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!

The Small RNA Calculator

Click here to try an example!


Small RNA Sequence [?]
Small RNA Sequence: enter the nucleotide sequence of a small RNA that binds to mRNA and regulates translation initiation, using A/G/C/T/U. (required).

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)

For Non-Commercial Use Only
Design Jobs: 7 queued, 17 currently running
Developed by Amin Espah Borujeni and Howard Salis.
Please inquire about proper citation before using these results in a publication.
Have a Question? Our Documentation, Publications, and References may have your answer!
We gratefully acknowledge research funding from the Defense Advanced Research Projects Agency, 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.
Method online since January 10th, 2011.