Diazonium ions are reactive intermediates derived by the metabolites of carcinogenic nitrosamines. They can react with DNA at many heteroatoms and form different adducts, which might eventually lead to cancer. Compared to other classical organic alkylating agents, simple diazonium ions react more selectively at oxygen atoms of nucleobases. The resulting oxygen adducts have been shown to be correlated with the mutagenicity of the parent nitrosamines. Therefore, it is of great importance to understand the factors that account for this preference of diazonium ions for oxygen atoms of nucleobases. This work was carried out to study the site selectivity in DNA alkylation by primary diazonium ions using 1-propyldiazonium ion as a tool. The 1-propyldiazonium ion can generate both n-propylation and iso-propylation products. The yield of iso-propylation at a given site is roughly a measurement of the association constant and the ratio of npro ylation to iso-propylation is roughly a measurement of nucleophilicity. Therefore, the individual effect of the association constants and nulceophilicity on the product yie s can be discussed by using 1-propyldiazonium ion. Alkylation of DNA as well as its monomers nucleosides by 1-propyldiazonium ion wa carried out. After hydrolysis, the reaction mixture was analyzed by HPLC and LC MS. The percent yields of n-propylation and iso-propylation products were then de rmined. It was found that the variation in the yields of iso-propylation in nucleoside re ctions is small and relatively random. In DNA, however, preferential iso-propylation in he minor groove was observed, indicating that the double helix favors the as ociation of 1-propyldiazonium in the minor groove. In the case of the ratio of n-propylation to io-pro Lion, The variation is also small in nucleoside reactions. In DNA, however, the ratios of n-propylation to iso-propylation for some sites show significant enhancement,whi1ethe others show much smaller enhancement or remain almost the same as cornr. ared the nucleosides. These results demonstrate that the double helix selectively enhance the nucleophilicity of certain sites. Thus, it is the structure of DNA that dictatesthe association constant and nucleophilicity, which in turn control the atom site selctivlty in DNA alkylation by primary diazonium ions.