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 Library Calculator
Title


Pre-Sequence [?]
Pre-Sequence: enter a nucleotide sequence (5 to 20 bp) that appears before the ribosome binding site, using A/G/C/T/U. The Pre-Sequence is important when the ribosome binding site is less than 35 nucleotides long. (optional)
Protein Coding Sequence [?]
Protein Coding Sequence: enter a nucleotide sequence (at least 50 bp) that encodes a protein, using A/G/C/T/U.
Begins with a start codon (ATG/GTG/TTG/CTG). (required)
 


Initial RBS Sequence with Optional Constraints [?]
Degenerate Ribosome Binding Site Sequence: enter a degenerate nucleotide sequence that defines a library of RBSs, using the 15 letter UIPAC degenerate nucleotide code: A/G/C/T/S/W/K/R/Y/M/D/B/H/V/N. S: G or C. W: A or T. K: G or T. R: A or G. Y: C or T. M: A or C. D: A, G, or T. B: C, G, or T. H: A, C, or T. V: A, C, or G. N: A, G, C, or T.
(optional)

Minimum Translation Initiation Rate [?]
RBS Library's Minimum Translation Initiation Rate: select the desired minimum rate of translation initiation within the optimized ribosome binding site library, on a proportional scale from 0.1 to 100,000 or more. This will determine the lowest protein expression level within the library. (required)
Maximum Translation Initiation Rate [?]
RBS Library's Maximum Translation Initiation Rate: select the desired maximum rate of translation initiation within the optimized ribosome binding site library, on a proportional scale from 0.1 to 100,000 or more. This will determine the highest protein expression level within the library. (required)


Estimated Library: x     Low Res    
    High Res
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.
(required)
(start typing)

Design Jobs: 11 queued, 15 currently running
For Non-Commercial Use Only. Click here for commercial usage.
When using these results, please reference: Iman Farasat, Manish Kushwaha, Jason Collens, Michael Easterbrook, Matthew Guido, and Howard M. Salis, "Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria", Molecular Systems Biology, v10(6), 2014
Method online since January 10th, 2011.
Have a Question? Our Documentation, Publications, and References may have your answer!
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.