While doing a traditional PCR with primers designed for real time PCR we perform a protocol which is also designed for real time PCR (no elongation / expansion) with an initial 50°C step that is normally to activate Uracil N-glycosylase (UNG). I could not find information for Uracil N-glycosylase (UNG) also used in tradtional PCR to remove carry over contamination. Unfortunately we yield a band in the blank from time to time and inconsistent results in PCR-products (without UNG). Is use of Uracil N-glycosylase (UNG) in this traditional PCR useful?
The use of UNG in pcr is a good method of lessening pcr contamination but it does rely on there being no contamination of ordinary pcr amplimer when you start using the ung. Ideally it should be used from the very first amplification because any pre existing contamination will be normal dna and the enzyme will not degrade this.
Your statement about inconsistent pcr results without UNG suggests that the pcr is better with UNG possibly due to Incorporation of U changing the melting chracteristics of the pcr product and making the pcr more efficient so in your case it does seem that it is useful.
As with all enzyme reactions the rate of reaction falls with falling substrate concentration so UNG can never remove absolutely all trace of previous pcr product but it can often keep the levels of contaminant so low that it does not visibly amplify
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