The structure of DNA dictates purine atom site selectivity in alkylation by primary diazonium ions.

The 1-propanediazonium ion, generated from N'-nitro-N-nitroso-N-propylguanidine in aqueous solutions, was reacted with the purine nucleosides dGuo and dAdo or single-stranded or double-stranded DNA. After nucleobase liberation by acid hydrolysis, the percent yields of products were determined by LC/MS using either isotopically distinct internal standards in the case of the nucleoside reactions or an internal standard and the ratios of response factors of all other products that were separately determined in the case of the reactions with DNA. In the reactions of nucleosides, products of both n-propylation and iso-propylation at all of the heroatoms were observed. For these reactions, the yields of the three most abundant n-propyl adducts of Gua are in the order O6 > N7 > N2, in the ratio of 9.0/6.4/1, while for Ade, the order of the yields of N-propyl products is N1 > N7 > N3 > N6 in the ratio 2.5/1.8/1.1/1. The ratios of n-propylated to iso-propylated products at each site, P(n)/P(i), generally a measure of enhancement of S(N)2 displacement on the diazonium ion, vary with each heteroatom but by no more than a factor of 6 for Gua and a factor of 3 for Ade. In the reactions with duplex DNA, products of reactions at all sites could not be detected. In addition, much larger selectivities are observed, similar to what has been observed by others in the reactions with ethanediazonium ion. Thus, P(n)/P(i) = 30, 21, and 0.9 for N7, O6, and N2 of Gua. Similarly, the values of P(n)/P(i) are 11 and 8 for N3 and N7 of Ade. Reactions with single-stranded DNA give values of P(n)/P(i) that are intermediate between the nucleoside reactions and the reactions of duplex DNA in most cases. The factors responsible for the relatively small atom site selectivities intrinsic to the nucleosides are analyzed, and reasons for enhanced S(N)2 nucleophilicity in duplex DNA are discussed.