Abstract: A method is disclosed for highly efficient DNA sequence alterations. The method is useful for editing chromosomes, to engineer cellular markers through insertion of genes, or to create epigenetic changes by using cas9-enzyme fusions where the enzymes can be DNA epigenetic modifying enzymes or chromatin modifying enzymes, etc. The technology also differs from all previously known technologies in that the CRISPR/Cas system can function in ways that are “clean”, i.e. they have not been in contact with any virus, or are carried DNA molecules that can insert into the chromosome in unintended locations.