Proton magnetic resonance studies of 2′-deoxynucleosides and nucleotides in the syn conformation

Proton magnetic resonance data for 6-methyl-2′-deoxyuridine and its 3′- and 5′-monophosphate derivatives are obtained in aqueous solution and compared with data for corresponding thymine derivatives. The data show that the derivatives of the 6-methyluracil base occupy the syn conformation. The presence of the syn base leads to a flattening of the sugar ring and destabilization of the g+ conformer about the C(4′)—C(5′) bond. This destabilization is particularly large at the 5′-nucleotide level and is discussed in terms of a repulsive interaction involving the 2-keto oxygen of the base and the negatively charged 5′-group.