Difference between revisions of "Part:BBa K4601133"
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<partinfo>BBa_K4601133 short</partinfo> | <partinfo>BBa_K4601133 short</partinfo> | ||
| − | + | This part is a synthetic RBS specifically designed for the LacZ-alpha (pUC19 like) ([[Part:BBa_K2448003|BBa_K2448003]]) using the [https://www.denovodna.com/ Salis Lab RBS Library Calculator v2.0] [1-3]. | |
| − | |||
===Usage and Biology=== | ===Usage and Biology=== | ||
| + | This RBS was used to drive the expression of LacZ-alpha (pUC19 like) ([[Part:BBa_K2448003|BBa_K2448003]]) under the control of the pOmpR promoter ([[Part:BBa_R0083|BBa_R0083]]) in the composite part [[Part:BBa_K4601233|BBa_K4601233]]. 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) : 35366.74 | ||
| + | dG_total (kcal/mol) : -7.46 | ||
| + | dG_mRNA_rRNA (kcal/mol) : -10.77 | ||
| + | dG_spacing (kcal/mol) : 0.01 | ||
| + | dG_stacking (kcal/mol) : -0.38 | ||
| + | dG_standby (kcal/mol) : 1.53 | ||
| + | dG_start (kcal/mol) : -2.76 | ||
| + | dG_mRNA (kcal/mol) : -4.92 | ||
| + | Warnings : none | ||
| + | This RBS was selected fortuitously during the cloning process from a library of 96 RBSes (ASWTTAATAATKTAKAGAGGVGGTATAK) for which the estimated Translation Initiation Rates (TIR) range from 4223.38 to 393272.53. | ||
| + | |||
| + | ===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. | ||
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<span class='h3bb'>Sequence and Features</span> | <span class='h3bb'>Sequence and Features</span> | ||
Latest revision as of 19:27, 2 October 2023
Synthetic RBS designed for LacZalpha
This part is a synthetic RBS specifically designed for the LacZ-alpha (pUC19 like) (BBa_K2448003) using the Salis Lab RBS Library Calculator v2.0 [1-3].
Usage and Biology
This RBS was used to drive the expression of LacZ-alpha (pUC19 like) (BBa_K2448003) under the control of the pOmpR promoter (BBa_R0083) in the composite part BBa_K4601233. 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) : 35366.74 dG_total (kcal/mol) : -7.46 dG_mRNA_rRNA (kcal/mol) : -10.77 dG_spacing (kcal/mol) : 0.01 dG_stacking (kcal/mol) : -0.38 dG_standby (kcal/mol) : 1.53 dG_start (kcal/mol) : -2.76 dG_mRNA (kcal/mol) : -4.92 Warnings : none
This RBS was selected fortuitously during the cloning process from a library of 96 RBSes (ASWTTAATAATKTAKAGAGGVGGTATAK) for which the estimated Translation Initiation Rates (TIR) range from 4223.38 to 393272.53.
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
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]