Gel Shifts: DIG labelling - (Jul/16/2007 )

Hi all,

I am labelling up a fragment for gel shift assays using the Roche EMSA kit. The size of my fragment is 8bp. While I have labelled a 29 bp fragment very well, the 8bp fragment just does not labell with DIG very well.

Does anyone have any experience of using small fragments in non-radioactive EMSAs? It would be great if you had any suggestions

why don't you use 8bp repeats? such as 3 ~4 repeat of your 8bp sequence (24~32bp)