The Salis Lab has recently discovered a new mechanism, called Ribosome Drafting, that controls a mRNA's translation rate. Learn more about it in our latest publication: Espah Borujeni and Salis. Translation Initiation is Controlled by RNA Folding Kinetics via a Ribosome Drafting Mechanism, Journal of the American Chemical Society, 2016

Are you engineering riboswitches? See our latest NAR Breakthrough Article Automated physics-based design of riboswitches from diverse RNA aptamers, Nucleic Acid Research, 2016. Are you engineering bacterial operons? In non-model hosts? Then our latest published work should also interest you: Kushwaha and Salis, A Portable Expression Resource for Engineering Cross-species Genetic Circuits and Pathways, Nature Communications, 2015. and Tian and Salis, A Predictive Biophysical Model of Translational Coupling to Coordinate and Control Protein Expression in Bacterial Operons, Nucleic Acid Research, 2015

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: 1 queued, 5 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.