Dipartimento di Fisica e Geologia, Università di Perugia, Perugia, Italy.
Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università Degli Studi di Milano, Milano, Italy.
J Chem Phys. 2024 Oct 7;161(13). doi: 10.1063/5.0226019.
Recent experiments have demonstrated the self-assembly and long-range ordering of concentrated aqueous solutions of DNA and RNA mononucleotides. These are found to form Watson-Crick pairs that stack into columns that become spatially organized into a columnar liquid-crystalline phase. In this work, we numerically investigate this phase behavior by adopting an extremely coarse-grained model in which nucleotides are represented as semi-disk-like polyhedra decorated with attractive (patchy) sites that mimic the stacking and pairing interactions. We carry out Monte Carlo simulations of these patchy polyhedra by adapting algorithms borrowed from computer graphics. This model reproduces the features of the experimental phase behavior, which essentially depends on the combination of pairing and stacking interactions.
最近的实验证明了 DNA 和 RNA 单核苷酸的浓缩水溶液的自组装和长程有序性。这些单核苷酸形成 Watson-Crick 碱基对，堆积成柱状，在空间上组织成柱状液晶相。在这项工作中，我们通过采用一种非常粗粒度的模型来数值研究这种相行为，其中核苷酸表示为带有吸引力（斑片状）位点的半圆盘状多面体，这些位点模拟了堆积和配对相互作用。我们通过从计算机图形学中借用算法来进行这些斑状多面体的蒙特卡罗模拟。该模型再现了实验相行为的特征，这主要取决于配对和堆积相互作用的组合。
