Ramsing N B, Jovin T M
Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, FRG.
Nucleic Acids Res. 1988 Jul 25;16(14A):6659-76. doi: 10.1093/nar/16.14.6659.
Three linear 21-nt oligonucleotides (C2, C3, C7) have been synthesized with different sequences of A and T residues. One pairwise combination, (C3, C7), hybridizes to form a conventional antiparallel duplex (aps-C3.C7), whereas the pair C2, C3 forms a duplex (ps-C2.C3) in which the two strands are in a parallel orientation and the A.T base-pairs in a reverse Watson-Crick configuration. The existence of the novel ps helical structure was established from the following criteria: (i) The electrophoretic mobilities of the ps and aps duplexes in native and denaturing polyacrylamide gels are similar. (ii) The ps duplex is not a substrate for T4 DNA ligase. (iii) Salt-dependent thermal transitions are observed for the two duplexes, but the melting temperatures of the ps molecules are 15 degrees C lower. (iv) The ultraviolet absorption and circular dichroism spectra of the ps duplex are indicative of a base-paired structure, but differ systematically from that of the aps helix. (v) Based on fluorescent measurements, the bis-benzimidazole drug BBI-258 shows a lower affinity for the ps compared to the aps duplex, whereas the opposite preference holds for the intercalator ethidium bromide. We conclude from the present study that parallel stranded DNA is a stable conformation which can arise by interaction between two conventional strands with appropriate sequence homology.
已合成了三种线性21个核苷酸的寡核苷酸（C2、C3、C7），它们具有不同的A和T残基序列。一种两两组合（C3，C7）杂交形成传统的反平行双链体（aps-C3.C7），而C2、C3这一对形成了一个双链体（ps-C2.C3），其中两条链呈平行取向，且A.T碱基对呈反向沃森-克里克构型。这种新型ps螺旋结构的存在是根据以下标准确定的：（i）ps和aps双链体在天然和变性聚丙烯酰胺凝胶中的电泳迁移率相似。（ii）ps双链体不是T4 DNA连接酶的底物。（iii）观察到两种双链体都有盐依赖性热转变，但ps分子的解链温度低15摄氏度。（iv）ps双链体的紫外吸收光谱和圆二色光谱表明其为碱基配对结构，但与aps螺旋的光谱有系统性差异。（v）基于荧光测量，双苯并咪唑药物BBI-258对ps双链体的亲和力比对aps双链体低，而嵌入剂溴化乙锭则表现出相反的偏好。我们从本研究得出结论，平行链DNA是一种稳定的构象，它可以通过两条具有适当序列同源性的传统链之间的相互作用而产生。
