For the prediction of the duplex fractions or for the prediction of the fractions of any secondary DNA structures (dimers or hairpin-loops), the program uses classic equations and thermodynamic parameters, which however do not consider the dynamics of the reactions (competitions and enzyme activity). There are no particular studies that take into account these dynamisms of reactions. The program, to improve the prediction, modifies the values of the thermodynamic equations. For this purpose particular parameters (Temperature factor) are used, which can be set in 'Advance Setting'. By default the program uses values derived from our laboratory experience, these represent only a first attempt to obtain a 'significant' prediction. These parameters and possibly other parameters will surely have to be applied and calibrated in the future.
Those who use our programs to analyze and/or design PCR reactions can contribute to the improvementof these predictions by sending the author (ivano.zara.bio@gmail.com) the results obtained in their real-time PCR experiments. |