Assembly and characterization of 8-arm and 12-arm DNA branched junctions
Assembly and characterization of 8-arm and 12-arm DNA branched junctions
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DOI：
10.1021/ja0693441
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发表时间：
2007-07-04
影响因子：
15
通讯作者：
Seeman, Nadrian C.
中科院分区：
文献类型：
--
作者：
Wang, Xing;Seeman, Nadrian C.
分支的DNA分子可以组装成物体和网络，由粘性末端的凝聚力指导。这些物种的连接性受到两侧分支点的臂数的限制。到目前为止，唯一的分支路口建设含有六个或更少的武器。我们报告的建设DNA分支路口，包含8或12个双螺旋臂周围的分支点。8臂接头的设计利用了先前方法的限制来阻止分支迁移，但是12臂接头的设计使用了新的原理来实现该目的。8臂连接稳定，每臂16个核苷酸对，但12臂连接稳定，每臂24个核苷酸对。Ferguson分析这些连接与3-，4-，5-和6-臂连接的组合表明摩擦常数随臂数增加而线性增加; 4-臂连接在4 ℃下不稳定地迁移，表明其结构域的堆叠。8臂和12臂接头中的所有链对羟基自由基自动足迹分析显示出相似的反应，表明它们缺乏任何显性堆叠结构。12臂连接的稳定性表明连接中的臂的数量不限于连接侧翼具有相邻相同碱基对的情况。构建8臂和12臂连接的能力增加了可以从分支DNA组件构建的对象、图形和网络的数量。原则上，与立方体紧密堆积相对应的棒状结构现在是DNA纳米技术组装的可能目标。
Branched DNA molecules can be assembled into objects and networks directed by sticky-ended cohesion. The connectivity of these species is limited by the number of arms flanking the branch point. To date, the only branched junctions constructed contain six or fewer arms. We report the construction of DNA branched junctions that contain either 8 or 12 double-helical arms surrounding a branch point. The design of the 8-arm junction exploits the limits of a previous approach to thwart branch migration, but the design of the 12-arm junction uses a new to principle achieve this end. The 8-arm junction is stable with 16 nucleotide pairs per arm, but the 12-arm junction has been stabilized by 24 nucleotide pairs per arm. Ferguson analysis of these junctions in combination with 3-, 4-, 5-, and 6-arm junctions indicates a linear increase in friction constant as the number of arms increases; the 4-arm junction migrates anomalously at 4 degrees C, suggesting stacking of its domains. All strands in both the 8-arm and 12-arm junctions show similar responses to hydroxyl radical autofootprinting analysis, indicating that they lack any dominant stacking structures. The stability of the 12-arm junction demonstrates that the number of arms in a junction is not limited to the case of having adjacent identical base pairs flanking the junction. The ability to construct 8-arm and 12-arm junctions increases the number of objects, graphs, and networks that can be built from branched DNA components. In principle, the stick structure corresponding to cubic close-packing is now a possible target for assembly by DNA nanotechnology.