One more bit re: the PCR question. Tm's for most DNA's of approx. 40 % G+C
are 85-90 C (in, e.g. TE buffer), such that with even 40-50% of the
template melted, it might still be possible to routinely amplify targets by
melting at say 88 C. I think David Juck makes a good point when he says
that subsequent denaturation of the much smaller amplicon could be much
easier (but only if it doesn't have a high G+C content). Before adding DMSO
or glycerol or whatever, I'd be inclined to just give it one shot at 88 C.
You might accomplish your objective without further fine-tuning. There
might also be the added benefit of less temperature-related damage to the DNA.