Their sequences are:
5'-Biotin-CAAAACAGCAGCAATCCAATGCGCAGACACCCGATTACAAATGC-3'
5'-Biotin-GTAGGAGACTCTGATGTGCTTCATGATCTTTTTTTTTTTTTTTT-3'
Both strands are labeled with Biotin from 5' end. They run through a PAGE where all conditions for them are equal. The result of the gel bands are different i.e. one sequence's band is upper than the others. The difference is meaningful as well, so there in no doubt about them.
The question here is what explanation should be considered for the different band positions in the gel while ssDNA sequences are different?
Do you mean that one of the sequence move longer than the other or that both show more than one band?
Are you performing the PAGE in denaturing or not-denaturing manner?
How do you visualize your PAGE bands?
in native PAGE these oligos will take up different conformations ( this is the basis of the SSCP method of mutation detection ) and this different conformation will cause different bases to show different charged moieties on the outside of the conformation meaning that each has a slightly different charge so moves through the gel at different speeds. It is to stop this kind of effect that denaturing PAG is used in order to force fewer alowable conformations of molecules keeping separations simpler
I performed a native PAGE. The applied voltage was 75V. The Polyacrylamide concentration in gel was 18%. I have also checked out the secondary structures of both strands with NUPACK software and it doesn't show much difference to make strands so different in shape.
To answer to the Massimo's question: yes I meant one is moving longer than the other one. I visualize the bands using EtBr.
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