Section 23.3.2.5.  Syn/anti glycosyl bond geometry

The glycosyl bond angle, χ, about the bond connecting a sugar ring to a base is a special case of torsion angle, and is defined by O4′—C1′—N1—C2 for pyrimidines and O4′—C1′—N9—C4 for purines. In A- and B-DNA, the normal range of χ is 160 to 300°. This is known as the anti conformation (right-hand side of Fig. 23.3.2.13) and swings the sugar ring out away from the minor groove edge of the base pair. In Z-DNA, pyrimidines also exhibit the anti glycosyl bond conformation, but purines adopt the syn geometry shown on the left-hand side of Fig. 23.3.2.13. Now the sugar ring is rotated so that it intrudes into the minor groove, and χ lies in the range 50 to 90°.

Figure 23.3.2.13| top | pdf | Syn versus anti orientation about the glycosyl bond connecting sugar and base. Right: anti conformation, with χ ca 210°. Left: syn conformation, with χ around 60°. Both A- and B-DNA only employ the anti geometry; Z-DNA uses anti for pyrimidines and syn for purines, as shown here. Note that the 5′-to-3′ direction in both rings is down into the paper. Hence, antiparallel backbone chains can be achieved only by a zigzag chain geometry with local chain reversals, as shown later in Fig. 23.3.3.4. Black dots labelled A, B and Z indicate the position of the helix axis relative to the base pairs in A-, B- and Z-DNA.