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Conformational energy calculations for dinucleotide molecules. A systematic study of dinucleotide conformation, with application to diadenosine pyrophosphate

A systematic study of the conformational states of the dinucleotide diadenosine 5′,5′‐pyrophosphate (AppA), an analog of the coenzyme NAD+, has been made using semi‐empirical energy calculations. Taking low‐energy mononucleotide structures as starting conformations, energy minimizations have been performed. The most stable structures exhibit stacking interactions between the adenine bases; there are many different stacked states of similar energy; their stability is derived from nonbonded interactions primarily between the bases but also from base–sugar interactions. The most common form of stacking in the most stable structures was found to be antiparallel A‐A helix. These findings are consistent with the experimental data, which suggest that AppA adopts predominantly a stacked state in solution, and this state incorporates a variety of stacked conformations.