CONFORMATION OF POLYNUCLEOTIDES

Abstract

The conformations of the five?membered rings and other relevant conformational features of deoxyribose, ribose, and arabinose have been analysed in this chapter and in the preceding two chapters. The analysis included fifteen arabinose, twenty?seven deoxyribose, and eighty ribose sugar moieties. Other structural features of these compounds, such as the geometries of the bases, the planarity of the bases, and the propeller?twist of the base pairs, wherever relevant, have also been obtained. These features are important in model?building studies of nucleic acids and polynucleotides. Average geometries for the commonly occurring bases in nucleic acids have not been obtained earlier. However, in this thesis, data from accurately determined crystal structures were used to derive base geometries. In general, it is found that almost all atoms of the base except O1? lie in a plane. The deviation of the C1? atom from the best plane of the base was found to be significant and systematically present. Although individual bases are planar in structures where bases are paired through hydrogen bonds, the two planes do not form a coplanar structure but show a twist. This propeller?twist for Watson–Crick base pairing ranges from +7° to +15°. This structural detail was considered in model?building studies of polynucleotides and nucleic acids. In addition, the conformational features around the phosphodiester bonds, which are important in model?building studies of nucleic acids, have been obtained from the crystal structures of dinucleoside monophosphates and other higher oligomers, and these are discussed in Chapter 12.