Abstract: The present invention provides a method for site-specific cleavage of double stranded DNA at sequences not less than eight base pairs long, comprising methylating he DNA with a sequence-specific methylase capable of recognizing and methylating a first sequence of the DNA, thereby generating a second sequence of the DNA capable of being recognized by a site-specific endonuclease, the first and second sequences having an overlapping part thereof; the length of the combined methylase and endonuclease recognition sites being not less than eight base pairs long, and cleaving the methylated DNA by treatment with the site-specific endonuclease. This method is useful for increasing the selectivity of cutting DNA stands using restriction endonucleases, thereby permitting the isolation of large DNA fragments and the generation of unique sites in DNA fragments, e.g., cloning vectors.