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Primer design: free energy


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#1 intern

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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?

#2 susanna

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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.

#3 intern

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Posted 13 November 2009 - 09:07 AM

Thank you :)




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