Perturbation Of A Rna Secondary Structure

Question

[Nicolas Rosewick]

Hi,

Is there a tool to pertub a secondary structure of a RNA by permutating its nucleotide sequence. In my case, I've a sequence encoding mutliple miRNAs (each pre-miR has a hairpin structure). I want to delete each of the hairpin structures by changing as little as possible the sequence.

The goal is to take this sequence encoding multiple miRNAs, to modify it to perturb the structure to delete the hairpins and to put it in a lentiviral vector and to see if it is processed

I posted a more biological question for the same topic on biology.stackexchange : http://biology.stackexchange.com/questions/680/rna-sequence-modification-which-newly-pattern-ive-to-avoid

Thanks a lot,

N.

[Nicolas Rosewick]

nobody ? I'll try to pertub only the 3' part of the stemloop (so the miRNA star) to delete the complementarity between the miR-5p and miR-3p . Anyone has an another idea to do this ?

Thanks

Answer 1

[Alastair Kerr]

I am unaware of a package that will perform that task without some intervention of your own.

I suggest that the best approach at the moment is to use tools from the Vienna RNA Package along with some scripting (bioperl, biopython...) to systematically change that sequence.

My workflow would be:

1. Create mutants using scripting language or manually
2. Use RNAfold* to create the 2d structure
3. Use RNAdistance* to compare secondary structure to original.
4. Sort all mutations by (3) and judge yourself where you should make the cut-off

(*both from the Vienna RNA package)

Note that RNAfold uses Watson-Crick base pairing only. There are other folding programs in development see the wikiomics page but I have yet to try one better then RNAfold for miRNAs.

[Nicolas Rosewick]

Yes that's a good start. I'll add a step at the end: the scrambled hairpin sequence must have a score under 17 with sRNAloop. Thanks

[Nicolas Rosewick]

It works well with RNAdistance ;)

Answer 2

[Ib84]

I'm not sure if it's what you are after, but the GeneGA tool does permutate sequences using a genetic / evolutionary algorithm with an objective function which maximizes free energy. Hence it strives to decrease secondary structure, but not sure if this is suited well to explicitely eliminate hairpins. Also, afaik, it is restricted to synomymous mutations, i.e. resulting protein sequence remains identical. Its purpose is to improve heterologeous expression by optimizing both codon usage and RNA secondary structure, with respect to recent findings of the so-called "ramp" (Tuller 2010, Science). Recommend to use with rstudio.