Biochem. J. (1972) 130, 453-465 Printed in Great Britain The Dimensions and Shapes of the Furanose Rings in Nucleic Acids By STRUTHER ARNOTT and D. W. L. HUKINS Department of Biological Sciences, Purdue University, Lafayette, Ind. 47907, U.S.A. (Received 30 May 1972) A survey was made of the geometry of furanose rings in ,-nucleotides and fl-nucleosides (as monomers related to nucleic acids) for which structures have been determined by X-ray crystallography. Mean values, and estimated standard deviations from them, were calculated for bond-lengths, bond-angles and conformation-angles. For para- meters with values dependent on ring-puckering, separate calculations were made for each ring type. (The rings are puckered in one of three conformations: C-2- or C-3-endo or C-3-exo; C-2-exo has not been observed.) The results were used to compute standard furanose rings with C-2-endo, C-3-endo and C-3-exo conformations for use in nucleic acid molecular model-building. The survey also showed that the only other conformation- angle in nucleotides dependent on the furanose ring conformation corresponds to the relative orientation of the purine (or pyrimidine) base and the ring. Molecules of biological polymers usually do not form crystalline arrays of sufficient extent and per- fection for them to yield many X-ray-diffraction signals corresponding to periodicities less than 2.OA (0.2nm). Polynucleotides are no exception, whether they are like DNA, elongated molecules in polycrystalline fibres, or like tRNA, folded molecules in single crystals. As a consequence, fine molecular structural details for polynucleotide chains cannot be obtained from X-ray-diffraction analyses unless the diffraction data from the polymer are supplemented by stereochemical information in the form of expected bond-lengths, bond-angles and sometimes even conformation-angles (rotations about bonds). X-ray analyses of fibrous polynucleotides by linked-atom least-squares methods (where the bond- lengths, bond-angles and sugar ring conformations are assumed to be fixed at the mean values observed in accurate, high-resolution X-ray-crystallographic studies of monomers) provide atomic positions with a precision of a few tenths of an A and experimental values for chain conformation-angles in the polymers with estimated standard deviations of several degrees. The correctness of the results (as distinct from their precision) depends on the error introduced by assignment of fixed values to certain features of the polymers. The furanose rings of nucleic acids are either ,-D-ribose (ribose) or P-D-erythropentose (deoxy- ribose). In early molecular model-building studies of DNA the deoxyribose ring was assumed to be planar (Crick & Watson, 1954). Spencer (1959) predicted that the furanose rings of nucleic acids would be puckered. This prediction was confirmed by sub- sequent crystallographic studies of nucleotides and Vol. 130 nucleosides and prompted Sundaralingam & Jensen (1965b) to define four main conformations in which either C-2 or C-3 (as defined in Fig. 1) is displaced furthest from the plane through C-1, 0-5 and C-4 either in the direction of C-5 (endo) or away from C-5 (exo). The number of X-ray-crystallo- graphic analyses of appropriate, accurately deter- mined nucleotide and nucleoside structures has doubled in the last 3 years (Table 1). We have made our survey so that the new stereochemical information from them can be exploited in the precise methods of analysing X-ray-diffraction data from fibrous polynucleotides (e.g. Arnott et al., 1969) and in X-ray-crystallographic studies of tRNA (Hampel etal., 1968; Blake etal., 1970; Cramer et al., 1970; Kim et al., 1971; Sakurai et al., 1971). In this survey we consider values of bond-lengths, bond-angles and conformation-angles. The mean values of these parameters have been reconciled by a linked-atom least-squares procedure to provide standard furanose rings for use (where appropriate) as fixed stereochemical features in nucleic acid models. Survey of Furanose Ring Geometry The structures considered are listed in Table 1. By the criteria of published agreement indices and estimated standard deviations, all have been deter- mined very accurately. Cyclic nucleotides have been omitted since their sugar ring conformations are often distorted by the additional phosphate ester linkage (Watenpaugh et al., 1968; Coulter, 1969; Coulter & Greaves, 1970; Saenger & Eckstein, 1970). Histograms were prepared for each bond-length, 15 453