Some New Polynucleotide Structures and Some New Thoughts About Old Structures

Abstract

For more than a quarter of a century, X-ray fibre diffraction analysis has been the most direct experimental technique to elucidate the structures of nucleic acids. The paucity of diffraction data from these fibres does not permit us to deduce atomic positions from electron density maps as in single crystal structure determination. The linked-atom treatment (1) using bond lengths and bond angles fixed at their respective average values, as obtained from a survey of nucleoside and nucleotide crystal structures enables to redefine the problem to one of dealing with the rotations about single bonds, α, β, γ, δ, ε, ζ and χ (Figure 1) as the major variable independent parameters. For simplicity of computation, the five-membered sugar ring is quite often frozen at one of the more commonly observed puckered shapes: C3'-endo (ζ ≃ 85°) and C2'-endo (ζ ≃ 156°) or a minor variant. When appropriate, the endocyclic conformation angles