Welch J B, Duckett D R, Lilley D M
Department of Biochemistry, The University, Dundee, UK.
Nucleic Acids Res. 1993 Sep 25;21(19):4548-55. doi: 10.1093/nar/21.19.4548.
We have studied a series of three-way DNA junctions containing unpaired bases on one strand at the branch-point of the junctions. The global conformation of the arms of the junctions has been analysed by means of polyacrylamide gel electrophoresis, as a function of conditions. We find that in the absence of added metal ions, all the results for all the junctions can be accounted for by extended structures, with the largest angle being that between the arms defined by the strand containing the extra bases. Upon addition of magnesium (II) or hexamine cobalt (III) ions, the electrophoretic patterns change markedly, indicative of ion-dependent folding transitions for some of the junctions. For the junction lacking the unpaired bases, the three inter-arm angles appear to be quite similar, suggesting an extended structure. However, the addition of unpaired bases permits the three-way junction to adopt a significantly different structure, in which one angle becomes smaller than the other two. These species also exhibit marked protection against osmium addition to thymine bases at the point of strand exchange. These results are consistent with a model in which two of the helical arms undergo coaxial stacking in the presence of magnesium ions, with the third arm defining an angle that depends upon the number of unpaired bases.
我们研究了一系列在分支点处一条链上含有未配对碱基的三链DNA连接体。通过聚丙烯酰胺凝胶电泳分析了连接体臂的整体构象与条件的函数关系。我们发现，在不添加金属离子的情况下，所有连接体的所有结果都可以用伸展结构来解释，其中最大的角度是由含有额外碱基的链所定义的臂之间的角度。加入镁（II）或六胺钴（III）离子后，电泳图谱发生明显变化，表明某些连接体存在离子依赖性折叠转变。对于缺乏未配对碱基的连接体，三个臂间角度似乎非常相似，表明是伸展结构。然而，加入未配对碱基使三链连接体能够采用显著不同的结构，其中一个角度比其他两个角度小。这些物种在链交换点处对锇添加到胸腺嘧啶碱基也表现出显著的保护作用。这些结果与一个模型一致，即在镁离子存在下，两个螺旋臂进行同轴堆积，第三个臂所定义的角度取决于未配对碱基的数量。
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