I have been having an ongoing issue with smeary/wavy DNA bands from plasmid prep at the HINDIII cut. This step seems to be the worst. I have tried using TAE and TBE Buffer, new ladder, fresh 1X loading dye, different methods of pour the gel, and now different types of agarose.
Originally we though it was the TBE buffer, it was a 10L 10X stock and we noticed it had formed a hard precipitate. I then made a 10X TAE stock fresh using the raw components which resulted in no change, I then bought 10X TBE stock because I though I might have made it wrong...still no change.
Next, I made a fresh stock of ladder and 1X loading dye in TE and still no change
Then, I tried making the gel differently. (Originially I thought it might be due to the gel solidifying slighlty before I have time to add SYBR dye). I've tried low melting point agarose and HR agarose and there is still not much difference.
I also tried titrating the amount of ladder to ensure that I am not adding too much DNA and still no change.
I only load 2ul of sample which is approx. 2ug of DNA. The size of the bands are 2.5Kb and .42KB. I normally run a 1% gel, but I'm trying a 1.5% today. I run gels at 130V for 45min.
Any suggestions on where I should go from here?