Team:EPF-Lausanne/Our Project/Assembly

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{{:Team:EPF-Lausanne/Templates/Header|title=Assembly Sequence}}
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#REDIRECT [[Team:EPF-Lausanne/Our_Project/Reporter_Systems]]
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TODO: describe here the sequence of assembly for our plasmids: what plasmids we build; where the parts came from;
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what had to be done. For example, why did we have to rebuild J61002 from scratch?
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This page will probably become very technical, in which case we will move it and replace by a succinct outline.
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The goal of this page is to keep everybody on the assembly team up to date on the ugly details of everybody's work.
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Leave nothing out!
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== Reporter Plasmid ==
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The reporter plasmid contains the mutated TetR operator coupled to a LacI inverter, so that in presence of TetR the reporter gene is ''activated''. Two reporter plasmids are built: one that contains and RFP reporter, and one that contains a Lysis gene, to lyse the cells that contain valid combinations of TetR and pTet mutants, in order to recover their DNA. Their structure is illustrated below.
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[[File:EPFL-Reporter_plasmids_both.png|700px|center]]
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== Backbone template assembly ==
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The '''first step''' of assembly was to make a J61002 backbone, containing pTet and RFP. We took the J61002 plasmid from the registry, containing ampicillin resistance, RFP and a ColE1 replication origin (medium copy number). By PCR, we then added the pTet promoter in front of RFP. Finally, the pTet-RFP and the backbone (plasmid without RFP) were assembled thank to Gibson.(<span style="color:red"> vincent, please confirm this!</span>). This was our first successful Gibson assembly.
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Vincent, please document this step. What template did you use, what primers, etc? Please include links to the
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sequences of the template, of the expected product, and if possible a table that summarizes that all,
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like Nadine did.
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{|
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! Part used for Gibson assembly 
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! Amplified from which template
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! Features added with the PCR primers 
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|-
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| J61002 backbone
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| J61002 plasmid - from delivery kit
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| none
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|-
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| pTet-RFP
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| J61002 plasmid - from delivery kit
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| pTet
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|}
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[[File:EPFL-J61002-pTet-RFP.png|400px]]
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The product of this assembly is the J61002-pTet-RFP 'backbone' plasmid. It contains an ampicillin resistance gene, as well as RFP repressed by pTet. This plasmid is used as a template for the second step of assembly, in which the LacI inverter and reporter genes are introduced.
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=== Adding the inverter and reporter ===
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The '''second step''' is to add the LacI inverter and reporter gene into the backbone. Let's run through the elements one by one. We need:
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* The '''backbone''', which already contains the '''pTet promoter'''
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* the '''LacI coding region''', repressed by the pTet promoter
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* a '''pLac promoter'''...
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* ...that represses expression of a '''reporter gene''' either RFP or the Lysis cassette.
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TODO: - illustrate which parts are copied from where.
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      - lookup biobrick numbers.
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      - illustrate Gibson overhangs
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The '''backbone''' is copied from the previously-assembled J61002-pTet-RFP. The RFP gene is '''not''' included in this copy; this allows the same PCR primers and products to be used for the assembly of both plasmids. The '''LacI''' coding region is copied from the Repressilator plasmid. In the case of the '''RFP''' plasmid, RFP is copied from the J61002-pTet-RFP plasmid, making a fragment separate from the backbone. In the case of the '''Lysis''' plasmid, the lysis device is copied from the T4 Lysis device plasmid, from the iGEM gene distribution. In both cases, the '''pLac''' promoter is introduced by the primer, using an overhang.
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{|
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! Part used for Gibson assembly 
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! Amplified from which template
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! Features added with the PCR primers
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|-
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| J61002-pTet backbone
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| J61002 pTet-RFP plasmid - from previous assembly
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| none
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| LacI with degradation tag (ssrA) and terminator (rrnB)
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| Repressilator plasmid
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| none
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| Plac-RFP
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| J61002 pTet-RFP plasmid - from previous assembly
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| Plac
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| Plac-lysis
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| T4 lysis plasmid
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| Plac
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|}
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== TetR plasmid ==
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This assembly was quite tricky, as we had to test 3 plasmids before succeeding.
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* We first took the J23019 plasmid from the registry and designed plasmids, but we never succeeded in amplifying something during PCRs. We assumed that probably the plasmid is not exactly the one described in the registry and went on with plasmid number 2.
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* Our second choice was pSB3C5, as we could partially reuse the primers designed for J23019. But the PCR results were very weak and the assembly failed.
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* So finally we used '''pSB3K1''', which is really similar to pSB3C5, designed new primers and succeeded in doing the Gibson assembly!
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We amplified this backbone, and added '''TetR''' under '''constitutive promoter''' to it.
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{|
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! Part used for Gibson assembly 
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! Amplified from which template
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! Features added with the PCR primers
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|-
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| pSB3K1 backbone
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| pSB3k1 plasmid - from registry 
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| none
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|-
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| Pconst-TetR
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| Repressilator plasmid
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| Constitutive promoter (pConst), RBS and spacer
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|}
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[[File:EPFL_Tetr_plasmid.jpg|300px]]
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This plasmid seems to contain RFP, although not present in the sequence on partregistry...
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{{:Team:EPF-Lausanne/Templates/Footer}}
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Latest revision as of 01:49, 22 September 2011

  1. REDIRECT Team:EPF-Lausanne/Our_Project/Reporter_Systems
Retrieved from "http://2011.igem.org/Team:EPF-Lausanne/Our_Project/Assembly"