Anomalous base-stacking of the N1-oxide of AMP.

The intermolecular association in aqueous solution of the N1-oxide nucleotide analog of adenosine-5'-monophosphate has been investigated by 1H-NMR spectroscopy over the concentration range 0.0006--0.6 M. The concentration profile of individual chemical shifts provides evidence for an unusual stacking pattern compared to that of the natural nucleotide AMP, involving only the imidazole moiety of the adenine base. The different stacking pattern of this nucleotide analog suggests that the exact stacking geometry of natural nucleotides interacting with nucleotide-depending enzymes, is achieved by adjusting to the geometry of the individual receptor molecule.