Difference between revisions of "Part:BBa K4601142"

 
 
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<partinfo>BBa_K4601142 short</partinfo>
 
<partinfo>BBa_K4601142 short</partinfo>
  
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This part is a synthetic RBS specifically designed for the AmpR β-lactamase enzyme ([[Part:BBa_K4601041|BBa_K4601041]]) using the [https://www.denovodna.com/ Salis Lab RBS Library Calculator v2.0] [1-3].
  
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===Usage and Biology===
 
===Usage and Biology===
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This RBS was used to drive the expression of AmpR β-lactamase enzyme ([[Part:BBa_K4601041|BBa_K4601041]]) under the control of the Na+ RiboSwitch v2 ([[Part:BBa_K4601022|BBa_K4601022]]) in the composite part [[Part:BBa_K4601242|BBa_K4601242]]. In this context, the predicted features of this RBS, according to Salis Lab RBS Calculator v2.1.1 [1,4-7],  are:
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Translation Initiation Rate (au) : 20865.92
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dG_total (kcal/mol) : -6.28
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dG_mRNA_rRNA (kcal/mol) : -34.45
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dG_spacing (kcal/mol) : 0.01
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dG_stacking (kcal/mol) : -0.52
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dG_standby (kcal/mol) : 0.04
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dG_start (kcal/mol) : -2.76
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dG_mRNA (kcal/mol) : -31.40
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Warnings : none
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This RBS was selected fortuitously during the cloning process from a library of 96 RBSes (GCGKYATTCGYKTTRAGGAGGTBTTA) for which the estimated Translation Initiation Rates (TIR) range from 2634.51 to 380322.47.
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===References===
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[1] Reis AC, Salis HM. An automated model test system for systematic development and improvement of gene expression models. ACS synthetic biology (2020) 9: 3145–3156.
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[2] Farasat I, Kushwaha M, Collens J, Easterbrook M, Guido M, Salis HM. Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria. Molecular Systems Biology (2014) 10: 731.
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[3] Ng CY, Farasat I, Maranas CD, Salis HM. Rational design of a synthetic Entner-Doudoroff pathway for improved and controllable NADPH regeneration. Metabolic Engineering (2015) 29: 86–96.
 +
 +
[4] Cetnar DP, Salis HM. Systematic quantification of sequence and structural determinants controlling mRNA stability in bacterial operons. ACS Synthetic Biology (2021) 10: 318–332.
 +
 +
[5] Espah Borujeni A, Cetnar D, Farasat I, Smith A, Lundgren N, Salis HM. Precise quantification of translation inhibition by mRNA structures that overlap with the ribosomal footprint in N-terminal coding sequences. Nucleic Acids Research (2017) 45: 5437–5448.
 +
 +
[6] Espah Borujeni A, Channarasappa AS, Salis HM. Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites. Nucleic Acids Research (2014) 42: 2646–2659.
 +
 +
[7] Salis HM, Mirsky EA, Voigt CA. Automated design of synthetic ribosome binding sites to control protein expression. Nature Biotechnology (2009) 27: 946–950.
  
 
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Latest revision as of 19:47, 2 October 2023


Synthetic RBS designed for AmpR

This part is a synthetic RBS specifically designed for the AmpR β-lactamase enzyme (BBa_K4601041) using the Salis Lab RBS Library Calculator v2.0 [1-3].

Usage and Biology

This RBS was used to drive the expression of AmpR β-lactamase enzyme (BBa_K4601041) under the control of the Na+ RiboSwitch v2 (BBa_K4601022) in the composite part BBa_K4601242. In this context, the predicted features of this RBS, according to Salis Lab RBS Calculator v2.1.1 [1,4-7], are: 

Translation Initiation Rate (au)	:	20865.92
dG_total (kcal/mol)	:	-6.28
dG_mRNA_rRNA (kcal/mol)	:	-34.45
dG_spacing (kcal/mol)	:	0.01
dG_stacking (kcal/mol)	:	-0.52
dG_standby (kcal/mol)	:	0.04
dG_start (kcal/mol)	:	-2.76
dG_mRNA (kcal/mol)	:	-31.40
Warnings	:	none

This RBS was selected fortuitously during the cloning process from a library of 96 RBSes (GCGKYATTCGYKTTRAGGAGGTBTTA) for which the estimated Translation Initiation Rates (TIR) range from 2634.51 to 380322.47.

References

[1] Reis AC, Salis HM. An automated model test system for systematic development and improvement of gene expression models. ACS synthetic biology (2020) 9: 3145–3156.

[2] Farasat I, Kushwaha M, Collens J, Easterbrook M, Guido M, Salis HM. Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria. Molecular Systems Biology (2014) 10: 731.

[3] Ng CY, Farasat I, Maranas CD, Salis HM. Rational design of a synthetic Entner-Doudoroff pathway for improved and controllable NADPH regeneration. Metabolic Engineering (2015) 29: 86–96.

[4] Cetnar DP, Salis HM. Systematic quantification of sequence and structural determinants controlling mRNA stability in bacterial operons. ACS Synthetic Biology (2021) 10: 318–332.

[5] Espah Borujeni A, Cetnar D, Farasat I, Smith A, Lundgren N, Salis HM. Precise quantification of translation inhibition by mRNA structures that overlap with the ribosomal footprint in N-terminal coding sequences. Nucleic Acids Research (2017) 45: 5437–5448.

[6] Espah Borujeni A, Channarasappa AS, Salis HM. Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites. Nucleic Acids Research (2014) 42: 2646–2659.

[7] Salis HM, Mirsky EA, Voigt CA. Automated design of synthetic ribosome binding sites to control protein expression. Nature Biotechnology (2009) 27: 946–950.

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]