Syn–Anti effects on the spatial configuration of polynucleotide chains

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Abstract
Semiempirical energy calculations have beeb performed on model nucleic acid systems to assess the preferred conformation of the rotation χ about the glycosidic linkage and also the effect of this rotation on the spatial configuration of the sugar‐phosphate chain backbone. The rotation angle ϕ˝ about bond C5′–C4′ in purine polyribonucleotides and 5′‐monoribonucleotides is found to depend on whether the conformational range of χ is syn or anti. The preferred conformation of χ in these molecules is also found to depend upon the nature of the attached base. The orientation of χ in poly rA chains is predicted to be predominantly anti, whereas in poly rG the syn conformer is expected to occur in significant proportions. The syn conformer is preferred almost exclusively in certain unusual purine polynucleotides, such as poly 8Br‐rA. It is noted that the preferred conformation of x in polynucleotides is not necessarily the same as that calculated for 5′‐mononucleotides and nucleosides. On the basis of these calculations, the influence of the orientation and nature of a purine base on the spatial configuration of a polynucleotide chain as a whole has been examined. The random coil dimensions of a syn polynucleotide chain are found to be larger than those of an anti chain as a consequence of the effect of a syn base on the local conformation of the chain skeleton. Finally, it is found that the occurrence of a syn base in an ordered polynucleotide chain may prevent the formation of normal stacking with the preceding base.