This post falls into the category of “things I couldn’t find myself online, so I’m posting for the sake of others with the same problem”. While there are a few articles and pages scattered around offering advice on PCR additives, the following excellent tips came from a random old faculty dude in my school:

• The best PCR additives for improving your chances of amplifying a target with strong secondary structure (including RT-PCR of folded RNAs, which is my big problem at the moment) are Dimethyl sulfoxide (DMSO) and Qiagen’s Q-solution.
• While a lot of websites will tell you to use DMSO at about 5-10% (of your final reaction mix, not the master mix), it can actually be brought up to about 30%. If you’re not getting results at a lower conc., try ramping it up.
• It’s crucial to use pure DMSO. It’s fairly cheap stuff so order some in if you are unsure.
• Although it is possible that DMSO will be slightly mutagenic, it’s really nothing to worry about unless you are going to be re-amplifying something multiple times, in which case you should be worrying about other sources of mutagenesis anyway.
• Q-solution is probably just betaine. While it’s true that you can buy raw betaine cheaper than Q-solution, if your lab is anything like mine there are probably a million tubes of Q-solution lying around in old, abandoned kits and hence it is probably the cheapest and most readily available additive. Use it at a final conc. of about 1M.

DISCLAIMER: I am but a humble research student and definitely not a master of PCR. I’m simply repeating advice that I found useful. This advice is given as-is and I take no responsibility for failed PCRs, nervous breakdowns or raidings of the lab next door’s chemicals cupboard.