I would really like to see a picture of a gel but my feeling is that the gel is probably fine but the pcr is not working. You can get a smear with one primer working which is usually because one primer has degraded on storage ( probably in water) or the pcr annealing temperature is too high for the lower annealing primer. My first try would be to order new primers and make them up in TE

We use 1.5% gels for PCR genotyping and analyze bands of that size all the time.  Even a 1% gel would work unless you are trying to distinguish bands that are very close.  Just pay attention to the dye front to know when to stop the gel and look.  I point this out because if the agarose percentage is too high, your gels might not solidify uniformly and it could cause distortions.  From your images, I also think you might just be loading too much material (the amount of DNA, not the volume is what matters).  If there is too much DNA, it won't behave like a sharp band.  Perhaps run a few dilutions of your PCR product in TE with loading dye (start with 1:5 or 1:10).  Of course, the best advice is to keep asking for help from people in your lab or other labs nearby; there isn't exactly a shortage of molecular biologists at your institution.

sorry Ari I did not see the pictures you posted. My last answer is wrong and I agree with Michael that it looks like  a problem with your gels or the running conditions

Hi Ari Mog,

You are lucky to have such a best despiration (Haha).

For first gel gel  running conditions which generates heat or buffers, casting  gel with less melting time, might be the problems. (I use 1XTAE, Themo master mix, 6X loading dye, low melting agarose for 1-1.5% gel for your conditions.)

Based on last gel picture, DNA ladder is perfect, so the gel casting, buffers and running conditions are good. Even non-specific bands due to primers should give sharp bands not smiley.  If I am correct the problem is associated with your loading or loading dye. If you are using the additional loading dye instead of premixed master mix, change the composition. Mix sample well with loading dye before loading.

All the best.

Ari Mog,

Dr. Michael's is one of the reason for your horrendous result.

Hello everyone,

Thank you so much for your help!! I did figure out the problem, and it was with the gel. It turns out that the 10X buffer was actually 1X buffer. Diluting that down 10X resulted in a 100-fold dilution, instead of a 10-fold dilution. Such an obvious problem! If only I had checked that before spending months on this problem!!

Thank you so much for your kindness, wishing you all the best!

thank you for the solution Ari,

it makes helping so much more enjoyable when we do find out what the solution was and also means that better answers can be sent for future people with problems