Dear Elaheh Hashemi,

I believe it will depend on how many U you have in your template using Dig-dUTPs. My concern is if you are not getting good labeling of your probe or whatever you trying to obtain. I used some time ago the dig labeling system from  Roche to label probe by pcr, but had lot of times bad results in terms of signal in my experiments. Then, I decide to clone my template to use later in pcr labeling with Roche system to obtain dig-labeled probe. Voila! I started to obtain good results. Therefore, if you do not have a clean template, potentially you will have low signal in downstream experiments.

Hope this may help you!

Good luck!

Herbert