We are currently testing the kinetics of the deprotection of CleanAmp™ dNTPs at lower temperatures such as 60°C.  Both the temperature and the pH of the PCR reaction affect the deprotection rate of the CleanAmp™ dNTPs where increased temperature and acidic conditions accelerate deprotection.

Our studies of deprotection at 55°C in 1X PCR buffer (pH 8.3) indicate that 40% of the dNTPs are deprotected after 2 hrs.  Although deprotection is slower than at the elevated temperatures of PCR (95°C), adjustments to your reaction conditions, such as higher dNTP concentrations will likely allow for success.

Our CleanAmp™ Primers contain a different modification, but provide Hot Start activation using the same principle.  At lower temperatures the rate of deprotection is slower, with a lower concentration of activated primers.  To counter act the slower rate, we recommend using a higher concentration of primers.