calculate the mRNA stability

Question

[Samane]

how can I calculate the mRNA stability, (after design the primer and PCR and final expression ( overlap PCR)) ?

which software is exist, or which site can help me?

and how many parameters should be checked,at it?

Answer 1

[Giovanni M Dall'Olio]

You can use for example the UNAFold software. For an example of how it is used, check figure S4 of this paper.

You can also check the list of RNA Structure Prediction Software in Wikipedia.

[Samane]

thank you so much .those link help me so

but I have a question, about mfold;

when it analyse my sequence which structure should be choose to describe?

structure 1, or not which has the lowest deltaG?

and how could I describe those information, for example TotaldeltaG was (ΔG = -163.60),but there are some details in it?(-1,-0.1,-9,....)

thank you.