Anti-Syn conformational range of pyrimidines with deoxyribofuranose

The ability of pyrimidine bases to adopt the syn conformation in DNA has been investigated. The distances between atoms on the sugar and base and the resulting steric energies have been calculated as a function of glycosidic torsion angle for the principal sugar puckers of the deoxyribose of cytosine. The results indicate that pyrimidines can assume both the anti and syn conformations for the 3E, 4E, 1E, 2E, 3E sugar puckers and syn for the 2E sugar pucker. For these sugar puckers the difference between the minimum energies of the anti and syn conformations is in the range of 0.1-2.0 kcal/mole, with the minimum syn energy being lower in the case of the 4E, 1E and 2E sugar puckers. It is particularly significant that cytosine can assume the syn conformation for the 3E sugar pucker commonly observed for the syn nucleotides in Z-DNA with both alternating pyrimidine/purine (APP) and non-APP sequences. The results of this investigation confirm that steric interactions resulting from putting a pyrimidine nucleotide in the syn conformation are not a major factor in the preference for APP base sequences in Z-DNA.