Hello, I am trying to optimize translating ribosome affinity purification to collect only translating coding RNAs. I used VHH magnetic gfp beads. After ribosome pull-down, I used TriZol for RNA isolation, and then, I applied DNaseI treatment for 1 h. To check genomic DNA contamination I performed PCR with GAPDH primers and my RNA was clean. After cDNA synthesis I made PCR with pri-mir-21 primers to check whether my RNA is only coding or total/non-specific RNA. I shouldn't have seen a band in GFP-TRAP cDNA ON AGE. This means, non-coding RNAs precipitated also :(. What could be the reason? How can I solve this non-specific non-coding RNA pull-down?

Thank you :)