BCD13 (Medium expression bi-cistronic RBS, engineered for downstream context-independence; see https://doi.org/10.1038/nmeth.2404).
121017U4mMoClo golden gate assembly BC part for UTR1 (very strong RBS). Please see Supplemental Documents for annotated Genbank file.
121018U5mMoClo golden gate assembly BC part for BCD14 (Medium expression bi-cistronic RBS, engineered for downstream context-independence; see https://doi.org/10.1038/nmeth.2404).
121019U6mMoClo golden gate assembly BC part for BCD20 (Medium expression bi-cistronic RBS, engineered for downstream context-independence; see https://doi.org/10.1038/nmeth.2404).
121020U7mMoClo golden gate assembly BC part for BCD16 (low expression bi-cistronic RBS, engineered for downstream context-independence; see https://doi.org/10.1038/nmeth.2404).
121021U8mMoClo golden gate assembly BC part for BCD24 (low expression bi-cistronic RBS, engineered for downstream context-independence; see https://doi.org/10.1038/nmeth.2404).
121022U9mMoClo golden gate assembly BC part for BCD22 (very low expression bi-cistronic RBS, engineered for downstream context-independence; see https://doi.org/10.1038/nmeth.2404).
121023U17mMoClo golden gate assembly BC part for Bujard RBS (strong RBS from https://doi.org/10.1093/nar/25.6.1203). Please see Supplemental Documents for annotated Genbank file.
121024U19mMoClo golden gate assembly BC part for MG-aptamer (fluorescent RNA aptamer of malachite green; see DOI: 10.1021/ja0529788) - Please see Supplemental Documents for annotated Genbank file
121025U22mMoClo golden gate assembly BC part (high expression bi-cistronic RBS, engineered for downstream context-independence; see https://doi.org/10.1038/nmeth.2404).
121026U24mMoClo golden gate assembly BC part for RiboJ-BCD2 (low expression bi-cistronic RBS, engineered for context-independence, prefixed by self-cleaving RiboJ; see https://doi.org/10.1038/nmeth.2404).
121027U25mMoClo golden gate assembly BC part for RiboJ-UTR1 (very strong RBS, prefixed by self-cleaving RiboJ for upstream context independence). Please see Supplemental Documents for annotated Genbank file.
121028T1mMoClo golden gate assembly DE part for T500 terminator Engineered terminator derived from bacteriophage 83; see DOI: 10.1126/science.284.5414.611).
121029T2mMoClo golden gate assembly DE part for Eck120033736 (164.6x-strength natural terminator; see DOI: 10.1038/nmeth.2515) - Please see Supplemental Documents for annotated Genbank file
121030T7mMoClo golden gate assembly DE part for tracrRNA terminator (natural terminator from S. pyogenes CRISPR-system tracrRNA). Please see Supplemental Documents for annotated Genbank file.
121031T12mMoClo golden gate assembly DE part ECK120029600 (378x-strength natural terminator; see DOI: 10.1038/nmeth.2515). Please see Supplemental Documents for annotated Genbank file.
121032T13mMoClo golden gate assembly DE part for ECK120033737 (313x-strength natural terminator; see DOI: 10.1038/nmeth.2515). Please see Supplemental Documents for annotated Genbank file.
121033T14mMoClo golden gate assembly DE part for L3S1P13 (178x-strength synthetic terminator; see DOI: 10.1038/nmeth.2515). Please see Supplemental Documents for annotated Genbank file.
121034T15mMoClo golden gate assembly DE part for L3S3P11 (173x-strength synthetic terminator, modified to remove BsaI cut site; see DOI: 10.1038/nmeth.2515).
121035T16mMoClo golden gate assembly DE part for L3S2P55 (256x-strength synthetic terminator; see DOI: 10.1038/nmeth.2515). Please see Supplemental Documents for annotated Genbank file.
121036T17mMoClo golden gate assembly DE part L3S2P11 (262x-strength synthetic terminator; see DOI: 10.1038/nmeth.2515). Please see Supplemental Documents for annotated Genbank file.
121037T18mMoClo golden gate assembly DE part for L3S2P21 (382x-strength synthetic terminator with BsaI cut site removed; see DOI: 10.1038/nmeth.2515).
121038UC16mMoClo golden gate assembly DE part for gQi gRNA (guide RNA for S. pyogenes Cas9; sequence from DOI: 10.1016/j.cell.2013.02.022). Please see Supplemental Documents for annotated Genbank file.
121039UC17mMoClo golden gate assembly DE part for gV1 gRNA (guide RNA for S. pyogenes Cas9; sequence from doi: [10.15252/msb.20145735]). Please see Supplemental Documents for annotated Genbank file.
121040UC20mMoClo golden gate assembly DE part for gN2 gRNA (guide RNA for S. pyogenes Cas9; sequence designed with NUPACK for stable tracrRNA structure and open targeting region).
121041UCT1mMoClo golden gate assembly DE part for gQi gRNA (guide RNA for S. pyogenes Cas9; sequence from DOI: 10.1016/j.cell.2013.02.022). Please see Supplemental Documents for annotated Genbank file.
121042V35mMoClo golden gate assembly AE destination vector DVCK-AE-GFP (ColE1/kan resistance destination vector with constitutive GFP expression for screening.
121043V37mMoClo golden gate assembly AE destination vector DVCK-AE-mScar (ColE1/kan resistance destination vector with constitutive mScarlet expressing for screening.

Antibodies from Article