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Amplification of bisulfite converted gDNA for sequencing - (Nov/21/2010 )

Greetings fellow scientists!
I am trying to amplify bisulfite converted genomic DNA for subsequent capillary sequencing, but I am experiencing problems. I have tried two different polymerases of which only the Dynazyme produces a band on a gel:

(1) AmpliTaq Gold polymerase
AmpliTaq Gold

(2) DynazymeII Hotstart polymerase
Dynazyme II Hotstart Pol

Does anyone have any insight to why AmpliTaq is not working but the Dynazyme is? I have tried varying reagent concentrations (including primers, template) and thermocycling conditions but to no success.

My other question is this: since I am going to sequence the amplicon (using Big Dye chemistry and capillary sequencing), is there any reason why I shouldn't use the DNA amplified with DynazymeII? From reading lots of papers, I see people using Taq polymerases, but they need the TA ends for cloning (followed by sequencing).

Thanks in advance :)

-Jack

Edit: The sequencing results are used for methylation analysis of promoter regions.

-Jackjonez-

hi there, different Cation concentration can also affect the PCR which is probably something you are seeing.

for PCR, cloning and then sequencing normal Taq is favoured to allow for TA-cloning into a sequencing vector. Both are hot starts so they should work.

-methylnick-