Our new paper is out (free full-text until May 13th!): Chiam Yu Ng et. al., Rational Design of a Synthetic Entner-Doudoroff Pathway for Improved and Controllable NADPH Regeneration, Metabolic Engineering, 2015

Highlights: We re-engineered the Entner–Doudoroff pathway from Zymomonas mobilis to increase NADPH regeneration in E. coli by 25-fold. Operons expressing the 5-enzyme pathway were designed by our Operon Calculator algorithm and integrated into the E. coli genome. Pathway variants were characterized using enzyme assays, a NADPH-binding fluorescent reporter, and a NADPH-dependent biosynthesis pathway. Enzyme expression levels were efficiently optimized by combining our RBS Library Calculator algorithm with the Church Lab's MAGE genome mutagenesis technique.

Did you design DNA using our algorithms? Please remember to cite! Links: RBS Calculator v2.0 RBS Library Calculator
Our website has been updated!

RBS Calculator

mRNA Sequence [?]
mRNA Sequence: enter the nucleotide sequence of an mRNA transcript, using A/G/C/T/U. (required)

Organism or (16S rRNA) [?]
Organism or 16S rRNA sequence: choose a bacterial species by typing in the first 3 letters of its name and selecting it from the list. Alternatively, you may enter the last 9 nucleotides of the 16S rRNA, using A/G/C/T/U.
(start typing)

Select a Free Energy Model [?]
Free Energy Model Version: Improved versions of our biophysical models are released once their experimental validation has shown a sufficiently large increase in accuracy.

Version 1.0: The original RBS Calculator free energy model, as described in Nature Biotechnology, 2009. This version employs the NuPACK software suite.

Version 1.1: More accurate calculation of the final state's free energy and a modified ribosome footprint length. These changes are described in Methods in Enzymology, v498, 2011. This version employs the ViennaRNA software suite.

Version 2.0: Includes additional interactions between the ribosomal platform and mRNA at upstream standby sites. These changes are described in Espah Borujeni, Channarasappa, and Salis, Nucleic Acid Research, v42 (4), 2014.
Design Jobs: 3 queued, 10 currently running
For Non-Commercial Use Only. Click here for commercial usage.
Have a Question? Our Documentation, Publications, and References may have your answer!
When using these results, please reference A. Espah Borujeni, A.S. Channarasappa, and H.M. Salis, "Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites", Nucleic Acid Research, 2013 and H.M. Salis, E.A. Mirsky, C.A. Voigt, Nat. Biotech., 2009
We gratefully acknowledge research funding from the Air Force Office of Scientific Research, the National Science Foundation, the Office of Naval Research, and an Amazon AWS Research Grant.
Computational resources are provided by the AWS Elastic Compute Cloud.