Moclo: Difference between revisions
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In order to take full advantage of the modularity and ease of use, one must spend significant time "domesticating" DNA parts by removing extra restriction sites and placing them into appropriate vectors which contain the typeIIs restriction sites in the right orientation. This work has been done by many labs (with equally many sticky end overhang standards). | In order to take full advantage of the modularity and ease of use, one must spend significant time "domesticating" DNA parts by removing extra restriction sites and placing them into appropriate vectors which contain the typeIIs restriction sites in the right orientation. This work has been done by many labs (with equally many sticky end overhang standards). | ||
One example of such a standard is the CIDAR library from Doug Densmore's lab | One example of such a standard is the CIDAR library from [http://pubs.acs.org/doi/pdf/10.1021/acssynbio.5b00124 Doug Densmore's lab] | ||
=CIDAR= | =CIDAR= | ||
Revision as of 02:25, 22 June 2016
Moclo is a type of cloning strategy that attempts to standardize the assembly of multiple DNA parts into finished constructs or 'devices'. The basic cloning method relies on the fact that typeIIs restriction enzymes cut outside their sequence of recognition. Unlike traditional restriction cloning, this means there is no chance that ligated pieces can be cut again by the same enzyme. This also gives you complete freedom in choosing the four base-pair sticky end, and allows multiple specific ligations to be accomplished with only one restriction enzyme.
In order to take full advantage of the modularity and ease of use, one must spend significant time "domesticating" DNA parts by removing extra restriction sites and placing them into appropriate vectors which contain the typeIIs restriction sites in the right orientation. This work has been done by many labs (with equally many sticky end overhang standards).
One example of such a standard is the CIDAR library from Doug Densmore's lab
CIDAR
| Name | Well | Type | Overhangs | Description | Link |
|---|---|---|---|---|---|
| J23100_AB | A1 | Promoter | AB | Weak Constitutive Promoter | https://benchling.com/s/gS6lXC3X/edit |
| J23100_EB | A2 | Promoter | EB | Weak Constitutive Promoter | https://benchling.com/s/aq8Gxp2O/edit |
| J23100_FB | A3 | Promoter | FB | Weak Constitutive Promoter | https://benchling.com/s/rTzq9ToN/edit |
| J23100_GB | A4 | Promoter | GB | Weak Constitutive Promoter | https://benchling.com/s/5yn5Zy6g/edit |
| J23102_AB | A5 | Promoter | AB | Strong Constitutive Promoter | https://benchling.com/s/aQOLd1xr/edit |
| J23102_EB | A6 | Promoter | EB | Strong Constitutive Promoter | https://benchling.com/s/zOCQC6dM/edit |
| J23102_FB | A7 | Promoter | FB | Strong Constitutive Promoter | https://benchling.com/s/1pfiY4NG/edit |
| J23102_GB | A8 | Promoter | GB | Strong Constitutive Promoter | https://benchling.com/s/LmBWThyt/edit |
| J23103_AB | A9 | Promoter | AB | Weak Constitutive Promoter | https://benchling.com/s/9KEsWqta/edit |
| J23103_EB | A10 | Promoter | EB | Weak Constitutive Promoter | https://benchling.com/s/ynovZBP9/edit |
| J23103_FB | A11 | Promoter | FB | Weak Constitutive Promoter | https://benchling.com/s/oZSwbWfi/edit |
| J23103_GB | A12 | Promoter | GB | Weak Constitutive Promoter | https://benchling.com/s/4qwyO9ja/edit |
| J23106_AB | B1 | Promoter | AB | Medium Constitutive Promoter | https://benchling.com/s/riO8LQFW/edit |
| J23106_EB | B2 | Promoter | EB | Medium Constitutive Promoter | https://benchling.com/s/ljtaz48p/edit |
| J23106_FB | B3 | Promoter | FB | Medium Constitutive Promoter | https://benchling.com/s/b8wazW5M/edit |
| J23106_GB | B4 | Promoter | GB | Medium Constitutive Promoter | https://benchling.com/s/UqDZklx7/edit |
| J23107_AB | B5 | Promoter | AB | Medium Constitutive Promoter | https://benchling.com/s/G8ouTflM/edit |
| J23107_EB | B6 | Promoter | EB | Medium Constitutive Promoter | https://benchling.com/s/SGzlA9lZ/edit |
| J23107_FB | B7 | Promoter | FB | Medium Constitutive Promoter | https://benchling.com/s/0mSZV0LM/edit |
| J23107_GB | B8 | Promoter | GB | Medium Constitutive Promoter | https://benchling.com/s/InUihbMF/edit |
| J23116_AB | B9 | Promoter | AB | Weak Constitutive Promoter | https://benchling.com/s/1mQPZFtM/edit |
| J23116_EB | B10 | Promoter | EB | Weak Constitutive Promoter | https://benchling.com/s/xqAO8tJl/edit |
| J23116_FB | B11 | Promoter | FB | Weak Constitutive Promoter | https://benchling.com/s/o8lvrIdJ/edit |
| J23116_GB | B12 | Promoter | GB | Weak Constitutive Promoter | https://benchling.com/s/YYNkGLBV/edit |
| R0010_AB | C1 | Promoter | AB | pLac LacI Repressible Promoter | https://benchling.com/s/etg7OrN6/edit |
| R0010_EB | C2 | Promoter | EB | pLac LacI Repressible Promoter | https://benchling.com/s/FamBps3h/edit |
| R0010_FB | C3 | Promoter | FB | pLac LacI Repressible Promoter | https://benchling.com/s/oi1T00L0/edit |
| R0010_GB | C4 | Promoter | GB | pLac LacI Repressible Promoter | https://benchling.com/s/Yw6bgPjg/edit |
| R0040_AB | C5 | Promoter | AB | pTet Strong TetR Repressible Promoter | https://benchling.com/s/3RYAjD6u/edit |
| R0040_EB | C6 | Promoter | EB | pTet Strong TetR Repressible Promoter | https://benchling.com/s/SNZHRImR/edit |
| R0040_FB | C7 | Promoter | FB | pTet Strong TetR Repressible Promoter | https://benchling.com/s/nyzVqekN/edit |
| R0040_GB | C8 | Promoter | GB | pTet Strong TetR Repressible Promoter | https://benchling.com/s/473M59P8/edit |
| R0063_AB | C9 | Promoter | AB | pLux Weak LuxR Repressible Promoter | https://benchling.com/s/EUFuZKHP/edit |
| R0063_EB | C10 | Promoter | EB | pLux Weak LuxR Repressible Promoter | https://benchling.com/s/PN1VmcWg/edit |
| R0063_FB | C11 | Promoter | FB | pLux Weak LuxR Repressible Promoter | https://benchling.com/s/xnA98Y5U/edit |
| R0063_GB | C12 | Promoter | GB | pLux Weak LuxR Repressible Promoter | https://benchling.com/s/jHQHwAaD/edit |
| I13453_AB | D1 | Promoter | AB | pBAD AraC Inducible Promoter | https://benchling.com/s/HE4joK6k/edit |
| I13453_EB | D2 | Promoter | EB | pBAD AraC Inducible Promoter | https://benchling.com/s/YC8NeyAe/edit |
| I13453_FB | D3 | Promoter | FB | pBAD AraC Inducible Promoter | https://benchling.com/s/c4zFwYww/edit |
| I13453_GB | D4 | Promoter | GB | pBAD AraC Inducible Promoter | https://benchling.com/s/i9YCgIRi/edit |
| B0032m_BC | D5 | RBS | BC | Weiss Medium Strength RBS | https://benchling.com/s/jwIsLDg9/edit |
| B0033m_BC | D6 | RBS | BC | Weiss Low strength RBS | https://benchling.com/s/FQFaG78R/edit |
| B0034m_BC | D7 | RBS | BC | Weiss High Strength RBS | https://benchling.com/s/kBNYDAHo/edit |
| BCD12_BC | D8 | RBS | BC | Medium Strength BCD RBS | https://benchling.com/s/mUcZUqJo/edit |
| BCD2_BC | D9 | RBS | BC | High Strength BCD RBS | https://benchling.com/s/jM8sZdRg/edit |
| BCD8_BC | D10 | RBS | BC | Low Strength BCD RBS | https://benchling.com/s/8UhD5Vaf/edit |
| C0012m_CD | D11 | CDS | CD | LacI Repressor protein | https://benchling.com/s/1RopAYaI/edit |
| C0040_CD | D12 | CDS | CD | TetR Repressor Protein | https://benchling.com/s/M9uZpTOg/edit |
| C0062_CD | E1 | CDS | CD | LuxR Repressor/Activator Protein | https://benchling.com/s/FFyxWiwT/edit |
| C0080_CD | E2 | CDS | CD | LuxR Repressor/Activator Protein | https://benchling.com/s/FFyxWiwT/edit |
| cre_CD | E3 | CDS | CD | Cre Recombinase Protein | https://benchling.com/s/CAXPcaMy/edit |
| E0030_CD | E4 | CDS | CD | Yellow Fluorescent Protein | https://benchling.com/s/cr12BVOE/edit |
| E0040m_CD | E5 | CDS | CD | Green Fluorescent Protein | https://benchling.com/s/cj91KrVH/edit |
| E1010m_CD | E6 | CDS | CD | Red Fluorescent Protein | https://benchling.com/s/1AbCv00F/edit |
| eBFP2_CD | E7 | CDS | CD | Blue Fluorescent Protein | https://benchling.com/s/bbkctFdr/edit |
| B0015_DE | E8 | Terminator | DE | Double Terminator | https://benchling.com/s/a1cHND33/edit |
| B0015_DF | E9 | Terminator | DF | Double Terminator | https://benchling.com/s/f6RaEG2K/edit |
| B0015_DG | E10 | Terminator | DG | Double Terminator | https://benchling.com/s/5pFYTkSF/edit |
| B0015_DH | E11 | Terminator | DH | Double Terminator | https://benchling.com/s/8st8vLlQ/edit |
| DVA_AB | E12 | Destination | AB | Moclo Part Destination Vector (stage 1), Promoter | https://benchling.com/s/slHkWK6p/edit |
| DVA_AE | F1 | Destination | AE | Moclo Device Destination Vector (stage 3) | https://benchling.com/s/JbqtviMA/edit |
| DVA_AF | F2 | Destination | AF | Moclo Device Destination Vector (stage 3) | https://benchling.com/s/NviiNLIp/edit |
| DVA_AG | F3 | Destination | AG | Moclo Device Destination Vector (stage 3) | https://benchling.com/s/pPe92CO5/edit |
| DVA_AH | F4 | Destination | AH | Moclo Device Destination Vector (stage 3) | https://benchling.com/s/iaYDvlV2/edit |
| DVA_BC | F5 | Destination | BC | Moclo Part Destination Vector (stage 1), UTR | https://benchling.com/s/o7TOrROp/edit |
| DVA_CD | F6 | Destination | CD | Moclo Part Destination Vector (stage 1), CDS | https://benchling.com/s/xgdB8Znv/edit |
| DVA_DE | F7 | Destination | DE | Moclo Part Destination Vector (stage 1), Terminator | https://benchling.com/s/mtpMynxT/edit |
| DVA_DF | F8 | Destination | DF | Moclo Part Destination Vector (stage 1), Terminator | https://benchling.com/s/53Whxb2s/edit |
| DVA_DG | F9 | Destination | DG | Moclo Part Destination Vector (stage 1), Terminator | https://benchling.com/s/bJdQOwZP/edit |
| DVA_DH | F10 | Destination | DH | Moclo Part Destination Vector (stage 1), Terminator | https://benchling.com/s/sGGQDAg6/edit |
| DVA_EB | F11 | Destination | EB | Moclo Part Destination Vector (stage 1), Promoter | https://benchling.com/s/i5JEIhUg/edit |
| DVA_EF | F12 | Destination | EF | Moclo Device Destination Vector (stage 3) | https://benchling.com/s/OlSBaZCj/edit |
| DVA_EG | G1 | Destination | EG | Moclo Device Destination Vector (stage 3) | https://benchling.com/s/xGeYtbZx/edit |
| DVA_EH | G2 | Destination | EH | Moclo Device Destination Vector (stage 3) | https://benchling.com/s/fnTqha2S/edit |
| DVA_FB | G3 | Destination | FB | Moclo Part Destination Vector (stage 1), Promoter | https://benchling.com/s/3CuYwFwU/edit |
| DVA_GB | G4 | Destination | GB | Moclo Part Destination Vector (stage 1), Promoter | https://benchling.com/s/UvuVapbV/edit |
| DVA | G5 | Vector | - | Vector for new Stage 1 or 3 vector | https://benchling.com/s/6hijqfvT/edit |
| pJ02B2Gm_AE | G6 | Device | AE | High GFP Expression Device, in Part Vector | https://benchling.com/s/mgYDcL4z/edit |
| pJ02B2Gm_EF | G7 | Device | EF | High GFP Expression Device, in Part Vector | https://benchling.com/s/3WQbdlzU/edit |
| pJ02B2Rm_AE | G8 | Device | AE | High RFP Expression Device, in Part Vector | https://benchling.com/s/Kb4AAbox/edit |
| pJ02B2Rm_EF | G9 | Device | EF | High RFP Expression Device, in Part Vector | https://benchling.com/s/FOM8uxtS/edit |
| pJ02B2Gm:Rm_AF | G10 | Device | AF | High GFP and High RFP expression Device, in Part Vector | https://benchling.com/s/D75ziv6K/edit |
| pJ02B2Rm:Gm_AF | G11 | Device | AF | High RFP and High GFP Expression Device, in Part Vector | https://benchling.com/s/OOkaVw1a/edit |
| pJ02B2Gm_AE | G12 | Device | AE | High GFP Expression Device, in Stage 2 Vector | https://benchling.com/s/ShVJxDdF/edit |
| pJ02B2Gm_EF | H1 | Device | EF | High GFP Expression Device, in Stage 2 Vector | https://benchling.com/s/uUTmefO7/edit |
| pJ02B2Rm_AE | H2 | Device | AE | High RFP Expression Device, in Stage 2 Vector | https://benchling.com/s/syrZcMB4/edit |
| pJ02B2Rm_EF | H3 | Device | EF | High RFP Expression Device, in Stage 2 Vector | https://benchling.com/s/nNICVGuk/edit |
| DVK_AE | H4 | Destination | AE | Moclo Device Destination Vector (stage 2) | https://benchling.com/s/sueyphOw/edit |
| DVK_AF | H5 | Destination | AF | Moclo Device Destination Vector (stage 2) | https://benchling.com/s/1i0mX41y/edit |
| DVK_EF | H6 | Destination | EF | Moclo Device Destination Vector (stage 2) | https://benchling.com/s/7FuJO5tD/edit |
| DVK_FG | H7 | Destination | FG | Moclo Device Destination Vector (stage 2) | https://benchling.com/s/Cz5hQ9wM/edit |
| DVK_GH | H8 | Destination | GH | Moclo Device Destination Vector (stage 2) | https://benchling.com/s/MFw9pNDU/edit |
| DVK | H9 | Vector | - | Vector for new Stage 2 vector | https://benchling.com/s/olS42cDR/edit |
