Single strand/Oligo structure

CramCycle

Designing oligos and looking for structure prediction programmes online. The only one I can find is the following: http://rna.urmc.rochester.edu/RNAstructureWeb/Servers/Predict1/Predict1.html

Does anyone know are there any others available. My background is originally in Proteins and there is an abundance of protein structure predictors available but DNA/RNA/nucleotide sequence structure predictors seem to be in short supply.

Any ideas?

CramCycle

A better question is that I want to measure distance in the folded state of the oligo between the first and last nucleotide, is there anything that has this possibility?

josey_whale

I find IDT's Oligo Analyzer tool very good for looking at hairpin structures in DNA oligos.

For looking at RNA, you have found the most widely used tool (m-Fold). Another useful tool that I have used is RNA-fold at U Vienna.

I don't think these allow you to calculate distances. The major problem here is that these folding programs only give 2-D structures. Of course these molecules do not fold in 2-D, so anything that you used to measure distances would be inaccurate anyways.

One way of doing would be to have a look at PDB files that contain protein-RNA complexes - that might give you some feel for the distance.

If all else fails, go back to the fact that 10 bases of dsDNA is 3.4nm in length and work from there.

CramCycle

josey_whale wrote: »

I find IDT's Oligo Analyzer tool very good for looking at hairpin structures in DNA oligos.

Brilliant, I actually order all my oligos from them, can't believe I missed that.

Much appreciated