The Barrier to Pseudorotation of Furanose Rings and its Biological Implications

Abstract

DNA has long been known to exhibit polymorphic forms; the B double helical structure (Watson and Crick, 1953) appears to be only one of a number of possible DNA conformations, as shown by recent X-ray single-crystal and fibre diffraction studies as well as molecular spectroscopic methods, especially nuclear magnetic resonance and circular dichroism data. Synthetic poly- and oligonucleotide DNA/RNA molecules have played an important role in these investigations (see, e.g., Arnott et al., 1970, 1981; Wang et al., 1979, 1982; Dickerson et al, 1981; Sarma, 1980; Nordheim et al., 1981; Neidle, 1983; Hall et al., 1984; Saenger, 1984). Both in solution and in the solid state, deoxyribonucleotide duplexes with Watson-Crick base-pairs are known to exist in at least three basic forms: A, B and Z. The substantial differences between these forms are correlated with different furanose puckers which, according to the nomenclature introduced by Altona and Sundaralingam (1972), are defined as C3’-endo (N) in the A-DNA form, and C2’-endo (S) in the B-DNA form. Figure 2.1 illustrates the puckering modes. For alternating CG sequences, in the Z-DNA and Z’-DNA forms all deoxyguanosine residues have the C3’-endo and C1’-exo pucker, respectively, while all deoxycytidines are C2’-endo. A second important difference in the DNA conformations is associated with the orientation of the bases about the glycosidic bond. In A- and B-DNA all bases are in the anti orientation. In Z-and Z’-DNA all guanosine residues are found in the syn orientation.