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N-terminal deletion primers

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Hi all
I need to construct a N-terminal deletion of a protein through PCR. I was told that the best way to do it is to amplify the C-terminal region with a Nde1 and BamH1 recognition site and insert it into a suitable vector.
I have a couple of questions regarding the primer design:
I assume that there has to be an ATG codon just before the C-terminus so that the translation starts there.Am I right??
Also, the BamH1 recognition site is GGATCC....will this additonal insertion in the primer affect its ability to anneal to the parent template?
Thanks!!
P.S: I am not a molecular biologist and hence not too familiar with PCR methods.
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