I'm having some trouble with genotyping for this one gene & hoping to get some insight! Our primers have an expected product size of ~600bp. As you can tell by the picture of the first run (darkfield), almost every lane showed a positive band. Based on the parents, it isn't possible for ALL the mice to have this gene (should be ~50/50).

Some things I've tried:

  • Increased the DNA template volume from 1µl to 2 & 4µl -- faint bands disappeared?
  • Ordered new primers -- same results
  • Re-extracted DNA from samples -- same results

Today I tried a touchdown PCR (-0.5C each cycle starting from 65C) and compared it to the regular program I've been using (60C annealing), with the new primers and re-extracted samples. The primers have a Tm of ~62C, and I've been running 33 cycles. And, it looks like it worked (inverted picture).

The negative control was water template, and the - & + were from previously verified samples. My questions are - why did this appear to work this time, and can I trust these bands? Thank you for any help/advice!!

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