The anomeric effect in the phosphodiester backbone of nucleic acids is a stereoelectronic effect that has conventionally been linked to interactions between lone pairs on the O(ester) atoms and P-O(ester) antibonding orbitals. The present study demonstrates that the anomeric effect in the phosphodiester backbone is significantly more complex than portrayed by this description. The presence of multiple lone pairs and antibonding orbitals around the phosphorus atom leads to additional contributions to the anomeric effect, especially involving the anionic oxygen lone pairs. On the basis of the structural changes and Natural Bond Orbital analysis it is shown that a complex balance between stereoelectronic effects involving both the ester and anionic oxygen lone pairs governs the conformational properties of the phosphodiester backbone. The N3'-phosphoramidate DNA backbone differs from the phosphodiester backbone due to the N3'-H moiety having only a single lone pair instead of the two lone pairs present on the O3' atom substituted. The present study uses N3'-phosphoramidate as a control to understand the changes in stereoelectronic effects as a result of changes in the structure and conformation. Two previously uncharacterized properties of the N3'-phosphoramidate backbone are also observed and explained through the complex balance of the postulated electronic delocalizations. The first observation is that the N3'-H moiety in N3'-phosphoramidate is a flexible moiety that can change the orientation of its hydrogen through inversion without a significant energetic penalty in both the gas phase and the aqueous phase. The second observation is that the stabilization of the C3'-endo conformation in N3'-phosphoramidate is primarily due to aqueous solvation rather than intrinsic gas-phase effects involving the reduced electronegativity of the 3'-substituent.