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==Exp. 2 Confirmation of CpG MIP capturing experiment by PCR== Another way to confirm the result of the MIP capturing experiment is to perform PCR on the circularization reactions with target-specific PCR primers. I will use the bisulfite converted DNA as positive controls. The primers used included HD48MIP 1-3. Template: 1ul (1:100 dilution of bifulfite converted gDNAs) 10X buffer: 2.5ul 10mM dNTP: 0.5ul 10uM Primer pair 0.5ul 50X SYBR I 0.2ul JumpStart Taq 0.25ul H2O 20ul Total number of reactions: 4 MIP reactions x 3 primer pairs + 2 control x 3 primer pairs = 18 94C 3min -> 30 cycles of (94C 30min -> 57C 45sec -> 72C 30sec) -> 72C 3min [[Image:2007-12-10-CpGMIP-PCR-PAGE-PCR.png|500px]] The results are noisy. The amplicons with Hd48MIP2 sort of suggest that there might be some targeted DNA being captured, but there are too many non-specific bands. Hd48MIP1&5 didn't even work at all. I will repeat this PCR using a touch-down protocol.
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