Dependence of Oligonucleotide Conformational Properties on Sugar Ring and Base-Sequence. 1H and 13C N.M.R. Studies

Abstract

Interest has developed in the possibility that base sequence might affect the local conformational properties of nucleic acids and may lead to specific recognition sites for protein or drug binding. Part of the interest stems from the fact that variations in DNA structure with base sequence have been observed; for example, the recent crystal structure of a DNA dodecamer by Dickerson and Drew (1981) showed several departures from the ideal, regular helical structure of B-DNA that might depend on base sequence; Klug and co-workers (1979) proposed a nonclassical “alternating B” configuration for poly(dA-dT) brought about by differential overlap of successive bases along the same chain; alternating C-G oligomers are known to form left-handed, zigzag, Z-DNA (Wang et al., 1979; Arnott et al., 1980; Drew et al., 1980). On the other hand base sequence dependent perturbations of structure are not found in the A-form of DNA (Shakked et al., 1981; Connor et al., 1982). An attempt has been made to rationalise the sequence dependent stacking of bases in B-DNA in terms of simple steric repulsive forces between purine bases in consecutive base-pairs but on opposite backbones, and to show that the repulsive forces between base-pairs are resisted by stresses in the helical backbone (Calladine, 1982).