TA Cloning - (Mar/14/2015 )

I would be doing a control ligation of a PCR product that was different from the one you are attempting. You say that your competent cells are good. The only way to know that is to either do such a control, or to quantify the competence, which will need to be at least 10^7 cfu/ug. You can measure the competence by serial dilution of a common plasmid (such as pUC19) to the 10 pg/ul level, then transforming. If you get no colonies, you have a problem.

Meg P. Anula on Sat Mar 21 11:21:58 2015 said:

Anyway, I have a question in mind, since this Econotaq polymerase master mix I used have this green dye in it, would it be okay not to purify it before i use on GC vector? Since you said purification can degrade the A-T overhangs so i wonder if it'd do the same for G-C as well.
 
Thanks.

I can't say, but given the fact that both polymerase and the cloning kit would be from the same company, they should have protocols optimized for their polymerases. If you look in their protocol before buying, you can see what they exactly recommend to do with the PCR product.
The degradation of overhangs may happen the same, or there may be differences between A and G nucleotide at the end, I don't know. Also dyes in PCR mixes are often inert for polymerases, if it's the same for enzymes doing ligation, that is a question.

But as I said, I would be really VERY angry on that company for the reason mentioned earlier, maybe considering never buying anything else from them, but that is up to you. There are plenty other mastermixes that don't require optimizing (or just DMSO or betain) but I understand you don't want to go through new PCR kit and everything again, when the TOPO kit may not even work.
But at least I would write them angry email, that they should mention this specific behaviour of their polymerase in the manual next time.