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
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)
 


Target Translation Initiation Rate [?]
Target Translation Initiation Rate: select the desired rate of translation initiation on a proportional scale from 0.1 to 100,000 or more. (required)


Proportional scale (0 to 100,000+) Goal: Maximize
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: 10 queued, 11 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.