Overmars F J, Pikkemaat J A, van den Elst H, van Boom J H, Altona C
Leiden Institut of Chemistry, Gorlaeus Laboratories, The Netherlands.
J Mol Biol. 1996 Feb 9;255(5):702-13. doi: 10.1006/jmbi.1996.0057.
DNA three-way junctions (TWJs) containing unpaired residues at the branch point can adopt a conformation in which one helix is stacked upon another, forming a coaxial, quasicontinuous double helix. As in four-way junctions (FWJs), two conformers with different stacking arrangements between the arms are possible. However, in both types of structures a markedly strong preference for one conformer has been observed. To investigate the basis for this preference, in particular the influence of the stacking proclivity of the base-pairs at the centre of the junction, two linear oligomers (36 nucleotides), TWJ1 and TWJ2, differing only in one base-pair (G.C versus C.G, respectively) at the branch point, were designed and chemically synthesized. Each one is expected to fold into a stable three-way junction, containing two unpaired thymidine bases at the junction region and two arms capped with a hairpin loop. The data obtained from 1H and 31P-NMR spectroscopy confirm that both oligomers are present as stable three-way junctions. In both TWJs two of the helical arms stack preferentially upon each other. However, the stacking arrangement is similar in both molecules. From this it is deduced that purine-purine stacking across the junction cannot be considered as a major factor that determines the preferred stacking arrangement.
在分支点含有未配对残基的DNA三向连接（TWJ）可采用一种构象，其中一条螺旋堆叠在另一条螺旋之上，形成同轴、准连续的双螺旋。与四向连接（FWJ）一样，臂之间可能存在两种具有不同堆叠排列的构象异构体。然而，在这两种类型的结构中，均观察到对一种构象异构体有明显的强烈偏好。为了研究这种偏好的基础，特别是连接点中心碱基对堆叠倾向的影响，设计并化学合成了两种线性寡聚物（36个核苷酸），TWJ1和TWJ2，它们仅在分支点的一个碱基对（分别为G.C对C.G）上不同。预计每一种都会折叠成一个稳定的三向连接，在连接区域含有两个未配对的胸腺嘧啶碱基，两条臂由发夹环封闭。从1H和31P-NMR光谱获得的数据证实，两种寡聚物均以稳定的三向连接形式存在。在两个TWJ中，两条螺旋臂优先相互堆叠。然而，两种分子中的堆叠排列相似。由此推断，连接点上嘌呤-嘌呤的堆叠不能被视为决定首选堆叠排列的主要因素。
