3' vs 5'G quartet

[umjawad]

Hi everyone!!

I am new here and hopefully can get some ideas from you about my project

I have a question with regard DNA folds into 4 stranded intermolecular G quadrplex, I have ordered 2 oligos:
5'-T7G5-3'
5'-G5T7-3'

as you notice, when generating the complex, they will have G qurtet located at either 3'or 5' side

my question is when running these two complexes in a native gel, they show different mobility as the 5'complex has lower moblilty than the 3'!!

not only that, but also they show different binding behavior to my cofactor and display different rate when try them in my chemical reaction. I believe that they have the same molecular weight, right??

any one has an explanation???

Thanks alot!!

[umjawad]

Hi!

No body reply !! seems that nobody has experienced this before