Difference between revisions of "Part:BBa B0034"
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===Usage and Biology===
 
===Usage and Biology===
 +
 +
Group: Valencia_UPV iGEM 2018
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<br>
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Author: Adrián Requena Gutiérrez, Carolina Ropero
 +
<br>
 +
Summary: We have adapted the part to be able to assemble transcriptional units with the Golden Gate method and we have done the characterization of this RBS.
 +
<br>
 +
Documentation:
 +
<br>
 +
BBa_K2656011 is the RBS [https://parts.igem.org/Part:BBa_B0034 B0034] standardized into the Golden Braid assembly method. It also includes the BioBrick equivalent scar in the 3' extreme, so the insertion of this supplementary bases ensure correct spacing for the CDS expression when assembled into a TU.
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Characterization of the this part was performed with the transcriptional unit [https://parts.igem.org/Part:BBa_K2656101 BBa_K2656101 ], which was used in a comparative RBS expression experiment with composite parts [https://parts.igem.org/Part:BBa_K2656101 BBa_K2656101] and [https://parts.igem.org/Part:BBa_K2656102 BBa_K2656102].
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They all were assembled in a Golden Braid alpha1 plasmid using the same promoter, CDS and terminator.
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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 rationale choose its [http://2018.igem.org/Team:Valencia_UPV/Modeling#optimization optimization values] based on each RBS tested.
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[[File:T--Valencia_UPV--optimization_exp1_RBS_graphUPV2018.png|900px|thumb|none|alt=RBS experiment 1.|Figure 1. RBS expression experiment with K2656009, K26560010 and K2656011 RBS basic parts]]
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{|class='wikitable'
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|colspan=4|Table 1. Optimized parameters from experimental data (BBa_K2656009 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 = 0.082 min-1
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|-
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|Dilution rate μ
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| μ = 0.01631 min-1
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|}
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 +
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.
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{|class='wikitable'
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|colspan=4|Table 2. BBa_K2656008 (GB BBa_B0032 RBS) 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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|0.371
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|-
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|p parameter ratio (pRBS/pref)
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|0.398
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|}
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 +
  
 
== IIT Madras 2016's Characterization ==
 
== IIT Madras 2016's Characterization ==

Revision as of 23:46, 16 October 2018

RBS (Elowitz 1999) -- defines RBS efficiency

RBS based on Elowitz repressilator.

Usage and Biology

Group: Valencia_UPV iGEM 2018
Author: Adrián Requena Gutiérrez, Carolina Ropero
Summary: We have adapted the part to be able to assemble transcriptional units with the Golden Gate method and we have done the characterization of this RBS.
Documentation:
BBa_K2656011 is the RBS B0034 standardized into the Golden Braid assembly method. It also includes the BioBrick equivalent scar in the 3' extreme, so the insertion of this supplementary bases ensure correct spacing for the CDS expression when assembled into a TU.

Characterization of the this part was performed with the transcriptional unit BBa_K2656101 , which was used in a comparative RBS expression experiment with composite parts BBa_K2656101 and BBa_K2656102. 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 [http://2018.igem.org/Team:Valencia_UPV/Modeling#optimization optimization values] based on each RBS tested.

RBS experiment 1.
Figure 1. RBS expression experiment with K2656009, K26560010 and K2656011 RBS basic parts


Table 1. Optimized parameters from experimental data (BBa_K2656009 RBS).
Parameter Value
Translation rate p p = 0.082 min-1
Dilution rate μ μ = 0.01631 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 (GB BBa_B0032 RBS) relative strength and p ratio.
Parameter Value
Relative strength 0.371
p parameter ratio (pRBS/pref) 0.398


IIT Madras 2016's Characterization

Characterization of popular BioBrick RBSs

Modelling

Global non-modularity towards promoters & protein coding parts and relative strength was estimated for RBSs B0030, B0032, B0034 in our [http://2016.igem.org/Team:IIT-Madras/Model#Modularity_of_RBS_parts modelling]

Experimentation

Biobrick RBSs B0030, B0031, B0032, B0034 were used in our 'Noise in Device' experiment to understand the role of RBS parts in giving rise to noise.

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]


Functional Parameters

biology-NA-
efficiency1

Note: The Elowitz RBS is the definition of efficiency 1.0.

Team Warsaw 2010's measurement

definition of 100% strength in our measurement.