Team:ETHZ Basel/Achievements/BioBrick Toolbox

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To construct the aimed fusion proteins, we first blunt-end cloned our BioBricks into the storage vector pSEVA132 <partinfo>BBa_K422002</partinfo> (Victor de Lorenzo's lab, KanR, pBBR1 ori).  
To construct the aimed fusion proteins, we first blunt-end cloned our BioBricks into the storage vector pSEVA132 <partinfo>BBa_K422002</partinfo> (Victor de Lorenzo's lab, KanR, pBBR1 ori).  
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All parts are sequence verified and compatible with BBF RFC28 (http://dspace.mit.edu/handle/1721.1/46721).
+
All parts are sequence verified and compatible with BBF RFC28 (http://dspace.mit.edu/handle/1721.1/46721)
-
Check out our general scheme for the easy construction of Tom Knight's OAS and BBF RFC28 compatible working vectors [https://2010.igem.org/Team:ETHZ_Basel/Biology/Cloning]!
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=== basic parts ===
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<center>
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{| class="wikitable sortable" border="0" style="text-align: left"
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|-bgcolor=#cccccc
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|+ align="top, left"|'''table 1''': Our BrickBox parts for the Chemotaxis BrickBox, the Anchor BrickBox, the Light Sensing BrickBox and the Reporter BrickBox.
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|+ align="bottom"|<nowiki>* compatible for insertion of microRNA binding sites</nowiki>
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|width=100px|ID||width=40px|Insert||width=40px|Orientation||width=100px|ID||width=40px|Insert||width=40px|Orientation||width=300px|Description
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== Chemotaxis BrickBox ==
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{| border="1"
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|-
|-
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! Name
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|<partinfo>BBa_K422003</partinfo>||CheB||A-part||<partinfo>BBa_K422003</partinfo>||CheB||C-part||Demthylase: Demethylates methyl accepting chemotaxis proteins MCPs
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! Insert
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! Orientation
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! Name
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! Insert
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! Orientation
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! Description
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! Favourite part
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|-
|-
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| <partinfo>BBa_K422003</partinfo>
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|<partinfo>BBa_K422005</partinfo>||CheR||A-part||<partinfo>BBa_K422003</partinfo>||CheR||C-part||Methyltransferase: Methylates methyl accepting chemotaxis proteins MCPs
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| CheB
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| A-part
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| <partinfo>BBa_K422004</partinfo>
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| CheB
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| C-part
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| Demthylase: Demethylates methyl accepting chemotaxis proteins MCPs
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|
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|-
|-
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| <partinfo>BBa_K422005</partinfo>
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|<partinfo>BBa_K422007</partinfo>||CheY||A-part||<partinfo>BBa_K422003</partinfo>||CheY||C-part||Induces tumbling by interacting with the flagellar switch protein FliM
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| CheR
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| A-part
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| <partinfo>BBa_K422006</partinfo>
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| CheR
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| C-part
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| Methyltransferase: Methylates methyl accepting chemotaxis proteins MCPs
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|  
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|-
|-
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| <partinfo>BBa_K422007</partinfo>
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|<partinfo>BBa_K422009</partinfo>||tetR||A-part|| || || ||Tetracyclin repressor: Binds to its operator tetO for spatial localization of a fusion protein to the DNA
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| CheY
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| A-part
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| <partinfo>BBa_K422008</partinfo>
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| CheY
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| C-part
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| Induces tumbling by interacting with the flagellar switch protein FliM
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|  
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|}
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== Anchor BrickBox ==
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{| border="1"
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|-
|-
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! Name
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|<partinfo>BBa_K422010</partinfo>||trig||A-part|| || || ||Ribosome binding domain of the trigger factor: Binds to the large subunit of the ribosome
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! Insert
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! Orientation
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! Description
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! Favourite part
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|-
|-
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| <partinfo>BBa_K422009</partinfo>
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| || || ||<partinfo>BBa_K422011</partinfo>||MreB||C-part||Prokaryotic actin homologue: Assembles into helical filaments underneath the cytoplasmic membrane
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| TetR
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| A-part
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| Tetracyclin repressor: Binds to its operator tetO for spatial localization of a fusion protein to the DNA.
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|
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|-
|-
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| <partinfo>BBa_K422010</partinfo>
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| || || ||<partinfo>BBa_K422012</partinfo>||Pif3||C-part||Phytochrome interacting factor: Binds Prf form of PhyB and rapidly dissociates in response to reconversion to the Pr state
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| trigA
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| A-part
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| Ribosome binding domain of the trigger factor: Binds to the large subunit of the ribosome.
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|
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|-
|-
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| <partinfo>BBa_K422011</partinfo>
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| || || ||<partinfo>BBa_K422013</partinfo>||PhyB||C-part||Phytochromes type II: Biologically inactive form Pr absorbs red light and active configuration Pfr far-red light
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| MreB
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| C-part
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| Prokaryotic actin homologue: Assembles into helical filaments underneath the cytoplasmic membrane.
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|  
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|}
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== Ligth sensor BrickBox ==
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{| border="1"
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|-
|-
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! Name
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|<partinfo>BBa_K422014</partinfo>||mcyPet||A-part|| || || ||CFP variant
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! Insert
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! Orientation
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! Description
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! Favourite part
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|-
|-
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| <partinfo>BBa_K422012</partinfo>
 
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| Pif3
 
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| C-part
 
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| Phytochrome interacting factor: Binds Prf form of PhyB and rapidly dissociates in response to reconversion to the Pr state.
 
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|
 
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|-
 
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| <partinfo>BBa_K422013</partinfo>
 
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| PhyB
 
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| C-part
 
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| Phytochromes type II: Biologically inactive form Pr absorbs red light and active configuration Pfr far-red light.
 
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|
 
|}
|}
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</center>
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+
We also gave a lot of thoughts how to make BBF RFC28 (method for combinatorial multi-part assembly based on the Type II restriction enzyme AarI) compatible with Tom Knight's OAS standard. Check out our general scheme for the easy construction of Tom Knight's OAS and BBF RFC28 compatible working vectors [https://2010.igem.org/Team:ETHZ_Basel/Biology/Cloning]!
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== Reporter BrickBox ==
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{| border="1"
+
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|-
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! Name
+
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! Insert
+
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! Orientation
+
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! Description
+
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! Favourite part
+
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|-
+
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| <partinfo>BBa_K422014</partinfo>
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| cyPet
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| A-part
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| CFP variant.
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|
+
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|}
+

Revision as of 11:36, 26 October 2010

BioBrick Toolbox

BioBrick assembly A-parts are used for N-Terminal and C-parts for C-terminal fusion. B-part is the linker that connects the two entities.

To construct the aimed fusion proteins, we first blunt-end cloned our BioBricks into the storage vector pSEVA132 <partinfo>BBa_K422002</partinfo> (Victor de Lorenzo's lab, KanR, pBBR1 ori). All parts are sequence verified and compatible with BBF RFC28 (http://dspace.mit.edu/handle/1721.1/46721)

basic parts

table 1: Our BrickBox parts for the Chemotaxis BrickBox, the Anchor BrickBox, the Light Sensing BrickBox and the Reporter BrickBox. * compatible for insertion of microRNA binding sites
IDInsertOrientationIDInsertOrientationDescription
<partinfo>BBa_K422003</partinfo>CheBA-part<partinfo>BBa_K422003</partinfo>CheBC-partDemthylase: Demethylates methyl accepting chemotaxis proteins MCPs
<partinfo>BBa_K422005</partinfo>CheRA-part<partinfo>BBa_K422003</partinfo>CheRC-partMethyltransferase: Methylates methyl accepting chemotaxis proteins MCPs
<partinfo>BBa_K422007</partinfo>CheYA-part<partinfo>BBa_K422003</partinfo>CheYC-partInduces tumbling by interacting with the flagellar switch protein FliM
<partinfo>BBa_K422009</partinfo>tetRA-part Tetracyclin repressor: Binds to its operator tetO for spatial localization of a fusion protein to the DNA
<partinfo>BBa_K422010</partinfo>trigA-part Ribosome binding domain of the trigger factor: Binds to the large subunit of the ribosome
<partinfo>BBa_K422011</partinfo>MreBC-partProkaryotic actin homologue: Assembles into helical filaments underneath the cytoplasmic membrane
<partinfo>BBa_K422012</partinfo>Pif3C-partPhytochrome interacting factor: Binds Prf form of PhyB and rapidly dissociates in response to reconversion to the Pr state
<partinfo>BBa_K422013</partinfo>PhyBC-partPhytochromes type II: Biologically inactive form Pr absorbs red light and active configuration Pfr far-red light
<partinfo>BBa_K422014</partinfo>mcyPetA-part CFP variant

We also gave a lot of thoughts how to make BBF RFC28 (method for combinatorial multi-part assembly based on the Type II restriction enzyme AarI) compatible with Tom Knight's OAS standard. Check out our general scheme for the easy construction of Tom Knight's OAS and BBF RFC28 compatible working vectors [1]!

Retrieved from "http://2010.igem.org/Team:ETHZ_Basel/Achievements/BioBrick_Toolbox"