Schreck John S, Ouldridge Thomas E, Romano Flavio, Louis Ard A, Doye Jonathan P K
Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom.
Rudolph Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom.
J Chem Phys. 2015 Apr 28;142(16):165101. doi: 10.1063/1.4917199.
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.
DNA纳米技术的进展激发了人们对可用于控制DNA纳米结构性质的简单基序的探索。一种这样的基序，即凸起双链体，已广泛应用于多面体笼、二维阵列和带状结构等，它是指在凸起环处连接的两个螺旋段。我们使用DNA的粗粒度模型来表征这种凸起双链体。我们发现这种基序可以呈现属于两个主要类别的结构：一类是系统中心处螺旋的堆积得以保留，几何形状大致呈直线，凸起位于双链体的一侧；另一类是中心处的堆积被破坏，从而使这个连接点可作为铰链并增加灵活性。小环有利于双链体中心处堆积得以保留的状态，环碱基要么翻转出来，要么并入双链体。具有较长环的双链体在凸起处更倾向于解堆积并采用开放结构。然而，当单链DNA的刚性显著且环抵抗压缩时，解堆积概率对于中等长度的环最高。这种基本结构基序的性质显然与某些纳米级物体的结构行为相关，其中与较大凸起相关的增强灵活性已被用于调整自组装产物以及所得纳米结构的详细几何形状。我们进一步证明了凸起在确定“Z形瓦片”（一种纳米结构的基本构建块）结构中的作用。
