What would you expect if a particular PCR protocol is carried out by setting the annealing temperature of primers at 42 or 45 degree centigrade whereas the actual (calculated) temperature of melting is 60 to 62 degree centigrade after adjusting parameters for monovalent cations (Na+, K+ and Tris+) as well as divalent (Mg2++), and dNTP's concentration. (Generally recommended is 5 degree below melting temperature).
a) All primer dimers settled at the bottom of the agarose gel?
b) Amplification of desired gene with multiple secondary bands?
c) Total smearing?
d) No amplification?
Can anyone explain the outcomes along with reason.
The outcome will depend on the sequence of the primers and the nature of the DNA samples you are trying to amplify, so there is no way predict what will happen in your case.
Why don't we focus on your specific issue? What are you trying to amplify? Why are you concerned about using a 60-62°C Tm?
As Daniel says "there is no way predict what will happen in your case"
It depend on how specific your primers are and how many other possibilities they have to bind. The math models to predict Tm aren't all that accurate either and many don't take into account salts and other components.
Touchdown PCR starts above or near the predicted Tm and by the end of the PCR may be 20 degrees below Tm, and it generally works very well with not a lot of dimer.
Daniel and Glenn are right and one or all of your suggestions could happen. I don't get it why you are not using the proper annealing temperature.
If your primers are highly specific then it should amplify OK. But if there is any partial homology with any other region of DNA then you are bound to get non-specific and irreproducible bands in your PCR product
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