Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom.
Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari, Via Torino 155, 30172 Venezia Mestre, Italy.
J Chem Phys. 2018 Apr 7;148(13):134910. doi: 10.1063/1.5019344.
Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculations with oxDNA, a nucleotide-based model of DNA, to parametrize a coarser kinetic model that can reach the time and length scales needed to study the assembly mechanisms of these structures. We test the model by performing a detailed study of the assembly pathways for a two-dimensional target structure made up of 334 unique strands each of which are 42 nucleotides long. Without adjustable parameters, the model reproduces a critical temperature for the formation of the assembly that is close to the temperature at which assembly first occurs in experiments. Furthermore, the model allows us to investigate in detail the nucleation barriers and the distribution of critical nucleus shapes for the assembly of a single target structure. The assembly intermediates are compact and highly connected (although not maximally so), and classical nucleation theory provides a good fit to the height and shape of the nucleation barrier at temperatures close to where assembly first occurs.
受最近使用单链 DNA 瓦片来构建复杂结构的成功启发，我们开发了一种两步粗粒化方法，该方法使用基于核苷酸的 DNA 模型 oxDNA 进行详细的热力学计算，以参数化更粗糙的动力学模型，该模型可以达到研究这些结构组装机制所需的时间和长度尺度。我们通过对由 334 个独特的单链组成的二维靶结构的组装途径进行详细研究来测试该模型，每个单链长 42 个核苷酸。在没有可调参数的情况下，该模型再现了组装形成的临界温度，该温度接近实验中组装首次发生的温度。此外，该模型使我们能够详细研究单个靶结构组装的成核势垒和临界核形状分布。组装中间体紧凑且高度连接（尽管不是最大程度的连接），经典成核理论很好地拟合了组装首次发生时接近的温度下成核势垒的高度和形状。
