This protocol is from the UC Davis labs:
(http://genome-lab.ucdavis.edu/Protocols/pcr_tips/pcr_reamplification.htm )
PCR Reamplification for Inadequate or Failed
Amplifications
Change your standard PCR protocol as follows:
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decrease the number of cycles by 10
raise the annealing temperature by 2°C
lower the final primer concentration by 0.1 uM
lower the final MgCl2 concentration by 0.5 mM (but not lower than 1.0 mM)
add 1.0 ul of the previous PCR reaction (cannot contain loading dye)
in addition, attempt reamplification of the negative control(s) from the
previous reaction to be sure the reamplification product is not contaminated
Other Notes from Various Sources
The only issue is not overloading a PCR reaction with too much of the original PCR product--make a dilution of 1/50 (30-35 cycle PCR) and even 1/1,000,000 for a 40-45 cycle PCR.
May need to titrate this out to find the proper dilution of the original PCR product to use in a
re-PCR.
An even easier approach is to stick a sterile toothpick or needle into the gel at the site of the
banded fragment, and to swish this through a new PCR reaction mix in order to inoculate it with
a tiny amount of specific DNA. (Kadokami, Y. and Lewis, R. V. (1994) BioTechniques 17, 438)
The sub-standard PCR product can also be resolved on a normal 1% agarose gel. In this case,
however, the agarose plug should not be allowed to dissolve in the 50 μl of ddH2O since
agarose in higher quantities inhibits PCR. The agarose plug should be warmed at 55°C for 10-15
minutes to facilitate the elution of the PCR product, and then the Eppendorf tube should be
centrifuged to compact the agarose on the bottom of the Eppendorf. When I reamplifying the
PCR product, the annealing temperature should be raised to 55°C or higher (depending on the
annealing temperature of the primers), remember that this time the match between the
priming sites and the primer is perfect.
(http://evoamazon.net/legal/index.php/protocols/laboratory/pcr/pcr-reamplification )