stratalinker: Oligo Damage?

Go to the profile of thelongwindingcode
Feb 20, 2018
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Hi, Does any one have any experience with the stratalinker? I am looking to immobilise a fluorophore labelled ss Oligo (~20-30bp).

It is standard in our lab to immobilize at 1 j/cm2, does anyone know of any data to suggest this could result in DNA damage for such short ss oligos? Of course, I want to be confident that when quantifying using my fluorophore, I am not under estimating due to the fact some oligos are damaged and therefore their fluorophore washed away.

Thank you!

1 Comments

Go to the profile of OldCloner
OldCloner 5 months ago

Hi LWC,

I’m not sure of the answer regarding damage to the oligo, but fluorophores themselves are subject to damage by light (why we keep them in amber colored tubes or wrapped in foil) so I would also be concerned about that. Can your substrate tolerate heat fixation (baking)? I suggest you contact your supplier of labeled oligos for their input-companies have a lot of knowledge of the properties of their products and should be able to help you choose a method. Fluorophores do tolerate electrophoresis oven temperatures during capillary sequencing; baking them might be OK.

Also, can I assume you will be some kind of standard curve with some known quantities of labeled oligos? If so, whatever happens to the unknowns will also happen to the standards, so that should compensate for any damping of the fluorescence.