Are you sure you are working with genomic DNA? This is fairly uncommon, particularly with working with restriction enzymes and PCR, which is often dealing with plasmid DNA only. How are you purifying your DNA? If it is with a MiniPrep kit, you are only extracting plasmid DNA (not genomic DNA). It is pretty common to do a restriction enzyme digest on plasmid DNA, use gel extraction and purification of a given fragment, then use only that fragment as the template for PCR.

Restriction endonucleases are initially bacterial enzymes that fight viral invasions. However, they are commercially available as a product of "genetic engineering". In general, when you want to digest your genomic DNA with a given restriction enzyme like HgaI or EcoRI or others, this DNA has to be amplified first.

Best wishes

Thanks for your comments, the restriction enzymes can be used with genomic DNA but depends on the size and purity of DNA. May be seen a smear or many bands in the gel, as the long genomic DNA have many of enzyme sites. Has anyone have do this before?