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Part:BBa_J61101
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.
Add more about the biology of this part here
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. It also includes the BioBrick equivalent scar in the 3' extreme, so the insertion of this supplementary bases ensure the correct spacing for the coding sequence expression when assembled in a composite part.
Characterization of the this part was performed with the transcriptional unit BBa_K2656104, which was used in a comparative RBS expression experiment with composite parts BBa_K265610 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 on each RBS.
| Table 1. Optimized parameters for the BBa_K2656008 RBS. | |||
| Parameter | Value | ||
| Translation rate p | p = 0.02889 min-1 | ||
| Dilution rate μ | μ = 0.0118 min-1 | ||
We have also calculated the relative force between the different RBS, taking BBa_K2656009 strong RBS as a reference. It has been defined as the quotient between the values of the protein in equilibrium of the results of the simulation of one RBS and the reference RBS. 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 | 0.032 | ||
| p parameter ratio (pRBS/pref) | 0.032 | ||
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]
Team Warsaw 2010's measurement
RBS strength (relative to B0034): 22,70%
Team TU Delft 2010's measurements
RBS strength: 11.9%, standard deviation: 2.14%RBS strength is relative to B0034, obtained from an average of 12 measurements. Protein production rate is calculated using our production model
//ribosome/prokaryote/ecoli
//chassis/prokaryote/ecoli
//direction/forward
//regulation/constitutive
| None |