Characterizing the bending and flexibility induced by bulges in DNA duplexes.
Characterizing the bending and flexibility induced by bulges in DNA duplexes.
复制标题
DOI：
10.1063/1.4917199
复制
发表时间：
2014-12
期刊：
影响因子：
--
通讯作者：
J. Schreck;T. Ouldridge;F. Romano;A. Louis;J. Doye
中科院分区：
文献类型：
--
作者：
J. Schreck;T. Ouldridge;F. Romano;A. Louis;J. Doye
DNA纳米技术的进步刺激了对可用于控制DNA纳米结构性质的简单基序的搜索。一个这样的基序，已被广泛用于结构，如多面体笼，二维阵列，和带，是一个凸起的双链体，即两个螺旋段连接在一个凸起环。我们使用一个粗粒度的DNA模型来描述这种凸出的双链体。我们发现，这种基序可以采用属于两个主要类别的结构：一个是在系统中心的螺旋堆叠被保留，几何形状大致是直的，凸起是在双链体的一侧，另一个是在中心的堆叠被打破，从而允许这种连接作为铰链和增加灵活性。小环有利于保持双链体中心堆叠的状态，环碱基翻转或并入双链体。具有较长环的双链体显示出更多的倾向于在凸起处解堆叠并采用开放结构。然而，当单链DNA的刚性很大并且环能抵抗压缩时，对于中间长度的环，解堆积的概率最高。这种基本结构基序的性质与某些纳米级物体的结构行为明显相关，其中与较大凸起相关的增强的柔性已用于调整自组装产物以及所得纳米结构的详细几何形状。我们进一步展示了凸起在确定“Z-瓦片”结构中的作用，“Z-瓦片”是纳米结构的基本构建块。
Advances in DNA nanotechnology have stimulated the search for simple motifs that can be used to control the properties of DNA nanostructures. One such motif, which has been used extensively in structures such as polyhedral cages, two-dimensional arrays, and ribbons, is a bulged duplex, that is, two helical segments that connect at a bulge loop. We use a coarse-grained model of DNA to characterize such bulged duplexes. We find that this motif can adopt structures belonging to two main classes: one where the stacking of the helices at the center of the system is preserved, the geometry is roughly straight, and the bulge is on one side of the duplex and the other where the stacking at the center is broken, thus allowing this junction to act as a hinge and increasing flexibility. Small loops favor states where stacking at the center of the duplex is preserved, with loop bases either flipped out or incorporated into the duplex. Duplexes with longer loops show more of a tendency to unstack at the bulge and adopt an open structure. The unstacking probability, however, is highest for loops of intermediate lengths, when the rigidity of single-stranded DNA is significant and the loop resists compression. The properties of this basic structural motif clearly correlate with the structural behavior of certain nano-scale objects, where the enhanced flexibility associated with larger bulges has been used to tune the self-assembly product as well as the detailed geometry of the resulting nanostructures. We further demonstrate the role of bulges in determining the structure of a "Z-tile," a basic building block for nanostructures.