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I'm investigating phylogenetic in Panax genus (Araliaceae). I tried some published PCR condition for amplification matK gene with pair of specific primers trnK3914F (5’-TGG GTT GCT AAC TCA ATG G-3’) and trnK2R (5'-AAC TAG TCG GAT GGA GTA G-3') (in attached files) but I could not recognize the desired band. My problem is no observed band. I had tried gradient PCR with Tm ranged from 45 to 68 deegrees also, The size of desired band is 1509 - 1512bp, so I also try to increase the time for strain elongation , but it also was not better.
With another region (ITS1-5.8S-ITS2), it was successful to amplify.
I can not explain why it has failed with matK gene. Please give me advices to modify the PCR condition. Please hint what I should modifify the procedure to do.
Le Ngoc Trieu