I am trying to gel extract my digested large-ish (8 kb) vector using low melting point agarose. Since its large, I have been using 0.8% to try to get good separation, but every gel I've been running is a smeary mess! I thought that it may be due to overloading of DNA, so I've played with that, and have ruled it out. I'm wondering whether it may be due to the low % of the low melting point agarose--I'm new to this type of agarose, so I don't know if this is a factor. Any ideas? I'm running the gels at 90V for about an hour, so I don't think this is an issue either.

I just want to confirm something for those people reading this post. Have you run this same sample on your usual agarose gels to ensure that what you have in your tube is not degraded?

Ryan

Yes I have...and I should also make it clear that the smear is above (higher mw) than where the band should be, and is not degregation. The smear stops where the expected band is, but I am having a hard time deciding where to cut because everything above it is a mess!

Sounds a little like you added a too much sample to the well. How 'long' is the smear? (from what size marker to your target size?)