I am planning to perform Methylight to bisulfite-converted cell-free DNA isolated from blood(Serum/plasma). Can you please suggest which DNA Polymerase with 5' to 3' exonuclease activity works best with cell-free DNA? (I will use Stratagene Mx3005p Real-Time PCR system)
While I have never done PCR on cell-free DNA (I'm a bacteriologist), I would guess that any high fidelity polymerase will work the same way in your system as in any other. Just choose something robust. Based on my experience, one or all of the following 3 (expensive) options will give you the results you need:
Extensor Long PCR ReddyMix Master Mix - Super robust, but only about 6X fidelity over Taq)
NEB Phusion Hot Start Flex 2x Master Mix - My current favorite. Not quite as robust as Extensor, but it is much higher fidelity and has amplified sequences that Extensor could not)
AccuPrime Pfx 1.1x Super Mix - Not as high fidelity as Phusion, but the 1.1 mix is a breeze to set up, and it usually works well.
https://www.thermofisher.com/order/catalog/product/AB0794B
https://www.neb.com/products/m0536-phusion-hot-start-flex-2x-master-mix
https://www.thermofisher.com/order/catalog/product/12344040
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