The invention features a method of promoting an alteration at a selected site in a target DNA, e.g., in the chromosomal DNA of a cell. The method includes providing, at the site: (a) a double stranded DNA sequence which includes a selected DNA sequence; (b) an agent which enhances homologous recombination, e.g., a Rad52 protein or a functional fragment thereof; and (c) an agent which inhibits non-homologous end joining, e.g., an agent which inactivates Ku such as an anti-Ku antibody or a Ku-binding oligomer or polymer, and allowing the alteration to occur. The agent which inhibits non-homologous end joining, e.g., a Ku inactivating agent such as an anti-Ku antibody, is preferably provided locally. Component (a), (b), and (c) can be introduced together, which is preferred, or separately.