The BioBricks Foundation:Standards/Technical/Formats: Difference between revisions
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<sub>Note, for coding parts, the prefix is shortened so that the ATG is fully part of the biobrick sequence.</sub> | <sub>Note, for coding parts, the prefix is shortened so that the ATG is fully part of the biobrick sequence.</sub> | ||
==== | [[http://parts.mit.edu/registry/index.php/Help:BioBrick_Prefix_and_Suffix | description at parts.mit.edu]] | ||
====Advantages==== | |||
* de-facto standard | * de-facto standard | ||
* well tested and documented | |||
====Disadvantages==== | |||
* no protein fusions (frame shift, stop codon) | * no protein fusions (frame shift, stop codon) | ||
* a single mutation (at the fused region) can upset the setup? | * a single mutation (at the fused region) can upset the setup? | ||
== "2.0" Biofusion (Silver lab) == | == "2.0" Biofusion (Silver lab) == | ||
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[[Image:Bbformats_biofusion.png]] | [[Image:Bbformats_biofusion.png]] | ||
[[http://www.openwetware.org/wiki/Silver:_BB_Strategy | description by Silver lab]] | |||
====Advantages==== | |||
* in-frame fusion of protein parts | * in-frame fusion of protein parts | ||
* compatible to 1.0 non-coding parts | * compatible to 1.0 non-coding parts | ||
* half-compatible to 1.0 protein parts (frame shift, but adapter/Kozak brick workaround) | * half-compatible to 1.0 protein parts (frame shift, but adapter/Kozak brick workaround) | ||
====Disadvantages==== | |||
* Arg in scar can be problematic | * Arg in scar can be problematic | ||
* N-terminal Thr-Arg = destabilization signal (N-end rule) | * N-terminal Thr-Arg = destabilization signal (N-end rule) | ||
* methylation site blocks cloning when prefix is followed by "TC" | * methylation site blocks cloning when prefix is followed by "TC" | ||
== "3.0" (Freiburg iGem team) == | == "3.0" (Freiburg iGem team) == | ||
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[[Image:Bbformats_freiburg.png]] | [[Image:Bbformats_freiburg.png]] | ||
[[http://parts.mit.edu/igem07/index.php/Freiburg07/report_fusion_parts | description by Freiburg iGem team]] | |||
====Advantages==== | |||
* in-frame fusion of protein parts | * in-frame fusion of protein parts | ||
* less intrusive protein scar | * less intrusive protein scar | ||
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* compatible to 1.0 and 2.0 non-coding parts | * compatible to 1.0 and 2.0 non-coding parts | ||
====Disadvantages==== | |||
* stand-alone protein expression (start + stop in prefix / suffix) | * stand-alone protein expression (start + stop in prefix / suffix) | ||
* not compatible to 1.0 protein parts (stop codon) | * not compatible to 1.0 protein parts (stop codon) | ||
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[[Image:Bbformats_crg.png]] | [[Image:Bbformats_crg.png]] | ||
====Advantages==== | |||
* in-frame fusion of protein parts | * in-frame fusion of protein parts | ||
* less intrusive protein scar | * less intrusive protein scar | ||
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* full backwards-compatibility (coding and non-coding 1.0 and 2.0 parts) | * full backwards-compatibility (coding and non-coding 1.0 and 2.0 parts) | ||
====Disadvantages==== | |||
* no stand-alone protein expression | * no stand-alone protein expression | ||
* not tested | |||
== different strategies == | == different strategies == | ||
[ add ] | [ add ] |
Revision as of 01:46, 27 February 2008
Biobrick Formats: This working group aims to specify Biobrick DNA formats.
Aim / Application scenarios for this standard
[ add ]
Overview over proposed Biobrick formats
All biobrick formats proposed so far follow the same basic scheme where restriction and ligation of two biobricks forms a new biobrick.
1.0 de-facto standard
This is the classic Biobrick format used by most iGem teams and most biobricks in the MIT registry.
Note, for coding parts, the prefix is shortened so that the ATG is fully part of the biobrick sequence.
[| description at parts.mit.edu]
Advantages
- de-facto standard
- well tested and documented
Disadvantages
- no protein fusions (frame shift, stop codon)
- a single mutation (at the fused region) can upset the setup?
"2.0" Biofusion (Silver lab)
The Silver lab modified the classic format to allow for protein fusions:
Advantages
- in-frame fusion of protein parts
- compatible to 1.0 non-coding parts
- half-compatible to 1.0 protein parts (frame shift, but adapter/Kozak brick workaround)
Disadvantages
- Arg in scar can be problematic
- N-terminal Thr-Arg = destabilization signal (N-end rule)
- methylation site blocks cloning when prefix is followed by "TC"
"3.0" (Freiburg iGem team)
The Freiburg 2007iGem team proposed a more radical modification or rather extension of 1.0, which would enable protein fusions but alleviate the disadvantages of the Biofusion format:
[| description by Freiburg iGem team]
Advantages
- in-frame fusion of protein parts
- less intrusive protein scar
- N-end rule safe (longer protein half-life)
- stand-alone protein expression (start + stop in prefix / suffix)
- compatible to 1.0 and 2.0 non-coding parts
Disadvantages
- stand-alone protein expression (start + stop in prefix / suffix)
- not compatible to 1.0 protein parts (stop codon)
- not compatible to 2.0 protein parts (frame shift + stop codon)
"2.0-3.0" (CRG proposal)
Biobrick users at the CRG propose a modification to the Freiburg format which would make 3.0 and 2.0 biobricks compatible with each other and allow 3.0 biobricks to be fused N-terminally to 1.0 protein coding parts. The modification sacrifices the possibility to have a single coding biobrick ready for expression (start and stop in the prefix and suffix are deleted). This may also be considered am advantage though, as it somewhat reduces the risk of uncontrolled expression leading to toxicity.
Advantages
- in-frame fusion of protein parts
- less intrusive protein scar
- N-end rule safe (longer protein half-life)
- full backwards-compatibility (coding and non-coding 1.0 and 2.0 parts)
Disadvantages
- no stand-alone protein expression
- not tested
different strategies
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