Mandal Taraknath, Kumar Mattaparthi Venkata Satish, Maiti Prabal K
Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science , Bangalore, Karnataka 560 012, India.
J Phys Chem B. 2014 Oct 9;118(40):11805-15. doi: 10.1021/jp504175f. Epub 2014 Sep 26.
We report DNA assisted self-assembly of polyamidoamine (PAMAM) dendrimers using all atom Molecular Dynamics (MD) simulations and present a molecular level picture of a DNA-linked PAMAM dendrimer nanocluster, which was first experimentally reported by Choi et al. (Nano Lett., 2004, 4, 391-397). We have used single stranded DNA (ssDNA) to direct the self-assembly process. To explore the effect of pH on this mechanism, we have used both the protonated (low pH) and nonprotonated (high pH) dendrimers. In all cases studied here, we observe that the DNA strand on one dendrimer unit drives self-assembly as it binds to the complementary DNA strand present on the other dendrimer unit, leading to the formation of a DNA-linked dendrimer dimeric complex. However, this binding process strongly depends on the charge of the dendrimer and length of the ssDNA. We observe that the complex with a nonprotonated dendrimer can maintain a DNA length dependent inter-dendrimer distance. In contrast, for complexes with a protonated dendrimer, the inter-dendrimer distance is independent of the DNA length. We attribute this observation to the electrostatic complexation of a negatively charged DNA strand with the positively charged protonated dendrimer.
我们通过全原子分子动力学（MD）模拟报告了聚酰胺胺（PAMAM）树枝状大分子的DNA辅助自组装，并展示了DNA连接的PAMAM树枝状大分子纳米簇的分子水平图像，这一图像最早由Choi等人通过实验报道（《纳米快报》，2004年，第4卷，第391 - 397页）。我们使用单链DNA（ssDNA）来指导自组装过程。为了探究pH对该机制的影响，我们使用了质子化（低pH）和非质子化（高pH）的树枝状大分子。在这里研究的所有情况下，我们观察到一个树枝状大分子单元上的DNA链与另一个树枝状大分子单元上存在的互补DNA链结合时会驱动自组装，从而导致形成DNA连接的树枝状大分子二聚体复合物。然而，这种结合过程强烈依赖于树枝状大分子的电荷和ssDNA的长度。我们观察到与非质子化树枝状大分子形成的复合物可以保持与DNA长度相关的树枝状大分子间距离。相比之下，对于与质子化树枝状大分子形成的复合物，树枝状大分子间距离与DNA长度无关。我们将这一观察结果归因于带负电荷的DNA链与带正电荷的质子化树枝状大分子之间的静电络合作用。
