Wang Y H, Griffith J
Lineberger Cancer Research Center, University of North Carolina, Chapel Hill 27514.
Biochemistry. 1991 Feb 5;30(5):1358-63. doi: 10.1021/bi00219a028.
We recently showed that bulged bases kink duplex DNA, with the degree of kinking increasing in roughly equal increments as the number of bases in the bulge increases from one to four [Hsieh, C.-H., & Griffith, J.D. (1989) Proc. Natl. Acad. Sci. U.S.A. 86, 4833-4837]. Here we have examined the kinking of DNA by single A, C, G, or T bulges with different neighboring base pairs. Synthetic 30 base pair (bp) duplex DNAs containing 2 single-base bulges spaced by 10 bp were ligated head to tail, and their electrophoretic behavior in highly cross-linked gels was examined. All bulge-containing DNAs showed marked electrophoretic retardations as compared to non-bulge-containing DNA. Regardless of the sequence of the flanking base pairs, purine bulges produced greater retardations than pyrimidine bulges. Furthermore, C and T bulges produced the same retardations as did G and A bulges. Bulged DNA containing different flanking base pairs showed marked differences in electrophoretic mobility. For C-bulged DNA, the greatest retardations were observed with G.C neighbors, the least with T.A neighbors, and an intermediate amount with a mixture of neighboring base pairs. For A-bulged DNA, the retardations were greatest with G.C neighbors, less with T.A neighbors, even less with a mixture of neighboring base pairs, and finally least with C.G neighbors. Thus flanking base pairs affect C-bulged DNA and A-bulged DNA differently, and G.C and C.G flanking base pairs were seen to have very different effects. These results imply an important role of base stacking in determining how neighboring base pairs influence the kinking of DNA by a single-base bulge.
我们最近发现，凸起的碱基会使双链DNA发生扭结，随着凸起中碱基数量从1个增加到4个，扭结程度大致以相等的增量增加[谢，C.-H.，& 格里菲思，J.D.（1989年）《美国国家科学院院刊》86，4833 - 4837]。在此，我们研究了由单个A、C、G或T凸起以及不同相邻碱基对引起的DNA扭结。将含有2个单碱基凸起且间隔10个碱基对的30碱基对（bp）合成双链DNA首尾相连进行连接，并检测它们在高度交联凝胶中的电泳行为。与不含凸起的DNA相比，所有含凸起的DNA均表现出明显的电泳迁移率减慢。无论侧翼碱基对的序列如何，嘌呤凸起产生的迁移率减慢比嘧啶凸起更大。此外，C和T凸起产生的迁移率减慢与G和A凸起相同。含有不同侧翼碱基对的凸起DNA在电泳迁移率上表现出明显差异。对于C凸起的DNA，与G.C相邻碱基对时观察到最大的迁移率减慢，与T.A相邻碱基对时最小，与相邻碱基对混合物时为中间值。对于A凸起的DNA，与G.C相邻碱基对时迁移率减慢最大，与T.A相邻碱基对时较小，与相邻碱基对混合物时更小，与C.G相邻碱基对时最小。因此，侧翼碱基对以不同方式影响C凸起的DNA和A凸起的DNA，并且G.C和C.G侧翼碱基对具有非常不同的影响。这些结果表明碱基堆积在确定相邻碱基对如何影响单碱基凸起引起的DNA扭结方面起着重要作用。
