柱撑DNA纳米管的纳米尺度结构和弹性
Nanoscale Structure and Elasticity of Pillared DNA Nanotubes
摘要：
我们提出了一个原子模型的柱撑DNA纳米管（DNT）和它们的弹性性能，这将有助于进一步研究这些纳米管在几个重要的纳米技术和生物学应用。特别是，我们引入了一个计算设计，以创建一个原子模型的6-螺旋DNT（6 HB）及其两个变种，6 HB两侧对称的两个双螺旋DNA柱（6 HB +2）和6 HB两侧对称的三个双螺旋DNA柱（6 HB +3）。200 ns的全原子模拟轨迹的存在下，明确的水和离子的分析表明，这些结构是稳定的，表现良好，在所有三种几何形状。对于6 HB DNT的所有变体，氢键都保持良好。我们计算这些纳米管的持久长度从它们的平衡弯曲角分布。其持续长度约为10 μm，比dsDNA大2个数量级。我们还发现了一个逐渐增加的持久性长度与越来越多的支柱，在定量协议与以前的实验结果。为了定量地了解这些管的拉伸模量，我们进行了非平衡转向分子动力学（SMD）。力延伸曲线的线性部分给出了对于没有柱的6 HB在6500 pN范围内的拉伸模量，对于具有三个柱的管，该拉伸模量增加到11，000 pN。从平衡MD模拟获得的轮廓长度分布计算的拉伸模量的值是类似于从非平衡SMD模拟获得的。支柱的添加使得这些DNT非常刚性。
英文摘要：
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 μm, 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.
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
