At Bitesize Bio, Shoba Anantha gives some tips on using touch-down PCR. She says this "very useful technique for improving PCR amplification specificity is trickier that it might seem at first." To reduce non-specific priming, she suggests keeping the reactions cold until it's time for thermal cycling and then she says that a hot-start is the best way to go. She also suggests limiting the number of cycles. "Too many cycles will lead to appearance of non-specific bands in the gel," Anantha writes.
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