Five novel 1,1'-binaphthalene analogues 1a-1e with triphenylphosphonium (TPP+) salts as a leaving group have been synthesized and characterized as photo-activatable DNA alkylating agents. Phototriggered release of the TPP+ group from 1a-1e generated naphthalenylmethyl-free radicals that were spontaneously transformed to the corresponding cations directly producing DNA interstrand cross-link (ICL) formation via alkylation. The substituents at position 4 not only affect the efficiency of ICL formation but also influence the reaction rate for DNA cross-linking. Groups with small or medium size favor ICL formation, while a bulky substituent (e.g., phenyl group) prevents DNA interstrand cross-linking. DNA alkylation by the naphthalenylmethyl cations photo-generated from 1a-1e occurs at dG, dC, and dA, while interstrand cross-linking took place with dG/dC base pairs. The TPP+ salts (1a-1e) are cations with both lipophilic and hydrophilic properties, which have great potential for biological applications.