dUTP/UNG is not that expensive actually. Many qPCR kits have include this in the 2X PCR Mix. There is not much different when you use dUTP/UNG. The only different thing is to set a single 50 ℃ hold for 2 min before denaturation stage and the following cycles in your qPCR machine.

Thanks! Is there anything to consider for downstream applications? Such as T/A cloning or making in situ probes?

I haven't try making the probe.

If you want to perform cloning, the ligation product should be transformed into a dUTPase and UNG defective host. Otherwise the product will be digested. I haven't try this yet so I don't know the detail.

Do you think that UNG (uracil DNA glycosylase ) can be used for carry-over prevention of PCR ? What about sodium bisulfite when treatment converts unmethylated cytosine bases into uracil residues, bisulfite treated DNA is sensitive to UNG treatment, not only contaminating products of previous PCR, but also the actual template will be degraded.

dUTP/UNG carry over prevention system is only used for many repeatitive PCRs such as genotypes or diagnostics to prevent the previous PCR product contamination of the new PCR rxns. If you do cloning, methylation detections, if you have good separation of PCR rxn area from PCR product detection area, there is no need to use dUTP/UNG carry over prevention system.

Thanks to everyone for the comments. I'm on sabbatical in a lab that does not have good separation of set up areas and gel boxes and I'm trying to figure out the best way to deal with the contamination problems that are developing! I'll keep all the advice in mind. Thanks!

Of course, I understand. Incidentally, does anyone know if surveyor nuclease will work with dUTP/UNG?

oops, I sent that too quickly. What I mean to ask is will surveyor nuclease be able to identify mismatches in a template that has incorporated dUTP (but obviously not digested with UNG). Thanks.