We are attempting to perform DMS (Dimethyl sulphate) footprinting with 6-FAM labelled oligonucleotide sequence. We are confused about the labelling of the DNA sequence by 6-FAM. Do we need to perform a ligand based PCR reaction or we can tag the DNA by 6-FAM for footprinting?
if you are extending off a dna oligo then just have it made with 6-fam at the 5'end by the company making yoiur oligos and column purified which is usually the default for dye labelled oligos.
Dear Paul Rutland,
Thank you for your answer, but we have 6-FAM in our laboratory, and unfortunately don't have any labelling kit. I am looking for a protocol which will help me labelling DNA with 6-FAM.
Thank you.
I still think that labelled oligos are the best but it is possible to label the 5' end of an oligo using carbodi imide chemistry to activate the dna then bind fluorescein to iti attach a thermo fisher methodology which may help
best wishes
paul
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