Difference between revisions of "Part:BBa K2656004"
 
(19 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_K2656004 is the constitutive promoter [https://parts.igem.org/Part:BBa_J23106 BBa_J23106] compatible with both Biobrick and [http://2018.igem.org/Team:Valencia_UPV/GB3 GoldenBraid 3.0] assemply 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].
 
  
 
<!-- 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]