My only experience is with Runx2 polyQ domain that is tough to amplify and will yield variable number of repeats. There are tricks however they might work partially or not at all in your particular experiment. Things to try are 5% DMSO, Betain, touch-down biphasic PCR, and if you have access to a thermocycler with temperature gradient block, then it's worth trying to figure out the annealing temperatures this way. Of course it's important that your F & R primers hit non-repetitive sequences with Tm higher than 70-72 deg C. If you're cloning your fragment is better to grow the bacteria at lower temperature and longer so that the repetitive elements don't get used for recombination events.

My only experience is with Runx2 polyQ domain that is tough to amplify and will yield variable number of repeats. There are tricks however they might work partially or not at all in your particular experiment. Things to try are 5% DMSO, Betain, touch-down biphasic PCR, and if you have access to a thermocycler with temperature gradient block, then it's worth trying to figure out the annealing temperatures this way. Of course it's important that your F & R primers hit non-repetitive sequences with Tm higher than 70-72 deg C. If you're cloning your fragment is better to grow the bacteria at lower temperature and longer so that the repetitive elements don't get used for recombination events.

When I was working with triplet repeat PCR, it was having problem most of the time. After that, we tried an enhancer prepared in our own lab and it worked very well. You can try it..

For 100ul of enhancer:

Betain 54ul

DSMO 6.7ul

DTT 6.7ul

H2O 27.6ul

Add 2.5ul of enhancer in 25ul total reaction volume. Good Luck.

I think you must be sure that there is no matching between the used primers in the reaction.