Abstract
This paper reports a systematic PCILO study of the conformation of the nucleic acid backbone. The authors principally studied the ω′ and ω phosphodiester torsion angles of the disugar triphosphate model as a simultaneous function of (1) the sugar nature, ribose or deoxyribose, (2) the different combinations of the sugar ring puckers C(2′)‐endo‐C(2′)‐endo, C(3′)‐endo‐C(3′)‐endo, C(3′)‐endo‐C(2′)‐endo, and C(2′)‐endo‐C(3′)‐endo, and (3) the different conformations around the ψ(C4′–C5′) exocyclic bond. The dependence of the (ω′,ω) conformational energy maps upon these different factors, is discussed. The results are in very good agreement with the observed structures of ribonucleic (RNA10, RNA11, A′‐RNA12, tRNA^Phe^) and deoxyribonucleic acids (D‐DNA, C‐DNA 9.3, B‐DNA 10, A‐DNA 11). Thus the validity of this model, the disugar triphosphate unit, is ensured.
The main conclusions that can be drawn from this systematic study are the following:
The torsion around P‐05′ (angle ω) is, as a general rule, more flexible than the torsion around P‐03′ (angle ω′).
There is no notable difference between the ribose–triphosphate units and the deoxyribose–triphosphate units for the C(3′)‐endo–C(3′)‐endo and C(3′)‐endo–C(2′)‐endo sugar puckers.
The deoxyribose–triphosphate units with C(2′)‐endo–C(2′)‐endo and C(2′)‐endo–C(3′)‐endo sugar puckers show much more ω′ flexibility than the ribose–triphosphate units with the same sugar puckers and cis position for the 2′hydroxyl group.
The preferred values of ω′ are independent of the sugar nature (ribose or deoxyribose) and of ψ values; they are correlated with the sugar pucker of the first sugar‐phosphate unit:
C(3′)‐endo‐C(3′)‐endo and C(3′)‐endo‐C(2′)‐endo puckers ⟹ ω′ ≃ 240° (g^−^ region)
C(2′)‐endo‐C(2′)‐endo and C(2′)‐endo‐C(3′)‐endo puckers ⟹ ω′ 180° (t region)
The preferred values of ω are independent of the nature and the puckering of the sugars; they are correlated with the rotational state of the torsion angle ψ(C4′–C5′): ψ ≃ 60° (gg) ⟹ ω ≃ 300° (g^−^), ψ ≃ 180° (gt) or 300° (tg) ⟹ ω ≃ 60° (g^+^)