Title: Nanoscale Structure and Elasticity of Pillared DNA Nanotubes Show Chinese title

Title: 纳米尺度结构和柱状DNA纳米管的弹性

Abstract: We present an atomistic model of pillared DNA nanotubes (DNTs) and their elastic properties which will facilitate further studies of these nanotubes in several important nanotechnological and biological applications. In particular, we introduce a computational design to create an atomistic model of a 6-helix DNT (6HB) along with its two variants, 6HB flanked symmetrically by two double helical DNA pillars (6HB+2) and 6HB flanked symmetrically by three double helical DNA pillars (6HB+3). Analysis of 200 ns all-atom simulation trajectories in the presence of explicit water and ions shows that these structures are stable and well behaved in all three geometries. Hydrogen bonding is well maintained for all variants of 6HB DNTs. We calculate the persistence length of these nanotubes from their equilibrium bend angle distributions. The values of persistence length are ~10 {\mu}m, which is 2 orders of magnitude larger than that of dsDNA. We also find a gradual increase of persistence length with an increasing number of pillars, in quantitative agreement with previous experimental findings. To have a quantitative understanding of the stretch modulus of these tubes we carried out nonequilibrium Steered Molecular Dynamics (SMD). The linear part of the force extension plot gives stretch modulus in the range of 6500 pN for 6HB without pillars which increases to 11,000 pN for tubes with three pillars. The values of the stretch modulus calculated from contour length distributions obtained from equilibrium MD simulations are similar to those obtained from nonequilibrium SMD simulations. The addition of pillars makes these DNTs very rigid. Show Chinese abstract

Abstract: 我们提出了一种柱状DNA纳米管（DNTs）的原子模型及其弹性特性，这将有助于在多个重要的纳米技术和生物应用中进一步研究这些纳米管。 特别是，我们介绍了一种计算设计，以创建一个6螺旋DNT（6HB）的原子模型及其两种变体，6HB两侧对称地由两个双螺旋DNA支柱包围（6HB+2）和6HB两侧对称地由三个双螺旋DNA支柱包围（6HB+3）。 在存在显式水和离子的情况下，对200 ns全原子模拟轨迹的分析表明，这些结构在所有三种几何形状中都是稳定且行为良好的。 所有6HB DNT变体的氢键都得到了良好保持。 我们从它们的平衡弯曲角度分布中计算了这些纳米管的持久长度。 持久长度的值约为10{\mu }m，比双链DNA的持久长度大两个数量级。 我们还发现，随着支柱数量的增加，持久长度逐渐增加，这与之前的实验结果在定量上是一致的。 为了对这些管的拉伸模量有定量理解，我们进行了非平衡定向分子动力学（SMD）模拟。 力-伸长图的线性部分给出了6HB无支柱时的拉伸模量范围为6500 pN，对于具有三个支柱的管则增加到11,000 pN。 从平衡MD模拟中获得的轮廓长度分布计算出的拉伸模量与从非平衡SMD模拟中得到的值相似。 添加支柱使这些DNT变得非常刚性。