I have been growing B16F10 Mouse Melanoma cells. I need to extract the genomic DNA and do PCR to amplify a specific region. However, no matter what temperature or magnesium concentration I use, I have no luck.
I obtained mouse DNA from someone who was genotyping mice. I tested the PCR oligos with that DNA, and the reaction worked, so it's not an oligo problem.
The genomic DNA had poor 260/230, about 0.6. I thought the EDTA levels may have been high, so I did an isopropanol precipitation to clean it up. This made the 260/230 ratios about 2.1. But the PCR still didn't work.
What I had noticed during the precipitation however was that the DNA pellets were gray to black. I assume this is melanin, because the cells are melanoma cells, and turn black.
Could this melanin be a problem in PCR?