Primer design: free energy
2 replies to this topic
Posted 13 November 2009 - 07:09 AM
I am new to primer design. I used OligoCalc to check my primers for self-complementarity and one of the sections gave me the thermodynamics of the primer. Does anyone know what the parameters/ranges are for the deltaG, deltaH, and deltaS?
Posted 13 November 2009 - 07:52 AM
you can also use oligo to check the formation of primerdimers and primerhairpins: herefore in the case of primerdimer, the deltaG has to be higher than -5 kcal/mol for 3'end and higher dan -6 kcal/mol for internal. For hairpins, the deltaG must be higher than -2 kcal/mol for 3'en en higher dan -3 kcal/mol for internal hairpins.