Dear Katarzyna, thanks for your reply, Can you tell me whether you are working on single stranded genome of double stranded? have you ever run a control PCR (without reverse transcription) to determine the DNA contamination of your RNA prep?

Dear Katarzyna, with double stranded DNA, I also have no problem as DNase digest it very well but I am facing problem with viral genome which remains as single stranded in some fraction in the cell and contaminate RNA prep.

Yu may try mungbean S1 nuclease to get rid of single stranded DNA

Dear Dr. Siva

Thanks for your reply.

Mungbean S1 nuclease digest both single stranded DNA as well as RNA which is not required as I need to quantify RNA to analyze gene expression. Its activity on single stranded RNA render its use unappropriated in my case.

OK. It is my vague memory of using S1 nuclease . I do stand corrected.

Perhaps you could use a cocktail of DNase I to generate smaller fragments together with a DNA-specific exonuclease to finish the job.

Dear Axel

Thanks a lot, by reading about EXoI I think it will work according to my need. In next few days, I will be doing experiments and will let you know how it actually performed for me.

Stay blessed!

Dear Muhammad, 

I'm running into a similar situation as you previously described, but with AAV. Could you kindly share your experience with ExoI for getting rid of ssDNA viral genomes? Also, do you do both DNaseI and ExoI treatment at the same time or separately?

Thanks a million,

Kexian

Dear all,

This thread is truly useful as I'm currently encountering very similar problems removing AAV genomes. So far I have tried treating my RNA samples with RQ1 RNase-Free DNase from Promega but still I have a RT-PCR product at the same Ct in my -RT control as in my test sample. I would like to try ExoI and would appreciate any tips/experiences.

Many thanks!

Marina