Molecular orbital calculations on the conformation of nucleic acids and their constituents: IX. The geometry of the phosphate group: Key to the conformation of polynucleotides?

Abstract

The PCILO (ω′—ω) conformational energy maps of dimethyl phosphate constructed with different geometries of the phosphate group corresponding to the known crystal structures of U 3′p 5′A and A 2′p 5′U show that the global minimum of each map corresponds to the observed crystallographic conformation of the dinucleoside monophosphate having the same phosphate geometry. This result indicates that the conformational preferences of these relatively large molecules are determined essentially by the geometrical properties of the phosphate group. In particular it is shown in this study that the right-handed helical conformation of the dinucleoside monophosphates is favoured when the O 5′PO(I) and O 3′PO(II) valence angles have values greater than their symmetrical value (i.e. the value in the corresponding symmetrical dimethylphosphate) and that the left-handed helical conformation is favoured when these same valence angles have values smaller than their symmetrical value. A further confirmation of this rule is accomplished by analysing the phosphate group geometry in the crystal structures of diethyl phosphates. Such an analysis shows that the agreement between the observed conformations and those predicted by the rule is excellent. Ab initio calculations performed on a few selected geometries of dimethyl phosphate confirm the PCILO results. They also demonstrate that the conformation of the methyl groups has an influence on the overall stability.