primer design for Syber Green - (Jul/03/2007 )
I'm designing sets of primers for syber green real time pcr. I use the premier program to analyze the primers. My question is regarding the delta G values I get when analyzing the formation of dimers and hairpin. What does these values stand for? what is concidered a good delta G value for the formation of dimers? hairpins?
i have here an article and i think IDT is a reliable company:
in general, the dG value indicates the spontaneity of a reaction.
positive dG = more reactants are produced (in case of PCR: single strands)
0 = equilibrium
negative dG = more products are formed spontaneous (double strands)
you should also check your amplicon for secondary structures especially in the primer binding regions, but i think the best way is to avoid any secondary structures if possible.