I am working with a pool of oligos. I first amplify them then transcribe into RNA. I then use this RNA in a co-ip to recover RNA bound to a specific protein. The problem is, I am not able to get rid of the original starting material (amplified DNA) that was not transcribed. RT-PCR of the enriched RNA from the CO-IP shows multiple band product (see image). I think that this may be due to amplification of contaminating DNA that I tried to get rid of after transcription.
I have used DNase treatment after transcription with varying conditions to try to optimize the enzyme. Dnase does not work very well. I have also tried spermidine to get rid of DNA and it did not work at all for me. Some people us LiCl.
Does anyone have a tested protocol that works really well to get rid of DNA?