primer dimer or what? - (Jul/31/2009 )
Recently I used a few pair of primers to test genomic DNA contamination in my cDNA (RT from total RNA). The primers are one in nontranscript region, the other in exon. If no genomic DNA contamination, it should has no band, right? But I always have a <75bp bands, even I tried several different pair. And when I do other traditional PCR, if my product has low yield, I have this suspicious band as well.
Is it a primer dimer? How can I avoid it?
If the expected size of your prodcut is > 75 bp, the the 75 bp one is most likely primer dimer. In this case probably you have to redesign your primers because your current primers form self or inter pairing.
Yes, more than likely. You can run a Control with no template and compare the bands. Also, if it's genomic DNA, your bands should sit high. If you also know that your target band is >75bp, that should answer your problem.