I believe this may be directly related to concentration of primers used, but like dNTPs, can primers also get used up fully in the course of a PCR? I am using primers for a housekeeping gene at a concentration of 10uM. I am doing these PCRs using cDNA from 5 different tissues. One of tissues does not give me any product with my housekeeping gene. The problem is further complicated by the fact that these primers are also giving me cross dimers which resolve at around 100bp, as does the amplicon for my housekeeping gene. Even a 3% gel is unable to resolve them separately. Furthermore, all my negative controls for the housekeeping gene give me a band, which is most likely the cross dimers. My opinion now is that in the case of my cDNA, all the primer might be getting used up and what i see on the gel is probably just the amplicon, whereas for my negative control, all the bands are due to the cross dimers. I have already tried increasing the annealing temperature, which does get rid of the bands but it also gets rid of my amplicons. Any suggestions, aside from designing better primers?