Inverse folding of a single RNA

Ligand-responsive RNA switch design

This design explores the sequence space to find RNA sequences that fold into the target structures in silico.
This design uses RNAfold to predict secondary structures.
Examples of runtimes can be browsed here.
Current limit of this server is >= 20 nt and <= 230 nt. If you use this web server, please cite these papers.
Step 1: Input your targets to the following form in S+ notation :
(If you would like to directly specify the targets in the standard dot-bracket notation, you can skip Step 1 & 2 and go to Step3).

Line 1: Target structure 1 (ligand-free state)
Line 2: Target structure 2 (ligand-binding state)
Note: The aptamer structure and sequence motif denoted by "A" must be specified in line 2.
This aptamer structure motif will be constrained when the ligand-binging state specified in line 2 is predicted by RNAfold.
Line 3 & 4 : Aptamer information must be specified in these lines as a set of structure and sequence motifs.
Note: The structure and sequence motifs specified by "A=" must be defined here (the user-specified aptamer structure and sequence).
Line 5 and more lines (optional) : The other structure and/or sequence motifs



 


Step 2: Click the above button to automatically generate your target(s) and sequence constraints in the standard dot-bracket notation; the generated structures and constraints are displayed in the form shown below.

Step 3: Confirm (or input) your targets in the following form (the targets are written in the standard dot-bracket notation [*?+@^ are also allowed]):
Line 1: Target secondary structure 1 (ligand-free state)
Line 2: Target secondary structure 2 (ligand-binding state)
Line 3: Sequence constraints
Line 4: Structure constraints to model the ligand-binding state



The central value of desired G+C content (%):
  The half-range of the allowed G+C content (%):


GA population size:


Initial random number:


Prohibited sequence motifs (if multiple motifs are specified, please concatenate them with comma.):


Prohibited polynucleotide tracts. Those with the length (in nucleotides) longer than the value specified here are prohibited:  


PolyA tract is:  
  PolyC tract is:  
  PolyG tract is:  
    PolyU tract is:  


The constraint for the energy difference between the two target structures (kcal/mol); should be a value >= 0.0:

We design the sequences with the predicted energy difference smaller than or equal to this specified energy difference.

The energy barrier height between the ligand-binding and ligand-free structures is

NOTE: Optimizing an energy barrier height (i.e., minimized or maximized) will take a long runtime.

Step 4: Click the next button to submit your design!