PCR simulation with PNAs
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@marissaruthlee-22003
Last seen 22 months ago

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

PCR DECIPHER PNA • 172 views
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Thanks for your question. AmplifyDNA() is intended solely for DNA oligonucleotides. PNAs require different thermodynamic parameters that are not supported by AmplifyDNA(). You may want to look for alternative solutions in this reference.

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