Figure 3.9. Backbone conformations in DNA and RNA. 2D scattergrams show conformations of 1861 nucleotides from 186 structures of uncomplexed DNA (dark blue), 5878nucleotidesfrom 261structures of DNA in complexes with proteins or drugs (yellow), and 3752 nucleotides from 132 structures of RNA (red). A, AII, BI, BII, ZI, and ZII are respective double helical forms, Zr/Zy are purine and pyrimidine steps, respectively, in the Z-form. (a) Conformations at the phosphodiester linkage O3’-P-O5’, ζ versus α;(b) torsions α versus γ; (c) relationship between the sugar pucker and the base orientation, δ versus χ. Torsion angles are defined in Figure 3.2.
Figure 3.11. Important structural forms of DNA. Molecules are colored by strand. (a) B-DNA dodecamer (Drew et al., 1989); (b) A-DNA octamer (McCall et al., 1985); (c) Z-DNA hexamer (Gessner et al., 1989); (d) DNA guanine tetraplex. Four guanine tetramers are flanked by two T-T-T-T loops, potassium cations are shown in magenta (Haider, Parkinson, and Neidle, 2003); (e) cytosine tetraplex, or i-motif (Chen et al., 1994). In (a), (b), and (c), two perpendicular views are shown. The minor groove is shown in the red line.
Figure 3.14. The structure of the complete 70s ribosome (Selmer et al., 2006). (See text for full caption.)
