crosslinking of DNA after modification? - (Nov/30/2004 )

I am still trying to optimize my bisulfite modification protocol. I ran it on some size marker DNA in order to compare to the original and quantify how much DNA is lost during the treatment. Not only do I lose a significant amount of the DNA (about 90% less intensity on the gel), there is a bright band "stuck" in the well. Is this really long pieces of DNA that have been crosslinked or ligated during treatment?

Thank you for any help you can give.

Hi,
did you already try to increase the concentration of the hydroquinone as suggested by Raizis et al (Analytical Biochemistry 226, 161-166, 1995).

Good luck!