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20mer Oligonucleotide running in the wrong direction - (Dec/07/2009 )

Hello Please, I need some help.

I am doing some work with a 20mer oligonucleotide.

Today I was running on 4% agarose with 0.5X TBE buffer at 35V stained with Syber green.

I noticed that my Oligonucleotide was running in the wrong direction ( It was running from "+" to " -").

I would really appreciate it if anyone can tell me why my oligonucleotide was running in the wrong direction.

Meanwhile when the oligonucleotide was labelled at the 3' end with biotin, the oligonucleotide ran in the appropriate direction ("-" to "+").

Please i can't seem to wrap my brain around this.

Thanks in anticipation of a speedy and favourable response.


are you sure that your leads were plugged into the correct poles?

if not, then your oligos may have been pushed by eof (electroosmotic flow) towards the negative pole. this usually requires high voltage to charge the glass plate and would be helped by reducing the negative charge of the oligo. (just a possibility, not likely).