How do you know that your primers are integrated into the genome and got amplified? I still believe that the multiple bands you got were due to primer unspecificity. First of all, I don’t know how you extracted DNA and also maintain the integrity of NgAgo proteins. Normally, after DNA extraction, most of the proteins should be denatured or degreaded. Therefore, it is hard to imagine that NgAgo functions during PCR reaction. Secondly, the sequences got amplified are not totally match with the PCR primers. If the primers are intersted into the genome, the matches should be much better, right? The genomic sequences are complicated, it is common to get unspecific amplifications. If you believe that the 5' phosphorylated oligo could affect the PCR results, can you find a way to get rid of the free oligos during genomic DNA extraction?