RBS

Part:BBa_K4592003

Designed by: Varun Kodur   Group: iGEM23_UCSC   (2023-10-11)


Synthetic RBS for Microcystis-optimized eGFP Expression

This part is a synthetic RBS generated using the Salis RBS Library Calculator v2.1.1 to express Microcystis-optimized eGFP (BBa_K4592001) in Microcystis aeruginosa with a high predicted translation initiation rate (TIR) of 817373.40 [1-3]. Predicted TIR values lack definitive units because the scale used by translation rate calculators is proportional [4].

Features of Synthetic RBS Predicted by Salis RBS Library Calculator v2.1.1:
Translation Initiation Rate (au): 817373.40
Total Gibbs Free Energy Change (kcal/mol): -14.43
Gibbs Free Energy Change of mRNA:rRNA Complex (kcal/mol): -13.26
Gibbs Free Energy Penalty for Non-optimal Spacing (kcal/mol): 0.01
Gibbs Free Energy Change of Stacked Nucleotides in Spacer Region (kcal/mol): -0.65
Gibbs Free Energy Penalty for Ribosome Binding to Standby Site (kcal/mol): 0.11
Gibbs Free Energy Change of mRNA:tRNA Complex (kcal/mol): -2.76
Gibbs Free Energy Change of mRNA Folded Complex (kcal/mol): -2.12

Usage and Biology

We have not been able to gather empirical data on the behavior of this RBS in UTEX 2385 M. aeruginosa as we were unable to assemble our plasmids and express them in UTEX 2385 M. aeruginosa before the Parts Pages Freeze. This page will be updated in the future with this information.

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]


References

[1] Reis, A. C., & Salis, H. M. (2020). An Automated Model Test System for Systematic Development and Improvement of Gene Expression Models. ACS synthetic biology, 9(11), 3145–3156. https://doi.org/10.1021/acssynbio.0c00394

[2] Farasat, I., Kushwaha, M., Collens, J., Easterbrook, M., Guido, M., & Salis, H. M. (2014). Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria. Molecular systems biology, 10(6), 731. https://doi.org/10.15252/msb.20134955

[3] Ng, C. Y., Farasat, I., Maranas, C. D., & Salis, H. M. (2015). Rational design of a synthetic Entner-Doudoroff pathway for improved and controllable NADPH regeneration. Metabolic engineering, 29, 86–96. https://doi.org/10.1016/j.ymben.2015.03.001

[4] Reeve, B., Hargest, T., Gilbert, C., & Ellis, T. (2014). Predicting translation initiation rates for designing synthetic biology. Frontiers in bioengineering and biotechnology, 2, 1. https://doi.org/10.3389/fbioe.2014.00001

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