I have been using Betaine for a while now in my master mix, but I am beginning to question its effectiveness. I know it supposedly serves a purpose to improve target specificity, but there are more instances in which it is not used. Any thoughts?
Betaine may be used in improving the sequencing reaction of GC-rich templates. But, what is important, it may "introduce" false heterozygotes and there are more "N" in the chromatogram, so it may not very useful if you are interested in mutation identification. Then, other additives are more useful.
I know betaine for GC rich templates and long PCRs, not actually specificity. For the latter issue TMAC (tetramethylammonium chloride) is a quite useful additive.
Also have a look on the concentrations as this has also an influences the effect of an additive.