I dont think it will be a problem. UNG with dUTP  is used to avoid carry over contamination. It is mostly an extra security measure than a necessity.  If your negative controls look good, you can go ahead. Good Luck.

The presence/absence of UNG should not make too much difference.  The nucleotide mix will include dUTP and this will make a difference in the melting temperature of your product--so there is a remote possibility that the efficiency of the PCR will be affected.  If you have been using a different mastermix, you might want to check that the optimal conditions that you have worked out will give clean results with the new mastermix, because there will probably be other differences, such as salts, buffers and additives that might make even more of a difference in the PCR than the UNG/dUTP.

The replies above are correct. UNG is only useful if the previous PCRs have been performed with dUTP incorporated. it will not get rid of any contamination without incorporated dU. As an alternative to UNG you can also use Arctic Shrimp DNAse incorporated in mixes. As it is quite expensive I use it during the cDNA synthesis steps. Always use only dedicated clean pipettes and filter tips in a sterile hood if possible. Do not use the same pipettes for samples and reagents, and do not use the same pipettes for high copy standards and low copy targets - i.e I use 3 separate sets of pipettes.

http://arcticzymes.com/technology/double-strand-specific-dnases/

Hi bita 

 use of UNG not only don't interfere your experiment but also helps to control possible contamination and carry over.

Luck