Which patterns do I have to avoid when modifying the 3'-UTR?

Question

I want to change a pre-miRNA sequence (in my case the pre-miRNA is encoding in a 3'UTR of a gene) and then put it in a lentivirus to see if it is still processed. After modification (permutation of ten regions of ~20 nt) which kind of newly appeared pattern I've to be careful about? I do not want to disturb the gene in which the miRNA is encoded

Answer 1

As I understand, you are going to modify the UTR because your sequence is located there. Sometimes happens, first take a look of the gene. If it is 'important', you should try to design a 'cleaner' way to analyse your hypothesis.

Dharmacon has a lot of products to study miRNAs and premiRNAs.

I would also take a look to the miRNAs that target that UTR, maybe it is not highly regulated by miRNAs.