I have been using a PCR master mix green coloured from a Promega ( green taq). But for my recent work in a particular gene that PCR master mix is not working. I borrowed Phusion DNA polymerase ( high fidelity Cat no: F-530XL) from a neighbouring lab for two samples and the amplification did take place. My aim is to amplify the gene promoter region ( PCR product size: 269 bp) and study Single nucleotide polymorphism in the region using RFLP technique. For this purpose I have introduced an restriction cut site ( AluI) near the 3' end of my Reverse primer ( single basepair mismatch) . While checking the details of this phusion DNA polymerase I found it has 3'-5' exonuclease activity and it is known for its accuracy. Hence I am anticipating that there is a chance that the polymerase might cut the error basepair for editing and accuracy maintenance. If this happens then I will have false results for my SNP study. I have never used a high fidelity polymerase before, I used taq polymerase which does not have 3'-5' exonuclease activity. In this regard I am confused which polymerase should I buy. I have seen in thermo catalogue there are normal taq polymerases , dreamtaq as well as many other options but I am unaware about their properties and which one to select. I donot have access to more phusion DNA polymerase or any other taq pol at this moment. This particular gene amplification has been complicated for from the beginning. I have 300+ patient DNA samples to look for SNPs so I am looking for an economic option as well. Kindly guide me what my options are regarding this and which polymerase should I opt for.
As for polymerase selection, you may find this chart useful:
https://www.neb.com/en-us/tools-and-resources/selection-charts/dna-polymerase-selection-chart
As for the rest, if you only have the promega mix available, try to optimize tmeperature/timing/salt cc
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