Difference between revisions of "Part:BBa K2656004"

 
 
(23 intermediate revisions by 4 users not shown)
Line 1: Line 1:
−
 
 
__NOTOC__
 
__NOTOC__
 
<partinfo>BBa_K2656004 short</partinfo>
 
<partinfo>BBa_K2656004 short</partinfo>
 +
[[File:T--Valencia_UPV--im11UPV2018.png|250px|thumb|centro|alt=domestication.|Figure 1. DNA basic parts domestication. First construction refers to promoter GB domestication. ]]
 +
 +
Part BBa_K2656004 is the constitutive low promoter [https://parts.igem.org/Part:BBa_J23106 BBa_J23106] adapted into the Golden Gate grammar. Thus, it is compatible with both Biobrick and [http://2018.igem.org/Team:Valencia_UPV/Design GoldenBraid] assembly methods.
 +
 +
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.
 +
 +
Characterization of the this part was performed with the transcriptional unit [https://parts.igem.org/Part:BBa_K2656105 BBa_K2656105], which was used in a comparative promoters expression experiment with composite parts [https://parts.igem.org/Part:BBa_K2656104 BBa_K2656106] and [https://parts.igem.org/Part:BBa_K2656107 BBa_K2656107].
 +
They all were assembled in a Golden Braid alpha1 plasmid using the same RBS, CDS and terminator:
 +
 +
<html>
 +
<ul>
 +
<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>
 +
<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>
 +
<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>
 +
</ul>
 +
</html>
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
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 for each promoter tested.
 +
 +
[[File:T--Valencia_UPV_promoter_UPV2018.png|900px|thumb|none|alt=RBS experiment.|Figure 1. Promoter expression experiment with  BBa_K2656004, K2656005 and BBa_K2656007 basic pieces]]
 +
 +
 +
{|class='wikitable'
 +
|colspan=4|Table 1. Optimized parameters for the BBa_K2656004 promoter.
 +
|-
 +
|'''Parameter'''
 +
|'''Value'''
 +
|-
 +
|Constitutive transcription rate CR
 +
|CR = 171.15 min-1
 +
|-
 +
|Dilution rate μ
 +
|μ = 0.01001 min-1
 +
|}
 +
 +
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.
 +
 +
{|class='wikitable'
 +
|colspan=4|Table 2. BBa_K2656004 relative strength and p ratio.
 +
|-
 +
|'''Parameter'''
 +
|'''Value'''
 +
|-
 +
|Relative strength
 +
|0.2603
 +
|-
 +
|p parameter ratio
 +
|0.3172
 +
|}
  
−
Part BBa_J23106 domesticated to the Golden Braid 3.0 grammar. Constitutive promoter. It can be used to assembly transcriptional units with the Golden Gate assembly method, and also, it can be used as a Biobrick.
 
  
 
<!-- Add more about the biology of this part here
 
<!-- Add more about the biology of this part here

Latest revision as of 01:46, 18 October 2018

Constitutive promoter J23106

domestication.
Figure 1. DNA basic parts domestication. First construction refers to promoter GB domestication.

Part BBa_K2656004 is the constitutive low promoter BBa_J23106 adapted into the Golden Gate grammar. Thus, it is compatible with both Biobrick and [http://2018.igem.org/Team:Valencia_UPV/Design GoldenBraid] 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_K2656105, which was used in a comparative promoters expression experiment with composite parts BBa_K2656106 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 for each promoter tested.

RBS experiment.
Figure 1. Promoter expression experiment with BBa_K2656004, K2656005 and BBa_K2656007 basic pieces


Table 1. Optimized parameters for the BBa_K2656004 promoter.
Parameter Value
Constitutive transcription rate CR CR = 171.15 min-1
Dilution rate μ μ = 0.01001 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_K2656004 relative strength and p ratio.
Parameter Value
Relative strength 0.2603
p parameter ratio 0.3172


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]