I am thinking to use 338F and 518R primers for DGGE analysis of bacterial consortium. Please suggest me the suitable primers, and is it necessary to use GC clamp for forward primer if I am not sequencing the DGGE products, as I want to check only the DGGE gel profile. please answer
the GC clamp has nothing to do with sequencing but is needed to make DGGE work. The high GC clamp stops one end of the amplimer from melting so that changes in the lower gc target can cause differential melting which causes the melting amplimer to stop in the gel at different positions. If there was no gc clamp then the amplimer would probably all melt at the same denaturing conditions even with different base changes making bases changes impossible to differentiate
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