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Riboswitch Calculator
Synthetic Riboswitch Examples from Amin Espah Borujeni et. al.

Title


Pre-Aptamer Sequence [?]
Pre-Aptamer RNA Sequence: enter the nucleotide sequence that appears before the RNA aptamer, using A/G/C/T/U.
The sequence should begin with the +1 of the mRNA transcript. (required)
Post-Aptamer Sequence [?]
Post-Aptamer RNA Sequence: enter the nucleotide sequence that appears after the RNA aptamer, using A/G/C/T/U.
The sequence should end just before the CDS (don't include the start codon). (required)
 

RNA Aptamers from the Aptagen Database (select one to retrieve its information)

Aptamer Sequence[?]
Aptamer RNA Sequence: enter the nucleotide sequence of the RNA aptamer, using A/G/C/T/U.
(required).

Ligand-bound Aptamer Structure[?]
Ligand-Bound Aptamer Structure: specify the base paired structure of the RNA aptamer when it is bound to its ligand.
For each nucleotide in the aptamer sequence, use left and right parentheses "( )" to indicate when two nucleotides are base paired and an "x" to indicate when a nucleotide is not base paired. Use brackets "[ ]" to indicate when two nucleotides base pair together to form a pseudoknot (a tertiary structure).

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)

Ligand-aptamer Binding Free Energy [?]
Ligand-Aptamer Binding Free Energy: enter the amount of free energy released when the ligand binds to the RNA aptamer, in units of kcal/mol.
(required)


Ligand-water volume ratio[?]
Ligand-water volume ratio: enter the ratio between the particle volume of a single ligand molecule and the particle volume of a single water molecule (typically 1 to 20 for small molecule ligands, 200 to 10000+ for proteins)


mRNA-water volume ratio[?]
mRNA-water volume ratio: enter the ratio between the particle volume of a single RNA molecule and the particle volume of a single water molecule (10000 for 16S rRNA, or about 5 per nt RNA)


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)

For Non-Commercial Use Only
Design Jobs: 2 queued, 6 currently running
When using these results, please reference: Amin Espah Borujeni, Dennis M. Mishler, Jingzhi Wang, Walker Huso, and Howard M. Salis, "Automated Physics-Based Design of Synthetic Riboswitches from Diverse RNA Aptamers", submitted
Method online since June 14th, 2014.
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.