How do small RNA- and DNA-Oligos (~20nt) differ in their electrophoretic mobility under denaturing conditions? I was just wondering whether there is a general difference in the migration of totally unfolded RNA-Oligos vs. DNA-Oligos (of the same base composition) e.g. due to different hydrations.
Thank you for your answers.
Hi Sven, RNA migrates more slowly than DNA.
Here is an article that will explain all (I think):
Bonifacio et al., Biophys J. 1997;73(3):1532-8
Just trying to put my 5 cents here (in case it is not mentioned in the article by Bonifacio et al): when the size of the RNA and DNA is relatively small (less than 20 nt), the presence of the phosphate group (and their total number) on the 5`-end will affect the migration rate of the oligo (makes it run faster).
Thank you Anna. I went through the Bonifacio paper (describing DNA and RNA duplexes) and wonder whether there is a similar effect for single stranded oligos.
Does anyone know?
Thanks Oleg, in the case of our oligonucleotides, both are 5'-P32 labled, so they have the same charge.
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