RNA gel shift - (Sep/06/2006 )

i've start trying RNA gel shift. From most literature, people would like to add RNase T1 and heparin sulfate in the binding reaction. RNase T1 is used to digest unbound RNA. But what's the use for heparin sulfate. In addition, some literatures show heparin sulfate, some show heparan sulfate and some show heparin. So, which one should i use and are there any suggestion using which brand? thanks!

i did several EMSA recently, and I 'guess' a RNA/Protein complex(es) is/are formed. I think it's specific as i can compete it away using cold probe. But the problem is, no matter how long i 'run' the gel, the band appears at the very top position. I am using 4% polyacryamide gel and run overnight already? will it be due to the large size of my probe, ~660 bp...