Sugar puckering

It can be seen that alkylation has changed the sugar-base conformation (distant from the site of alkylation) from anti (as in deoxyadenosine and in B-DNA) to syn (as in alkylated deoxyadenosine and in some bases in Z-DNA). The sugar puckers are either C2 -endo or C3 -endo. A second structural feature of great interest in these crystals is that the more planar anthracene portion of the PAH is stacked between adenine residues of other molecules throughout the crystal. The highly buckled region of the PAH does not take part... 

Receptor sites. The intercalation and kinked sites in DNA used in this study are listed in Table V. Three theoretically determined intercalation sites (I, II and III) permit the study to be conducted with the DNA unwound by 7°-12°, lU-l8° and 25°-32° with parallel base pairs separated by 6.76 A and with alternating (a) sugar puckers (67,68) Attention will be confined to site I because it was found to be the most favorable in the present studies. Several kink (K) sites have been identified (66). The constraint that proper hybridization exists about N2(g) and CIO of BPDEs stimulated an investigation in kinked DNA. In an idealized structure the pyrene moiety is approximately parallel to one of the base pairs as shown... 

Fig. 7.25 Theoretical and experimental rcCH CH values to define the sugar pucker.

The Watson and Crick model for DNA as a double helix is only a generalized model to describe much more complex structures. Along with the typical double helix there exist structural elements such as supercoils, kinks, cruciforms, bends, loops, and triple strands as well as major and minor grooves. Each of these structural elements can vary in length, shape, location, and frequency. Even the simple DNA double helix can vary in pitch (number of bases per helical turn), sugar pucker conformation, and helical sense (whether the helix is left-or right-handed). 

This mixed sugar pucker conformation is associated with an extension of the -polynucleotide chain. 

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