EMSA results have other bands in control DNA - (Mar/21/2007 )

I have done gel shifts with my PCR and gel purified DNA(+ 3' biotin label) and in the control lane, there is other bands that show up when I scan the gel with a LI-CORE scanner? Does anyone know what these bands could be or how the DNA could be retarded in the gel to run slower. I have done some troubleshooting and the bands are still present when I have just DNA and water. Thanks

am I understanding this correctly? you have a control lane with nothing but DNA and water, and you're seeing multiple bands? is this DNA from your PCR? this would indicate that your PCR has quite a bit of non-specific product. this needs to be dealt with before you can do gel-shifts; you are possibly getting a bunch of non-specific binding of TFs to your non-specific product