Is the Tm calculation equation for degenerative primer the same as the ordinary one or there is a special equation for it?

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Wafa Habbal

TIB Molbiol offers a web-based calculator for a complete product description of any oligonucleotide at https://www.tib-molbiol.com/cgi-bin/WebObjects/TIB-MOLBIOL.woa/4/wo/2jOAglRmWbb1a3Z2fzjibM/4.0.0.11.1.15.1.1.2.5.1

By the way, did the two papers use different 'melting points' or 'annealing temperatures'? Melting points are usually calculated while annealing temperatures are empirically defined; so the latter might differ according to the experiment conditions.

Yordan Muhovski

Hi,

PCR using degenerate primers depends on several conditions, elevated MgCl and primer concentrations , up to 1µM. As I see your primers are with not very high degenerate score so try to sue touchdown PCR with the proposed temperatures as final end and see what is going on the gel. good luck!