it would also be helpful to know if you ran a positive control and whether it worked and also whether you can see the size standard on your checker gel and if you have used these primers successfully before. he annealing temperature would be useful but ,as Laurence says...give people some detail to work with please

did you run a positive and negative control? please give more information on dna extraction and PCR. did you mesured DNA in nanodrop? what is the yield in tthat case?

Hello Maryann, i do agree with all the comments made  before now. So i also advice you check the Yeast DNA extraction protocol you used to be sure that the DNA was actually extracted. Run positive and negative control too.

I do agree with all the above suggestions. Please check your DNA extraction protocol. Use Soil DNA extraction kits.check primers

Firstly check extraction, generaly kits are better than hand-made protocols, asi is mentioned above.

Check extracted DNA on gel. If there is a band it is OK. If not, it can be OK anyway. Don`t stress yourself by measuing on nanodrop.

PCR: Probably your sample contain humic acids or other PCR inhibitors. It is very common on organic and forest top-soils. For example DNA from compost or bio-sludge is almost always non-usable directly. Try to dilute DNA to 1/2, 1/4, 1/8, and 1/16 of original concentration.

Do PCR with all concentrations and check it on gel. Choose a concentration with best band on gel 

Principe: You will dillute DNA, but also inhibitors, lower concentration of inhibitors will allows polymerase to work.  With lower inhibitors, bands will be better, but when concentration of DNA will be very low, band will be weak. It is also called DNA spiking-SPUD. More theory in link.

You can also try purify your DNA, but inhibitors are malicious and this process is hard even some suppliers declare their products as perfect inhibitors removers.

You can also add Bovine albumin serum, which will catch some inhibitors, generally I use 1ul of BSA for each 1ul of Taq polymerase. You can change polymerase to more robust one. You can add more MgCl2 if your extraction protocol contains lot of EDTA.

You also may do one positive control i.e. DNA isolated from some fungus. (generally it can be almost any fungus, because ITS3GC and ITS4 are very low specific)

In Ingeny PhorU DGGE apparatus combination of ITS3GC and ITS4 will probably result to double banding -each OTU will be presented as 2 bands. Thus, I recommend FF390 and FR1GC primers.

If any more questions.... just ask.

http://www.gene-quantification.eu/nolan-spud-2006.pdf