Difference between revisions of "Part:BBa K2656007"
 
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__NOTOC__
 
__NOTOC__
 
<partinfo>BBa_K2656007 short</partinfo>
 
<partinfo>BBa_K2656007 short</partinfo>
  
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Part BBa_K2656007 is the constitutive promoter [https://parts.igem.org/Part:BBa_J23101 BBa_J23101] compatible with both Biobrick and [http://2018.igem.org/Team:Valencia_UPV/GB3 Golden Braid ] assembly methods. It can be combined with other compatible parts from our [http://2018.igem.org/Team:Valencia_UPV/Part_Collection Valencia UPV IGEM 2018 Printeria Collection] to assemble transcriptional units with the [http://2018.igem.org/Team:Valencia_UPV/Protocols Golden Gate assembly protocol].
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[[File:T--Valencia_UPV--im11UPV2018.png|250px|thumb|centro|alt=domestication.|Figure 1. DNA basic parts domestication. First construction refers to promoter domestication into the Golden Gate grammar. ]]
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Part BBa_K2656007 is the constitutive strong promoter [https://parts.igem.org/Part:BBa_J23101 BBa_J23101] adapted into the Golden Gate grammar. Thus, it is compatible with both Biobrick and [http://2018.igem.org/Team:Valencia_UPV/Design Golden Braid] assembly methods.  
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Following the <html><a href="https://static.igem.org/mediawiki/parts/b/bc/T--Valencia_UPV--protocols.pdf#page=27"> Golden Gate assembly protocol </a></html>, it can be combined with other GB compatible parts from our [http://2018.igem.org/Team:Valencia_UPV/Part_Collection Valencia UPV IGEM 2018 Printeria Collection] to assemble transcriptional units in a BsaI Type IIS one-pot reaction.
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Characterization of the this part was performed with the transcriptional unit [https://parts.igem.org/Part:BBa_K2656107 BBa_K2656107], which was used in a comparative promoters expression experiment with composite parts [https://parts.igem.org/Part:BBa_K2656105 BBa_K2656105] and [https://parts.igem.org/Part:BBa_K2656107 BBa_K2656107].
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They all were assembled in a Golden Braid alpha1 plasmid using the same RBS, CDS and terminator:
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<html>
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<ul>
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<li></html>RBS [https://parts.igem.org/Part:BBa_K2656009 BBa_K2656009]: the [https://parts.igem.org/Part:B0030 B0030] RBS in its Golden Braid compatible version from our [http://2018.igem.org/Team:Valencia_UPV/Part_Collection Part Collection]<html></li>
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<li></html>CDS [https://parts.igem.org/Part:BBa_K2656022 BBa_K2656022]: the [https://parts.igem.org/Part:E0040 E0040] GFPmut3b sequence in its Golden Braid standardized version from our [http://2018.igem.org/Team:Valencia_UPV/Part_Collection Part Collection]<html></li>
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<li></html>Terminator [https://parts.igem.org/Part:BBa_K2656026 BBa_K2656026]: the [https://parts.igem.org/Part:BBa_B0015 B0015] transcriptional terminator in its Golden Braid compatible version from our [http://2018.igem.org/Team:Valencia_UPV/Part_Collection Part Collection]<html></li>
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</ul>
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</html>
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By using this [http://2018.igem.org/Team:Valencia_UPV/Experiments#exp_protocol experimental protocol], we have obtained the parameters to valide our  [http://2018.igem.org/Team:Valencia_UPV/Modeling#models constitutive model] and so rationale choose its optimized values based on each promoter tested.
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[[File:T--Valencia_UPV_promoter_UPV2018.png|900px|thumb|none|alt=promoter experiment. |Figure 2. Promoter expression experiment with  BBa_K2656004, K2656005 and BBa_K2656007 basic pieces]]
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{|class='wikitable'
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|colspan=4|Table 1. Optimized parameters for the BBa_K2656007 promoter.
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|-
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|'''Parameter'''
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|'''Value'''
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|-
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|Constitutive transcription rate CR
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|CR = 486.25 min-1
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|-
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|Dilution rate μ
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|μ = 0.0058 min-1
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|}
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We have also calculated the relative force between the different promoters, taking [https://parts.igem.org/Part:BBa_K2656005 BBa_K2656005 promoter] as a reference.  Likewise, the promoter ratio (p parameter ratio) of the different promoters referring to the stronger one has been calculated.
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{|class='wikitable'
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|colspan=4|Table 2. BBa_K2656007 relative strength and p ratio.
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|-
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|'''Parameter'''
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|'''Value'''
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|-
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|Relative strength
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|0.9367
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|-
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|p parameter ratio
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|0.9013
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|}
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<!-- Add more about the biology of this part here
 
<!-- Add more about the biology of this part here

Latest revision as of 01:19, 18 October 2018

Constitutive promoter J23101

domestication.
Figure 1. DNA basic parts domestication. First construction refers to promoter domestication into the Golden Gate grammar.

Part BBa_K2656007 is the constitutive strong promoter BBa_J23101 adapted into the Golden Gate grammar. Thus, it is compatible with both Biobrick and [http://2018.igem.org/Team:Valencia_UPV/Design Golden Braid] assembly methods.

Following the Golden Gate assembly protocol , it can be combined with other GB compatible parts from our [http://2018.igem.org/Team:Valencia_UPV/Part_Collection Valencia UPV IGEM 2018 Printeria Collection] to assemble transcriptional units in a BsaI Type IIS one-pot reaction.

Characterization of the this part was performed with the transcriptional unit BBa_K2656107, which was used in a comparative promoters expression experiment with composite parts BBa_K2656105 and BBa_K2656107. They all were assembled in a Golden Braid alpha1 plasmid using the same RBS, CDS and terminator:

  • RBS BBa_K2656009: the B0030 RBS in its Golden Braid compatible version from our [http://2018.igem.org/Team:Valencia_UPV/Part_Collection Part Collection]
  • CDS BBa_K2656022: the E0040 GFPmut3b sequence in its Golden Braid standardized version from our [http://2018.igem.org/Team:Valencia_UPV/Part_Collection Part Collection]
  • Terminator BBa_K2656026: the B0015 transcriptional terminator in its Golden Braid compatible version from our [http://2018.igem.org/Team:Valencia_UPV/Part_Collection Part Collection]

By using this [http://2018.igem.org/Team:Valencia_UPV/Experiments#exp_protocol experimental protocol], we have obtained the parameters to valide our [http://2018.igem.org/Team:Valencia_UPV/Modeling#models constitutive model] and so rationale choose its optimized values based on each promoter tested.

promoter experiment.
Figure 2. Promoter expression experiment with BBa_K2656004, K2656005 and BBa_K2656007 basic pieces


Table 1. Optimized parameters for the BBa_K2656007 promoter.
Parameter Value
Constitutive transcription rate CR CR = 486.25 min-1
Dilution rate μ μ = 0.0058 min-1

We have also calculated the relative force between the different promoters, taking BBa_K2656005 promoter as a reference. Likewise, the promoter ratio (p parameter ratio) of the different promoters referring to the stronger one has been calculated.

Table 2. BBa_K2656007 relative strength and p ratio.
Parameter Value
Relative strength 0.9367
p parameter ratio 0.9013


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 11
    Illegal NheI site found at 34
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]