Wiechelman K, Taylor E R
Department of Chemistry, University of Southwestern Louisiana, Lafayette 70504-4370, USA.
J Biomol Struct Dyn. 1998 Jun;15(6):1181-94. doi: 10.1080/07391102.1998.10509012.
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.
人们已经对嘧啶碱基在DNA中采取顺式构象的能力进行了研究。对于胞嘧啶脱氧核糖的主要糖环构象,已计算出糖和碱基上原子之间的距离以及由此产生的空间能作为糖苷扭转角的函数。结果表明,对于3E、4E、1E、2E、3E糖环构象,嘧啶可以采取反式和顺式构象,对于2E糖环构象则采取顺式构象。对于这些糖环构象,反式和顺式构象的最低能量之差在0.1 - 2.0千卡/摩尔范围内,在4E、1E和2E糖环构象的情况下,顺式的最低能量更低。特别重要的是,胞嘧啶对于Z - DNA中顺式核苷酸常见的3E糖环构象可以采取顺式构象,无论是交替嘧啶/嘌呤(APP)序列还是非APP序列。这项研究的结果证实,将嘧啶核苷酸置于顺式构象所产生的空间相互作用不是Z - DNA中APP碱基序列偏好的主要因素。