electronlone pair with either phosphorus d orbitals or, more likely, with the PO anti-bonding orbital.
The interaction has been calculated at 30 kJ mol^1 more favourable than the extended W-conformation
for the COPOC system. Other non-bonded interactions dictate that and both have values
close to 300° in helical structures though values of60° are seen in some dinucleoside phosphate
structures.
Other PO conformations have been observed in non-helical nucleotides while left-handed helices
also require changed PO conformations. These changes take place largely in the rotamers for . In
Z-DNA, these aresc for guanines but broadly antiperiplanarfor the cytosines whereas issc for
cytosines but broadly synperiplanarfor guanines (Section 2.2.2).
DNA and RNA Structure 23
Figure 2.13 Preferred nucleotide conformations:scfor C-4–C-5(left); apfor C-5–O-5(centre); and ap/–ac
for C-3–O-3(right)
Figure 2.14 (Upper) Gauche conformation for phosphate diesters showing the antiperiplanar alignment of an
occupied non-bonding oxygen orbital with the adjacent PO bond. (Lower) Contour map for PO
bond rotations calculated for diribose triphosphate (energies in kJ mol^1 )
(Adapted from G. Govil, Biopolymers, 1976, 15 , 2303–2307. © (1976), with permission from
John Wiley and Sons, Inc.)