Do you know of any bioinformatic tools for testing PNAs with PCR simulation?

I have tried using Amplify() in DECIPHER to test candidate PNAs, but (perhaps not surprisingly) this did not do a good job of predicting PNA success in the lab.

Here’s what I tried: (1) added the PNA as an additional “primer” in the reaction, (2) subtracted amplicons produced by the PNA, and (3) identified the amplicons as target or host w/ blast to quantify host DNA contamination.

If you have any recommendations or “hacks” for using tools to solve this PNA simulation problem, that’d would be greatly appreciated!

Thanks, Marissa