Best in this case means: specific priming, long templates (amplifying whole plasmids >5 kb), and fast.
I use NEB Q5 polymerase now which meets all of these requirements, but is very expensive from my country's distributor. Q5 is a big improvement over what I've used previously (PfuUltra being 2nd best).
Q5 PCRs give good yield ~95% of the time on the first try and ~100% of the other times can be easily fixed with small tweaks, even with very poor primers (very low GC; many mismatches). A very good fidelity with 2 errors observed over ~1M bp of sequenced clones made from Q5 PCR products.
I use Phusion but it is not much cheaper than Q5 and I am really satisfied. However, if you ask around you may be able to find a clone of Phusion (or Q5) and that would trim you costs!!
Hi Zach
I used PrimeSTAR GXL DNA Polymerase from TAKARA and successfully amplified a whole vector which was around 11 kb. It is high fidelity and in my case, it worked perfectly.
Thanks Hugo... the new Phusion Hot Start II is somewhat cheaper here than Q5 so probably I'll get a sample and give it a shot.
Amin: I had a sample of that before but never got around to trying it; Takara SapphireAmp is AMAZING for colony PCR.
Zach, Dima and I have been using KOD Neo Plus from Toyobo. I haven't amplified anything over 3-4kb but he uses it routinely for plasmids and swears by it Not sure the costs outside of Japan but it was definitely cheaper compared to other hi-fi long range polymerases. Compared to Q5 which I also use and feel the same way as you about it, it does better with less template. I use Q5 only b/c they make a lazy man's version of it as a 2X master mix and of course, funds are not an issue in our lab.
http://www.toyobo-global.com/seihin/xr/lifescience/products/pcr_016.html
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