Difference between revisions of "Part:BBa J61100"
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Documentation:
 
Documentation:
 
In order to create our complete [http://2018.igem.org/Team:Valencia_UPV/Part_Collection part collection] of parts compatible with the Golden Gate assembly method, we made the part [https://parts.igem.org/Part:BBa_K2656008 BBa_K2656008] which is this part adapted to the Golden Gate technology.
 
In order to create our complete [http://2018.igem.org/Team:Valencia_UPV/Part_Collection part collection] of parts compatible with the Golden Gate assembly method, we made the part [https://parts.igem.org/Part:BBa_K2656008 BBa_K2656008] which is this part adapted to the Golden Gate technology.
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Characterization of the this part was performed with the transcriptional unit [https://parts.igem.org/Part:BBa_K2656100 BBa_K2656100], which was used in a comparative RBS expression experiment with composite parts [https://parts.igem.org/Part:BBa_K2656104 BBa_K2656104] and [https://parts.igem.org/Part:BBa_K2656101 BBa_K2656101].
 +
They all were assembled in a Golden Braid alpha1 plasmid using the same promoter, CDS and terminator.
 +
 +
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 rationale choose its optimized values based for each RBS.
 +
 +
[[File:T--Valencia_UPV--optimization_exp2_RBS_all_graph_expUPV2018.png|900px|thumb|none|alt=RBS experiment.|Figure 1. RBS expression experiment with K2656008, K2656009 and K2656012 basic pieces]]
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[[File:T--Valencia_UPV--optimization_exp2_RBS_2obj_graph_expUPV2018.png|900px|thumb|none|alt=RBS experiment.|Figure 2. RBS expression experiment with K2656008 and K2656012 basic pieces]]
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{|class='wikitable'
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|colspan=4|Table 1. Optimized parameters for the BBa_K2656008 RBS.
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|-
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|'''Parameter'''
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|'''Value'''
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|-
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|Translation rate p
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|p = 0.04089 min-1
 +
|-
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|Dilution rate μ
 +
|μ = 0.01288 min-1
 +
|}
 +
 +
We have also calculated the relative force between the different RBS, taking [https://parts.igem.org/Part:BBa_K2656009 BBa_K2656009 strong RBS] as a reference. Likewise, a ratio between p parameters of the different RBS parts and p parameter of the reference RBS has been calculated.
 +
 +
{|class='wikitable'
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|colspan=4|Table 2. BBa_K2656008 relative strength and p ratio.
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|-
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|'''Parameter'''
 +
|'''Value'''
 +
|-
 +
|Relative strength
 +
|0.042
 +
|-
 +
|p parameter ratio (pRBS/pref)
 +
|0.044
 +
|}
 +
  
 
<!-- Uncomment this to enable Functional Parameter display  
 
<!-- Uncomment this to enable Functional Parameter display  

Revision as of 19:11, 17 October 2018

Ribosome Binding Site Family Member .
Parts J61100-J61150 are a family of similar ribosome binding site basic parts identified from a saturation mutagenic library. 

 Library    TCTAGAGAAAGANNNGANNNACTAGT
 J61100     tctagaGAAAGAGGGGACAAactagt
 J61101     tctagaGAAAGACAGGACCCactagt
 J61102     tctagaGAAAGATCCGATGTactagt
 J61103     tctagaGAAAGATTAGACAAactagt
 J61104     tctagaGAAAGAAGGGACAGactagt
 J61105     tctagaGAAAGACATGACGTactagt
 J61106     tctagaGAAAGATAGGAGACactagt
 J61107     tctagaGAAAGAAGAGACTCactagt
 J61108     tctagaGAAAGACGAGATATactagt
 J61109     tctagaGAAAGACTGGAGACactagt
 J61110     tctagaGAAAGAGGCGAATTactagt
 J61111     tctagaGAAAGAGGCGATACactagt
 J61112     tctagaGAAAGAGGTGACATactagt
 J61113     tctagaGAAAGAGTGGAAAAactagt
 J61114     tctagaGAAAGATGAGAAGAactagt
 J61115     tctagaGAAAGAAGGGATACactagt
 J61116     tctagaGAAAGACATGAGGCactagt
 J61117     tctagaGAAAGACATGAGTTactagt
 J61118     tctagaGAAAGAGACGAATCactagt
 J61119     tctagaGAAAGATTTGATATactagt
 J61120     tctagaGAAAGACGCGAGAAactagt
 J61121     tctagaGAAAGAGACGAGTCactagt
 J61122     tctagaGAAAGAGAGGAGCCactagt
 J61123     tctagaGAAAGAGATGACTAactagt
 J61124     tctagaGAAAGAGCCGACATactagt
 J61125     tctagaGAAAGAGCCGAGTTactagt
 J61126     tctagaGAAAGAGGTGACTCactagt
 J61127     tctagaGAAAGAGTGGAACTactagt
 J61128     tctagaGAAAGATAGGACTCactagt
 J61129     tctagaGAAAGATTGGACGTactagt
 J61130     tctagaGAAAGAAACGACATactagt
 J61131     tctagaGAAAGAACCGAATTactagt
 J61132     tctagaGAAAGACAGGATTAactagt
 J61133     tctagaGAAAGACCCGAGACactagt
 J61134     tctagaGAAAGACCGGAAATactagt
 J61135     tctagaGAAAGACCGGAGACactagt
 J61136     tctagaGAAAGAGCTGAGCAactagt
 J61137     tctagaGAAAGAGTAGATCAactagt
 J61138     tctagaGAAAGATATGAATAactagt
 J61139     tctagaGAAAGATTAGAGTCactagt

These parts are present in plasmid pSB1A2, but there is also a constitutive promoter (J23100-derived) inserted into the XbaI site. So, for example, the EcoRI/PstI region of part J61100 reads: 

 Biobrick 5'    XbaI                    J23100              XbaI    RBS Part     Biobrick 3'
 gaattcgcggccgcttctagaGTTGACGGCTAGCTCAGTCCTAGGTACAGTGCTAGCTtctagaGAAAGAGGGGACAAactagtagcggccgctgcag

This feature in no way prevents the use of these parts in standard Biobrick assembly. Normal prefix insertion into EcoRI/XbaI will delete this promoter element. Suffix insertion into SpeI/PstI will retain this promoter, but it can of course be removed later by a prefix insertion.

Note also that the base 5' to the SpeI site is allowed to float in these parts and is therefore rarely "T". The "G" downstream of the XbaI site obeys the standard. Because the database does not permit variation at this position, the predicted sequences of composite parts derived from these parts will be incorrect at this position.

More on this family of parts and their quantitative behavior is described here.

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]

Team Warsaw 2010's measurement

RBS strength (relative to B0034): 4,29%

Team TU Delft 2010's measurements

RBS strength: 2.0%, standard deviation: 0.512%
RBS strength is relative to B0034, obtained from an average of 12 measurements. Protein production rate is calculated using our production model

Contribution

Group: Valencia_UPV iGEM 2018
Author: Adrián Requena Gutiérrez, Carolina Ropero
Summary: We adapted the part to be able to assemble transcriptional units with the Golden Gate assembly method
Documentation: In order to create our complete [http://2018.igem.org/Team:Valencia_UPV/Part_Collection part collection] of parts compatible with the Golden Gate assembly method, we made the part BBa_K2656008 which is this part adapted to the Golden Gate technology.

Characterization of the this part was performed with the transcriptional unit BBa_K2656100, which was used in a comparative RBS expression experiment with composite parts BBa_K2656104 and BBa_K2656101. They all were assembled in a Golden Braid alpha1 plasmid using the same promoter, CDS and terminator.

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 rationale choose its optimized values based for each RBS.

RBS experiment.
Figure 1. RBS expression experiment with K2656008, K2656009 and K2656012 basic pieces
RBS experiment.
Figure 2. RBS expression experiment with K2656008 and K2656012 basic pieces
Table 1. Optimized parameters for the BBa_K2656008 RBS.
Parameter Value
Translation rate p p = 0.04089 min-1
Dilution rate μ μ = 0.01288 min-1

We have also calculated the relative force between the different RBS, taking BBa_K2656009 strong RBS as a reference. Likewise, a ratio between p parameters of the different RBS parts and p parameter of the reference RBS has been calculated.

Table 2. BBa_K2656008 relative strength and p ratio.
Parameter Value
Relative strength 0.042
p parameter ratio (pRBS/pref) 0.044