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I have a DNA fragment that contains the gene of interest sandwiched by restriction enzyme sites. Then, can PCR amplify the entire fragment, recognizing the restriction enzyme sites?

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  • $\begingroup$ Why not? PCR amplifies any sequence. $\endgroup$
    – WYSIWYG
    Jun 22, 2016 at 13:05

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If you aren't digesting prior to amplification, sure. Nothing in PCR cares about whether or not some other protein interacts with the site. There are thousands of restriction enzymes in nature. No one would ever be able to do PCR if you had to avoid every single potential restriction site.

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    $\begingroup$ Just a minor comment: some restriction enzymes like XbaI are sensitive to DNA methylation, so XbaI works on your PCR product but may not work on your gene. $\endgroup$
    – Ashafix
    Jun 22, 2016 at 22:16

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